Amino Acids (BC, OC)

• Description

  • Organic molecules with an amine ($N{H}_2$$NH_2$) group, a carboxyl ($COOH$$COOH$) group, and a side chain (R-group) attached to an alpha carbon.

  • Serve as building blocks of proteins.

• Absolute configuration at the α position

  • Most naturally occurring amino acids in eukaryotes are L-amino acids.

  • The chiral center at the α carbon generally has the S configuration (except cysteine which is R).

• Amino acids as dipolar ions

  • At physiological pH (~7.4), amino acids exist as zwitterions with both a positively charged ammonium group ($N{H}_3^{+}$$NH_3^+$) and a negatively charged carboxylate group ($CO{O}^{-}$$COO^-$).

• Classifications

  • By side chain: nonpolar, polar, acidic, basic, aromatic, sulfur-containing.

  • By nutritional requirement: essential vs. nonessential.

• Acidic or basic

  • Acidic: aspartic acid, glutamic acid (side chain $COOH$$COOH$ groups).

  • Basic: lysine, arginine, histidine (side chain nitrogen groups).

• Hydrophobic or hydrophilic

  • Hydrophobic: nonpolar side chains (e.g., leucine, valine).

  • Hydrophilic: polar, charged side chains (e.g., serine, glutamate).

• Reactions

  • Peptide bond formation via condensation (amine of one with carboxyl of another).

  • Side chain modifications (e.g., phosphorylation, glycosylation).

• Sulfur linkage for cysteine and cystine

  • Two cysteine residues can form a disulfide bond ($S-S$$S-S$) to yield cystine, stabilizing tertiary structure.

• Peptide linkage: polypeptides and proteins

  • Peptide bonds link amino acids in a linear chain.

  • Polypeptides fold into functional proteins.

• Hydrolysis

  • Peptide bonds can be broken by hydrolytic enzymes or acid/base hydrolysis.

Protein Structure (BIO, BC, OC)

• Structure

  • Proteins have hierarchical structures: primary, secondary, tertiary, quaternary.

• 1° structure of proteins

  • Linear sequence of amino acids linked by peptide bonds.

• 2° structure of proteins

  • Local folding patterns such as α-helices and β-sheets stabilized by hydrogen bonds.

• 3° structure of proteins; role of proline, cysteine, hydrophobic bonding

  • Overall 3D shape.

  • Stabilized by side chain interactions: hydrophobic interactions, hydrogen bonds, ionic bonds.

  • Disulfide bonds (cysteine), proline often induces kinks in polypeptide chains.

• 4° structure of proteins (BIO, BC)

  • Arrangement of multiple polypeptide subunits into a functional complex.

• Conformational stability

  • Protein stability depends on noncovalent interactions and disulfide bonds.

• Denaturing and folding

  • Denaturing: loss of 3D structure due to heat, pH changes, chemicals.

  • Folding: guided by chaperone proteins, returns polypeptide to native state.

• Hydrophobic interactions

  • Nonpolar side chains cluster in the interior of the protein, stabilizing structure.

• Solvation layer (entropy) (BC)

  • Water forms a solvation shell around the protein.

  • Proper folding decreases the ordered water layer, increasing entropy.

• Separation techniques

  • Chromatography, electrophoresis, isoelectric focusing.

• Isoelectric point

  • pH at which the protein/zwitterion has no net charge.

• Electrophoresis

  • Separation of proteins based on charge and size in an electric field.

Non-Enzymatic Protein Function (BIO, BC)

• Binding (BC)

  • Proteins can bind ligands (e.g., hemoglobin binding O${}_2$$_2$).

• Immune system

  • Antibodies bind antigens; specificity due to variable regions.

• Motors

  • Motor proteins (myosin, kinesin, dynein) move along cytoskeletal filaments using ATP.

Enzyme Structure and Function (BIO, BC)

• Function of enzymes in catalyzing biological reactions

  • Lower activation energy, increase reaction rate without being consumed.

• Enzyme classification by reaction type

  • Oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases.

• Reduction of activation energy

  • Stabilizing transition states, providing alternative reaction pathways.

• Substrates and enzyme specificity

  • Enzymes bind specific substrates at active sites.

• Active Site Model

  • Specific region where substrate binds and reaction occurs.

• Induced-fit Model

  • Active site conformational change upon substrate binding.

• Mechanism of catalysis

  • Acid-base catalysis, covalent catalysis, metal ion catalysis, proximity/orientation effects.

• Cofactors

  • Inorganic ions (e.g., Mg${}^{2+}$$^{2+}$) required for enzyme function.

• Coenzymes

  • Organic molecules (e.g., NAD${}^{+}$$^+$, FAD) that assist enzymes.

• Water-soluble vitamins

  • Often precursors for coenzymes (e.g., B vitamins).

• Effects of local conditions on enzyme activity

  • Temperature, pH, substrate concentration affect enzymatic rates.

Control of Enzyme Activity (BIO, BC)

• Kinetics

  • Study of reaction rates and how they change in response to variables.

• General (catalysis)

  • Rate = k [substrate]^n, depends on enzyme mechanism.

• Michaelis–Menten

  • V = (Vmax [S])/(Km + [S])

  • Km reflects enzyme affinity for substrate.

• Cooperativity

  • Binding of one substrate affects affinity at other sites (sigmoidal curve).

• Feedback regulation

  • End products can inhibit or stimulate enzyme activity upstream.

• Inhibition – types

  • Reversible vs. irreversible.

• Competitive

  • Inhibitor competes with substrate at active site; increases Km, no change in Vmax.

• Non-competitive

  • Inhibitor binds enzyme and enzyme-substrate complex equally; no change in Km, decreases Vmax.

• Mixed (BC)

  • Inhibitor binds enzyme and enzyme-substrate complex with different affinities; changes both Km and Vmax in various ways.

• Uncompetitive (BC)

  • Inhibitor only binds to enzyme-substrate complex; decreases Km and Vmax.

• Regulatory enzymes

  • Enzymes regulated by other molecules to control metabolic pathways.

• Allosteric enzymes

  • Binding at sites other than active site modulates activity.

• Covalently-modified enzymes

  • Phosphorylation, acetylation, etc. alter enzyme activity.

• Zymogen

  • Inactive enzyme precursor activated by cleavage.

Nucleic Acid Structure and Function (BIO, BC)

• Description

  • Nucleic acids: DNA and RNA, polymers of nucleotides.

• Nucleotides and nucleosides

  • Nucleoside: sugar + base

  • Nucleotide: sugar + base + phosphate

• Sugar phosphate backbone

  • Repeating sugar-phosphate units linked by phosphodiester bonds.

• Pyrimidine, purine residues

  • Purines: A, G

  • Pyrimidines: C, T (in DNA), U (in RNA)

• Deoxyribonucleic acid (DNA): double helix, Watson–Crick model of DNA structure

  • Antiparallel strands, complementary base pairing, right-handed helix.

• Base pairing specificity: A with T, G with C

  • A-T pairs have 2 hydrogen bonds, G-C pairs have 3 hydrogen bonds.

• Function in transmission of genetic information (BIO)

  • DNA stores genetic information; RNA conveys it for protein synthesis.

• DNA denaturation, reannealing, hybridization

  • Heat or chemicals can denature DNA; complementary strands reanneal when conditions normalize.

  • Hybridization: pairing of complementary nucleic acid strands from different sources.

DNA Replication (BIO)

• Mechanism of replication: separation of strands, specific coupling of free nucleic acids

  • Helicase unwinds, DNA polymerase adds complementary bases.

• Semi-conservative nature of replication

  • Each new DNA molecule has one old and one new strand.

• Specific enzymes involved in replication

  • DNA polymerase, primase, ligase, helicase, topoisomerase.

• Origins of replication, multiple origins in eukaryotes

  • Replication begins at specific sequences; eukaryotic chromosomes have multiple origins.

• Replicating the ends of DNA molecules

  • Telomerase adds repetitive sequences to telomeres.

Repair of DNA (BIO)

• Repair during replication

  • Proofreading by DNA polymerase, mismatch repair.

• Repair of mutations

  • Base excision repair, nucleotide excision repair, double-strand break repair.

Genetic Code (BIO)

• Central Dogma: DNA → RNA → protein

  • Information flows from DNA to RNA to protein.

• The triplet code

  • Three nucleotides = one codon specifying one amino acid.

• Codon–anticodon relationship

  • tRNA anticodons pair with mRNA codons during translation.

• Degenerate code, wobble pairing

  • Multiple codons for one amino acid.

  • Wobble: third base often flexible.

• Missense, nonsense codons

  • Missense: codon change to encode a different amino acid.

  • Nonsense: codon changed to a stop codon.

• Initiation, termination codons

  • Start codon: AUG (Met)

  • Stop codons: UAA, UAG, UGA.

• Messenger RNA (mRNA)

  • Carries coded genetic message from DNA to ribosome.

Transcription (BIO)

• Transfer RNA (tRNA); ribosomal RNA (rRNA)

  • tRNA: brings amino acids to ribosome.

  • rRNA: structural and catalytic part of ribosome.

• Mechanism of transcription

  • RNA polymerase synthesizes RNA from DNA template.

• mRNA processing in eukaryotes, introns, exons

  • 5' cap, poly-A tail, splicing out introns, leaving exons.

• Ribozymes, spliceosomes, small nuclear ribonucleoproteins (snRNPs), small nuclear RNAs (snRNAs)

  • Spliceosomes (snRNPs + snRNA) remove introns.

  • Ribozymes: RNA enzymes.

• Functional and evolutionary importance of introns

  • Regulatory roles, alternative splicing increases protein diversity.

Translation (BIO)

• Roles of mRNA, tRNA, rRNA

  • mRNA: template.

  • tRNA: adaptor, reads codon and brings correct amino acid.

  • rRNA: catalyzes peptide bond formation.

• Role and structure of ribosomes

  • Two subunits: large and small.

  • E, P, A sites for tRNA binding and peptide bond formation.

• Initiation, termination co-factors

  • Initiation factors help assemble ribosome at start codon.

  • Release factors recognize stop codons, terminate translation.

• Post-translational modification of proteins

  • Folding, cleavage, addition of groups (phosphates, carbohydrates, lipids).

Eukaryotic Chromosome Organization (BIO)

• Chromosomal proteins

  • Histones package DNA into nucleosomes.

• Single copy vs. repetitive DNA

  • Single copy sequences often genes, repetitive sequences often structural.

• Supercoiling

  • DNA tightly wound for compaction.

• Heterochromatin vs. euchromatin

  • Heterochromatin: tightly packed, transcriptionally inactive.

  • Euchromatin: loosely packed, active transcription.

• Telomeres, centromeres

  • Telomeres: repetitive ends of chromosomes protecting them.

  • Centromeres: region where sister chromatids attach.

Control of Gene Expression in Prokaryotes (BIO)

• Operon Concept, Jacob–Monod Model

  • Operons: clusters of genes under one promoter.

• Gene repression in bacteria

  • Repressors bind operators to prevent transcription.

• Positive control in bacteria

  • Activators enhance transcription.

Control of Gene Expression in Eukaryotes (BIO)

• Transcriptional regulation

  • Controlled by transcription factors, enhancers, silencers.

• DNA binding proteins, transcription factors

  • Bind specific DNA sequences to regulate transcription.

• Gene amplification and duplication

  • Increase gene product by increasing gene copies.

• Post-transcriptional control, basic concept of splicing (introns, exons)

  • Alternative splicing can produce different mRNAs from one gene.

• Cancer as a failure of normal cellular controls, oncogenes, tumor suppressor genes

  • Mutations in oncogenes or tumor suppressors lead to uncontrolled growth.

• Regulation of chromatin structure

  • Acetylation, methylation affect DNA accessibility.

• DNA methylation

  • Usually represses gene expression.

• Role of non-coding RNAs

  • miRNA, siRNA regulate gene expression post-transcriptionally.

Recombinant DNA and Biotechnology (BIO)

• Gene cloning

  • Inserting DNA into vectors to replicate in host cells.

• Restriction enzymes

  • Cut DNA at specific sequences.

• DNA libraries

  • Collections of DNA fragments stored in vectors.

• Generation of cDNA

  • Reverse transcriptase converts mRNA to complementary DNA.

