Title: Jack Sparrow Biochem / Biochemistry / Biochemistry Chapter 1
Tags: #JackSparrow::#B/B::#Biochemistry::#Chapter.1

Q: What is an amino acid?
A: An amino acid is a molecule that contains an amino group (-NH_2) and a carboxyl group (-COOH).

Q: What is a side chain?
A: A side chain, or R group, is the part of the amino acid that defines and specifies the various amino acids.

Q: What are the proteinogenic amino acids?
A: Proteinogenic amino acids are the 20 alpha amino acids encoded by the human genetic code.  These are the only amino acids with which you need to have a memorized familiarity.

Q: With the exception of glycine, all amino acids are [...]
A: chiral

Q: All chiral amino acids in eukaryotes are [L- or D- amino acids?]
A: L

Q: What are Glycine's structure, character, three letter abbreviation, and one letter abbreviation?
A: Glycine, Gly, or G is a non-polar aliphatic amino acid.  Also unique in that it is non-chiral!

Q: What are Valine's structure, character, three letter abbreviation, and one letter abbreviation?
A: Valine, Val, or V is a non-polar, aliphatic amino acid.

Q: What are Leucine's structure, character, three letter abbreviation, and one letter abbreviation?
A: Leucine, Leu, or L is a non-polar aliphatic amino acid.

Q: What are Alanine's structure, character, three letter abbreviation, and one letter abbreviation?
A: Alanine, Ala, or A is a non-polar aliphatic amino acid.

Q: What are Isoleucine's structure, character, three letter abbreviation, and one letter abbreviation?
A: Isoleucine, Ile, or I is a non-polar, aliphatic amino acid.

Q: What are Methionine's structure, character, three letter abbreviation, and one letter abbreviation?
A: Methionine, Met, or M is a (relatively) non-polar amino acid.  It is also one of the only two amino acids that contains sulfur!

Q: What are Proline's structure, character, three letter abbreviation, and one letter abbreviation?
A: Proline, Pro, or P is a non-polar amino acid.  It is also unique in its cyclic structure, which severly hampers proline's flexibility.
Is what damages the secondary structures of secondary proteins if in the middle (found in kinks/turns of beta) so usually in the start of alpha helices and beta sheets

Q: What are Tryptophan's structure, character, three letter abbreviation, and one letter abbreviation?
A: Tryptophan, Trp, or W is a nonpolar aromatic amino acid.
Twyptophan --> W

Q: What are Phenylalanine's structure, character, three letter abbreviation, and one letter abbreviation?
A: Phenylalanine, Phe, or F is an nonpolar, aromatic amino acid.

Q: What are Tyrosine's structure, character, three letter abbreviation, and one letter abbreviation?
A: Tyrosine, Tyr, or Y is a just barely polar aromatic amino acid.
Tyr --> Y

Q: What are Serine's structure, character, three letter abbreviation, and one letter abbreviation?
A: Serine, Ser, or S is a polar amino acid.

Q: What are Threonine's structure, character, three letter abbreviation, and one letter abbreviation?
A: Threonine, Thr, or T is a polar amino acid.

Q: What are Asparagine's structure, character, three letter abbreviation, and one letter abbreviation?
A: Asparagine, Asn, or N is a polar amino acid with an amide bond in the side chain.
Asn --> N

Q: What are Glutamine's structure, character, three letter abbreviation, and one letter abbreviation?
A: Glutamine, Gln, or Q is a polar amino acid with an amide bond in the side chain.

Q: What are Cysteine's structure, character, three letter abbreviation, and one letter abbreviation?
A: Cysteine, Cys, or C is a polar amino acid.  It is also one of the only two amino acids with a sulfur, and it is unique in that it can engage in disulfide bonds with other nearby cysteines.

Q: What are Aspartic Acid's structure, character, three letter abbreviation, and one letter abbreviation?
A: Aspartic Acid, Asp, or D is an hydrophillic/acidic/negatively charged amino acid. (aspartate is deprotonated form)

Q: What are Glutamic Acid's structure, character, three letter abbreviation, and one letter abbreviation?
A: Glutamic Acid, Glu, or E is an hydrophillic/acidic/negatively charged amino acid.
E is missing from Glu --> E

Q: What are Arginine's structure, character, three letter abbreviation, and one letter abbreviation?
A: Arginine, Arg, or R is a basic/positively charged amino acid.

