Title: Jack Sparrow Biochem / Biochemistry / Biochemistry Chapter 7
Tags: #JackSparrow::#B/B::#Biochemistry::#Chapter.7

Q: What is the central dogma of biology?
A: The central dogma refers to the way proteins are made in our body.  First, DNA is transcribed into RNA, then RNA is translated into protein.

Q: What are the three main types of RNA?
A: 1.  mRNA
2.  tRNA
3.  rRNA

Q: What is a codon?
A: A codon is any three nucleotides in a row.  Codons are what the ribosome reads to translate mRNA into Amino Acids.

Q: What is mRNA?
A: mRNA is the link between DNA and proteins.  DNA is transcribed into mRNA, which travels out of the nucleus to the ribosomes where it can be translated into proteins.

Q: What does it mean for eukaryotic mRNA to be monocistronic?
A: Monocistronic RNA is mRNA that can only be translated into one protein product.  That means every single on of the thousands of proteins we contain has its own mRNA strand.

Q: What does it mean for prokaryotic mRNA to be polycistronic?
A: Polycistronic mRNA is mRNA that can be translated into more than one protein product.  This means that 10 different proteins in a bacteria may all be made from the same strand of mRNA.  This is possible because you can get a different protein product if you don't translate all of the mRNA or don't start the translation in the same place.

Q: What is tRNA?
A: tRNA is responsible for translating the language of nucleic acids into amino acids at the ribosome.  Each tRNA molecule contains a folded strand of RNA that includes a three nucleotide anticodon and an amino acid.  The anticodon of tRNA binds to the codon of mRNA and brings with it the appropriate amino acid.

Q: What does it mean when someone says a tRNA molecule is charged or activated?
A: tRNA molecules don't always have an amino acid attached.  A charged or activated tRNA molecule is a tRNA with an amino acid attached.

Q: What is aminoacyl-tRNA synthetase?
A: Aminoacyl-tRNA Synthetases are a class of enzymes that attach specific amino acids to specific tRNA molecules (based on the anticodon).  Each type of amino acid is activated by a different aminoacyl-tRNA synthetase.  Amino Acids are always added to the free hydroxyl at the 3' end of the tRNA.

Q: What is rRNA?
A: rRNA is synthesized in the nucleolus and functions as an important structural component of ribosomes.  rRna molecules can also act as ribozymes.

Q: What is a ribozyme?
A: A ribozyme is a strand of RNA with enzymatic properties.

What are the three stop codons?

Q: What is the start codon?
A: AUG
Mnemonic: School starts in AUGust.

Q: Describe start and stop codons
A: Start and stop codons are the codons that start and stop protein translation respectively.  In other words, ribosomes will not start translating mRNA into amino acids unless it sees an AUG codon.  On the other hand, translation will not stop until a UAA, UGA, or UAG codon appears.

Q: What is translation?
A: Translation is the process of protein synthesis in the ribosome using an mRNA template.

Q: What does it mean when we say codons are specific?
A: Codons are specific because each individual only codes for one amino acid.

Q: What does it mean when we say codons are degenerate?
A: Codons are degenerate because there are multiple different codons that code for the same amino acid.  This is most notably seen in third base wobble.

Q: What is third base wobble?
A: Third base wobble is the tendency for the third base in a codon to not be as important in determing the amino acid for which the codon codes.  Third base wobble is an evolutionary development designed to protect our body from mutations.

Q: What are the three types of point mutations?
A: 1.  Silent Mutation
2.  Missense Mutation
3.  Nonsense Mutation

Q: What is a silent mutation?
A: A silent mutation is when the third codon of a nucleotide is swapped out for another, but the same amino acid is coded, resulting in no actual change in the protein product.

Q: What is a missense mutation?
A: A missense mutation is a mutation where an altered codon substitues a different amino acid.  The effect on the protein product is variable.  If the new amino acid is very different from the unmutated amino acid than the protein's function can be affected.
If the new amino acid is not very different from the unmutated amino acid, than the protein's function is less likely to be affected.

Q: What is a nonsense mutation?
A: A nonsense mutation is a mutation where an altered codon results in a premature STOP codon.  These mutations almost always lead to non-functional proteins.

Q: What is the reading frame?
A: The reading frame refers to the way the entire strand of DNA and RNA is framed in terms of triplets (codons).  The reading frame is important for understanding frameshift mutations.
By adding or substracting a base, you don't just affect that one base, you shift the ENTIRE reading frame.

