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Principles: Biochemistry > Gene Regulation and Protein Synthesis > Flashcards

Gene Regulation and Protein Synthesis Flashcards

1
Q

structure of RNA

A

single stranded

local stretches of intramolecular base-pairing (sums and loops)

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2
Q

3 main RNA classes

A

rRNA - combines with proteins to form ribosomes where protein synthesis takes place, stable
tRNA - carries amino acids to be incorporated into protein, stable
mRNA - carries genetic info for protein synthesis

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3
Q

what is the most common type of RNA in cells

A

rRNA - 80%
tRNA - 15%
mRNA - 5%

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4
Q

describe the structure and function of tRNA

A

adapters between nucleic acid code and amino acid code
anti-codon consists of 3 nucleotides
3D structure

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5
Q

where is the attachment site for specific amino acid

A

anticodon sequence codes for specific amino acid

added to free 3’ end OH attachment site

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6
Q

how is RNA made

A

use one DNA strand to copy nucleotide sequence

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7
Q

how many types of RNA polymerase do eukaryotic cells have

A

3 - Pol I, Pol II, Pol III

Pol II synthesises all mRNA

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8
Q

5 steps of transcription

A

RNA polymerase II binding - detection of initiation sites (promotors) on DNA, transcription factors required (NO PRIMER)
DNA chain separation - local unwinding of DNA to gain access to nucleotide sequence
Transcription initiation - selection of first nucleotide of growing RNA
Elongation - addition of further nucleotides to RNA chain
Termination - release of finished RNA

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9
Q

role of RNA polymerase

A

bind promotors (DNA sequence), specific to RNA pol II
Transcription starts at nucleotide +1
TATA box is present about 25 nucleotides upstream before transcriptional start

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10
Q

what is TBP

A

TATA box binding protein
recognises TATA box
introduces kink into DNA (determines transcriptional start and direction)
Provides platform for further transcription factors & RNA polymerase

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11
Q

what is TFIID

A

general transcription after

required for all pol II transcribed genes

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12
Q

how is transcription initiated

A

general transcription factors
Pol II & TFIIF extend transcript on their own
TFIID remains at promotor, a new initiation complex can assemble allowing transcription at low basal rate

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13
Q

what happens during transcription elongation

A

transcription bubble moves in one direction along DNA

DNA is unwound infant of DNA polymerase then rewound behind it

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14
Q

in what direction is RNA chain synthesised

A

in a 5’ to 3’ direction
new RNA is complementary to template strand
identical to the coding strand (U replaces T)

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15
Q

how Is transcription terminated

A

new RNA strand makes stem loop structure followed by stretch of Us
A specific enzyme cleaves finished RNA, releasing it

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16
Q

how is transcription regulated

A

requires specific transcription factors (DNA binding proteins, DNA binding domain and transcriptional activation which causes other protein/factors to increase rate of transcription)
Bind to specific DNA sequences near promotor enhance/ repress transcription (loop back on itself)

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17
Q

how are genes expressed

A

in response to specific stimuli eg hormones, cell stress

transcription factor activated by modification eg by extracellular factors phosphorylation/cleavage

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18
Q

describe steroid receptors and how they are activated

A 
transcription factors (nucelar hormone receptors)
DNA-binding and ligand-binding domain highly conserved
in cell cytoplasm (inactive)
when ligand (steroid) binds move to nucleus and bind to DNA at steroid response elements
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19
Q

describe the activation of the glucocorticoid receptor

A

steroids transported in blood (by albumin binding)
enter large cell by diffusion
bind to inactive steroid receptor in cytoplasm causing receptor activation
translocates to nucleus
binds to response elements (as homodimer)
coordinated regulation of genes

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20
Q

are all genes expressed

A

no
some at basal rate
some never expressed DNA will be tightly coiled around histone, packaged away - never transcribed
genes are regulated by transcription factors

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21
Q

what are coding regions

A

exons, disturbed by non coding regions - introns

all transcribed into pre-mRNA

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22
Q

what is splicing

A

removal of introns before translation forming mRNA, only exons in mature mRNA
works in 5’ to 3’ direction
this is how one gene can make different proteins depending on whats classed as an intron and exon

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23
Q

how is the end of mRNA processed

A

addition of poly(A)tail

capping - addition of 5’ cap

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24
Q

what are codon anti-codon base pairs

A

during translation anticodons of tRNA molecules form base pairs with codons on mRNA
3 nucleotides
genetic code based on triplets