Q: What are Lysine's structure, character, three letter abbreviation, and one letter abbreviation?
A: Lysine, Lys, K ; Lysine is hydrophilic/basic/positively charged

Q: What are Histidine's structure, character, three letter abbreviation, and one letter abbreviation?
A: Histidine, His, or H is a basic/positively charged amino acid.

Q: What does it mean to be amphoteric?
A: An amphoteric substance is something that can react like an acid or a base.
Amino acids are amphoteric because the carboxyl group can donate protons and the amino group can accept protons.

Q: At low ph, ionizable groups tend to be [protonated or deprotonated?]
A: protonated

Q: At high ph, ionizable groups tend to be [protonated or deprotonated?]
A: deprotonated

Q: If the pH is lower than the pKa of a group, then the group will be [protonated or deprotonated?]
A: protonated

Q: If the pH is higher than the pKa of a group, then the group will be [protonated or deprotonated?]
A: deprotonated

Q: What is a zwitterion?
A: A zwitterion is a molecule with both a positive and a negative charge simultaneously.  This is seen in amino acids at neutral and body pH's.

Q: What will the titration curve of an amino acid look like?
A: The titration curve of an amino acid will look like the combination of two monoprotic titration curves (or three if the side chain has an ionizable group)

Q: What is the isoelectric point (pI)?
A: Isoelectric point or pI is the pH at which the amino acid is completely neutral as a result of all positive and negative charges balancing out.

Q: How does one calculate isoelectric point?
A: One must take the pKa's of the functional groups that provide the protein with a +1 and a -1 charge respectively.  Then, one simply averages them.  For amino acids with no ionizable side chain, this is simply the average of the pKa of the carboxyl group and the pKa of the amino group.
Note, for amino acids with ionizable side chains, it is important to correctly select the 2 pKa's that correspond to -1 and +1 charge out of the three available pKa's.
Remember: If pH is higher than pKa it "wins the proton"

Q: Amino acids with acidic side chains have [high or low?] pI's?
A: low

Q: Amino acids with basic side chains have [high or low?] pI's?
A: high
Extra: Trends follow pH

Q: What is a peptide?
A: A peptide is a chain of amino acids.

Q: What is a residue?
A: A residue is just another name for amino acid.  It is usually used when referring to amino acids in a peptide.

Q: What is an oligopeptide?
A: An oligopeptide is a relatively small peptide of up to only 20 residues.

Q: What is a polypeptide?
A: A polypeptide is any chain of amino acids that is longer than 20 amino acids.

Q: What is a peptide bond?
A: Peptide bond is just a specific name for the amide bond that holds amino acids together.

Q: Peptide Bond Formation occurs via [what kind of reaction?]
A: condensation aka dehydration
Extra: Remember, dehydration reactions displace a water from the molecules reacting.

Q: What is meant by the term N-terminus?
A: An N-terminus is the free amino group at the very beginning of a peptide.

Q: What is meant by the term C-terminus?
A: A C-terminus is the free carboxyl group at the very end of a peptide.

Q: In what direction are peptides drawn?
A: Left to right from N-terminus to C-terminus.

Q: Describe the strength of the peptide bond.
A: The peptide bond is resonance stabilized, and is thus very strong.  More often than not, we need to use special enzymes to break these bonds down.

Q: What are the four levels of structure seen in proteins?
A: 1.  Primary Structure
2.  Secondary Structure
3.  Tertiary Structure
4.  Quaternary Structure

Q: What is primary structure and what is its characteristic bond?
A: Primary structure refers to the actual sequence of amino acids in the protein.  These amino acids are held together by peptide bonds.

Q: What is secondary structure and what is its characteristic bond?
A: Secondary structure refers to the formation of repeating patterns of pleated sheets and alpha helices.  These patterns are held together by hydrogen bonds between the carboxyl and amino group backbone of the amino acids.

Q: What is tertiary structure and what is its characteristic bond?
A: Tertiary structure refers to the three dimensional folding of the polypeptide chain into its final form.
These forms are held together by:
1. Hydrogen bonds between side chains,
2. Salt bridges between positively and negatively charged side chains
3. Disulfide bonds between cysteine residues.