Q: What is a frameshift mutation and what are the two types?
A: A frameshift mutation is a mutation that shifts the entire reading frame of the genetic information.
1.  Frameshift Deletion - a base is deleted and the frame shifts down one base.
2.  Framsehift Insertion - a base is added and the frame shifts up one base.
Notice, if three bases were removed at once, the frame would actually be conserved.

Q: Generally speaking, [frameshifts or point mutations?] are more likely to result in nonfunctional proteins.
A: frameshifts

Q: What is transcription?
A: Transcription is the process by which mRNA is synthesized by RNA polymerase from a strand of template DNA.

Q: What needs to happen before RNA pol can access DNA and transcribe it?
A: Just like in DNA replication, helicase needs to unwind the DNA and Topoisomerase nicks the strand further down to prevent super coiling.

Q: What is the template strand?
A: The template strand (also called the antisense strand) is the DNA strand that is read by RNA pol to create the mRNA transcript.  The bases of the mRNA Transcript will be antiparallel and complementary to the template strand.

Q: What is the coding strand?
A: The coding strand is the DNA strand that is not read by RNA pol.  The bases of the mRNA Transcript will be parallel and equivalent to the bases in the coding strand, it's just that there will be U's instead of T's.
Use the coding strand to determine the mRNA transcript of a segment of DNA!  It's a lot easier than reading the template strand backwards and complimentarily.

Q: Does RNA polymerase just randomly transcribe segments of DNA as they open up?
A: No.  RNA polymersase searches for specializeed DNA regions known as promoter regions and only transcribes starting at those.

Q: What are the three types of RNA pol in eukaryotes?
A: 1.  RNA pol 1 - Located in Nucleolus, synthesizes rRNA.
2.  RNA pol 2 - Located in the nucleus, transcribes DNA and some small nuclear RNA.  This is the transcription RNA pol.
3.  RNA pol 3 - Located in the Nucleus, synthesizes tRNA and some rRNA.

Q: What is the TATA box?
A: The TATA box is the binding site within the promoter region in eukaryotic DNA to which RNA pol binds.  The TATA box is able to be separated easily because of the relative weakness of T-A bonds compared to G-C bonds.

Q: What are transcription factors?
A: Transcription factors are proteins that bind to DNA and either help or hurt the transcription of certain genes.  In the case of helping, transcription factors help RNA pol find and bind to the DNA of interest.

Q: In what direction does RNA polymerase read and synthesize?
A: RNA pol reads in the 3'->5' direction so that it can synthesize nucleotides in the 5'->3' direction.
Nucleotides are always synthesized in the 5' -> 3' direction!

Q: What is hnRNA?
A: hnRNA is heterogenous nuclear RNA.  hnRNA is RNA after it has been transcribed from DNA but before it has been post-transcriptionaly modified.  Because the hnRNA has not been processed yet, it will be a perfect RNA version of the DNA strand.

Q: What is postranscriptional processing?
A: Postranscriptional processing is a series of modifications made to hnRNA to make into mRNA.  The three most important post transcriptional processes are...
1.  Intron/Exon Splicing
2.  5' Cap
3.  3' Poly-A tail

Q: Describe Splicing
A: Splicing is the process of cutting out non-coding sequences of DNA (introns) and reconnecting the coding sequences (exons)

Q: What is a lariat?
A: A lariat is a name for a lasso shaped structure.  In the context of biochemistry, it refers to the way introns are spliced out of the rna transcript.

Q: What is the spliceosome and what is it made of?
A: The spliceosome is the specialized complex that handles the splicing of rna.  It is comprised of small nuclear RNA (snRNA) and small nuclear ribonucleoproteins (snRNPS).

Q: Why do we even have introns?  What is the point of chunks of rna that don't code for anything?
A: To this day, the evolutionary function of introns in eukaryotic cells is not well understood.  However, scientists hypothesize that introns play an important role in maintaining the appropriate size of our genome and for regulating gene expression.

Q: What is the purpose of the 5' Cap?
A: The 5' cap is a methylated GTP molecule.  This molecule protects the mRNA from degredation in the cytoplasm.  It is also recognized by the ribosome as a binding site.

Q: What is meant by alternative splicing?
A: Depending on how a single transcript of hRNA is spliced, you can get different proteins.  This is hypothesized to make it so we can fit more potential proteins into a smaller amount of DNA/RNA.  For example, the same segment of DNA and the hRNA transcript that goes with it could be spliced 5 different ways to make 5 completely different proteins.

