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HFF - Exam 3 > Test 3 - Quiz 7 - Protein Meta (DNA/mRNA) > Flashcards

Test 3 - Quiz 7 - Protein Meta (DNA/mRNA) Flashcards

1
Q

What are the two main sources of amino acids?

A

Diet - Essential/Non-Essential

Synthesis - Glucose and CAC carbons from other pathways

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2
Q

AA concentration is tightly controlled, and the production of amino acids is dictated by what?

A

Demands of synthesis - This is a stead state process. There is not a pool of AA’s in storage just waiting to be deployed.

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3
Q

What are the nonessential amino acids?

A 
Alan - Alanine
Ate - Aspartate
Asparagus - Asparagine
Glumating - Glutamate
South - Serine
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4
Q

What are the conditionally essential amino acids?

A 
Argyle - Arginine
Can - Cysteine
Get - Glycine
Gutta - Glutamine
Percha - Proline
Tyrone - Tyrosine
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5
Q

What are the essential amino acids?

A 
P - Phe
V - Val
T - Threo
T - Trypto 
M - Met
H - His
I - Isoleu
L - Lys
L - Leu
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6
Q

What is ornithine?

A

Non-common AA, but is essential for urea excretion

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7
Q

Ribose 5-phosphate can produce what amino acid?

A

Histidine

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8
Q

3-Phosphoglycerate can produce what amino acid? Which can then produce which two amino acids?

A

Serine

Glycine
Cysteine

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9
Q

Erythrose 4-phosphate and Phosphoenolpyruvate can produce what 3 amino acids?

A

Tryptophan
Phenylalanine
Tyrosine

PET PT

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10
Q

Pyruvate can produce which 4 amino acids?

A

Alanine
Valine
Leucine
Isoleucine

VAIL Py

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11
Q

Oxaloacetate can produce which amino acid, and then what 4 amino acids can be produced from that?

A

Aspartate

Asparagine
Methionine
Threonine
Lysine

OA MALT

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12
Q

Alpha-ketoglutarate can produce which amino acid, and which 3 AAs can be produced from that?

A

Glutamate

Glutamine
Proline
Arginine

Alpha G GPA

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13
Q

DNA is primarily found in what form?

A

Nucleosome (DNA wrapped around histones)

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14
Q

What is a non-coding portion of DNA that is spliced from mRNA?

A

Intron

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15
Q

What encodes for an amino acid sequence?

A

Exon

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16
Q

What is the promoter region?

A

Transcription factor and RNA polymerase binding site

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17
Q

What is an enhancer or silencer?

A

Binding of proteins that promote or inhibit transcription

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18
Q

What is the open reading frame?

A

Amino acid encoding region containing both introns and exons

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19
Q

What is a UTR?

A

Untranslated region - necessary for RNA processing

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20
Q

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?

A

rRna
mRNA
tRNA

ROCKY MOUNTAIN TRUCKS

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21
Q

The DNA non-template strand can also be called what?

A

The coding strand

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22
Q

The RNA strand is read off of what strand and why this strand?

A

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.

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23
Q

What are the 5 steps of transcription?

P
TB
CTD-P, P escapes
E by Efs 
Efs dissociate and CTD-P —> CTD
A

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)

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24
Q

What is placed onto an mRNA strand after the introns have been excised?

A

5’ cap and a poly-A tail

*This constitutes a “mature” mRNA strand

25
Q

Transcription is regulated at what level?

A

DNA

26
Q

There are 2 types of negative regulation. Tell me how transcription is induced and how it is inhibited.

A

1- Molecular signal causes dissociation of repressor. This INDUCES transcription.

2- Molecular signal causes binding of repressor to DNA. This INHIBITS transcription.

27
Q

There are 2 types of positive regulation. Tell me about them.

A

1- Molecular signal causes dissociation of activator from DNA. This INHIBITS transcription

2- Molecular signal causes binding of activator to DNA. This INDUCES transcription

28
Q

Both positive and negative regulation occur in what region?

A

PROMOTER

29
Q

What are the 3 processing steps of mRNA that turn it into a mature strand?

A

Addition of a 5’ cap (modified GTP)
Intron splicing
Addition of a poly-A tail

30
Q

What 2 things does the 5’ cap do?

A

Protects mRNA

Tethers the mRNA until transcription is complete

31
Q

There are 4 classes of introns encoded into RNA. 2 classes are self-splicing, however, how are most introns spliced?

A

Via spliceosome complexes

*These associate with RNA polymerase

32
Q

What happens to the introns once they are spliced?

A

They are released into the nuclear space and degraded

33
Q

What is the main source of variation that allows a limited number of genes to encode for a myriad of protein options?

A

Splicing variance

34
Q

What does the poly-A tail do for the mRNA strand?

A

Protects the mRNA tail

Anchors mRNA during translation

35
Q

Where is mRNA sent for translation, and via what?

A

Cytoplasm

Nuclear export

36
Q

What is inosinate in tRNA?

A

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.

37
Q

DNA as a “proofing” enzyme, while RNA does not. What is the result?

AND, what is the compensation for that?

A

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.

38
Q

What is the summary of translation?

A

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

39
Q

What drives the initiation step of translation?

A

ATP/GTP

40
Q

In the elongation step, how is the mRNA strand read and in what orientation is the polypeptide chain formed?

A

5’ to 3’

N terminus —> C terminus

41
Q

Elongation is dependent upon what?

A

GTP hydrolysis

42
Q

What is elongation?

A

Building the amino acid chain

43
Q

What are the 3 sites on the ribosomal unit?

A

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

44
Q

What happens at the A-site?

A

The A-site binds the incoming tRNA with the mRNA codon, if they match. This begins the peptide bond linkage.

45
Q

What happens at the P-site?

A

It holds the tRNA while a polypeptide bond is created

46
Q

What happens at the E-site?

A

tRNA back bone, minus the amino acid, is rejected. Bye Felicia.

47
Q

What does eukaryotic releasing factor?

A

It causes the break-up of mRNA and the ribosome at termination

48
Q

What are the two locations that are important in protein synthesis?

A

ER

Cytosol/cytoplasm

49
Q

What brings the polypeptide chain to the ER, and what happens?

A

SRP Cycle (Signal recognition particle)

There are SRP receptors on the wall of the ER that will bind to the ribosome

50
Q

Once at the ER, what happens to the new protein?

A

It will stay or be granuled/vesicled out

51
Q

What decides whether or not an mRNA strand will by synthesized in the cytoplasm vs the ER?

A

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

52
Q

What are 3 post-translational modification that occur w/in the ER?

A

Protein folding and structure

Proteolytic cleavage

Post-translational modifications

53
Q

What are the 5 specific post-translational modifications?

A 
Glycosylation
Acetylation
Phosphorylation
Methylation
Acylation
54
Q

What are three proteins associated with mRNA doing its thing in the cytoplasm?

A

Nuclear proteins
Structure-associated proteins
Membrane-associated proteins

55
Q

What are three proteins associated with mRNA doing its thing in the ER?

A

Integral membrane proteins
Intravesicular proteins
Secreted proteins

56
Q

What targets proteins for destruction?

A

Ubiquitin

57
Q

What are the two organelles used for molecular degradation?

A

Proteosome

Lysosome

58
Q

What does a proteosome degrade?

A

Cytoplasmic proteins

59
Q

What does a lysosome degrade?

A

Vesicular and membrane proteins

HFF - Exam 3 (19 decks)

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