• Hybridization

  • Base pairing between complementary nucleic acid strands.

• Expressing cloned genes

  • Using expression vectors in bacteria or eukaryotes.

• Polymerase chain reaction

  • Amplifies DNA using repeated cycles of replication.

• Gel electrophoresis and Southern blotting

  • Separates DNA by size; Southern blot detects specific DNA fragments.

• DNA sequencing

  • Determines the order of nucleotides.

• Analyzing gene expression

  • Microarrays, Northern blot, RT-PCR.

• Determining gene function

  • Knockouts, knockdowns, transgenic organisms.

• Stem cells

  • Undifferentiated cells can develop into various cell types.

• Practical applications of DNA technology: medical applications, human gene therapy, pharmaceuticals, forensic evidence, environmental cleanup, agriculture

  • Recombinant insulin, gene therapy, GM crops.

• Safety and ethics of DNA technology

  • Considerations of GMO impact, gene editing ethics, CRISPR.

Evidence that DNA is Genetic Material (BIO)

Mendelian Concepts (BIO)

• Phenotype and Genotype:

  • Genotype: Genetic makeup of an organism.

  • Phenotype: Observable traits expressed by the organism.

• Gene:

  • A unit of hereditary information located at a specific locus on a chromosome.

• Locus:

  • The specific physical location of a gene on a chromosome.

• Allele:

  • Different versions of a gene at the same locus.

  • Single allele: One version of a gene.

  • Multiple alleles: More than two possible alleles exist in a population for a given locus.

• Homozygosity and Heterozygosity:

  • Homozygous: Having two identical alleles at a given locus ($AA$$AA$ or $aa$$aa$).

  • Heterozygous: Having two different alleles at a locus ($Aa$$Aa$).

• Wild-type:

  • The most common or "normal" phenotype/allele found in a natural population.

• Recessiveness:

  • A recessive allele only manifests its phenotype when in a homozygous state ($aa$$aa$).

• Complete Dominance:

  • The phenotype of the dominant allele completely masks the recessive allele in a heterozygote ($Aa$$Aa$ shows the dominant trait).

• Co-dominance:

  • Both alleles in a heterozygote are fully expressed, resulting in a phenotype that simultaneously displays both traits (e.g., blood type $AB$$AB$).

• Incomplete Dominance:

  • The heterozygote phenotype is intermediate between the two homozygotes (e.g., red ($RR$$RR$) and white ($rr$$rr$) flowers produce pink ($Rr$$Rr$) offspring).

• Leakage:

  • Gene flow between species that can introduce new alleles into a population.

• Penetrance:

  • The probability that a person with a particular genotype will express the associated phenotype.

• Expressivity:

  • The degree to which a genotype is expressed in the phenotype; can vary between individuals.

• Hybridization: Viability:

  • Mating between genetically distinct individuals; may result in sterile hybrids (e.g., mule) if the two parent species have incompatible chromosomes.

• Gene Pool:

  • The complete set of all genes and alleles present in a population at a given time.

Meiosis and Other Factors Affecting Genetic Variability (BIO)**

• Significance of Meiosis:

  • Meiosis produces haploid gametes ($n$$n$) from diploid cells ($2n$$2n$), allowing sexual reproduction and genetic diversity.

• Differences Between Meiosis and Mitosis:

  • Meiosis includes two rounds of division (meiosis I and II) and results in four non-identical haploid cells.

  • Mitosis results in two identical diploid daughter cells.

• Segregation of Genes:

  • During meiosis I, homologous chromosomes separate, ensuring each gamete receives one allele from each gene pair.

• Independent Assortment:

  • Alleles of different genes assort independently during gamete formation, contributing to genetic variation.

• Linkage:

  • Genes located close together on the same chromosome tend to be inherited together, violating independent assortment.

• Recombination:

  • The exchange of genetic material between homologous chromosomes during crossing-over in prophase I.

• Single Crossovers:

  • A single exchange of genetic material between two homologous chromosomes.

• Double Crossovers:

  • Two separate crossover events occur between homologous chromosomes, providing even greater genetic diversity.

• Synaptonemal Complex:

  • A protein structure that forms between homologous chromosomes during meiosis I, facilitating crossing-over.

• Tetrad:

  • The structure of two homologous chromosomes and their sister chromatids paired during prophase I of meiosis.

• Sex-linked Characteristics:

  • Traits determined by genes on sex chromosomes (often the $X$$X$ chromosome) that show different patterns of inheritance in males vs. females.

• Very Few Genes on Y Chromosome:

  • The $Y$$Y$ chromosome is small and has relatively few genes; often carries genes involved in male sex determination.

• Sex Determination:

  • In humans, presence of the $Y$$Y$ chromosome generally determines maleness.

• Cytoplasmic/Extranuclear Inheritance:

  • Genes in organelles (mitochondria, chloroplasts) are inherited independently of the nucleus, often maternally.

• Mutation:

  • Any change in the DNA sequence can produce new alleles and increase genetic variability.

• Types of Mutations:

  • Random: Spontaneous without known cause.

  • Translation Error: Errors in protein synthesis at the ribosome level.

  • Transcription Error: Errors made during RNA synthesis.

  • Base Substitution (Point Mutation): One nucleotide replaced by another.

  • Inversion: A segment of a chromosome is reversed end-to-end.

  • Addition (Insertion): Extra nucleotides inserted into DNA.

  • Deletion: Removal of nucleotides from DNA.

  • Translocation: A segment of one chromosome moves to another chromosome.

  • Mispairing: Non-complementary bases pair during replication.

• Advantageous vs. Deleterious Mutation:

  • Advantageous: Increases an organism’s fitness.

  • Deleterious: Decreases fitness or is harmful.

• Inborn Errors of Metabolism:

  • Genetic disorders resulting from mutations in metabolic enzymes.

• Mutagens to Carcinogens:

  • Many mutagens (chemicals, radiation) can cause mutations leading to cancer; these mutagens are considered carcinogens.

• Genetic Drift:

  • Random changes in allele frequencies in small populations, which can reduce genetic diversity over time.

• Synapsis or Crossing-over Mechanism for Increasing Genetic Diversity:

  • By exchanging genetic material between homologous chromosomes, new allele combinations are created.

Analytic Methods (BIO)

• Hardy–Weinberg Principle:

  • Describes allele frequencies in a non-evolving population.

  • $p+q=1$$p + q = 1$ (allele frequencies) and $p^2+2pq+q^2=1$$p^2 + 2pq + q^2 = 1$ (genotype frequencies).

• Testcross (Backcross):

  • Breeding an organism with a dominant phenotype but unknown genotype with a homozygous recessive to determine the unknown genotype.

• Concepts of Parental, F1, and F2 Generations:

  • Parental (P): Original individuals in a cross.

  • F1 Generation: Offspring of the parental generation.

  • F2 Generation: Offspring of the F1 generation.

• Gene Mapping: Crossover Frequencies:

  • The likelihood of crossover between two genes is proportional to the distance between them; used to create linkage maps.

• Biometry (Statistical Methods):

  • Applying statistical analysis to biological data to interpret inheritance patterns, gene frequencies, and population genetics.

Evolution (BIO)

• Natural Selection:

  • Organisms with heritable traits better suited to the environment tend to survive and reproduce more successfully.

• Fitness Concept:

  • Fitness is measured by an individual’s genetic contribution to the next generation ($\text{reproductive success}$$\text{reproductive success}$).

• Selection by Differential Reproduction:

  • Individuals with traits that improve reproductive success become more common over generations.

• Concepts of Natural and Group Selection:

  • Natural Selection: Acts on individuals.

  • Group Selection: Selection that benefits a group’s survival, though debated in evolutionary biology.

• Evolutionary Success as Increase in Percent Representation in the Gene Pool:

  • Traits that increase in frequency in the gene pool over time are considered evolutionary successes.

• Speciation:

  • The formation of new and distinct species from existing species.

• Polymorphism:

  • The presence of two or more distinct forms (alleles/traits) in a population.

• Adaptation and Specialization:

  • Adaptations are traits that enhance survival and reproduction. Over time, populations can become specialized for certain niches.

• Inbreeding:

  • Mating between closely related individuals, can increase homozygosity and the expression of deleterious recessive traits.

• Outbreeding:

  • Mating between unrelated individuals, usually increases genetic diversity.

• Bottlenecks:

  • Severe reduction in population size leading to loss of genetic variation.

• Evolutionary Time as Measured by Gradual Random Changes in Genome:

  • Molecular clocks measure evolutionary time by the accumulation of random mutations.

Principles of Bioenergetics (BC, GC)

• Bioenergetics/thermodynamics

  • Study of energy flow and transformation in biological systems

  • Relies on laws of thermodynamics

  • Biological systems are open: exchange matter and energy with surroundings

• Free energy/Keq

  • Gibbs free energy $G$$G$ measures the spontaneity of a reaction

  • $K_{eq}$$K_{eq}$ is the equilibrium constant, relating product and reactant concentrations at equilibrium

• Equilibrium constant

  • $K_{eq}=\frac{[products]}{[reactants]}$$K_{eq} = \frac{[products]}{[reactants]}$ at equilibrium

  • If $K_{eq}>1$$K_{eq} > 1$, products favored; if $K_{eq}<1$$K_{eq} < 1$, reactants favored

• Relationship of the equilibrium constant and ∆G°

  • $∆G°=-RT\ln K_{eq}$$∆G° = -RT \ln K_{eq}$

  • If $K_{eq}>1$$K_{eq} > 1$, $∆G°<0$$∆G° < 0$ (spontaneous under standard conditions)

• Concentration

  • Actual $∆G$$∆G$ depends on reactant and product concentrations

  • $∆G=∆G°+RT\ln \frac{[products]}{[reactants]}$$∆G = ∆G° + RT \ln \frac{[products]}{[reactants]}$

• Le Châtelier’s Principle

  • Changes in concentration, pressure, or temperature shift equilibrium to restore balance

• Endothermic/exothermic reactions

  • Endothermic: absorb heat ($∆H>0$$∆H > 0$)

  • Exothermic: release heat ($∆H<0$$∆H < 0$)

• Free energy: G

  • $G=H-TS$$G = H - TS$

  • Predicts direction of reaction

  • Negative $∆G$$∆G$: spontaneous process

• Spontaneous reactions and ∆G°

  • If $∆G°<0$$∆G° < 0$, reaction is spontaneous under standard conditions

• Phosphoryl group transfers and ATP

  • ATP is a major energy currency

  • Phosphoryl transfer used to drive unfavorable reactions

• ATP hydrolysis ∆G << 0

  • ATP hydrolysis is highly exergonic

  • Releases energy to power cellular processes

• ATP group transfers

  • Transfer of phosphoryl groups from ATP to substrates to form higher-energy intermediates

• Biological oxidation-reduction

  • Redox reactions move electrons from electron donors to acceptors

  • Essential in catabolism and energy production

• Half-reactions

  • Redox reactions separated into two half-reactions: oxidation and reduction

• Soluble electron carriers

  • Molecules like $NA{D}^{+}$$NAD^{+}$, $NAD{P}^{+}$$NADP^{+}$, $FAD$$FAD$, and $FMN$$FMN$ transport electrons

• Flavoproteins

  • Proteins with flavin groups ($FAD$$FAD$, $FMN$$FMN$) acting as electron carriers

Carbohydrates (BC, OC)

• Description

  • Polyhydroxy aldehydes or ketones and derivatives

  • Common energy sources and structural elements

• Nomenclature and classification, common names

  • Classified by number of carbons (triose, tetrose, pentose, hexose)

  • Aldose (aldehyde group) or ketose (ketone group)

  • Common examples: glucose, fructose, galactose

• Absolute configuration

  • D- and L- configuration based on the chiral carbon furthest from carbonyl

• Cyclic structure and conformations of hexoses

  • Five- or six-membered ring structures (furanose/pyranose forms)

  • Haworth projections

• Epimers and anomers

  • Epimers differ at one stereocenter

  • Anomers differ at the anomeric carbon (α or β)

• Hydrolysis of the glycoside linkage

  • Glycosidic bonds broken by hydrolysis to yield free monosaccharides

• Monosaccharides

  • Single carbohydrate units: glucose, fructose, etc.