Q: What is the purpose of the 3' Poly- A tail?
A: The 3' Poly A Tail is a long chain of Adenines.  The Poly A tail is a shield for the mRNA transcript in the cytoplasm.  As soon as the mRNA transcript hits the cytoplasm, the poly A tail starts to get destroyed.  The longer the Poly A tail, the more time the mRNA transcript has to get translated.

Q: What is a UTR?
A: UTR stands for untranslated region.  It refers to small portions at the ends of the RNA transcript that do not get translated.  Remember, Translation always starts at AUG and ends at stop codons, so UTR's are just the mRNA before the start codon and after the stop codon.

Q: What is the ribosome?
A: The ribosome is a structure made of proteins and RNA that associates with mRNA in the cytoplasm and constructs chains of amino acids using tRNA's.

Q: What are the three binding sites for tRNA's in ribosomes?
A: 1.  A - AminoAcyl Site
2.  P - Peptidyl Site
3.  E - Exit Site

Q: What are the three main steps of translation?
A: 1.  Initiation
2.  Elongation
3.  Termination

Q: What are the necessary requirements for each step of translation?
A: 1.  Initiation - Initiation Factors and GTP
2.  Elongation- Elongation Factors and GTP
3.  Termination - Releases Factors and GTP

Q: What is the Shine-Dalgarno sequence?
A: The Shine-Dalgarno sequence is seen in prokaryotes.  It is a piece of RNA in the 5' UTR that allows the small sub unit of the ribosome to bind.

Q: If prokaryotes use the Shine-Dalgarno sequence to recruit the small sub unit of the ribosome, how do eukaryotes do it?
A: Eukaryotes use the 5' cap to recruit the small sub unit of the ribosome.

Q: Describe Initiation
A: First, the small ribosomal sub unit binds to the mRNA (using shine-dalgarno in prokaryotes or the 5-cap in eukaryotes).
Second, the activated initiator tRNA binds to the start codon through base pairing at the P site of the ribosome.
Third, the large sub unit binds to the small sub unit with the help of initiation factors, forming the completed initiation complex.

Q: Describe the role of the A site
A: The A site holds the incoming aminoacyl-tRNA.  This is the next amino acid that is being added to the growing chain.

Q: Describe the role of the P site?
A: The P site holds the tRNA that carries the growing polypeptide chain.  It is also where methionine (starting AA) binds during initiation.  In this part of the ribosome, an enzyme called peptidyl transferase uses GTP to transfer the peptide chain from the tRNA in the P site to the tRNA A site.

Q: Describe the role of the E site.
A: After a tRNA in the P site loses its peptide chain, it is transferred to the E site where it pauses for just a second before dissociating back into solution so it can be recharged.

Q: What are Elongation Factors?
A: Elongation Factors are proteins that speed up elongation by bringing in tRNAs and GTP.  Elongation Factors also get rid of GDP (used up GTP) so that fresh GTP's can take their place.

Q: What is a signal sequence?
A: A signal sequence is a part of an mRNA transcript that directs the ribosome to move to the rough ER and finish translation there.  Signal sequences are meant for proteins that won't be in the cytoplasm, which includes secretory proteins, membrane proteins, and lysosome proteins.

Q: Describe Elongation.
A: First, the appropriate tRNA will enter the A-site of the complete ribosome.
Second, GTP is used to transfer the polypeptide from the tRNA in the P site to the tRNA in the A site.
Third, GTP is used to move the tRNA from the P site into the E site, and the tRNA in the A site to the P site.  This also moves the ribosome one codon down the mRNA.
Fourth/First, the tRNA leaves the E site and the next appropriate tRNA binds the A site.

Q: Describe Termination?
A: When a stop codon moves into the A site, a protein called Release Factor binds to the codon and causes the peptide to be hydrolyzed and released from the tRNA.  The ribosome will dissociate shortly after.

Q: What is post-translational processing and what are the commom types?
A: Post-Translational processing refers to any modifications made to a protein after it has already been translated.
1.  Phosphorylation
2.  Carboxylation
3.  Glycosylation
4.  Prenylation

Q: Generally speaking, how does phosphorylation affect proteins?
A: Phosphorylation is used to activate or deactivate proteins, especially enzymes.

Q: Generally speaking, how does carboxylation affect proteins?
A: Carboxylating proteins is usually done so that the protein can have calcium binding sites.

