Protein Metabolism: Amino Acid and Protein Synthesis

Question 1

what are the 2 main sources of amino acids?

Answer 1

diet and synthesis

Question 2

describe the diet as an amino acid source

Answer 2

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

Question 3

describe synthesis as a source of amino acids

Answer 3

• glucose
• citric acid cycle carbons from other pathways

Question 4

___ concentrations are tightly controlled

Answer 4

amino acid

Question 5

T or F:

there is an explicit long-term amino acid storage system

Answer 5

false

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

Question 6

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

Answer 6

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

Question 7

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

Answer 7

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

Question 8

glucose provides ___ backbones for amino acid synthesis

Answer 8

carbon

Question 9

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

Answer 9

11

Question 10

which 2 reaction types are involved in amino acid synthesis?

Answer 10

transaminase and single carbon group reactions

Question 11

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

Answer 11

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

Question 12

describe the steps of transcription and translation

Answer 12

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

Question 13

describe how DNA is highly organized and compact

Answer 13

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

Question 14

what are introns and exons?

Answer 14

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

Question 15

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

Answer 15

1.5%

Question 16

approximately how many human genes are there?

Answer 16

25,000

Question 17

DNA encodes for ___, which encodes for ___

Answer 17

• mRNA
• polypeptides

Question 18

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

Answer 18

DNA, pre-mRNA, and mRNA, respectively

Question 19

what are regulatory regions?

Answer 19

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

Question 20

what is an open reading frame?

Answer 20

amino acid encoding region containing introns and exons

Question 21

what is the UTR?

Answer 21

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

Question 22

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

Answer 22

• 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

Question 23

how are RNA polymerases recruited to promoter regions?

Answer 23

transcription factor complexes will recruit them

Question 24

describe the steps of transcription

Answer 24

Question 25

describe the direction of transcription

Answer 25

Question 26

describe how transcription is negatively regulated at the DNA level

Answer 26

Question 27

describe how transcription is positively regulated at the DNA level

Answer 27

Question 28

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

Answer 28

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

Question 29

describe addition of 5' cap in mRNA processing

Answer 29

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

Question 30

describe the intron splicing step of mRNA processing

Answer 30

* 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

Question 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?

Answer 31

* thyroid - calcitonin * brain - CGRP

Question 32

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

Answer 32

* 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**

Question 33

describe nuclear export

Answer 33

transports mRNA to the cytoplasm for translation

Question 34

translation can occur in which two places?

Answer 34

free in cytosol or in the ER

Question 35

what are mRNA codons?

Answer 35

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

Question 36

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

Answer 36

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

Question 37

what does inosinate do?

Answer 37

allows for variance in last (3rd) codon\*\*, providing resistance to mutation \*\*degenerate code, due to wobble (3rd) base

Question 38

describe the steps of translation

Answer 38

Question 39

what is responsible for activation?

Answer 39

aminoacylating tRNAs

Question 40

what happens in initiation?

Answer 40

* 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

Question 41

describe elongation

Answer 41

* 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

Question 42

describe termination

Answer 42

eRF3 - eukaryotic releasing factor

Question 43

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

Answer 43

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

Question 44

describe post-translational modifications. where do they occur?

Answer 44

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

Question 45

describe glycoprotein formation in the ER

Answer 45

Question 46

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

Answer 46

* nuclear proteins * structurally associated proteins * membrane-associated proteins

Question 47

what do the proteosome and lysosome do?

Answer 47

degrade proteins

Question 48

what is ubiquitin's role in degradation of proteins?

Answer 48

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

Question 49

describe the proteins that proteosomes and lysosomes degrade

Answer 49

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