Protein Metabolism: Amino Acid and Protein Synthesis Flashcards Preview

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

Flashcards in Protein Metabolism: Amino Acid and Protein Synthesis Deck (49):
1

what are the 2 main sources of amino acids?

diet and synthesis

2

describe the diet as an amino acid source

  • essential and non-essential amino acids
  • nitrogen/amine groups

3

describe synthesis as a source of amino acids

  • glucose
  • citric acid cycle carbons from other pathways

4

___ concentrations are tightly controlled

amino acid

5

T or F:

there is an explicit long-term amino acid storage system

false

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

6

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

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

7

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

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

8

glucose provides ___ backbones for amino acid synthesis

carbon

9

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

11

10

which 2 reaction types are involved in amino acid synthesis?

transaminase and single carbon group reactions

11

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

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

12

describe the steps of transcription and translation

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

13

describe how DNA is highly organized and compact

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

14

what are introns and exons?

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

15

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

1.5%

16

approximately how many human genes are there?

25,000

17

DNA encodes for ___, which encodes for ___

  • mRNA
  • polypeptides

18

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

DNA, pre-mRNA, and mRNA, respectively

19

what are regulatory regions?

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

20

what is an open reading frame?

amino acid encoding region containing introns and exons

21

what is the UTR?

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

22

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

  • 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

how are RNA polymerases recruited to promoter regions?

transcription factor complexes will recruit them

24

describe the steps of transcription

25

describe the direction of transcription

26

describe how transcription is negatively regulated at the DNA level

27

describe how transcription is positively regulated at the DNA level

28

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

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

29

describe addition of 5' cap in mRNA processing

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

30

describe the intron splicing step of mRNA processing

  • 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

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?

  • thyroid - calcitonin
  • brain - CGRP

32

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

  • 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

describe nuclear export

transports mRNA to the cytoplasm for translation

34

translation can occur in which two places?

free in cytosol or in the ER

35

what are mRNA codons?

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

36

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

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

37

what does inosinate do?

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

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

38

describe the steps of translation

39

what is responsible for activation?

aminoacylating tRNAs

40

what happens in initiation?

  • 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

describe elongation

  • 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

describe termination

eRF3 - eukaryotic releasing factor

43

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

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

44

describe post-translational modifications. where do they occur?

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

45

describe glycoprotein formation in the ER

46

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

  • nuclear proteins
  • structurally associated proteins
  • membrane-associated proteins

47

what do the proteosome and lysosome do?

degrade proteins

48

what is ubiquitin's role in degradation of proteins?

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

49

describe the proteins that proteosomes and lysosomes degrade

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