Test 3 - Quiz 7 - Protein Meta (DNA/mRNA) Flashcards
What are the two main sources of amino acids?
Diet - Essential/Non-Essential
Synthesis - Glucose and CAC carbons from other pathways
AA concentration is tightly controlled, and the production of amino acids is dictated by what?
Demands of synthesis - This is a stead state process. There is not a pool of AA’s in storage just waiting to be deployed.
What are the nonessential amino acids?
Alan - Alanine Ate - Aspartate Asparagus - Asparagine Glumating - Glutamate South - Serine
What are the conditionally essential amino acids?
Argyle - Arginine Can - Cysteine Get - Glycine Gutta - Glutamine Percha - Proline Tyrone - Tyrosine
What are the essential amino acids?
P - Phe V - Val T - Threo T - Trypto M - Met H - His I - Isoleu L - Lys L - Leu
What is ornithine?
Non-common AA, but is essential for urea excretion
Ribose 5-phosphate can produce what amino acid?
Histidine
3-Phosphoglycerate can produce what amino acid? Which can then produce which two amino acids?
Serine
Glycine
Cysteine
Erythrose 4-phosphate and Phosphoenolpyruvate can produce what 3 amino acids?
Tryptophan
Phenylalanine
Tyrosine
PET PT
Pyruvate can produce which 4 amino acids?
Alanine
Valine
Leucine
Isoleucine
VAIL Py
Oxaloacetate can produce which amino acid, and then what 4 amino acids can be produced from that?
Aspartate
Asparagine
Methionine
Threonine
Lysine
OA MALT
Alpha-ketoglutarate can produce which amino acid, and which 3 AAs can be produced from that?
Glutamate
Glutamine
Proline
Arginine
Alpha G GPA
DNA is primarily found in what form?
Nucleosome (DNA wrapped around histones)
What is a non-coding portion of DNA that is spliced from mRNA?
Intron
What encodes for an amino acid sequence?
Exon
What is the promoter region?
Transcription factor and RNA polymerase binding site
What is an enhancer or silencer?
Binding of proteins that promote or inhibit transcription
What is the open reading frame?
Amino acid encoding region containing both introns and exons
What is a UTR?
Untranslated region - necessary for RNA processing
RNA Polymerase I synthesizes what type of RNA?
RNA Polymerase II synthesizes what type of RNA?
RNA Polymerase III synthesizes what type of RNA?
What is your saying for this?
rRna
mRNA
tRNA
ROCKY MOUNTAIN TRUCKS
The DNA non-template strand can also be called what?
The coding strand
The RNA strand is read off of what strand and why this strand?
The DNA template strand
The DNA nontemplate strand is in the 5’ to 3’ orientation. mRNA is synthesized in that direction, so there has to be an intermediate strand in the 3’ to 5’ orientation to allow the mRNA strand to be formed correctly.
*As a shortcut, look at the DNA nontemplate strand and replace the T’s with U’s.
What are the 5 steps of transcription?
P TB CTD-P, P escapes E by Efs Efs dissociate and CTD-P —> CTD
Poly II is recruited to the DNA by transcription factors
Transcription bubble forms
The CTD is phosphorylated during initiation and the polymerase escapes the promoter
Transcription elongation is aided by elongation factors
Elongation factors dissociate, and the CTD is dephosphorylated as transcription stops (facilitated by termination factors)
What is placed onto an mRNA strand after the introns have been excised?
5’ cap and a poly-A tail
*This constitutes a “mature” mRNA strand
Transcription is regulated at what level?
DNA
There are 2 types of negative regulation. Tell me how transcription is induced and how it is inhibited.
1- Molecular signal causes dissociation of repressor. This INDUCES transcription.
2- Molecular signal causes binding of repressor to DNA. This INHIBITS transcription.
There are 2 types of positive regulation. Tell me about them.
1- Molecular signal causes dissociation of activator from DNA. This INHIBITS transcription
2- Molecular signal causes binding of activator to DNA. This INDUCES transcription
Both positive and negative regulation occur in what region?
