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025. My MCM Test 2 > Functions and Dysfunction of Protein Processing > Flashcards

Functions and Dysfunction of Protein Processing Flashcards

1
Q

What are the start and stop codons?

A

AUG : Methionine : Start

UAA, UGA, UAG : Stop

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2
Q

What is a silent mutation?

A

A mutation where the amino acid is not changed

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3
Q

What is a missense mutation?

A

A mutation in mRNA that only changes the amino acid in the protein, if change is similar to original AA, not bad. If you go from Lysine–> Valine = Sickle Cell Anemia

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4
Q

What is a nonsense mutation?

A

A mutation where a codon is changed into a stop codon causing premature chain termination. The product is either degraded or formed as a truncated version

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5
Q

Frameshift mutation

A

One or more nucleotides are inserted or delted into the ORF…. causes change in the codon sequence and an alteration in the amino acid sequence (duchenne muscular dystrophy)

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6
Q

What does mature mRNA consist of?

A

5’ Cap (7-methylguanosine cap), Poly (A) tail, 5’ untrasnlated region, coding region, and 3’ unstranslated region

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7
Q

What are the 2 important structures of tRNA?

A

Anticodon loop and 3’ CCA terminal region

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8
Q

What does the anticodon loop of tRNA do?

A

It contains a set of 3 nucleotides that pair with a complementary codon in mRNA.

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9
Q

What does the 3’ CCA terminal region do?

A

binds the amino acid that matches the corresponding codon

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10
Q

What do aminoacyl tRNA synthestases do?

A

The synthestase is specific to each amino acid and binds the correct AA to its corresponding tRNA.

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11
Q

What is the two step process of the activation of AAs?

A
  1. Aminoacyl tRNA synthetase catalyzes addition of AMP (originally ATP) to COOH end of AA.
  2. AA is trasnferred to cognate tRNA (by high energy bond at top)
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12
Q

What are the differences between the ribosomes of prokaryotes and eukaryotes and what are they made up of?

A

Ribosomes are made up of proteins and rRNA, they assemble together to activate with mRNA
Prok: have a 50S and 30S subunit (70S) (inhibited by antibiotics)
Euk: have a 60S and 40S subunit (80S)

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13
Q

What do EPA sites in the ribosomal complex do?

A

Acceptor (A) site: mRNA codon exposed to receive aminoacyl tRNA (except MET)
Peptidyl (P) site: aminacyl tRNA is attached
Empty (E) exit site: occupied by empty tRNA before leaving ribosome

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14
Q

What are the three steps of translation and what direction does it occur in?

A

Occurs in 5’ to 3’ direction

  1. Initiation: mRNA, small ribo, and initiator tRNA join (pre-initiator complex)
  2. Elongation: AA atached to intiating Met by forming peptide bond
  3. Termination: peptide chain released from ribo complex
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15
Q

How do you know where to start translation?

A

all mRNA molecules contain signals that define the beginning of each encoded polypeptide chain

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16
Q

What happens once pre-initiator complex is assembled?

A

initiator tRNA-methionine (also called methioninyl tRNA ineukaryotes) which GTP is bound to, is attached to P site of small SU, and slides along mRNA start codon is found. GTP is hydrolyzed, IFs dissociate, large ribo SU binds. Translation begins

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17
Q

What happens during elongation?

A

Activated AA attached to intiating methionine via peptide bond.

  1. new aminoacyl tRNA is attached so that anticodon base pairs with the codon position on A site. (prior to this, the aminoacyl is attached to GTP bound elongation factor-Tu which helps find A site)
  2. When loaded, GTP hydrolysis and release of elongation factor (if correct match, if not then will dissociate)
  3. Peptide bond formed between A and P AAs, catalyzed by peptidyl transferase
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18
Q

What happens during termination step of translation?

A
  1. triggered by stop codons (UAA UGA UAG)
  2. signals to ribosome to stop, brings in release factors (RF) which bind to A site, cleaving the ester bond between the c terminus of the polypeptide and the tRNA (adds h2o on end to form COOH end of PP).
  3. Protein released, GTP hydrolysis dissociates ribosomal complex
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19
Q

Tetracycline

A

Prok elongation inhibitor: binds to 30S, blocking entry of aminoacyl tRNA

20
Q

Chloramphenicol

A

Prok elongation inhibitor: inhibits peptidyl trasnferase

21
Q

Clindamycin and Erythromycin

A

Prok elongation inhibitors: binds to large 50S, blocking translocation of the ribosome

22
Q

Streptomycin

A

Prok elongation inhibitor: Binds to 30s, interferes with bind fmet-tRNA, also with 50S

23
Q

Cycloheximide

A

Euk elongation inhibitor: inhibits peptidyl transferase

24
Q

Diphtheria toxin

A

Euk elongation inhibitor: inactives GTP bound eEF2 interfering with ribosomal translocation

25
Q

Shiga toxin and Ricin

A

Euk elongation inhibitor: binds to large 60S, blocking entry of aminocyl-tRNA to ribo complex

26
Q

Puromycin

A

Prok/Euk elongation inhibitor: causes premature chain termination because acts as 3’ end, and released

27
Q

What is the cytoplasmic pathway?