• Disaccharides

  • Two monosaccharides linked: lactose, sucrose, maltose

• Polysaccharides

  • Long chains of monosaccharides: glycogen, starch, cellulose

Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway (BIO, BC)

• Glycolysis (aerobic), substrates and products

  • Converts glucose to pyruvate

  • Net yield: 2 $ATP$$ATP$, 2 $NADH$$NADH$, 2 pyruvate per glucose

• Feeder pathways: glycogen, starch metabolism

  • Glycogen and starch broken down to glucose units that enter glycolysis

• Fermentation (anaerobic glycolysis)

  • Regenerates $NA{D}^{+}$$NAD^{+}$ from $NADH$$NADH$ in absence of oxygen

  • Produces lactate in animals or ethanol in yeast

• Gluconeogenesis (BC)

  • Synthesis of glucose from non-carbohydrate precursors

  • Occurs mainly in liver and kidneys

• Pentose phosphate pathway (BC)

  • Produces $NADPH$$NADPH$ and ribose-5-phosphate for nucleotide synthesis

  • Oxidative and non-oxidative phases

• Net molecular and energetic results of respiration processes

  • Complete oxidation of glucose yields $C{O}_2$$CO_2$, $H_{2}O$$H_2O$, and large amounts of $ATP$$ATP$

Principles of Metabolic Regulation (BC)

• Regulation of metabolic pathways (BIO, BC)

  • Enzyme activity controlled by allosteric regulators, covalent modification, and hormone signaling

• Maintenance of a dynamic steady state

  • Concentrations of metabolites remain relatively constant despite changes

• Regulation of glycolysis and gluconeogenesis

  • Key enzymes: PFK-1 for glycolysis, fructose-1,6-bisphosphatase for gluconeogenesis

  • Regulated by energy charge, citrate, $ATP$$ATP$, $AMP$$AMP$

• Metabolism of glycogen

  • Glycogen synthesis and breakdown regulated by glycogen synthase and glycogen phosphorylase

• Regulation of glycogen synthesis and breakdown

  • Hormones (insulin, glucagon, epinephrine) control enzyme phosphorylation states

• Allosteric and hormonal control

  • Allosteric effectors regulate enzyme activity rapidly

  • Hormones provide slower, sustained control

• Analysis of metabolic control

  • Understanding flux through pathways and points of regulation

Citric Acid Cycle (BIO, BC)

• Acetyl-CoA production (BC)

  • From pyruvate via pyruvate dehydrogenase complex

  • From fatty acids and amino acids

• Reactions of the cycle, substrates and products

  • Oxidation of acetyl-CoA to $C{O}_2$$CO_2$

  • Produces $NADH$$NADH$, $FAD{H}_2$$FADH_2$, and $GTP$$GTP$

• Regulation of the cycle

  • Controlled by energy needs: $ATP$$ATP$, $NADH$$NADH$ levels

• Net molecular and energetic results of respiration processes

  • High-energy electron carriers and $GTP$$GTP$ generated for ATP synthesis

Metabolism of Fatty Acids and Proteins (BIO, BC)

• Description of fatty acids (BC)

  • Long-chain carboxylic acids

• Digestion, mobilization, and transport of fats

  • Bile salts emulsify fats

  • Chylomicrons transport dietary triglycerides

• Oxidation of fatty acids

  • Beta-oxidation in mitochondria

  • Each cycle shortens chain by two carbons, producing $NADH$$NADH$, $FAD{H}_2$$FADH_2$, and acetyl-CoA

• Saturated fats

  • No double bonds, higher melting points

• Unsaturated fats

  • One or more double bonds, generally healthier

• Ketone bodies (BC)

  • Produced from acetyl-CoA when carbohydrate is scarce

  • Used as alternative fuel by brain and muscles

• Anabolism of fats (BIO)

  • Fatty acid synthesis in cytosol from acetyl-CoA

• Non-template synthesis: biosynthesis of lipids and polysaccharides (BIO)

  • Constructed without a direct nucleic acid template

• Metabolism of proteins (BIO)

  • Amino acids used for energy, gluconeogenesis, or ketogenesis when excess protein is consumed

Oxidative Phosphorylation (BIO, BC)

• Electron transport chain and oxidative phosphorylation, substrates and products, general features of the pathway

  • Occurs in inner mitochondrial membrane

  • Electrons from $NADH$$NADH$ and $FAD{H}_2$$FADH_2$ transferred through complexes

  • Oxygen is final electron acceptor

• Electron transfer in mitochondria

  • Complexes I-IV pump protons to generate proton gradient

• NADH, NADPH

  • $NADH$$NADH$ donates electrons to ETC for ATP production

  • $NADPH$$NADPH$ used in biosynthetic reactions

• Flavoproteins

  • Contain $FAD$$FAD$ or $FMN$$FMN$ as prosthetic groups

  • Important electron carriers

• Cytochromes

  • Electron carriers with heme groups

• ATP synthase, chemiosmotic coupling

  • Proton gradient drives $ATP$$ATP$ synthesis

• Proton motive force

  • Gradient of H+ across inner mitochondrial membrane

• Net molecular and energetic results of respiration processes

  • Complete oxidation of glucose yields ~30-32 ATP

• Regulation of oxidative phosphorylation

  • Based on ADP availability (respiratory control)

• Mitochondria, apoptosis, oxidative stress (BC)

  • Mitochondria can initiate apoptosis

  • Reactive oxygen species can cause damage

Hormonal Regulation and Integration of Metabolism (BC)

• Higher level integration of hormone structure and function

  • Hormones coordinate metabolism across different tissues

• Tissue specific metabolism

  • Liver, muscle, adipose, and brain have unique metabolic roles

• Hormonal regulation of fuel metabolism

  • Insulin promotes storage

  • Glucagon and epinephrine promote mobilization of fuels

• Obesity and regulation of body mass

  • Long-term regulation via leptin and other signals

  • Balancing energy intake and expenditure

Plasma Membrane (BIO, BC)

• General function in cell containment

  • Forms the boundary of the cell, separating the intracellular environment from the extracellular space

  • Maintains cellular integrity, regulates passage of substances in and out

• Composition of membranes

  • Primarily composed of phospholipids, cholesterol, proteins, and carbohydrates

  • Lipids arranged as a bilayer with hydrophobic tails inward and hydrophilic heads outward

• Lipid components (BIO, BC, OC)

  • Phospholipids (and phosphatids)

    • Amphipathic molecules with a phosphate-containing hydrophilic head and two hydrophobic fatty acid tails

    • Common phospholipids: phosphatidylcholine, phosphatidylserine, phosphatidylethanolamine

  • Steroids

    • Cholesterol intercalates between phospholipids, increasing fluidity at low temperatures and decreasing it at high temperatures

  • Waxes

    • Lipids with long-chain fatty acids linked to long-chain alcohols

    • Mostly present in plant cell membranes, providing rigidity and waterproofing

• Protein components

  • Integral (transmembrane) proteins span the membrane

  • Peripheral proteins associate with membrane surfaces

  • Functions include signaling, transport, structural support, and enzymatic activity

• Fluid mosaic model

  • Membrane viewed as a dynamic, fluid matrix of lipids and proteins

  • Proteins and lipids can move laterally within the layer

• Membrane dynamics

  • Lateral diffusion of lipids and proteins

  • Changes in fluidity due to temperature, lipid composition, and cholesterol

• Solute transport across membranes

  • Controlled by membrane proteins and lipid bilayer permeability

• Thermodynamic considerations

  • Spontaneous movement of molecules down concentration gradients (no input of energy)

  • Active transport requires energy input (ATP)

• Osmosis

  • Passive diffusion of $H_{2}O$$H_2O$ across a selectively permeable membrane from low solute concentration to high solute concentration regions

• Colligative properties; osmotic pressure (GC)

  • Osmotic pressure depends on the total number of solute particles

  • Described by van ’t Hoff equation: $\pi =iMRT$$\pi = i M R T$

• Passive transport

  • Diffusion, facilitated diffusion (via channels or carriers)

  • No energy expenditure required

• Active transport

  • Movement of solutes against their concentration gradient

  • Requires energy (ATP hydrolysis or ion gradients)

• Sodium/potassium pump

  • Pumps 3 Na+ out and 2 K+ in per ATP

  • Establishes electrochemical gradient across the membrane

• Membrane channels

  • Ion channels (voltage-gated, ligand-gated, mechanically gated)

  • Aquaporins for water transport

• Membrane potential

  • Voltage difference across the membrane due to ion distribution

  • Resting membrane potential typically around –70 mV in neurons

• Membrane receptors

  • Proteins that bind signaling molecules (ligands) and initiate cellular responses

• Exocytosis and endocytosis

  • Exocytosis: secretory vesicles fuse with membrane to release contents

  • Endocytosis: uptake of external materials via membrane invagination

• Intercellular junctions (BIO)

  • Structures connecting cells to form tissues and allow communication

• Gap junctions

  • Connexin proteins form channels for direct cytoplasmic exchange between cells

• Tight junctions

  • Seal adjacent cells together, preventing leakage of extracellular fluid

• Desmosomes

  • Anchoring junctions providing mechanical stability and resistance to stress

Membrane-Bound Organelles and Defining Characteristics of Eukaryotic Cells (BIO)

• Defining characteristics of eukaryotic cells: membrane bound nucleus, presence of organelles, mitotic division

  • Eukaryotes have true nucleus and complex internal compartmentalization

  • Undergo mitosis for cell division

• Nucleus

  • Contains genetic material (DNA) organized into chromosomes

  • Site of DNA replication and transcription

• Compartmentalization, storage of genetic information

  • Nuclear envelope encloses DNA

  • Chromatin organization and regulation of gene expression

• Nucleolus: location and function

  • Located within the nucleus

  • Site of ribosomal RNA synthesis and ribosome subunit assembly

• Nuclear envelope, nuclear pores

  • Double membrane structure around nucleus

  • Nuclear pores allow regulated transport of molecules (mRNA, proteins) between nucleus and cytoplasm

• Mitochondria

  • Site of ATP production through oxidative phosphorylation

  • Has its own DNA and can self-replicate

• Site of ATP production

  • Inner mitochondrial membrane houses the electron transport chain

  • ATP synthase generates ATP from proton gradient

• Inner and outer membrane structure (BIO, BC)

  • Outer membrane: relatively porous

  • Inner membrane: folded into cristae, less permeable, location of respiratory complexes

• Self-replication

  • Mitochondria divide by binary fission, independent of cell division

• Lysosomes: membrane-bound vesicles containing hydrolytic enzymes

  • Digest cellular debris, waste materials, and ingested substances

• Endoplasmic reticulum

  • Rough and smooth components

    • Rough ER: studded with ribosomes for protein synthesis

    • Smooth ER: involved in lipid synthesis, detoxification

  • Rough endoplasmic reticulum site of ribosomes

    • Important for co-translational translocation of secretory and membrane proteins

  • Double membrane structure

    • Continuous with the nuclear envelope

  • Role in membrane biosynthesis

    • Synthesizes phospholipids and integral membrane proteins

  • Role in biosynthesis of secreted proteins

    • Proteins destined for secretion or organelles first enter RER lumen

• Golgi apparatus: general structure and role in packaging and secretion

  • Stacks of flattened, membrane-bound sacs (cisternae)

  • Modifies, sorts, and packages proteins from ER for transport to final destinations

• Peroxisomes: organelles that collect peroxides

  • Contain oxidative enzymes that degrade fatty acids and detoxify harmful substances

  • Produce and break down $H_2{O}_2$$H_2O_2$

Cytoskeleton (BIO)

• General function in cell support and movement

  • Provides structural integrity, anchors organelles, and facilitates intracellular transport and cellular motility

• Microfilaments: composition and role in cleavage and contractility

  • Composed of actin

  • Involved in muscle contraction, cytokinesis (cleavage furrow), and cell motility

• Microtubules: composition and role in support and transport

  • Composed of tubulin dimers

  • Provide tracks for vesicle transport, form spindle apparatus during mitosis, and support cilia and flagella

• Intermediate filaments, role in support

  • Composed of various fibrous proteins (keratins, vimentin)

  • Provide mechanical strength, maintain cell shape

• Composition and function of cilia and flagella

  • Axoneme structure of microtubule doublets (9+2 arrangement)

  • Cilia: numerous, short, for moving fluid along cell surfaces

  • Flagella: longer, fewer, for propelling cells (e.g., sperm)

• Centrioles, microtubule organizing centers

  • Pair of cylindrical structures in centrosome

  • Initiate and organize microtubule growth, important in mitotic spindle formation

Tissues Formed From Eukaryotic Cells (BIO)

• Epithelial cells

  • Line cavities and surfaces

  • Involved in absorption, secretion, and protection

  • Form glands

• Connective tissue cells

  • Provide structural support and connect tissues

  • Include bone, cartilage, blood, adipose tissue, and tendons

Cell Theory (BIO)

• History and development

  • Early observation of cells by Robert Hooke and Anton van Leeuwenhoek

  • Schleiden and Schwann proposed that all living organisms are composed of cells

  • Virchow added that all cells arise from pre-existing cells

• Impact on biology

  • Established cells as the fundamental unit of life

  • Led to understanding that physiological functions are carried out by cells

  • Formed the basis for modern cellular and molecular biology

Classification and Structure of Prokaryotic Cells (BIO)

• Prokaryotic domains

  • Archaea

  • Bacteria

• Archaea

  • Often live in extreme environments (e.g., hot springs, high salinity)

  • Possess unique membrane lipids and cell wall components

  • Have genes and enzymes similar to eukaryotes in some aspects

• Bacteria

  • Ubiquitous, found in diverse habitats

  • Contain cell walls composed of peptidoglycan

  • Exhibit various metabolic pathways (photosynthetic, heterotrophic, etc.)