25
Q

how many combinations code for 20 amino acids

A

64 amino acids

26
Q

what is the start codon

A

AUG - methionine

27
Q

what does degenerate mean

A

many codons make the same amino acid

28
Q

define unambiguous

A

each codon codes for only one amino acid - stop

29
Q

what is the stop codon

A

UAA
UAG
UGA

30
Q

what determines where translation takes place

A

reading frames 3 different types

coding frame will give longest stretch without a stop codon in between

31
Q

components of translation

A 
amino acids 
tRNAs 
Aminoacyl-tRNA synthetases
ribosomes
mRNA
ATP & GTP as sources of energy
a specific set of protein factors for each of (initiation of protein synthesis, elongation of polypeptide chain/translocation, termination)
32
Q

what is the role of aminoacyl-tRNA

A

synthetases bind amino acids to their corresponding tRNA molecule (highly specific)
at least one for each amino acid
ATP provides energy for formation of covalent bond
catalysis ATP to ADP

33
Q

how many molecules of rRNA are in a ribosome

A

4

also hae protein components

34
Q

what are the 3 binding sites on a ribosome

A 
E = exit
P = peptidyl
A = Aminoacyl
35
Q

how is translation initiated

A

initiation factors

36
Q

where does the energy for translation come from

A

hydrolysis of GTP supplies energy for initiation

37
Q

what happens when mRNA comes in contact with rRNA

A

small ribosomal subunit binds to 5’ end of mRNA

moves along mRNA until AUG start codon found (ATP dependant)

38
Q

describe initiation of translation process

A

special initiator tRNA with UAC anticodon base pairs with start codon (carries methionine)
large subunit joins assembly and initiator tRNA is located at site P

39
Q

role of elongation factor EF-1a

A

brings next aminoayl-tRNA to A site
GTP is hydrolysed
EF released from tRNA
second EF regenerates EF 1 to pick up next amino-acyl-tRNA

40
Q

how do peptide bonds form between adjacent amino acids at ribosome

A

peptidyl transferase catalyses peptide bond formation between amino acid in P and A sites so peptide is in A site

41
Q

What moves ribosome along mRNA

A

EF-2

42
Q

what does the tRNA do once it has dropped its amino acid off at site P

A

empty tRNA enters E site so can exit and reload
tRNA with growing peptide moves from A to P site, A site empty for next amino acid
right > left
E P A

43
Q

what bond is between amino acids

A

peptide

44
Q

when does termination of translation occur

A

when A site of ribosome encounters stop codon

no aminoacyl-tRNA base-pairs with stop codon

45
Q

what happens during termination

A

release factorRF binds to stop codon
GTP hydrolysis
finished protein cleaved off tRNA
components dislocate

46
Q

what is the polysome

A

many ribosomes acting on one mRNA strand to synthesise polypeptide at same time working
ribosomes added in 5’ to 3’ direction

47
Q

what is a point mutation

A

change in single base in DNA

48
Q

what is a missense mutation

A

results in change of amino acid sequence

can change protein function eg haemoglobin in sickle cell

49
Q

what are the 3 types of point mutation

A

missence
nonsense
silent

50
Q

what is a nonsense mutation

A

creates termination codon

changes length of protein due to premature stop of translation

51
Q

what is a silent mutation

A

no change of amino acid sequence
due to degeneracy of genetic code
no effect on protein function

52
Q

what is a frameshift mutation

A

addition/deletion of single base

changes reading frame of translation

53
Q

what are chromosomal mutations

A

affect larger portions of genome
deletion
duplication
translocation inversion

54
Q

what happens to finished protein

A

targeting - moving protein to final cellular destination, many possible locations, depends on amino acids in sequence
modification - addition functional groups
degradation - unwanted/damaged proteins removed

55
Q

what do free ribosomes in cystol make proteins destined for

A

cystol
nucleus
mitochondria
translocated (post-translationally)

56
Q

what doe bound ribosomes on rough ER make proteins destined for

A 
plasma membrane
ER 
Golgi-apparatus
secretion
translocated (co-translocationally)
57
Q

what is gycosylation

A

addition and processing of carbohydrates in ER and golgi

58
Q

what happens during post-translational modifications

A

formation of disulphide bonds in ER
folding/assembly multisubuni proteins in ER
specific proteolytic cleavage in ER/gogli/secretory vesicles
hereditary for of emphysema - misfiling of protein antitrypsi in ER

Principles: Biochemistry (6 decks)

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