A

for newly synthesized proteins destined for cytosol, mitcochondria, nucleus, and peroxisomes

28
Q

What is the secretory pathway?

A

for newly synthesized proteins destined for ER, lysosomes, plasma membranes, or for secretion. (first 20 AA residues of PP have ER targeting signals) this is the N-terminal positively charged alpha helix ER signal peptide

29
Q

Where do new proteins with no translocation signal go?

A

stay in the cytoplasm

30
Q

Where do new proteins with N-terminal hydrophoic alpha helix signal peptides go?

A

to mitochondria, goes through TOM (outer transporter) and TIM (inner transporter) which leaves them unfolded. The unfolded proteins are bound to chaperones (HSP70) that heat shock the proteins to keep them safe/ protected.

31
Q

Where do new proteins with four continouse basic residues go (ei. KKKRRK) most commonly Lys and Arg?

A

go to nucleus by nuclear pores, small able to pass through. Large (>40kDa) need nuclear localization signals.

32
Q

Where do new proteins with C-terminal SKL signal sequence go?

A

peroxisomes

33
Q

Where do new proteins with C-terminal KDEL retention signal go?

A

rough ER lumen (some will get sent to golgi, but will be sent bach to rough ER)

34
Q

Where do new proteins with mannose 6-phosphate signal go (associated with I-cell disease)?

A

lysosomes

35
Q

Where do new proteins with Tryptophan-rich domain signal regions go?

A

they get secreted out by vesicles

36
Q

Where do new proteins with N-terminal apolar regions (stop-transfer sequence) go?

A

they get released into membranes

37
Q

Steps for translation in secretory pathway…

A
  1. Each protein has ER targerting signal peptide which properties consist of 1-2 basic AA near N terminus & extremely hydrophobic seq on C terminus
  2. Signal recognition particle (SRP) binds to signal and ribo during trans, it wraps around complex, holding it to ER membrane by its receptor, stoping translation temporarily
  3. Protein directed into ER, enzymes cleave signal to release protein, recycled, undergoes PTM.
38
Q

How does post-translational protein folding work?

A

Small proteins can fold themselves. Large proteins cannot, need chaperones HSP70 (protect protein and help fold into tertiary structure) and chaperonins HSP60 (barrel shaped)

39
Q

Chaperonin HSP60

A

uses ATP to fold large proteins into proper structure

40
Q

How does post-translational proteolytic cleavage work?

A

converts inactive forms (zymogens) to active enzymes by cleaving. (trypsinogen/chymotrypsinogen –> trypsin and chymotrypsin)

41
Q

Post-translation modification: Glycosylation, types and how they work

A

O-glycosidic, ‘O-links’ formed with the hydroxyl groups of Serine or Threonine or N-glycosidic linkage ‘N-links’ formed with Asparagine to form mannose rich type or precursor of sugar transferred from phospho dolichol, complex type

42
Q

Post-translation modification: Phosphorylation, how it works

A

Forms ester bond between phosphate and OH of AA using serine/threonine and tyrosine kinase. Phosphate removed by phosphotases. This regulates enzyme activity and protein functions for signaling. Also done in cell growth, proliferation, differentiation, oncogensis

43
Q

Post-translation modification: disulfide bond formation

A

Stabilize proteins, bonds formed between thiol (SH) group of 2 cysteine (4cystine) residues. occurs in ER lumen, helped by protein disulfide isomerase.

44
Q

Post-translation modification: Acetylation

A

Occurs on lysine residues, uses acetyl-CoA as acetyl donor group. HAT and HDAC, pattern of histone modification heritable.

45
Q

Post-translation modification: collagen

A

lysines modified to form 5-hydroxlysines, other rxns as well… important for assemply of collagen. ascorbic acid essential for lysyl and prolyl hydroxylases. Defects in these reults in skin joint disorders such as ehlers-danlos

025. My MCM Test 2 (15 decks)

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