• Major classifications of bacteria by shape

  • Bacilli (rod-shaped)

  • Spirilli (spiral-shaped)

  • Cocci (spherical)

• Lack of nuclear membrane and mitotic apparatus

  • DNA is found in a nucleoid region

  • Cell division occurs by binary fission, no mitosis

• Lack of typical eukaryotic organelles

  • No membrane-bound organelles like mitochondria or chloroplasts

• Presence of cell wall in bacteria

  • Provides structural support and shape

  • Protects against osmotic pressure changes

• Flagellar propulsion, mechanism

  • Simple rotary motor embedded in cell membrane

  • Uses a proton gradient to power the rotation

  • Enables movement toward favorable environments (chemotaxis)

Growth and Physiology of Prokaryotic Cells (BIO)

• Reproduction by fission

  • Binary fission: a simple form of asexual reproduction

  • Rapid cell division under favorable conditions

• High degree of genetic adaptability, acquisition of antibiotic resistance

  • Horizontal gene transfer (transformation, conjugation, transduction)

  • Mutation and selection enhance adaptability

• Exponential growth

  • Population can double in a short time (e.g., every 20 minutes)

• Existence of anaerobic and aerobic variants

  • Obligate aerobes require $O_2$$O_2$

  • Obligate anaerobes are poisoned by $O_2$$O_2$

  • Facultative anaerobes can switch between aerobic and anaerobic metabolism

• Parasitic and symbiotic

  • Some live inside host cells, causing disease

  • Others form mutually beneficial relationships (e.g., gut flora)

• Chemotaxis

  • Movement toward chemical attractants (nutrients) or away from repellents

  • Mediated by cell surface receptors and flagellar rotation

Genetics of Prokaryotic Cells (BIO)

• Existence of plasmids, extragenomic DNA

  • Circular DNA molecules separate from chromosomal DNA

  • Often carry antibiotic resistance or virulence genes

• Transformation: incorporation into bacterial genome of DNA fragments from external medium

  • Uptake of free DNA from environment

  • Can lead to new phenotypic traits

• Conjugation

  • Direct transfer of DNA via a conjugation bridge (pilus)

  • Plasmid or chromosomal segments can be transferred

• Transposons (also present in eukaryotic cells)

  • Mobile genetic elements that can move within the genome

  • Can cause mutations, gene duplications

Virus Structure (BIO)

• General structural characteristics (nucleic acid and protein, enveloped and nonenveloped)

  • Core of either DNA or RNA (single-stranded or double-stranded)

  • Protein capsid surrounds genetic material

  • Some have lipid envelopes acquired from host membranes

• Lack organelles and nucleus

  • No metabolic machinery on their own

  • Rely entirely on host cell functions for replication

• Structural aspects of typical bacteriophage

  • Icosahedral head containing genetic material

  • Tail fibers that attach to bacterial surface

  • Tail sheath for injecting genetic material

• Genomic content — RNA or DNA

  • RNA viruses include retroviruses, influenza viruses

  • DNA viruses include adenoviruses, herpesviruses

• Size relative to bacteria and eukaryotic cells

  • Generally much smaller than bacteria

  • Cannot be seen under a light microscope

Viral Life Cycle (BIO)

• Self-replicating biological units that must reproduce within specific host cell

  • Obligate intracellular parasites

• Generalized phage and animal virus life cycles

  • Attachment: virus binds to host cell receptor

  • Penetration: viral genome enters host cell

  • Synthesis: host machinery replicates viral genome and proteins

  • Assembly: new virus particles self-assemble

  • Release: new virions leave host cell (lysis or budding)

• Attachment to host, penetration of cell membrane or cell wall, and entry of viral genetic material

  • Specific recognition of host receptor sites

• Use of host synthetic mechanism to replicate viral components

  • Host ribosomes translate viral proteins

  • Host enzymes replicate viral nucleic acids

• Self-assembly and release of new viral particles

  • Capsid proteins and nucleic acids spontaneously assemble into virions

  • Release often causes host cell death (lysis)

• Transduction: transfer of genetic material by viruses

  • Occurs when a phage accidentally packages host DNA

• Retrovirus life cycle: integration into host DNA, reverse transcriptase, HIV

  • Viral RNA reverse transcribed into DNA

  • Integrated into host genome and transcribed/translated along with host genes

  • Produces new viral particles that bud from host cell

• Prions and viroids: subviral particles

  • Prions: misfolded proteins causing transmissible spongiform encephalopathies

  • Viroids: small circular RNA molecules that infect plants, lack a capsid

Mitosis (BIO)

• Mitotic process: prophase, metaphase, anaphase, telophase, interphase

  • Prophase: chromosomes condense, centrioles move to opposite poles, spindle fibers form, nuclear membrane begins to break down

  • Metaphase: chromosomes align along the metaphase plate, kinetochores attach to spindle fibers

  • Anaphase: sister chromatids separate and are pulled to opposite poles, centromeres split

  • Telophase: nuclear membranes re-form around separated sets of chromosomes, chromosomes begin to decondense

  • Interphase (G1, S, G2): period between divisions, DNA replicates, cell grows, prepares for mitosis

• Mitotic structures

  • Centrioles: cylindrical structures that help organize the spindle apparatus

  • Asters: star-shaped microtubule arrays that anchor centrioles at the poles

  • Spindles: microtubule fibers that separate chromosomes during mitosis

• Chromatids, centromeres, kinetochores

  • Chromatids: two identical DNA strands (sister chromatids) joined by a centromere

  • Centromeres: central region joining sister chromatids

  • Kinetochores: protein complexes on centromeres that attach chromosomes to spindle fibers

• Nuclear membrane breakdown and reorganization

  • During prophase: nuclear envelope disassembles to allow spindle fibers to reach chromosomes

  • During telophase: nuclear envelopes reform around two separate sets of chromosomes

• Mechanisms of chromosome movement

  • Microtubule dynamics: polymerization and depolymerization of tubulin subunits

  • Motor proteins (dynein, kinesin) help move chromatids along spindle fibers

• Phases of cell cycle: G0, G1, S, G2, M

  • G0: resting phase, cells not actively dividing

  • G1: cell growth, organelle duplication

  • S: DNA synthesis, replication of genome

  • G2: preparation for mitosis, protein synthesis

  • M: mitosis and cytokinesis, cell divides into two daughter cells

• Growth arrest

  • Cells may enter G0 due to lack of growth signals or nutrient limitations

  • Senescent cells permanently stop dividing

• Control of cell cycle

  • Cyclins and cyclin-dependent kinases (CDKs) regulate progression

  • Checkpoints (G1/S, G2/M, spindle checkpoint) ensure accurate replication and division

• Loss of cell cycle controls in cancer cells

  • Mutations in oncogenes and tumor suppressors disrupt regulation

  • Uncontrolled proliferation leads to tumor formation

Biosignalling (BC)

• Oncogenes, apoptosis

  • Oncogenes: mutated genes that promote uncontrolled cell division

  • Apoptosis: programmed cell death, eliminates damaged or unnecessary cells

  • Signaling pathways: growth factors, kinase cascades, second messengers influence gene expression and cell fate

Reproductive System (BIO)

• Gametogenesis by meiosis

  • Occurs in gonads (ovaries and testes)

  • Reduces chromosome number by half to produce haploid gametes

• Ovum and sperm

  • Ovum: large, non-motile, nutrient-rich cell produced by the female

  • Sperm: small, motile, streamlined cell produced by the male

• Differences in formation

  • Oogenesis: one mature ovum produced per meiotic event, cytoplasm unevenly distributed

  • Spermatogenesis: four sperm produced per meiotic event, cytoplasm evenly divided

• Differences in morphology

  • Ovum: large, lots of cytoplasm and organelles

  • Sperm: minimal cytoplasm, contains flagellum for movement

• Relative contribution to next generation

  • Ovum: provides most of the cytoplasm, organelles (including mitochondria) to the zygote

  • Sperm: provides paternal DNA and centrioles

• Reproductive sequence: fertilization; implantation; development; birth

  • Fertilization: sperm and ovum fuse to form a zygote

  • Implantation: blastocyst attaches to uterine wall

  • Development: embryo undergoes cell division, differentiation, organogenesis

  • Birth: culmination of gestation resulting in newborn

Embryogenesis (BIO)

• Stages of early development (order and general features of each)

  • Fertilization: union of haploid gametes to form diploid zygote

  • Cleavage: rapid mitotic divisions without significant growth

  • Blastula formation: hollow ball of cells

  • Gastrulation: formation of three germ layers

  • Neurulation: formation of the neural tube from ectoderm

• Fertilization

  • Occurs in the fallopian tube

  • Acrosomal enzymes help sperm penetrate egg

  • Resulting zygote travels to uterus

• Cleavage

  • Early mitotic divisions increase cell number without increasing overall size

  • Creates a morula (solid ball of cells)

• Blastula formation

  • Fluid-filled cavity (blastocoel) forms within the embryo

  • Blastocyst implants in the uterine lining

• Gastrulation

  • Cell movements form the primary germ layers: endoderm, mesoderm, ectoderm

• First cell movements

  • Cells invaginate, ingress, or involute to establish distinct layers

• Formation of primary germ layers (endoderm, mesoderm, ectoderm)

  • Endoderm: forms digestive tract lining, respiratory system, liver, pancreas

  • Mesoderm: forms muscle, bone, connective tissue, circulatory system, kidneys

  • Ectoderm: forms skin, nervous system, lens of eye

• Neurulation

  • Notochord induces ectoderm to fold into neural tube

  • Neural tube becomes central nervous system

• Major structures arising out of primary germ layers

  • Endoderm: gut, lungs, liver

  • Mesoderm: heart, skeletal muscle, red blood cells

  • Ectoderm: neurons, skin cells, hair

• Neural crest

  • Cells at edge of neural fold migrate to form peripheral nervous system, melanocytes, and facial cartilage

• Environment–gene interaction in development

  • Gene expression influenced by factors such as temperature, nutrient availability, signaling molecules

Mechanisms of Development (BIO)

• Cell specialization

  • Process by which cells become uniquely suited for particular functions

• Determination

  • Cell fate is committed, even if not fully expressed

• Differentiation

  • Process of a determined cell becoming structurally and functionally distinct

• Tissue types

  • Epithelial, connective, muscle, and nervous tissues

• Cell–cell communication in development

  • Inductive signals from neighboring cells influence cell fate

  • Juxtacrine, paracrine, endocrine, and synaptic signaling guide tissue patterning

• Cell migration

  • Cells move to specific locations for proper tissue and organ formation

• Pluripotency: stem cells

  • Stem cells retain the ability to differentiate into multiple cell types

  • Embryonic stem cells are pluripotent, adult stem cells are more restricted

• Gene regulation in development

  • Transcription factors, enhancers, and silencers regulate gene expression patterns

