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Biochemistry > Protein Translation and Post-Translational Processing > Flashcards

Protein Translation and Post-Translational Processing Flashcards

1
Q

2 types of eukaryotic ribosomes

A
  1. Cytosolic

2. Mitochondrial

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2
Q

Composition of cytosolic ribosomes

A

Small subunit is 40S, composed of 34 proteins and 18S RNA; large subunit is 60S, composed of 50 proteins and 25S, 5.8S, and 5S RNAs – assembled size is 80S

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3
Q

Composition of mitochondrial ribosomes

A

Small subunit is 30S-35S, composed of 19S RNA; large subunit is 40S-45S, composed of 16S RNA; together there are 7-100 proteins (more than prokaryotic) – assembled size is 55S

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4
Q

Composition of prokaryotic ribosomes

A

Small subunit is 30S, composed of 21 proteins and 16S RNA; large subunit is 50S, composed of 34 proteins and 23S and 5S RNAs – assembled size is 70S – very different from eukaryotic ribosomes which make them drug targets

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5
Q

Polysomes

A

Group of ribosomes on an mRNA (usually translated by more than one ribosome at a time)

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6
Q

Phases of translation

A
  1. Initiation phase (ribosome assembly)
  2. Elongation phase
  3. Termination phase
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7
Q

Initiation phase

A
  1. eIF2a needs to be activated by phosphorylation from GTP binding
  2. Ternary complex (eIF2a + GTP + methionine-tRNAmet) is formed
  3. Ternary complex binds to small ribosomal subunit
  4. mRNA molecule binds to structure to form pre-initiation complex
  5. Pre-initiation complex becomes initiation complex with binding to the large subunit
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8
Q

Ternary complex

A

eIF2a + GTP + methionine-tRNAmet

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9
Q

Elongation phase

A
  1. Ribosome has assembled and tRNAmet is in P site
  2. Peptide + tRNA is brought to A site, along with EF-1 (elongation factor) + GTP
  3. Peptide bond is formed between amino acids
  4. EF-2 (+ GTP) helps ribosome move one codon further on mRNA so that two tRNAs are moved to E and P site, enabling empty tRNA to leave and new peptide-containing tRNA to fill A site
  5. Continues until protein has been completely synthesized
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10
Q

Where does the energy required for elongation phase come from?

A

GTP (bound to elongating factors EF-1 and EF-2)

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11
Q

Termination phase

A
  1. Ribosome reaches stop codon in A site (either UGA, UAA, or UAG)
  2. Release factor protein (RF) pairs with stop codon (NOT a tRNA)
  3. Peptide is released from P site when GTP on RF is hydrolyzed
  4. Ribosome breaks up and is recycled
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12
Q

How do antibiotics act?

A

Selectively inhibiting prokaryotic ribosomes (70S ribosomes) to inhibit growth of prokaryotes

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13
Q

Streptomycin

A

Binds to small subunit to inhibit initiation and cause mistranslation of codons

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14
Q

Neomycin and gentamicin

A

Bind to ribosomes and cause mistranslation of codons

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15
Q

Tetracycline

A

Blocks A site to prevent tRNA binding

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16
Q

Chloramphenicol

A

Prevents peptidyl bond formation

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17
Q

How do toxins act?

A

Interferes with the functions of eukaryotic ribosomes (80S ribosomes)

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18
Q

Ricin

A

Glycosidase that removes adenine bases from various positions of rRNA in large subunit to inactivate it (ribosome inactivating protein, RIP)

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19
Q

Diphtheria toxin

A

Ribosyltransferase protein produced by Corynebacterium diphtheriae that inactivates EF-2 by ADP ribosylation (EF-2 has unique amino acid that can be ribosylated by diphtheria toxin, causes protein synthesis to stop)

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20
Q

2 mechanisms for regulation of translation

A
  1. Recognition of start codon
  2. Activity of initiation factors
    * *Causes changes to occur rapidly so induction or shutdown or protein production can happen immediately after stimulus**
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21
Q

Regulation by recognition of start codon

A

Binding of regulatory protein in 5’ UTR of certain mRNAs prevents recognition of start codon to block translation until binding protein is removed (VERY SPECIFIC) – ex. regulates iron storage and transport proteins