PROMOTER
What are the 3 processing steps of mRNA that turn it into a mature strand?
Addition of a 5’ cap (modified GTP)
Intron splicing
Addition of a poly-A tail
What 2 things does the 5’ cap do?
Protects mRNA
Tethers the mRNA until transcription is complete
There are 4 classes of introns encoded into RNA. 2 classes are self-splicing, however, how are most introns spliced?
Via spliceosome complexes
*These associate with RNA polymerase
What happens to the introns once they are spliced?
They are released into the nuclear space and degraded
What is the main source of variation that allows a limited number of genes to encode for a myriad of protein options?
Splicing variance
What does the poly-A tail do for the mRNA strand?
Protects the mRNA tail
Anchors mRNA during translation
Where is mRNA sent for translation, and via what?
Cytoplasm
Nuclear export
What is inosinate in tRNA?
It is a wild card that can bind A, C, or U. This allows for a “wobble” where an anticodon can bind multiple types of codons.
DNA as a “proofing” enzyme, while RNA does not. What is the result?
AND, what is the compensation for that?
More errors occur in RNA than in DNA.
The code is degenerate. This means that changing the third base pair letter will usually result in a small error in the code, or it will code for the same amino acid. Ex. UUA and UUG both code for Leu.
What is the summary of translation?
Activate - tRNA is aminoacylated
Initiate - mRNA and amionacylated tRNA bind to the small ribosomal subunit. Then, the large subunit binds as well
Elongate - Cycles of amionacyl-tRNA binding and peptide bond formation occur until stop codon is encountered
Terminate - Stop codon is encountered, and mRNA dissociates and subunits are recycled
Fold - Protein folds
What drives the initiation step of translation?
ATP/GTP
In the elongation step, how is the mRNA strand read and in what orientation is the polypeptide chain formed?
5’ to 3’
N terminus —> C terminus
Elongation is dependent upon what?
GTP hydrolysis
What is elongation?
Building the amino acid chain
What are the 3 sites on the ribosomal unit?
A - aminoacyl
P - Peptidyl
E - Exit
**The 3 sites are oriented 5’ to 3’ E-P-A b/c ribosomes move toward the 3’ end of mRNA
What happens at the A-site?
The A-site binds the incoming tRNA with the mRNA codon, if they match. This begins the peptide bond linkage.
What happens at the P-site?
It holds the tRNA while a polypeptide bond is created
What happens at the E-site?
tRNA back bone, minus the amino acid, is rejected. Bye Felicia.
What does eukaryotic releasing factor?
It causes the break-up of mRNA and the ribosome at termination
What are the two locations that are important in protein synthesis?
ER
Cytosol/cytoplasm
What brings the polypeptide chain to the ER, and what happens?
SRP Cycle (Signal recognition particle)
There are SRP receptors on the wall of the ER that will bind to the ribosome
Once at the ER, what happens to the new protein?
It will stay or be granuled/vesicled out
What decides whether or not an mRNA strand will by synthesized in the cytoplasm vs the ER?
The AA sequence itself is the decider (mediated by SRP, if applicable). A small portion at the beginning of the chain will signal the SRP and it will then start the process of going to the ER
What are 3 post-translational modification that occur w/in the ER?
Protein folding and structure
Proteolytic cleavage
Post-translational modifications
What are the 5 specific post-translational modifications?
Glycosylation Acetylation Phosphorylation Methylation Acylation
What are three proteins associated with mRNA doing its thing in the cytoplasm?
Nuclear proteins
Structure-associated proteins
Membrane-associated proteins
What are three proteins associated with mRNA doing its thing in the ER?
Integral membrane proteins
Intravesicular proteins
Secreted proteins
What targets proteins for destruction?
Ubiquitin
What are the two organelles used for molecular degradation?
Proteosome
Lysosome
What does a proteosome degrade?
Cytoplasmic proteins
What does a lysosome degrade?
Vesicular and membrane proteins