• Programmed cell death

  • Apoptosis removes unnecessary structures, shapes organs, and prevents abnormal cell accumulation

• Existence of regenerative capacity in various species

  • Some animals (amphibians, planarians) can regenerate limbs or organs

  • Mammalian regenerative capacity is more limited (liver regeneration in humans)

• Senescence and aging

  • Gradual decline in cell function and division

  • Accumulation of DNA damage and telomere shortening leads to aging

Nervous System: Structure and Function (BIO)

• Major functions

  • High-level control and integration of body systems

  • Adaptive response to external stimuli

• Organization of vertebrate nervous system

  • Central nervous system (CNS): brain and spinal cord

  • Peripheral nervous system (PNS): cranial and spinal nerves

    • Sensory (afferent) neurons: carry information from receptors to CNS

    • Motor (efferent) neurons: carry information from CNS to effectors (muscles and glands)

• Sympathetic and parasympathetic divisions: antagonistic effects on organs

  • Sympathetic: fight-or-flight responses

  • Parasympathetic: rest-and-digest responses

• Reflexes

  • Simple automatic responses to stimuli

  • Reflex arc: sensory neuron → interneuron (in spinal cord) → motor neuron → effector

• Feedback loops

  • Negative feedback: reduces deviation from set point

  • Positive feedback: amplifies a response

• Role of spinal cord and supraspinal circuits

  • Spinal cord: mediates simple reflexes, transmits signals to and from brain

  • Supraspinal input: brain involvement to modulate reflexes and complex movements

• Integration with endocrine system

  • Hypothalamus links nervous and endocrine systems

  • Hormonal feedback loops modulate neural activity and vice versa

Nerve Cell (BIO)

• Cell body

  • Contains nucleus and organelles

• Dendrites

  • Receive incoming signals from other neurons

• Axon

  • Transmits action potentials away from cell body

  • Myelin sheath (produced by Schwann cells in PNS, oligodendrocytes in CNS) insulates axon

    • Nodes of Ranvier: gaps in myelin where action potentials jump (saltatory conduction)

• Synapse

  • Junction between two neurons or a neuron and effector cell

  • Neurotransmitters released into synaptic cleft bind receptors on postsynaptic cell

• Resting potential

  • Typical neuron resting potential: about $-70$$-70$ mV

  • Maintained by selective permeability and Na+/K+ pump

• Action potential

  • Rapid depolarization (Na+ influx) followed by repolarization (K+ efflux)

  • Threshold: all-or-none firing once stimulus exceeds critical level

• Summation

  • Excitatory and inhibitory inputs combine, determining if neuron fires

  • Frequency of firing encodes intensity of signal

• Glial cells (neuroglia)

  • Support, nourish, and protect neurons

  • Types include astrocytes, Schwann cells, oligodendrocytes, microglia

Electrochemistry (GC)

• Concentration cells

  • Electrons flow from area of lower ion concentration to higher ion concentration to equalize potential

  • Nernst equation quantifies the potential based on ion concentrations

Biosignalling (BC)

• Gated ion channels

  • Voltage-gated: open/close in response to membrane potential changes

  • Ligand-gated: open/close in response to binding of a specific molecule

• Receptor enzymes

  • Have enzymatic activity (e.g., receptor tyrosine kinases)

• G protein-coupled receptors

  • Activated by ligand binding, trigger second messenger cascades

Lipids (BC, OC)

• Description; structure

  • Hydrophobic molecules including fats, phospholipids, and steroids

• Steroids

  • Four fused ring structure

  • Include cholesterol and hormone precursors

• Terpenes and terpenoids

  • Lipids built from isoprene units

  • Terpenoids are modified terpenes (e.g., with oxygen-containing groups)

Endocrine System: Hormones and Their Sources (BIO)

• Function of endocrine system

  • Chemical control of cell, tissue, and organ activity

• Endocrine glands and hormones

  • Hormones secreted directly into bloodstream

  • Major glands: hypothalamus, pituitary, thyroid, parathyroid, adrenal, pancreas, gonads

  • Hormones can be peptides, steroids, or amino acid derivatives

• Neuroendocrinology

  • Relationship between nervous system and hormonal systems

  • Hypothalamus and pituitary coordinate endocrine responses

Endocrine System: Mechanisms of Hormone Action (BIO)

• Cellular mechanisms

  • Hormone binds to receptor → initiates intracellular signaling

  • Steroid hormones: diffuse into cell, affect gene transcription

  • Peptide hormones: bind cell surface receptors, use second messengers (e.g., cAMP)

• Transport in blood

  • Some hormones bound to carrier proteins, others free in plasma

• Specificity

  • Only target tissues with corresponding receptors respond

• Integration with nervous system

  • Feedback control loops (negative feedback)

  • Hypothalamic-pituitary axis coordination

• Regulation by second messengers

  • cAMP, IP3, Ca2+ mediate cellular responses

Respiratory System (BIO)

• General function

  • Exchanges gases between the atmosphere and blood

  • Supplies $O_2$$O_2$ to the body and removes $C{O}_2$$CO_2$

• Gas exchange, thermoregulation

  • Gas exchange occurs at alveoli where $O_2$$O_2$ diffuses into blood and $C{O}_2$$CO_2$ diffuses out

  • Thermoregulation involves warming and humidifying inhaled air and releasing heat during exhalation

• Protection against disease: particulate matter

  • Entrapment of particles by nasal hairs and mucus

  • Removal via mucociliary escalator

• Structure of lungs and alveoli

  • Lungs are spongy organs composed of branching bronchi leading to bronchioles ending in alveolar sacs

  • Alveoli are tiny sacs with thin walls surrounded by capillaries to facilitate gas exchange

• Breathing mechanisms

  • Inhalation increases thoracic volume, decreasing pressure and drawing air in

  • Exhalation typically passive due to lung recoil and muscle relaxation

• Diaphragm, rib cage, differential pressure

  • Diaphragm contracts downward, expanding thoracic cavity and decreasing intrapleural pressure

  • Intercostal muscles lift rib cage, increasing thoracic volume

• Resiliency and surface tension effects

  • Elastic fibers in lung tissue allow recoil

  • Surfactant reduces alveolar surface tension, preventing collapse

• Thermoregulation: nasal and tracheal capillary beds; evaporation, panting

  • Nasal passages rich in blood vessels warm and moisten incoming air

  • Evaporative cooling via panting or increased respiratory rate helps regulate body temperature

• Particulate filtration: nasal hairs, mucus/cilia system in lungs

  • Nasal hairs filter large particles

  • Mucus traps particles; cilia sweep mucus upwards toward pharynx

• Alveolar gas exchange

  • Alveoli provide large surface area for diffusion

  • Thin barrier between alveolar air and capillary blood optimizes gas diffusion

• Diffusion, differential partial pressure

  • Gas diffusion driven by differences in partial pressures of $O_2$$O_2$ and $C{O}_2$$CO_2$

  • $O_2$$O_2$ moves from higher partial pressure in alveoli to lower partial pressure in blood

• Henry’s Law (GC)

  • The amount of gas dissolved in liquid is proportional to its partial pressure and solubility: $C = k_H \times P$

• pH control

  • Respiratory rate influences blood $C{O}_2$$CO_2$ levels

  • Changes in $C{O}_2$$CO_2$ alter $H^{+}$$H^+$ concentration and thus blood pH

• Regulation by nervous control

  • Medulla oblongata and pons regulate respiratory rate

  • Chemoreceptors sense changes in $C{O}_2$$CO_2$, $O_2$$O_2$, and pH

• CO2 sensitivity

  • Increased $C{O}_2$$CO_2$ and lowered pH stimulate increased ventilation

  • Body is more sensitive to changes in $C{O}_2$$CO_2$ than $O_2$$O_2$ under normal conditions

Circulatory System (BIO)

• Functions: circulation of oxygen, nutrients, hormones, ions and fluids, removal of metabolic waste

  • Delivers $O_2$$O_2$ and nutrients to tissues

  • Removes $C{O}_2$$CO_2$ and waste products

  • Distributes hormones and maintains homeostasis

• Role in thermoregulation

  • Adjusting blood flow to the skin can conserve or dissipate heat

  • Vasodilation and vasoconstriction regulate heat exchange

• Four-chambered heart: structure and function

  • Two atria receive blood; two ventricles pump blood out

  • Valves ensure one-way flow

• Endothelial cells

  • Line blood vessels and regulate exchange, blood flow, and clotting

• Systolic and diastolic pressure

  • Systolic: pressure during ventricular contraction

  • Diastolic: pressure during ventricular relaxation

• Pulmonary and systemic circulation

  • Pulmonary: right ventricle to lungs and back to left atrium

  • Systemic: left ventricle to body tissues and back to right atrium

• Arterial and venous systems (arteries, arterioles, venules, veins)

  • Arteries carry blood away from heart under high pressure

  • Veins carry blood back to heart under lower pressure; often have valves

• Structural and functional differences

  • Arteries: thick, muscular walls to withstand high pressure

  • Veins: thinner walls, larger lumens, valves to prevent backflow

• Pressure and flow characteristics

  • Blood flow driven by pressure gradient

  • Highest pressure in arteries, lowest in veins

• Capillary beds

  • Sites of exchange between blood and tissues

  • Thin endothelial walls facilitate diffusion

• Mechanisms of gas and solute exchange

  • Diffusion, filtration, and osmosis

  • Bulk flow of fluids driven by hydrostatic and osmotic pressures

• Mechanism of heat exchange

  • Blood flow to skin affects radiant and evaporative heat loss

• Source of peripheral resistance

  • Mainly arterioles through vasoconstriction and vasodilation

  • Resistance affects blood pressure and flow

• Composition of blood

  • Plasma (water, ions, proteins), red blood cells, white blood cells, platelets

• Plasma, chemicals, blood cells

  • Plasma contains albumin, immunoglobulins, fibrinogen

  • RBCs transport $O_2$$O_2$

  • WBCs defend against infection

  • Platelets involved in clotting

• Erythrocyte production and destruction; spleen, bone marrow

  • RBCs produced in bone marrow

  • Lifespan ~120 days; old RBCs removed by spleen and liver

• Regulation of plasma volume

  • Kidneys adjust water and electrolyte balance

  • Hormones (ADH, aldosterone) regulate blood volume

• Coagulation, clotting mechanisms

  • Platelet plug formation and activation of clotting cascade

  • Fibrin mesh stabilizes clot

• Oxygen transport by blood

  • RBCs contain hemoglobin that binds $O_2$$O_2$

• Hemoglobin, hematocrit

  • Hemoglobin: protein with heme groups that bind $O_2$$O_2$

  • Hematocrit: percentage of blood volume occupied by RBCs

• Oxygen content

  • Dependent on hemoglobin concentration and saturation

• Oxygen affinity

  • Affected by pH (Bohr effect), temperature, $C{O}_2$$CO_2$, and 2,3-BPG

• Carbon dioxide transport and level in blood

  • Most $C{O}_2$$CO_2$ transported as bicarbonate ($HC{O}_3^{-}$$HCO_3^-$)

  • Some bound to hemoglobin, some dissolved in plasma

• Nervous and endocrine control

  • Sympathetic and parasympathetic nerves alter heart rate and vessel diameter

  • Hormones (epinephrine, angiotensin II) affect cardiac output and blood pressure

Lymphatic System (BIO)

• Structure of lymphatic system

  • Network of vessels returning excess fluid to the circulatory system

  • Lymph nodes interspersed along vessels

• Major functions

  • Fluid balance by returning interstitial fluid to bloodstream

  • Immune surveillance and response

• Equalization of fluid distribution

  • Prevents edema by collecting and returning fluid lost from capillaries

• Transport of proteins and large glycerides

  • Lymph vessels can absorb and transport large molecules not easily taken up by capillaries

• Production of lymphocytes involved in immune reactions

  • Lymph nodes and organs (spleen, thymus) produce and house lymphocytes

• Return of materials to the blood

  • Lymph eventually drains into the subclavian veins

Immune System (BIO)

• Innate (non-specific) vs. adaptive (specific) immunity

  • Innate: rapid, non-specific responses (barriers, inflammation, phagocytes)