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22
Q

Regulation by activity of initiation factors

A

Phosphorylation of eIF2a (part of ternary complex) to inactivate it and cause overall inhibition of translation

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23
Q

Chaperone proteins and role in protein folding

A

Associate with partially folded polypeptides and guide folding process by binding to hydrophobic regions of folding polypeptide; concentrated in cytosol and ER – important for survival of stress (ex. heat shock proteins, HSPs) – defects cause protein folding disorders such as Charcot Marie Tooth Disease

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24
Q

Hsp90

A

Binds to ATP and misfolded proteins and uses pincer movement to loosen up target protein and give it another chance to fold correctly

25
Q

Where does synthesis of exported proteins occur?

A

Endoplasmic reticulum

26
Q

Synthesis of exported proteins

A
  1. Hydrophobic signal sequence emerges from ribosome
  2. Signal recognition particle (SRP) binds to signal sequence and complex moves to ER
  3. SRP dissociates and translation continues in the ER (peptide is threaded into ER)
  4. Signal peptidase cleaves signal peptide from nascent protein
27
Q

What causes the unfolded protein response (UPR)?

A

Caused by certain physiological stressors that impair proper folding of proteins in the ER – accumulation of unfolded proteins in ER triggers UPR

28
Q

What happens in cells during UPR?

A
  1. General protein translation is inhibited
  2. Specific induction of chaperone production (HSP) to improve chances of proper folding
  3. Apoptosis (if unfolded proteins exceed capacity for repair)
29
Q

Why is glycosylation important?

A
  1. Changes physical properties of protein by increasing solubility, stability, and size
  2. Carbohydrates on protein surface are important recognition sites
30
Q

Mechanism of glycosyltransferases

A

Catalyze glycosylation by transfering sugar from activated sugar nucleotide to acceptor substrate

31
Q

Specificity of glycosyltransferases

A

Specific for:

  1. Activated sugar nucleotide donor (ex. UDP-mannose)
  2. Acceptor (ex, β-1,4 linked mannoses)
  3. Linkage formed (ex. β-1,4 linkage)
32
Q

Where does glycosylation occur?

A

Begins in ER and continues in Golgi

33
Q

N-linked vs. O-linked glycosylation

A

N-linked: starts in ER before protein folding is complete, adds sugars to asparagine residue in protein, and yields high mannose and complex types of N-glycosylated products
O-linked: starts in Golgi after protein folding is complete, adds sugars to serine or threonine residues in protein, and yields proteoglycans of the extracellular matrix and H-antigen on surface of red blood cells (requires more specific info)

34
Q

N-linked glycosylation

A
  1. Synthesis of universal oligosaccharide in ER
  2. Transfer of oligosaccharide from dolichol phosphate to asparagine
  3. Highly specific modification of universal oligosaccharide in Golgi
35
Q

Congenital disorders of glycosylation (CDGs)

A

Affect N-linked glycosylation
CDG-I: Defective synthesis of lipid-linked oligosaccharide precursor (12 variants)
CDG-II: Defective trimming of oligosaccharide chain (6 variants)

36
Q

O-linked glycosylation

A
  1. In Golgi, glycosyltransferases transfer sugars to serine or threonine residues of fully-folded proteins
  2. Adds N-acetylgalactosamine to begin
  3. Other glycosyltransferases add other sugars sequentially until finished
37
Q

N-linked glycosylated proteins

A
  1. High mannose type

2. Complex type (contains mannose and 5 other carbs)

38
Q

O-linked glycosylated proteins

A
  1. Proteoglycans of extracellular matrix

2. H-antigen on surface of red blood cells

39
Q

H-antigen on RBCs and its differing alleles

A

Surface antigen that enables immune system to discriminate between itself and foreign particles
A = N-acetylgalactosamine
B = galactose
O = nothing added

40
Q

Significance of dolichol phosphate

A

Lipid attached to ER membrane that has been pyrophosphorylated and has sugar molecules added to it (14 total) by activated sugar nucleotides

41
Q

Post-translational modification of amino acids

A
  • -Hydroxylation of proline
  • -Acetylation of lysine
  • -Cysteine to formylglycine
  • -Trimming at N-terminus
  • -Addition of hydrophobic moieties
  • -Changes at C-terminus
42
Q

Proline hydroxylation

A

Important for collagen triple helix; failure results in collagen disorders (ex. scurvy, Ehlers Danlos syndrome, osteogenesis imperfecta, etc.)

