Protein Metabolism: Amino Acid and Protein Synthesis Flashcards
what are the 2 main sources of amino acids?
diet and synthesis
describe the diet as an amino acid source
- essential and non-essential amino acids
- nitrogen/amine groups
describe synthesis as a source of amino acids
- glucose
- citric acid cycle carbons from other pathways
___ concentrations are tightly controlled
amino acid
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
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
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
glucose provides ___ backbones for amino acid synthesis
carbon
only ___ out of the 20 common amino acids are synthesized by humans
11
which 2 reaction types are involved in amino acid synthesis?
transaminase and single carbon group reactions
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)
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
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
what are introns and exons?
- intron - non-coding and spliced from RNA
- exon - encodes for amino acid sequence
what percent of mammalian DNA codes for amino acid chains for proteins?
1.5%
approximately how many human genes are there?
25,000
DNA encodes for ___, which encodes for ___
- mRNA
- polypeptides
what is responsible for transcription, post-transcription modification, and translation?
DNA, pre-mRNA, and mRNA, respectively
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
what is an open reading frame?
amino acid encoding region containing introns and exons
what is the UTR?
- untranslated regions necessary for RNA processing
- do not actually encode for protein
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
how are RNA polymerases recruited to promoter regions?
transcription factor complexes will recruit them
describe the steps of transcription
describe the direction of transcription
describe how transcription is negatively regulated at the DNA level
describe how transcription is positively regulated at the DNA level
after mRNA is produced, what 3 steps occur in RNA processing?
- addition of a 5’ cap
- intron splicing
- addition of a poly(A) tail
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
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
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
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
describe nuclear export
transports mRNA to the cytoplasm for translation
translation can occur in which two places?
free in cytosol or in the ER
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
which amino acids are stop codons? which one is the initiation codon?
- stop: UAA, UAG, UGA
- initiation: AUG (methionine)
what does inosinate do?
allows for variance in last (3rd) codon**, providing resistance to mutation
**degenerate code, due to wobble (3rd) base
describe the steps of translation
what is responsible for activation?
aminoacylating tRNAs
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
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
describe termination
eRF3 - eukaryotic releasing factor
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
describe post-translational modifications. where do they occur?
- occur in the ER
- protein folding and structure
- proteolytic cleavage
- post-translational modifications:
- glycosylation
- acetylation
- phosphorylation
- methylation
- acylation
describe glycoprotein formation in the ER
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
what do the proteosome and lysosome do?
degrade proteins
what is ubiquitin’s role in degradation of proteins?
it can target proteins for destruction (usually requires multiple ubiquitins to bind)
describe the proteins that proteosomes and lysosomes degrade
- proteosome: degrades cytoplasmic proteins
- lysosome: degrades vesicular and membrane proteins
