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Biochem > Mclaughlin 1 > Flashcards

Mclaughlin 1 Flashcards

0
Q

What is kwashiorkor starvation?

A

Protein malnutrition- a lot of calories, not enough proteins (mostly in children)

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1
Q

What is marasmus starvation?

A

Total calorie starvation

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2
Q

What is cachexie starvation?

A

Seen in cancer patients - dont know why they’re losing weight

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3
Q

Alpha amanitine, RNA pol II ricin, and 60s ribosomal diphtheria toxin are all examples of:

A

Toxins that inhibit protein synthesis

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4
Q

What does diphtheria toxin do

A

catalyzes the ADP-ribosylation of,

and inactivates, eEF-2. In this way, it acts as a translation inhibitor.

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5
Q

Are mutation more dangerous in embryos or adults? why?

A

embyros, their cells are more rapidly dividing -> any mutation will be propogated more often and to more cells

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6
Q

In rapidly growing cells, protein synthesis accounts for how much energy and wieght?

A

80% of the cells energy

50% of its dry weight are proteins

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7
Q

What are 4 transcription inhibiting toxins listed in lecture?

A

alpha amanitine
Ricin
ditheria toxin
trichothecene mycotoxins?

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8
Q

What are the three most important take aways from the protein synthesis postulates?

A

There is a genetic code.
There is an RNA copy of the DNA (mRNA), which carries the code.
There is a complex apparatus (ribosome and tRNA)
for translating the code carried by that mRNA.

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9
Q

What is the significance of Polynucleotide phosphorylase?

A

Help in cracking the genetic code - can make poly nucleotide tails

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10
Q

What are four major discoveries of the genetic code?

A
  1. The code is triplet, unpunctuated and nonoverlapping.
  2. The Genetic Code is Unambiguous - each triplet codes for only one amino acid
  3. The code is degenerate - one amino acid is coded for in different ways
  4. The Genetic Code is NOT quite universal
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11
Q

What are the exceptions to the unambiguous rule of the genetic code?

A

AUG - codes for both Methionine and N-formyl-Methionine

UGA - codes for selenocysteine and is a stop codon.

UAG - codes for pyrrolysine and is a stop codon

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12
Q

What is the importance of selenocytosine, the 21st amino acid?

A

antioxidant defense, thyroid hormone metabolism, lymphocyte activation, and myocyte regeneration
mutation of selenoprotein - abnormal thryoid hormone reg.

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13
Q

The code is so degenerate that only two amino acids are only coded for by one sequence, which two are they?

A

Methionine and tryptophan

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14
Q

How come the code isn’t 100% universal?

A

Because the mitochondrial DNA codes for different things than ours, thus mitochondrial protein synthesis resembles prokaryotic protein synthesis more than it does eukaryotic protein synthesis

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15
Q

Which amino acid stands for I? Where is it found and what is its importance?

A

Inosine. Found in tRNA and it can bind to either ACU. This allows for the wobble in the thrid amino acid position of tRNA

16
Q

Is the frequency of proteins similar between prokayotes and eucaryotes?

A

NO

17
Q

What are the four steps of proteins synthesis?

A

Initiation
Elongation
termination
disassembly

18
Q

How is mRNA translated and proteins synthesized (directionally)?

A

mRNA is translated 5’ -> 3’
Proteins are synthesized from the N-terminus to the C-terminus
N corresponds with 5’
C corresponds with 3’

19
Q

What is the difference between eukaryotic and prokaryotic translation?

A

Prokaryotic is not separated in both space and time, eukaryotic is (mRNA made in nucleus and proteins in cytoplasm)

20
Q

What 3 things are required for translation?

A

mRNA
functionally active ribosome
amino acylated tRNA

21
Q

Where are pseudouridine and andribothymidine found?

A

In tRNA, made through post translational modification.

22
Q

Where does the amino acid bind on the tRNA, what is the sequence?

A

It attaches to the 3’ end; -C-C-AOH

23
Q

What is a ribosome made of?