  • Adaptive: specific recognition via lymphocytes and memory cells

• Adaptive immune system cells

  • T-lymphocytes and B-lymphocytes with antigen-specific receptors

• T-lymphocytes

  • Mature in thymus

  • Helper T cells coordinate response; cytotoxic T cells kill infected cells

• B-lymphocytes

  • Mature in bone marrow

  • Produce antibodies that bind specific antigens

• Innate immune system cells

  • Macrophages, neutrophils, natural killer cells

  • Recognize common pathogen-associated patterns

• Macrophages

  • Phagocytose pathogens and present antigens

• Phagocytes

  • Engulf and destroy pathogens or debris

• Tissues

  • Bone marrow: site of blood cell production

  • Spleen: filters blood, immune cell interactions

  • Thymus: T cell maturation

  • Lymph nodes: filter lymph, site for immune activation

• Concept of antigen and antibody

  • Antigen: foreign molecule that elicits an immune response

  • Antibody: protein that specifically binds antigens

• Antigen presentation

  • Antigen-presenting cells (APCs) display antigen fragments on MHC molecules to T cells

• Clonal selection

  • Lymphocytes with receptors for specific antigen proliferate upon activation

• Antigen-antibody recognition

  • Antibodies bind specific antigen epitopes

  • Leads to neutralization, opsonization, or complement activation

• Structure of antibody molecule

  • Y-shaped protein with variable regions that bind antigen

  • Constant region determines antibody class

• Recognition of self vs. non-self, autoimmune diseases

  • Immune tolerance prevents targeting of self

  • Autoimmune disorders occur when self-tolerance fails

• Major histocompatibility complex

  • MHC class I on all nucleated cells presents endogenous antigens

  • MHC class II on APCs presents exogenous antigens

Digestive System (BIO)

• Ingestion

  • Introduction of food into the oral cavity

  • Mechanical breakdown by teeth and tongue

• Saliva as lubrication and source of enzymes

  • Salivary amylase begins carbohydrate digestion

  • Mucus moistens and lubricates food bolus

• Ingestion; esophagus, transport function

  • Muscular tube connecting mouth to stomach

  • Peristalsis propels bolus downward

• Stomach

  • Storage and churning of food into chyme

  • Low pH from gastric acid denatures proteins, activates pepsin

  • Gastric juice contains hydrochloric acid and pepsinogen

  • Mucal protection (mucus lining) prevents self-digestion

• Production of digestive enzymes, site of digestion

  • Mainly in the small intestine and accessory organs (pancreas)

  • Enzymes break down macromolecules into absorbable units

• Structure (gross)

  • Mouth → Esophagus → Stomach → Small Intestine → Large Intestine → Rectum

• Liver

  • Structural relationship of liver within gastrointestinal system: connected via bile ducts to gallbladder and small intestine

  • Production of bile for fat emulsification

  • Role in blood glucose regulation (glycogenesis, glycogenolysis, gluconeogenesis)

  • Detoxification of harmful substances (e.g., ammonia to urea)

• Bile

  • Storage in gall bladder

  • Function: emulsifies fats, increasing surface area for lipase action

• Pancreas

  • Production of enzymes: pancreatic amylase, lipase, proteases

  • Transport of enzymes to small intestine via pancreatic duct

• Small Intestine

  • Absorption of food molecules and $H_{2}O$$H_2O$

    • Villi and microvilli increase surface area

  • Function and structure of villi: finger-like projections with capillaries and lacteals for nutrient uptake

  • Production of enzymes (maltase, sucrase, lactase, peptidases)

  • Neutralization of stomach acid by bicarbonate secretions

  • Structure (anatomic subdivisions): duodenum, jejunum, ileum

• Large Intestine

  • Absorption of $H_{2}O$$H_2O$

  • Bacterial flora produce vitamins (e.g., K) and ferment undigested materials

  • Structure (gross): cecum, colon, rectum

• Rectum: storage and elimination of waste, feces

  • Muscular control: internal and external sphincters

• Peristalsis

  • Wave-like muscular contractions throughout the GI tract

• Endocrine control

  • Hormones: gastrin, secretin, cholecystokinin regulate secretion and motility

  • Target tissues: stomach, pancreas, gallbladder, intestinal smooth muscle

• Nervous control: the enteric nervous system

  • Intrinsic plexus regulating peristalsis and secretion

  • Influenced by autonomic nervous system

Excretory System (BIO)

• Roles in homeostasis

  • Blood pressure: regulation via renin-angiotensin system

  • Osmoregulation: control of water and electrolyte balance

  • Acid–base balance: excretion or retention of H+ and bicarbonate

  • Removal of soluble nitrogenous waste (urea, uric acid)

• Kidney structure

  • Cortex: outer region containing glomeruli, proximal and distal tubules

  • Medulla: inner region with loops of Henle and collecting ducts

• Nephron structure

  • Glomerulus: tuft of capillaries for filtration

  • Bowman’s capsule: collects filtrate

  • Proximal tubule: reabsorption of glucose, amino acids, $H_{2}O$$H_2O$, ions

  • Loop of Henle: establishes osmotic gradient for $H_{2}O$$H_2O$ reabsorption

  • Distal tubule: regulated secretion and reabsorption

  • Collecting duct: final concentration of urine, under hormonal control (ADH)

• Formation of urine

  • Glomerular filtration: passive filtration of plasma

  • Secretion and reabsorption of solutes: selective modification of tubular fluid

  • Concentration of urine: counter-current multiplier mechanism

• Counter-current multiplier mechanism

  • Creates an osmotic gradient in medulla to facilitate water reabsorption

• Storage and elimination: ureter, bladder, urethra

  • Ureter: transports urine from kidney to bladder

  • Bladder: stores urine until voiding

  • Urethra: passageway for urine excretion

• Osmoregulation: capillary reabsorption of $H_{2}O$$H_2O$, amino acids, glucose, ions

  • Maintains proper fluid and solute balance

• Muscular control: sphincter muscle

  • Internal (involuntary) and external (voluntary) sphincters regulate urination

Reproductive System (BIO)

• Male and female reproductive structures and their functions

  • Males: testes (sperm and testosterone production), epididymis, vas deferens, prostate, penis

  • Females: ovaries (oocytes and estrogen/progesterone), fallopian tubes, uterus, vagina

• Gonads

  • Testes and ovaries

  • Produce gametes (sperm, eggs) and sex hormones

• Genitalia

  • External reproductive structures (penis, vulva) for copulation and protective function

• Differences between male and female structures

  • Internal ducts, presence of uterus in females

  • External genital configurations

• Hormonal control of reproduction

  • Hypothalamic-pituitary-gonadal axis (GnRH, LH, FSH)

  • Testosterone, estrogen, progesterone regulate gametogenesis and secondary sex characteristics

• Male and female sexual development

  • Determined by genetic and hormonal factors (SRY gene, hormonal environment)

• Female reproductive cycle

  • Ovarian cycle (follicular phase, ovulation, luteal phase)

  • Uterine cycle (menstrual, proliferative, secretory phases)

• Pregnancy, parturition, lactation

  • Pregnancy: embryo/fetus development in uterus

  • Parturition: childbirth via hormonal signaling (oxytocin)

  • Lactation: milk production in mammary glands, stimulated by prolactin and oxytocin

• Integration with nervous control

  • Parasympathetic and sympathetic innervations modulate arousal and erectile response

  • Sensory feedback influences hormonal release

Muscle System (BIO)

• Important functions

  • Support: maintaining posture and stability

  • Mobility: enabling movement of body parts

  • Peripheral circulatory assistance: muscle contractions aid venous return

  • Thermoregulation (shivering reflex): heat production through involuntary contraction

• Structure of three basic muscle types: striated, smooth, cardiac

  • Striated (skeletal): voluntary, multinucleated, sarcomere organization

  • Smooth: involuntary, found in walls of hollow organs

  • Cardiac: involuntary, striated, intercalated discs

• Muscle structure and control of contraction

  • T-tubule system: facilitates rapid conduction of action potentials into muscle fibers

  • Contractile apparatus: actin (thin) and myosin (thick) filaments

  • Sarcoplasmic reticulum: stores and releases Ca2+ for contraction

  • Fiber type: slow-twitch (red), fast-twitch (white)

  • Contractile velocity of different muscle types related to fiber composition

• Regulation of cardiac muscle contraction

  • Inherent pacemaker cells, autonomic innervation, and gap junctions

• Oxygen debt: fatigue

  • Accumulation of lactic acid, depletion of ATP/oxygen leads to reduced contractile ability

• Nervous control

  • Motor neurons innervate skeletal muscle fibers at neuromuscular junction

  • Neuromuscular junction, motor end plates: site of acetylcholine release and muscle excitation

  • Sympathetic and parasympathetic innervation: affects heart rate and smooth muscle activity

  • Voluntary (somatic) and involuntary (autonomic) muscles

Specialized Cell - Muscle Cell (BIO)

• Structural characteristics of striated, smooth, and cardiac muscle

  • Striated: sarcomeres, multiple nuclei, voluntary control

  • Smooth: spindle-shaped, single nucleus, no sarcomeres, involuntary

  • Cardiac: branching, striated, intercalated discs, involuntary

• Abundant mitochondria in red muscle cells: ATP source

  • Provide energy for sustained contractions

• Organization of contractile elements: actin and myosin filaments, crossbridges, sliding filament model

  • ATP binding and hydrolysis cycle myosin power strokes, pulling actin

• Sarcomeres: I and A bands, M and Z lines, H zone

  • I band: only actin

  • A band: length of myosin filament (remains constant)

  • Z line: boundary of sarcomere

  • M line: midpoint of sarcomere

  • H zone: only myosin (shortens during contraction)

• Presence of troponin and tropomyosin

  • Regulatory proteins controlling actin-myosin binding

• Calcium regulation of contraction

  • Ca2+ binds troponin, shifts tropomyosin, exposes myosin binding sites on actin

Skeletal System (BIO)

• Functions

  • Structural rigidity and support for the body

  • Calcium storage and release to maintain blood Ca2+ levels

  • Physical protection of internal organs (e.g., skull protecting brain)

• Skeletal structure

  • Specialization of bone types, structures: long bones, flat bones, irregular bones

  • Joint structures: synovial, cartilaginous, fibrous

  • Endoskeleton vs. exoskeleton: internal vs. external support

• Bone structure

  • Calcium/protein matrix: hydroxyapatite (calcium phosphate) and collagen

  • Cellular composition of bone: osteoblasts (build), osteoclasts (break down), osteocytes (maintenance)

• Cartilage: structure and function

  • Flexible, avascular connective tissue

  • Provides cushioning and support at joints

• Ligaments, tendons

  • Ligaments connect bone to bone

  • Tendons connect muscle to bone

• Endocrine control

  • Hormones (PTH, calcitonin, vitamin D) regulate bone remodeling and calcium levels

Skin System (BIO)

• Structure

  • Layer differentiation: epidermis (outer), dermis (middle), hypodermis/subcutaneous (inner)

  • Cell types: keratinocytes, melanocytes, Langerhans cells

  • Relative impermeability to $H_{2}O$$H_2O$: prevents dehydration

• Functions in homeostasis and osmoregulation

  • Barrier to fluid loss, regulation of electrolyte balance

• Functions in thermoregulation

  • Insulation via fat layer

  • Evaporative cooling via sweat

  • Vasoconstriction and vasodilation to regulate heat loss

• Hair, erectile musculature

  • Hair traps air for insulation

  • Arrector pili muscles cause hair to stand (goosebumps)

• Fat layer for insulation

  • Adipose tissue in hypodermis helps retain heat

• Sweat glands, location in dermis

  • Produce sweat for evaporative cooling

• Vasoconstriction and vasodilation in surface capillaries

  • Control blood flow and heat dissipation

• Physical protection

  • Nails, calluses, hair protect against abrasion

  • Prevents entry of disease organisms

• Hormonal control: sweating, vasodilation, and vasoconstriction

  • Influenced by autonomic nervous system and hormones (e.g., epinephrine)

Translational Motion (PHY)

• Units and dimensions

  • Physical quantities are measured in base units (e.g., meters, kilograms, seconds) and can be expressed in derived units (e.g., m/s for velocity).

  • Dimensions describe the nature of a physical quantity (e.g., length [L], time [T], mass [M]) and can be used to check the consistency of equations.

