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Biochem > 05 > Flashcards

05 Flashcards

1
Q

What is transcription

A

copying DNA to RNA
Using RNA polymerase that catylizes the polymerization of nucleotides to form a single strand of RNA

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1
Q

Describe the central dogma

A

how info flows in a biological system

DNA (transcribed) –> RNA (translated) –> Protein

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2
Q

Where does transcription occur

A

occurs at gene regions within DNA –> each gene has a promoter region where RNA polymerase binds and starts (initiates) transcription

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3
Q

Which direction is the polynucleotide strand synthesied

A

5’ –> 3’

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4
Q

Which strand will the RNA strand match on DNA

A

matches coding strand

copies from template strande

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5
Q

What is the difference between rna polymerase and dna polymerase

A
  1. rna polymerase don’t need a primer to start synthesis
  2. proofreading on rna polymerase is a seperate protein –> the same part of the enzyme will “turnaround” and go backwards, removing the incorrect base and then starting again
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6
Q

What are the types of RNA polymerases, what do they do

A

RNA polymerase 1: rRNA
RNA polymerase 2: mRNA
RNA polymerase 3: small RNA (tRNA, 5S, rRNA)

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7
Q

What is a genome

A

contains many genes which provide the instructions for specific proteins

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8
Q

What are the parts of a gene

A

promotor region: where RNA polymerase binds to start transcription

transcribed region: part that gets turned into the mRNA

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9
Q

What modifications are made to RNA before it can be transported out of the nucleus

A

5’ cap
Poly A tail

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10
Q

What are the non coding regions called on eukaryotic genes

A

introns
must be removed

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11
Q

What are transcription factors

A

help recruit RNA polymerase and stabilize it on the DNA
allows transcription to start

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12
Q

What is the TATA box

A

in the promotor region

RNA polyermase binds to it becasue the bonds between A and T are weaker so easier to seperate for transcription

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13
Q

What is the sigma factor

A

in the promotor region

causes the strands to seperate

sigma factor is released and the DNA re-anneals behind the transcript
- becasue DNA re-anneals, supercoiling does not occur

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14
Q

What is an operon

A

on bacterial cells and may have several genes that are all under the control of a single promotor

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15
Q

What does an operon produce

A

a polycistronic transcript that is translated to several proteins
- can synthesize many related proteins at the same time

cistron = transcript

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16
Q

What does the 5’ cap do

A

a guanasine that is methylated by S-adenosylmethionine
(SAM) –> regenerated by the vitamin’s folate and B12, so this can’t occur if vitamin deficiencies exist

  1. stabilizes the mRNA
  2. Helps the mRNA translocate to the cytoplasm
  3. helps interact with ribosomes to start translation
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17
Q

What is a poly A polymerase

A

catalyzes the addition of A’s (can be >200) from ATP after transcription is finished

no string of Ts on DNA, so modification is not coded in the DNA

The poly A tail is a protein binding site that protexts the mRNA transcript from being degraded in the cytosol

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18
Q

What is a spliceosome

A

nucleotide sequence that borders the intron and is recognized by a protein complex
- introns have a specific sequence at the begginign and end to signal the spliceosome

binds to the intron region of mRNA and cuts it out

19
Q

What is the purpose of alternative splicing

A

can produce different variations of proteins some the same transcript

20
Q

What do rRNAs do after transcription

A

associate with proteins and form an intact ribosome that can translate mRNAs into proteins