Q: Generally speaking, how does glycosylation affect proteins?
A: Glycosylation is usually conducted in the ER and the golgi apparatus.  Glycosylation is most often used as a signal for where the protein is supposed to end up in the cell.  For example, a certain type of glycosylation might make a protein go to the lysosome while other glycosylations might make the protein go to the mitochondria.

Q: Generally speaking, how does prenylation affect proteins?
A: Prenylation (addition of lipid groups) is usually conducted on membrane bound enzymes so that they can associate with the membrane well.

Q: What is the main way that prokaryotes regulate how much of their genome they are expressing?
A: Operons

Q: What are the 5 main ways that Eukaryotes regulate how much of their genome they are expressing?
A: 1.  Transcription Factors
2.  Enhancers
3.  Gene duplication
4.  Histone Acetylation
5.  DNA methylation

Q: Describe the structure of an operon?
A: An operon is a cluster of genes transcribed as a single mRNA.
The main pieces of an operon from left to right are the Regulator gene, the Promotor site, The Operator site, and The Structural gene

Q: What is an operon and what are the two types?
A: An operon is like an on/off switch for certain genes in the prokaryotic chromosome.
1.  Inducible Systems
2.  Repressible Systems

Q: Describe an Inducible System operon?
A: In an inducible system, an ever-present repressor protein (coded for by the regulator) binds to the operator and stops RNA polymerase from transcribing it.
However, if an inducer is present, then it will bind to the repressor and stop it from repressing the gene.  This allows the operon to be transcribed.
This is useful because it ties transcription of these genes to the presence of a specific molecule, which means that the gene is only on when the cell feels like it is needed.
The classic inducible system is the lac operon, an operon that allows bacteria to digest lactose when it is in high enough concentrations.

Q: What is a negative control mechanism?
A: Negative control mechanisms are systems in which the binding of a molecule reduces transcriptional activity.  E.g. Repressor proteins

Q: What is a positive control mechanism?
A: A positive control mechanism is a system in which the binding of a molecule increases transcriptional activity.  E.g. Inducer molecules

Q: What is an inducer?
A: An inducer is a molecule that binds to a repressor to remove it from the operon.

Q: Describe a Repressible System operon
A: In a repressible system, an ever-present repressor protein (coded for by the regulator) cannot bind to the operator on its own, so RNA polymerase can transcribe it.
However, if a co-repressor is present, then it will bind the repressor and allow it to repress the gene.  This stops the operon from being transcribed.
This is useful because it ties transcription of these genes to the presence of a specific molecule, which means that the gene gets turned off when the cell feels its no longer needed.
The classic repressible system is the trp operon, an operon that allows bacteria to synthesize trp when it is low in the cell.

Q: What is an enhancer?
A: An enhancer is a group of transcription factors that bind elements far away from the gene in question in order to enhance the transcription of said gene.  The large distance between the enhancer and the genes it enhances almost always lead to the DNA bending to bring them close together.

Q: What is Gene Duplication?
A: Gene duplication is when certain cells modify their genome by adding more copies of a gene.  As is expected, the more copies you have of a gene, the more you express the protein associated with the protein.  For example, a skin cell might have many many copies of the keratin expressing gene because of its primary importance there.

Q: How exactly do histones get DNA to wrap so tightly?
A: Histones are studded with positively charged lysine residues, which bind tightly to the negative phosphate backbone of DNA.

Q: What is Histone Acetylation?
A: Histone acetylation is when the positively charged lysine residues are acetylated, which reduces their positive charge and weakens the binding of the histone with DNA.  This results in loose DNA that can be more easily transcribed.

Q: What is DNA methylation?
A: DNA Methylation is when C and A Nucleotides are methylated.  Methyl groups carry electron density in their bonds, which increases the negative charge of the DNA, which strengthens the interaction between histones and DNA.  This results in tight DNA that is harder/unable to transcribe.

Q: What are chaperones?
A: Chaperones are a special protein that wraps around newly synthesized proteins in order to protect them and change the microenvironment in which the protein folds.

Q: What are the main three differences between DNA and RNA?
A: 1.  RNA has Ribose, DNA has Deoxyribose
2.  RNA has Uracil, DNA has Thymine
3.  RNA is single stranded, DNA is double stranded. (except in viruses!)

Q: What is the main difference between enhancers and promoters?
A: Enhancers are more than 25 base pairs away from the transcription site.
Promoters are within 25 base pairs of the transcription site.