• Vectors, components

  • A vector has both magnitude and direction, such as displacement or velocity.

  • Any vector can be resolved into perpendicular components (e.g., x and y directions) to simplify analysis.

• Vector addition

  • Vector addition follows the tip-to-tail method; the resultant vector is found by combining components.

  • Addition is commutative and associative.

• Speed, velocity (average and instantaneous)

  • Speed is the scalar magnitude of velocity and does not include direction.

  • Velocity is a vector defined as displacement over time; average velocity uses total displacement over total time, while instantaneous velocity is the limit as time approaches zero.

• Acceleration

  • Acceleration is a vector that describes the rate of change of velocity over time.

  • Units are $m/s^2$$m/s^2$.

  • Constant acceleration equations include $v=v_0+at$$v = v_0 + at$ and $x=x_0+v_{0}t+\frac{1}{2}a{t}^2$$x = x_0 + v_0 t + \tfrac{1}{2}at^2$.

Force (PHY)

• Newton’s First Law, inertia

  • An object remains at rest or in uniform motion unless acted upon by a net external force.

  • Inertia is related to mass, the property that resists changes in motion.

• Newton’s Second Law ($F=ma$$F = ma$)

  • The net force on an object is equal to its mass times its acceleration.

  • Units: Newtons ($N=kg\cdot m/s^2$$N = kg \cdot m/s^2$).

• Newton’s Third Law, forces equal and opposite

  • For every action force, there is an equal and opposite reaction force.

  • These forces act on different objects and do not cancel each other out.

• Friction, static and kinetic

  • Friction opposes motion between surfaces in contact.

  • Static friction prevents motion until a threshold, while kinetic friction acts during relative motion.

  • Kinetic friction magnitude is often $f_k={\mu }_{k}N$$f_k = \mu_k N$, where $N$$N$ is the normal force.

• Center of mass

  • The point at which the mass distribution of an object or system is balanced.

  • For a system of particles, $x_{cm}=\frac{\sum m_i{x}_i}{\sum m_i}$$x_{cm} = \frac{\sum m_i x_i}{\sum m_i}$.

Equilibrium (PHY)

• Vector analysis of forces acting on a point object

  • In equilibrium, the net force on the object is zero.

  • Sum of all vector forces in each dimension must be zero, leading to no acceleration.

• Torques, lever arms

  • Torque is the rotational equivalent of force, $\tau =rF\sin \theta$$\tau = rF \sin\theta$.

  • The lever arm is the perpendicular distance from the pivot to the line of action of the force.

  • For rotational equilibrium, the net torque around a pivot is zero.

Work (PHY)

• Work done by a constant force: $W=Fd\cos \theta$$W = F d \cos\theta$

  • Work is the energy transferred by a force applied over a displacement.

  • If force and displacement are perpendicular, no work is done.

• Mechanical advantage

  • Using simple machines (e.g., levers, pulleys) to reduce the force required to do a certain amount of work.

• Work Kinetic Energy Theorem

  • The net work done on an object is equal to its change in kinetic energy: $W_{net}=\mathrm{\Delta }KE$$W_{net} = \Delta KE$.

• Conservative forces

  • Forces that have associated potential energies and do not dissipate mechanical energy.

  • Examples include gravity and elastic (spring) forces.

Energy of Point Object Systems (PHY)

• Kinetic Energy: $KE=\frac{1}{2}m{v}^2$$KE = \tfrac{1}{2} mv^2$; units

  • Units: Joules ($J=kg\cdot m^2/s^2$$J = kg \cdot m^2 / s^2$).

  • Kinetic energy depends on mass and the square of velocity.

• Potential Energy

  • Stored energy due to position or configuration.

• $PE=mgh$$PE = mgh$ (gravitational, local)

  • Near Earth’s surface, gravitational potential energy depends on height above a reference point.

• $PE=\frac{1}{2}k{x}^2$$PE = \tfrac{1}{2} kx^2$ (spring)

  • Elastic potential energy stored in a spring (Hooke’s Law).

• Conservation of energy

  • In a closed system with no non-conservative forces, total mechanical energy is constant: $K{E}_i+P{E}_i=K{E}_f+P{E}_f$$KE_i + PE_i = KE_f + PE_f$.

• Power, units

  • Power is the rate of work done: $P=\frac{W}{t}$$P = \frac{W}{t}$.

  • Units: Watts ($W=J/s$$W = J/s$).

Periodic Motion (PHY)

• Amplitude, frequency, phase

  • Amplitude: maximum displacement from equilibrium.

  • Frequency: number of cycles per unit time ($f=1/T$$f = 1/T$).

  • Phase: initial angle or starting point of the motion cycle.

• Transverse and longitudinal waves: wavelength and propagation speed

  • Transverse waves oscillate perpendicular to the direction of propagation (e.g., light waves).

  • Longitudinal waves oscillate parallel to direction of propagation (e.g., sound waves).

  • Wavelength ($\lambda$$\lambda$) is the spatial period of the wave.

  • Wave speed $v=\lambda f$$v = \lambda f$.

Fluids (PHY)

• Density, specific gravity

  • Density ($\rho$$\rho$): mass per unit volume ($\rho =\frac{m}{V}$$\rho = \frac{m}{V}$)

  • Specific gravity: ratio of a substance's density to the density of water ($\text{SG}=\frac{{\rho }_{\text{substance}}}{{\rho }_{H_{2}O}}$$\text{SG} = \frac{\rho_{\text{substance}}}{\rho_{H_2O}}$)

• Buoyancy, Archimedes’ Principle

  • Buoyant force ($F_b$$F_b$) equals the weight of the fluid displaced: $F_b={\rho }_{\text{fluid}}{V}_{\text{submerged}}g$$F_b = \rho_{\text{fluid}} V_{\text{submerged}} g$

  • Determines whether an object floats, sinks, or remains neutrally buoyant

• Hydrostatic pressure

  • Pressure due to the weight of a fluid at a given depth: $P=P_{\text{atm}}+\rho gh$$P = P_{\text{atm}} + \rho g h$

• Pascal’s Law

  • Pressure applied to an enclosed fluid is transmitted undiminished to all parts of the fluid and walls of the container

• Hydrostatic pressure; $P=\rho gh$$P = \rho g h$ (pressure vs. depth)

  • Pressure increases linearly with depth in a fluid

• Viscosity: Poiseuille Flow

  • Viscosity ($\eta$$\eta$) measures fluid's resistance to flow

  • Laminar flow in a tube: Poiseuille’s Law relates flow rate ($Q$$Q$) to radius ($r$$r$), viscosity ($\eta$$\eta$), length ($L$$L$), and pressure difference ($\mathrm{\Delta }P$$\Delta P$): $Q=\frac{\pi r^4\mathrm{\Delta }P}{8\eta L}$$Q = \frac{\pi r^4 \Delta P}{8 \eta L}$

• Continuity equation ($A\cdot v=\text{constant}$$A \cdot v = \text{constant}$)

  • For incompressible fluids, volume flow rate is constant throughout a pipe: $A_1{v}_1=A_2{v}_2$$A_1 v_1 = A_2 v_2$

• Concept of turbulence at high velocities

  • Flow transitions from laminar to turbulent when Reynolds number exceeds a critical value

• Surface tension

  • Results from cohesive forces between fluid molecules; causes liquids to minimize surface area

• Bernoulli’s equation

  • Describes conservation of energy in fluid flow: $P+\frac{1}{2}\rho v^2+\rho gh=\text{constant}$$P + \frac{1}{2}\rho v^2 + \rho g h = \text{constant}$

  • Higher velocity flow regions correspond to lower pressure

• Venturi effect, pitot tube

  • Venturi effect: reduction in fluid pressure when fluid flows through a constricted section

  • Pitot tube measures fluid flow velocity using pressure differences

Circulatory System (BIO)

• Arterial and venous systems; pressure and flow characteristics

  • Arteries: high pressure, thicker walls, pulse flow

  • Veins: lower pressure, valves to prevent backflow, rely on skeletal muscle pumps

  • Blood flow driven by pressure gradients from heart contractions

Gas Phase (GC, PHY)

• Absolute temperature, (K) Kelvin Scale

  • $T_{\text{K}}=T_{\text{°C}}+273.15$$T_{\text{K}} = T_{\text{°C}} + 273.15$

• Pressure, simple mercury barometer

  • Measures atmospheric pressure ($P_{\text{atm}}\approx 760\text{ mmHg}$$P_{\text{atm}} \approx 760 \text{ mmHg}$ at sea level)

• Molar volume at 0°C and 1 atm = 22.4 L/mol

  • For an ideal gas, 1 mole occupies 22.4 L at STP

• Ideal gas

  • Hypothetical gas that follows $PV=nRT$$PV = nRT$

• Definition

  • Ideal gases have no intermolecular forces and occupy no volume

• Ideal Gas Law: $PV=nRT$$PV = nRT$

  • Relates pressure, volume, moles, and temperature

• Boyle’s Law: $PV=\text{constant}$$PV = \text{constant}$

  • At constant $T$$T$ and $n$$n$, decreasing volume increases pressure

• Charles’ Law: $\frac{V}{T}=\text{constant}$$\frac{V}{T} = \text{constant}$

  • At constant $P$$P$ and $n$$n$, volume increases linearly with temperature

• Avogadro’s Law: $\frac{V}{n}=\text{constant}$$\frac{V}{n} = \text{constant}$

  • At constant $P$$P$ and $T$$T$, volume is proportional to number of moles

• Kinetic Molecular Theory of Gases

  • Gas particles in constant random motion

  • No intermolecular attractions, elastic collisions, and average kinetic energy proportional to $T$$T$

• Heat capacity at constant volume and at constant pressure (PHY)

  • $C_V$$C_V$ and $C_P$$C_P$ differ due to work done during expansion at constant pressure ($C_P>C_V$$C_P > C_V$ for ideal gases)

• Boltzmann’s Constant (PHY)

  • Relates average kinetic energy of particles in a gas to temperature ($k_B=1.380649\times {10}^{-23}\text{ J/K}$$k_B = 1.380649 \times 10^{-23} \text{ J/K}$)

• Deviation of real gas behavior from Ideal Gas Law

  • Qualitative: Real gases have finite particle volumes and intermolecular forces

  • Quantitative (Van der Waals’ Equation):

    • $(P+a(\frac{n}{V}{)}^2)(V-nb)=nRT$$(P + a(\frac{n}{V})^2)(V - nb) = nRT$

    • Corrects for intermolecular forces ($a$$a$) and finite molecular volume ($b$$b$)

• Partial pressure, mole fraction

  • Partial pressure $P_i=X_i{P}_{\text{total}}$$P_i = X_i P_{\text{total}}$ where $X_i=\frac{n_i}{n_{\text{total}}}$$X_i = \frac{n_i}{n_{\text{total}}}$

• Dalton’s Law relating partial pressure to composition

  • Total pressure is sum of partial pressures: $P_{\text{total}}=\sum P_i$$P_{\text{total}} = \sum P_i$

Electrostatics (PHY)

• Charge, conductors, charge conservation

  • Charge is a fundamental property of matter that comes in two types: positive and negative

  • Conductors are materials that allow free flow of charge; electrons move easily through them

  • Charge conservation states that total charge in a closed system remains constant

• Insulators

  • Materials that do not allow free flow of charge; electrons are bound tightly and do not move freely

• Coulomb’s Law

  • The electrostatic force between two point charges is given by $F=k\frac{q_1{q}_2}{r^2}$$F = k \frac{q_1 q_2}{r^2}$, where $k$$k$ is Coulomb’s constant, $q_1$$q_1$ and $q_2$$q_2$ are charges, and $r$$r$ is their separation

• Electric field E

  • An electric field at a point in space is defined as the force per unit charge at that point, $E=\frac{F}{q}$$E = \frac{F}{q}$

• Field lines

  • Imaginary lines that represent the direction and strength of an electric field; they emanate from positive charges and terminate on negative charges

• Field due to charge distribution

  • Superposition principle allows calculation of total field by summing contributions from all charges

• Electrostatic energy, electric potential at a point in space

  • Electric potential is the potential energy per unit charge, $V=\frac{U}{q}$$V = \frac{U}{q}$