43
Q

Lysine acetylation

A

Used for lysine residues in histones; influences gene expression patterns on genomic scale by determining how tightly histones bind

44
Q

Cysteine to formylglycine

A

Thiol-group in cysteine can be converted to aldehyde to form Cα-formylglycine, which is important for lysosomal sulfatases; failure can cause multiple sulfatase deficiency (MSD), in which glycosaminoglycans accumulate in lysosome

45
Q

Trimming at N-terminus

A

Proteolysis removes methionine at the N-terminus and modifies accordingly

46
Q

Addition of hydrophobic moieties

A

Membrane proteins need hydrophobic moieties to tether them inside the hydrophobic membrane– often linked to long-chain hydrophobic molecules to change surface properties

47
Q

4 ways hydrophobic molecules are added to proteins

A
  • -N-terminal myristoylation (addition of myristic acid)
  • -Palmitoylation (addition of palmitic acid) at cysteine near C-terminus
  • -Prenylation (addition of isoprenoids) of cysteine close to C-terminus
  • -Addition of glycosylphosphatidyl-inositol (GPI) anchor to C-terminus
48
Q

Protein sorting

A

Sending specific proteins to specific organelles in the cell (ex. lysosomes, cell membrane, mitochondria, etc.)

49
Q

Protein targeting to lysosomes

A

High-mannose glycoproteins are phosphorylated at mannose residues, which signals proteins into lysosomes

50
Q

Protein import into mitochondria

A
  1. Mitochondrial proteins are synthesized as large preproteins with N-terminal pre-sequence
  2. Chaperones stabilize mitochondrial proteins in unfolded form
  3. Pre-sequences interact with a receptor in outer mitochondrial membrane
  4. Protein complex consisting of TOMs (translocases of outer mitochondrial matrix) and TIMs (inner matrix) provides channel to enter
  5. Pre-sequence is cleaved by matrix proteases
  6. Localization in inner/outer membranes requires second pre-sequence
51
Q

Deafness-dystonia syndrome

A

Rare mitochondrial disorder caused by mutation in TIM, impairing cellular energy production by preventing assembly of fully functional mitochondria

52
Q

Cystic fibrosis

A

Normally caused by deletion of one codon from CFTR1 gene that interfering with folding and glycosylation, causing CFTR protein to be degraded

53
Q

I-cell disease

A

Causes impairment of phosphate transfer to mannose, resulting in lysosomal proteins not reaching their compartment which compromises their function and causes undegraded proteins to accumulate; lysosomal degradation of proteins and carbohydrates is impaired and lysosomes appear dense

54
Q

2 locations of protein degradation

A
  1. Lysosome (nonspecific degradation of extracellular and intracellular proteins)
  2. Proteasome (required for specific degradation of cytoplasmic proteins)
55
Q

Lysosomal degradation

A

Lysosomes contain acid hydrolases for nonspecific degradation of all types of extracellular and intracellular proteins; function in autophagy and endocytic pathway

56
Q

Proteasomal degradation

A

Proteasomes are large multiprotein complexes in cytoplasm and nucleus that selectively degrade cytoplasmic proteins; degradation requires poly-ubiquitination (transfer of multiple ubiquitin proteins to target protein), which is done by E1, E2, and E3 enzymes

57
Q

What are the purposes of ubiquitination?

A
  1. Regulates protein activity (ex. cyclins)

2. Marks misfolded proteins

58
Q

Ubiquitination process in proteasomes

A
  1. Activated by E1 enzymes
  2. Conjugated to E2 enzymes
  3. Litigated to targets by E3 enzymes (identifies for ubiquitination, many types of E3 that are very specific)
59
Q

Factors that determine protein half-life

A
  1. Conformation (misfolding –> degradation)
  2. N-terminus (Ser/Met = more stable than Arg/Lys)
  3. Other sequence elements such as PEST (proline-glutamine-serine-threonine) shorten lifespan

Biochemistry (14 decks)

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