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Biochemistry > Protein Metabolism: Amino Acid and Protein Synthesis > Flashcards

Protein Metabolism: Amino Acid and Protein Synthesis Flashcards

1
Q

what are the 2 main sources of amino acids?

A

diet and synthesis

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2
Q

describe the diet as an amino acid source

A
  • essential and non-essential amino acids
  • nitrogen/amine groups
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3
Q

describe synthesis as a source of amino acids

A
  • glucose
  • citric acid cycle carbons from other pathways
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4
Q

___ concentrations are tightly controlled

A

amino acid

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5
Q

T or F:

there is an explicit long-term amino acid storage system

A

false

production of amino acids is dictaed by demands of synthesis since there is no long-term storage system

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6
Q

synthesis of amino acids is a steady state process. what does that mean?

A
  • the body is always producing amino acids
  • specific amino acids are produced as needed based on demands
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7
Q

describe the primary amino acid synthesis pathways. what are the 7 precursors?

A
  • glycolysis
    • 3-phosphoglycerate
    • phosphoenolpyruvate
    • pyruvate
  • pentose phosphate pathway
    • ribose 5-phosphate
    • erythrose 6-phosphate
  • citric acid cycle
    • oxaloacetate
    • alpha-ketoglutarate
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8
Q

glucose provides ___ backbones for amino acid synthesis

A

carbon

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9
Q

only ___ out of the 20 common amino acids are synthesized by humans

A

11

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10
Q

which 2 reaction types are involved in amino acid synthesis?

A

transaminase and single carbon group reactions

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11
Q

name the amino acid biosynthetic families and group them by metabolic precursor. which are essential? nonessential?

A

starred amino acids are essential (acquired from diet), all others are nonessential (produced in humans)

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12
Q

describe the steps of transcription and translation

A
  • ongoing, steady-state process of protein production
  • regulated at several levels
  • limited amino acid palette (20)
  • extensive transcriptional and post-translational processing
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13
Q

describe how DNA is highly organized and compact

A
  • primarily in nucleosome form
  • mitosis forms chromosomes (only in chromosomal state when preparing to undergo division)
  • 46 chromosomes
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14
Q

what are introns and exons?

A
  • intron - non-coding and spliced from RNA
  • exon - encodes for amino acid sequence
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15
Q

what percent of mammalian DNA codes for amino acid chains for proteins?

A

1.5%

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16
Q

approximately how many human genes are there?

A

25,000

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17
Q

DNA encodes for ___, which encodes for ___

A
  • mRNA
  • polypeptides
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18
Q

what is responsible for transcription, post-transcription modification, and translation?

A

DNA, pre-mRNA, and mRNA, respectively

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19
Q

what are regulatory regions?

A

areas from which transcription is initiated and regulated

  • enhancer/silencer - binding of proteins that promote or inhibit transcription
  • promoter region - transcription factor and RNA polymerase binding
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20
Q

what is an open reading frame?

A

amino acid encoding region containing introns and exons

21
Q

what is the UTR?

A
  • untranslated regions necessary for RNA processing
  • do not actually encode for protein
22
Q

what do RNA polymerase I, II, and III synthesize?

A
  • RNA polymerase I - synthesizes ribosomal RNA (rRNA)
  • RNA polymerase II - synthesizes messenger RNA (mRNA)
  • RNA polymerase III - synthesizes transfer RNA (tRNA)

these are multiprotein complexes

polymerases separate DNA strands

transcription initiated by DNA binding

23
Q

how are RNA polymerases recruited to promoter regions?

A

transcription factor complexes will recruit them

24
Q

describe the steps of transcription

A
25
Q

describe the direction of transcription

A
26
Q

describe how transcription is negatively regulated at the DNA level

A
27
Q

describe how transcription is positively regulated at the DNA level

A
28
Q

after mRNA is produced, what 3 steps occur in RNA processing?

A
  1. addition of a 5’ cap
  2. intron splicing
  3. addition of a poly(A) tail
29
Q

describe addition of 5’ cap in mRNA processing

A
  • protects mRNA
  • bound by ribosomes to initiate translation
  • cap-binding complex tethers the mRNA until transcription is complete
30
Q

describe the intron splicing step of mRNA processing

A
  • four classes of introns encoded into RNA
    • 2 classes are self-splicing
    • most introns are spliced by spliceosome complexes
  • spliceosomes associate with RNA polymerase
  • introns are released into the nuclear space and degraded
31
Q

splicing variance creates different nRNAs and products. as an example, what proteins are produced from the same primary transcript (gene) in the thyroid vs. brain?

A
  • thyroid - calcitonin
  • brain - CGRP
32
Q

describe the termination and poly(A) tail step in mRNA processing

A
  • highly conserved cleavage sequence
    • AAUAAA upstream sequence
    • G and U rich residues downstream
  • polyadenylate polymerase adds 80-250 A residues
  • protects mRNA tail
  • anchors mRNA during translation
  • poly A addition occurs independent of RNA polymerase
33
Q

describe nuclear export

A

transports mRNA to the cytoplasm for translation

34
Q

translation can occur in which two places?

A

free in cytosol or in the ER

35
Q

what are mRNA codons?

A
  • triplet of nucleotides that specify an amino acid in the protein polypeptide chain
  • determine amino acid sequence
  • mRNA is composed of codons
36
Q

which amino acids are stop codons? which one is the initiation codon?

A
  • stop: UAA, UAG, UGA
  • initiation: AUG (methionine)
37
Q

what does inosinate do?

A

allows for variance in last (3rd) codon**, providing resistance to mutation

**degenerate code, due to wobble (3rd) base

38
Q

describe the steps of translation

A
39
Q

what is responsible for activation?

A

aminoacylating tRNAs

40
Q

what happens in initiation?

A
  • building of the ribosomal complex
  • ATP/GTP hydrolysis drives initiation
  • 5’ cap and 3’ end are bound in place; without this, initiation cannot happen

know this general process

41
Q

describe elongation

A
  • start codon binds to mRNA and peptidyl domain
  • amino acids move through aminoacyl until matching code is produced
  • mRNA read 5’ to 3’
  • polypeptide chain: N to C terminus
  • GTP hydrolysis dependent
42
Q

describe termination

A

eRF3 - eukaryotic releasing factor

43
Q

synthesis location affects protein targeting and transport. describe the effects of protein targeting and transport at the endoplasmic reticulum.

A
  • integral membrane proteins
  • intravesicular proteins
  • secreted proteins
  • signal recognition particle (SRP) cycle
44
Q

describe post-translational modifications. where do they occur?

A
  • occur in the ER
  1. protein folding and structure
  2. proteolytic cleavage
  3. post-translational modifications:
  • glycosylation
  • acetylation
  • phosphorylation
  • methylation
  • acylation
45
Q

describe glycoprotein formation in the ER

A
46
Q

synthesis location affects protein targeting and transport. describe the effects of protein targeting and transport in the cytoplasmic space.

A
  • nuclear proteins
  • structurally associated proteins
  • membrane-associated proteins
47
Q

what do the proteosome and lysosome do?

A

degrade proteins

48
Q

what is ubiquitin’s role in degradation of proteins?

A

it can target proteins for destruction (usually requires multiple ubiquitins to bind)

49
Q

describe the proteins that proteosomes and lysosomes degrade

A
  • proteosome: degrades cytoplasmic proteins
  • lysosome: degrades vesicular and membrane proteins

Biochemistry (32 decks)

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