21
Q

What do tRNAs do after transcription

A

after, they are left with an “anti-codon” region that binds to a specific RNA sequence

on the other end, there is a region that binds to a speicifc amino acid

tRNA translates na mRNA sequence into an amino acid

22
Q

Which direction is mRNA translated

A

5’ –> 3’
from the amino (N)-terminus to the carboxy (C)-terminus

23
Q

What joins amino acids

A

carboxylic acid group of one aa and the amino group of the next aa

Carbons and nitrogens of the aa form the backbone of the polypeptide

24
Q

What type of reaction creates peptide bonds

A

condensation reaction –> water is released

25
Q

Why are groups of 3 used for the genetic code

A

4 nucleotides = 4 amino acids

4x4 = 16 (not enough aa)
4x4x4 = 64 combinations

26
Q

What does a degenerate code mean

A

more than one codon can code for the same amino acid

27
Q

What does an unambiguous code mean

A

each codon always codes for the same amino acid

28
Q

What does a wobble on a codon mean

A

3rd position has a variation
- base-pairing in this spot might be weaker
- may deviate from the base-pairing rules or there can be an unusual base in this position on the anticodon that can pair with more than one base (only in the tRNA)

29
Q

TF the genetic code is not universal

A

false
most organisms use the same code
- some exceptions where a few different codons for amino acids in our mitochondrial DNA

no puntuation in the code and it doesn’t overlap

30
Q

Why does the coding sequence always start as AUG

A

there are 3 possible “reading frames” in which the code could be read (depending on where you start)
- different frames would produce very different proteins

31
Q

TF mutations can be passed down generations

A

True
they cannot be repaired

32
Q

What are the point mutations

A

silent
mssense
nonsense

33
Q

What is a silent mutation

A

no effect on the protein sequence

34
Q

What is a missense mutation

A

results in an amino acid substitution

35
Q

What is a nonsense mutation

A

substitutes a stop codon for an amino acid

36
Q

What is a frameshift mutation

A

insertion or deletion on nucleotides
- insertion of a stop codon
or
- if not in a group of 3 –> reading frame is shifted

37
Q

TF ATP is required for tRNA to catalyze the addition of amino acids

A

true
aa is attached –> tRNA is considered “charged”

38
Q

How are polypeptides synthesized

A

by ribosomes using mRNA as the instructions

  1. charged tRNAs enter the ribosome and donate their aa to the growing chain (forming a peptide bond) while the anticodon is attached to the mRNA
  2. tRNA is released and the charged tRNA that codes for the next aa in the reading frame become attached
39
Q

Describe the steps for translation

A
  1. initiation:
    - formation of a complex between the methionyl-tRNAi, initation factors, the mRNA and the small ribosomal subunit and large subunit

large subunit: aminoacyl (A) site, peptidyl (P) site, ejection (E) site

  1. elongation:
    - peptidyl transferase (the rRNA, an enzyme, NO protein) catalyzes the formation of the peptide bonds for each aa in the chain
    A) peptide bond is formed between the tRNA in the P-site and the tRNA in the A-site
    B) the tRNA slide over and the used tRNA is now in the exit site and is released
    C) the tRNA previously in the A-site, now contained the polypeptide chains and is now in the P-site
    D) A new charged tRNA enters the A-site to begin the next bond formation
  2. Termination:
    - the elongation steps continue until a stop codon is reached
    - no tRNA that match these codons
    - release factors bind to the ribosome, allowing for termination to occur
    - the polypeptide is hydrolyzed from the tRNA and the ribosome dissociates, ready to restart the process on a new mRNA
40
Q

TF the process of translation requires a lot of energy by the cell

A

True

41
Q

What are polysomes

A

multiple ribosomes binding to a single mRNA (depends on the length of the mRNA)
- allows multiple copies of a protein to be translated from a single mRNA

42
Q

What are chaperone prtoeins

A

proteins that bind to the polypeptide and help it to into its native structure

43
Q

What happens to new proteins with signal sequences

A

targeted to various compartments where they function
- proteins incorporated into membranes or organelles are translated into the ER due to signal-recognition particle (SRP) that causes the ribosome to dock onto the ER to complete synthesis of the protein

44
Q

How are proteins synthesized into the ER

A

proteins translated into the lumen of the ER are carried in vesicles to the golgi complex
nost destined to stay in the gogli or go back to the ER –> leave in vesicles from the other side of the golgi

vesicles either become lysoso mes or fuse with the cell membrane to release secreted proteins or integrate membrane-spanning proteins in the cells outer lipid bilayer

Biochem (11 decks)

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