  • Electrostatic energy stored in a configuration of charges can be found by summing the work required to assemble those charges

Circuit Elements (PHY)

• Current I = 6Q/6t, sign conventions, units

  • Electric current is the rate of flow of charge, $I=\frac{\mathrm{\Delta }Q}{\mathrm{\Delta }t}$$I = \frac{\Delta Q}{\Delta t}$

  • Measured in amperes (A)

  • Direction of conventional current is from positive to negative terminals

• Electromotive force, voltage

  • EMF (electromotive force) is the potential difference produced by a source, measured in volts (V)

  • Voltage is the potential difference between two points in a circuit

• Resistance

  • A measure of how much a component impedes current flow; measured in ohms ($\mathrm{\Omega }$$\Omega$)

• Ohm’s Law: I = V/R

  • States that current is proportional to voltage and inversely proportional to resistance, $I=\frac{V}{R}$$I = \frac{V}{R}$

• Resistors in series

  • Equivalent resistance $R_{eq}=R_1+R_2+...$$R_{eq} = R_1 + R_2 + ...$

• Resistors in parallel

  • Equivalent resistance $1/R_{eq}=1/R_1+1/R_2+...$$1/R_{eq} = 1/R_1 + 1/R_2 + ...$

• Resistivity: q = R•A / L

  • Resistivity relates the resistance of a material to its geometry: $R=\rho \frac{L}{A}$$R = \rho \frac{L}{A}$

  • $\rho$$\rho$ is resistivity, $L$$L$ is length, and $A$$A$ is cross-sectional area

• Capacitance

  • The ability of a device to store charge per unit voltage, $C=\frac{Q}{V}$$C = \frac{Q}{V}$

• Parallel plate capacitor

  • Two parallel plates separated by a distance form a capacitor with $C=\frac{{ϵ}_{0}A}{d}$$C = \frac{\epsilon_0 A}{d}$ in vacuum or air

• Energy of charged capacitor

  • Energy stored in a capacitor $U=\frac{1}{2}C{V}^2$$U = \frac{1}{2}CV^2$

• Capacitors in series

  • Equivalent capacitance $1/C_{eq}=1/C_1+1/C_2+...$$1/C_{eq} = 1/C_1 + 1/C_2 + ...$

• Capacitors in parallel

  • Equivalent capacitance $C_{eq}=C_1+C_2+...$$C_{eq} = C_1 + C_2 + ...$

• Dielectrics

  • Insulating materials placed between capacitor plates that increase the capacitance by reducing the effective electric field

• Conductivity

  • Inverse of resistivity, describes how easily current flows in a material

• Metallic

  • Conductors where electrons flow freely

• Electrolytic

  • Conductive solutions with ions as charge carriers

• Meters

  • Ammeters measure current and are placed in series

  • Voltmeters measure voltage and are placed in parallel

Magnetism (PHY)

• Definition of magnetic field B

  • A magnetic field is a field that exerts forces on moving charges and magnetic materials; measured in teslas (T)

• Motion of charged particles in magnetic fields; Lorentz force

  • A charged particle moving in a magnetic field experiences a force $F=qvB\sin \left(\theta \right)$$F = qvB \sin(\theta)$, where $v$$v$ is velocity and $\theta$$\theta$ is the angle between velocity and field

Electrochemistry (GC)

• Electrolytic cell

  • An electrochemical cell that uses external energy to drive a nonspontaneous reaction

• Electrolysis

  • Decomposition of substances using electric current

• Anode, cathode

  • Anode is the electrode where oxidation occurs

  • Cathode is the electrode where reduction occurs

• Electrolyte

  • Ionic medium that conducts electricity between electrodes

• Faraday’s Law relating amount of elements deposited (or gas liberated) at an electrode to current

  • The mass of substance deposited is proportional to the total charge passed

• Electron flow; oxidation, and reduction at the electrodes

  • Electrons flow from anode to cathode

  • Oxidation is loss of electrons, reduction is gain of electrons

• Galvanic or Voltaic cells

  • Spontaneous chemical reactions produce electrical energy

• Half-reactions

  • Reactions at each electrode; show electron transfer explicitly

• Reduction potentials; cell potential

  • Each half-reaction has a standard reduction potential; the cell potential is the difference between the two half-reactions

• Direction of electron flow

  • Electrons flow from the electrode with lower reduction potential to higher reduction potential

• Concentration cell

  • A galvanic cell with identical electrodes but different ion concentrations; voltage generated due to concentration difference

• Batteries

  • Commercially available electrochemical cells or series of cells

• Electromotive force, Voltage

  • EMF is the potential difference that drives current flow in a cell

• Lead-storage batteries

  • Rechargeable batteries using lead and lead dioxide electrodes in sulfuric acid

• Nickel-cadmium batteries

  • Rechargeable batteries with nickel oxide hydroxide and cadmium electrodes in a potassium hydroxide solution

Specialized Cell - Nerve Cell (BIO)

• Myelin sheath, Schwann cells, insulation of axon

  • Myelin sheath is a lipid-rich layer produced by Schwann cells in the peripheral nervous system; it insulates the axon and speeds up signal conduction

• Nodes of Ranvier: propagation of nerve impulse along axon

  • Gaps in the myelin sheath that allow action potentials to jump from node to node, increasing conduction velocity

Sound (PHY)

• Production of sound

  • Sound originates from vibrating objects; vibrations create pressure waves in media (solids, liquids, gases)

  • These pressure waves propagate as longitudinal waves where particles oscillate parallel to direction of wave travel

• Relative speed of sound in solids, liquids, and gases

  • Generally fastest in solids, slower in liquids, and slowest in gases

  • Speed depends on medium’s stiffness and density

• Intensity of sound, decibel units, log scale

  • Intensity is power per unit area ($I=P/A$$I = P/A$) measured in $W/m^2$$W/m^2$

  • Decibels (dB) use a logarithmic scale: $dB=10\log \left(I/I_0\right)$$dB = 10 \, \log(I/I_0)$ with $I_0$$I_0$ = threshold intensity

• Attenuation (Damping)

  • Reduction in amplitude (and intensity) of a sound wave as it propagates due to absorption and scattering

  • Higher frequency sounds attenuate more rapidly

• Doppler Effect: moving sound source or observer, reflection of sound from a moving object

  • Observed frequency changes if source or observer is moving

  • For source moving towards observer, frequency increases; moving away, frequency decreases

  • Reflections from moving objects (e.g., Doppler radar) also shift frequency

• Pitch

  • Related to perceived frequency of the sound wave

  • Higher frequency corresponds to higher pitch

• Resonance in pipes and strings

  • Standing waves form when certain wavelengths fit integer multiples in pipes or strings

  • Resonant frequencies produce large amplitude vibrations

• Ultrasound

  • Sound waves above human hearing range ($>20,000Hz$$> 20,000 \, Hz$)

  • Used in medical imaging and industrial flaw detection

• Shock waves

  • Produced when an object moves faster than the speed of sound, causing a large amplitude pressure front (sonic boom)

Light, Electromagnetic Radiation (PHY)

• Concept of Interference; Young Double-slit Experiment

  • Interference occurs when two waves overlap, producing regions of constructive and destructive interference

  • Young’s double-slit: coherent light through two slits creates interference pattern of bright and dark fringes

• Thin films, diffraction grating, single-slit diffraction

  • Thin films: interference from light reflected off top and bottom surfaces leads to color patterns

  • Diffraction grating: large number of closely spaced slits disperses light into spectrum

  • Single-slit diffraction: a single aperture creates a diffraction pattern with a central maximum and smaller side maxima

• Other diffraction phenomena, X-ray diffraction

  • X-ray diffraction used to determine crystal structures; constructive interference occurs at specific angles related to lattice spacing

• Polarization of light: linear and circular

  • Polarized light has electric field oscillating in a particular direction

  • Circular polarization results from two perpendicular waves differing in phase by 90°

• Properties of electromagnetic radiation

  • EM radiation consists of oscillating electric and magnetic fields, perpendicular to each other and to direction of propagation

  • Speed in vacuum is constant ($c\approx 3\times {10}^{8}m/s$$c \approx 3 \times 10^8 \, m/s$)

• Velocity equals constant c, in vacuo

  • All EM waves travel at $c$$c$ in vacuum

• Electromagnetic radiation consists of perpendicularly oscillating electric and magnetic fields; direction of propagation is perpendicular to both

  • Forms a transverse wave

• Classification of electromagnetic spectrum, photon energy E = hf

  • $E=hf$$E = h f$ where $h$$h$ is Planck’s constant, $f$$f$ is frequency

  • Spectrum ranges from radio (low frequency, low energy) to gamma (high frequency, high energy)

• Visual spectrum, color

  • Visible light: approximately $400-700nm$$400-700 \, nm$

  • Different wavelengths correspond to different perceived colors

Molecular Structure and Absorption Spectra (OC)

• Infrared region

  • IR spectroscopy identifies functional groups by characteristic vibrational frequencies

• Intramolecular vibrations and rotations

  • Molecules absorb IR at frequencies matching vibrational modes

• Recognizing common characteristic group absorptions, fingerprint region

  • Functional groups have predictable IR absorption bands

  • Fingerprint region (around $600-1400c{m}^{-1}$$600-1400 \, cm^{-1}$) unique to each molecule

• Visible region (GC)

  • Electronic transitions in visible region cause color perception

• Absorption in visible region gives complementary color (e.g., carotene)

  • Compound absorbing certain wavelength appears as the complementary color

• Effect of structural changes on absorption (e.g., indicators)

  • Changes in conjugation or environment shift absorption maxima

  • pH indicators change color by altering conjugation or protonation states

• Ultraviolet region

  • UV spectroscopy probes electronic transitions ($\pi \to {\pi }^{\ast }$$\pi \to \pi^{*}$, $n\to {\pi }^{\ast }$$n \to \pi^{*}$)

• π-Electron and non-bonding electron transitions

  • Conjugated systems absorb at longer wavelengths (lower energy)

• Conjugated systems

  • More conjugation leads to bathochromic shift (red shift) in absorption

• NMR spectroscopy

  • Uses magnetic fields to study hydrogen nuclei environments

• Protons in a magnetic field; equivalent protons

  • Chemical shift influenced by electron environment

  • Equivalent protons produce one NMR signal

• Spin-spin splitting

  • Neighboring protons split signals into multiplets following n+1 rule

Geometrical Optics (PHY)

• Reflection from plane surface: angle of incidence equals angle of reflection

  • ${\theta }_{incident}={\theta }_{reflected}$$\theta_{incident} = \theta_{reflected}$ measured from normal

• Refraction, refractive index n; Snell’s law: n1 sin Δ1 = n2 sin Δ2

  • Snell’s law: $n_1\sin \left({\theta }_1\right)=n_2\sin \left({\theta }_2\right)$$n_1 \sin(\theta_1) = n_2 \sin(\theta_2)$

  • $n=c/v$$n = c/v$ where $v$$v$ is speed of light in medium

• Dispersion, change of index of refraction with wavelength

  • Different wavelengths have slightly different refractive indices, causing white light to spread into colors

• Conditions for total internal reflection

  • Occurs when light travels from higher n to lower n at angle greater than critical angle

• Spherical mirrors

  • Concave mirrors converge light; convex mirrors diverge light

• Center of curvature

  • Point on optical axis around which mirror surface is defined

• Focal length

  • Half the radius of curvature for spherical mirrors

• Real and virtual images

  • Real images form where rays converge; virtual images form where rays appear to diverge from

• Thin lenses

  • Converging (convex) lenses focus light; diverging (concave) lenses spread light

• Use of formula 1/p + 1/q = 1/f, with sign conventions

  • Lens equation: $1/p+1/q=1/f$$1/p + 1/q = 1/f$; p = object distance, q = image distance, f = focal length

• Lens strength, diopters

  • Lens power $P=1/f$$P = 1/f$ in meters, measured in diopters (D)

• Combination of lenses

  • Powers add: $P_{total}=P_1+P_2$$P_{total} = P_1 + P_2$

• Lens aberration

  • Imperfections causing distortion: chromatic and spherical aberrations

• Optical Instruments, including the human eye

  • Eye acts as converging lens system focusing light onto retina

  • Instruments like microscopes and telescopes use lens combinations to magnify images