Q: What is quaternary structure?
A: Quaternary structure refers to the overall structure obtained when two or more separate polypeptides in tertiary structure combine.

Q: What is sequencing?
A: Sequencing is a laboratory technique that allows one to determine the primary structure of a protein.  This is most easily done by using the DNA that coded for the protein, although the protein itself can be used if necessary.
As you can see below, you can figure out the sequence by trying to replicate the DNA while adding ddnucleotides, which halt replication.  For example, if only one nucleotide is produced from the DNA in the ddATP beaker, then I know the first nucleotide in the DNA is A.  This can be repeated to get the whole sequence of DNA, which can then be translated into the amino acids present.

Q: What is an alpha helix?
A: An alpha helix is a rodlike structure in which the peptide chain coils clockwise around a central axis.

Q: What is a beta pleated sheet?
A: A beta pleated sheet is a structure in which peptide chains lie alongside one another, forming rows.

Q: Describe the special role played by proline in secondary structure
A: Proline's rigid ring structure makes it unsuitable for inclusion in the middle of alpha helices and beta pleated sheets.  When introduced into the middle of these structures, proline produces kinks in the secondary structure.  However, proline's rigidity makes it useful at the start of alpha helices and in the turns taken by beta pleated sheets.  These are the two locations one is likely to find proline.

Q: What are the two main structural classes of proteins?
A: 1.  Fibrous Proteins
2.  Globular proteins

Q: What is a fibrous protein?
A: A fibrous protein is a protein that resembles long sheets or strands.

Q: What is a globular protein?
A: A globular protein is a protein that is spherical and round

Q: During the formation of tertiary structure, hydrophobic amino acids are pushed [into the core or to the exterior?]
A: into the core

Q: What is Cystine?
A: Cystine is the name used to refer to the disulfide bond made between two cysteine's in a protein.

Q: The formation of a disulfide bond is a [reduction or oxidation?] reaction
A: oxidation

Q: What is denaturation?
A: Denaturation is the process by which a protein loses its tertiary structure.  This is usually accomplished through disruption of the bonds that hold tertiary structure together.
Most common causes of denaturation are by solutes or by heat.

Q: What is a solvation layer?
A: A solvation layer is a layer formed around a molecule by nearby solvent molecules.  These result as a consequence of electrostatic interactions.

Q: Why is the pushing of nonpolar amino acids into the core of a protein spontaneous?
A: When there are nonpolar amino acids on the outside of the protein, water cannot hydrogen bind with the protein, which means it can only hydrogen bind with itself.  This reduces water's options, which lowers its entropy, which makes this process unfavorable.
On the other hand, if water can hydrogen bind with the outside of the protein (polar AA's on the exterior), that gives water more options and lowers the entropy of the system, which is favorable.

Q: What is a subunit?
A: A sub unit refers to one of the functional tertiary peptides comprising the overall quaternary peptide.

Q: What roles can the formation of quaternary structure serve?
A: 1.  Quaternary structure can stabilize a protein
2.  Quaternary structure can reduce the amount of DNA needed to encode a protein complex
3.  Quaternary structure can bring catalytic sites together, which allows intermediates to be shuttled directly to the next step.
4.  Quaternary structure can induce cooperativity, also known as allosteric effects.

Q: What is a conjugated protein?
A: A conjugated protein is a protein that derives part of its function from the presence of prosthetic groups.

Q: What is a prosthetic group?
A: A prosthetic group is a covalently attached molecule that allows a protein to function.  Prosthetic groups can be organic molecules such as vitamins or metal ions, like iron.

Q: What is a lipoproptein?
A: A lipoprotein is a protein with a lipid based prosthetic group.

Q: What is a glycoprotein?
A: A glycoprotein is a protein with a carbohydrate based prosthetic group.

Q: What is a nucleoprotein?
A: A nucleoprotein is a protein with a nucleotide based prosthetic group.

Q: What are common ways to denature a protein?
A: 1.  Heat.  As temp increases, hydrogen bonds and salt bridges destabilize.
2.  Solutes such as urea and beta mercaptoethanol can disrupt disulfide bridges, causing denaturation.
3.  Detergents can solubilize proteins, which disrupts noncovalent bonds and therefore promotes denaturation.