A

Small subunit 30S (prokaryotes) 40S (eukaryotes)
(decoding centre)

Large subunit 50S (prokaryotes) 60S (eukaryotes)
(peptidyl transferase centre)

24
Q

What is tRNA synthatase and why is it significant?

A

protein that binds the amino acid to the tRNA. It is highly specific to the structure of the tRNA thus ensure the correct amino acid.
*It has two sites a synthesizing site and also a editing site. It can remove wrong amino acids added by using 2 ATP

25
Q

How is tRNA synthatase usually named?

A

(amino acid) tRNA synthatase

26
Q

Which amino acid has two forms of tRNA encoding for it?

How do they differ?

A

tRNA encoding for methionine (initiator and also elongating tRNA)
initiator tRNA binds in P site and elongator binds to A site
-initiator knows to bind to P site because it is formylated (formic acid) to the amino terminus (which uses initiating factor 2)
-elongator tRNA isn’t formylated -> it binds to elongating factoer Tu

27
Q

The formylating enzyme for tRNA is found in what kind of cells?

A

Only prokaryotic!

28
Q

What are the steps of protein initiation?

A

IF-3 binds to small subunit freeing from large subunit
IF-1 assists IF-3 and small subunit binding, it also blocks the A site ensuring proper initiation
IF-2 bound to tRNA with F-methionine and mRNA (shine-delgarno sequence) bind to small subunit
IF-1,2,3 disociate with large subunit binding.

29
Q

what is the shine-delgarno sequence?

A

Sequence on mRNA that is before the start codon AUG (signals initiation). It matches up with sequence on rRNA in small subunit

30
Q

What are the steps in protein elongation? (just the first part with EF-Tu)

A

EF-Tu +GTP + aminoacyl - tRNA binds to A site (tRNA is in a distorted conformatoin)
Checks to make sure tRNA is correct -> if not then sends it away
GTP-> GDP and EF-Tu undergoes huge conformational shift and relases tRNA, relaxing its conformation (called accommodation)
accommodation also enables the ribosome to catalyze the formation of a polypeptide bond
Double checks to make sure it is the correct tRNA -> if not sends away

31
Q

part two of elongation (EF-G) Translocatoin

A

Translocation
The unbound tRNA in P site moves to E site
EF-G bound to GTP comes into the A site translocating the tRNA in the A site to the P site
(the shape and size of EF-G is comparable to EF-Tu+aminoacyl tRNA

32
Q

How does termination occur? What is significant about termination and the creation of multiple proteins?

A

Once the ribosome hits a UGA,UAA,UAG sequence a release factor (RF) binds to the ribosome and breaks the polypeptide-tRNA bond, releasing a free polypeptide.
After the polypeptide has been released, the ribosome is released from the mRNA. Translation is a non-destructive process (Other ribosomes continue to translate mRNA)

33
Q

What is peptidyl transferase?

A

It is what cleaves the polypeptide-tRNA bond -> uses hydrolysis.

34
Q

how do the half lifes of tRNA, rRNA and mRNA relate?

how does this effect the rate of translation?

A

rRNA - longest half life - protected by proteins
tRNA - middle has alot of modified base pairs and is protected by EF-Tu
mRNA - very unstable -> to regulate translation rare amino acids slows translation -> less proteins are made

35
Q

What is a significant difference between protein synthesis in prokayrotes and eukaryotes?

A

In eukaryotic cell, protein synthesis takes place in the cytoplasm while transcription and RNA processing take place in the nucleus.
In bacteria, these two processes can be coupled so that protein synthesis can start even before transcription has finished.

36
Q

What do these drugs do?

A

Strep - prevents initiation
Tetracyclines- prevents aminoacyl tRNA to bind to A site
Puromyocin- looks like aminoacyl tRNA, binds and doesn’t allow elongation
Clindamyocin & erythamyocin - blocks translocation by binding to 50S irreversibly
Diphtheria toxin - blocks EF-2, blocks Translocation

Biochem (3 decks)

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