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A Level Biology > Eukaryotic Gene Expression > Flashcards

Eukaryotic Gene Expression Flashcards

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1
Q

Define Transcription

A

The process in which a complementary RNA copy is made under the direction of the template strand of a specific region of the DNA molecule, catalysed by RNA polymerase

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2
Q

Define Gene

A
  • A section of the DNA that contains the information in the form of a specific sequence of nucleotides to direct the synthesis of one polypeptide chain or RNA
  • A unit of inheritance located on the locus of a chromosome
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3
Q

What does the promoter consist of

A
  • RNA polymerase binding site
  • Transcription start site (anything upstream of this is not transcribed)
  • TATA box
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4
Q

TATA box

A
  • Contains TATAAA sequence, located 25 bp upstream of transcription start site
  • Serves as a binding site for the general transcription factor (TFIID) & facilitates the binding of RNA polymerase
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5
Q

Role of promoter

A
  • Determines which of the two strands of the DNA helix is used as the template strand
  • Is not transcribed
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6
Q

What is the transcription unit

A

The segment of DNA that is transcribed into a single-stranded RNA molecule (pre-mRNA). Only one of the two DNA strands serves as a template for transcription

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7
Q

How is the transcription unit read

A
  • Read in a 3’ to 5’ direction

- RNA synthesised in 5’ to 3’ direction

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8
Q

Template DNA sequence…

A

is complementary to that of RNA and serves as a template to direct the synthesis of RNA molecule

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9
Q

Non-template strand

A
  • DNA strand is not transcribed

- Sequence is exactly the same as that of RNA except nitrogenous base T is replaced by U in RNA

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10
Q

Termination sequence (found at end of gene)

A
  • Codes for a polyadenylation sequence (AAUAAA) in pre-mRNA
  • Results in transcription termination
  • IS transcribed
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11
Q

4 Components of transcription machinery

A
  1. Gene (DNA template)
  2. RNA polymerase (enzyme)
  3. General/Basal transcription factors (Proteins)
  4. RIbonucleotides (Monomers)
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12
Q

Components on a gene

A

Promoter, coding sequence, non-coding sequence, termination sequence

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13
Q

What is RNA polymerase

A
  • enzyme comprising of several protein subunits
  • found in the cytoplasm
  • synthesises RNA using ribonuceloside triphosphates (NTP) as its substrate
  • Reads DNA template in 3’ to 5’ direction
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14
Q

What can bind RNA polymerase bind

A
  1. Template
  2. Promoter
  3. Nucleoside
    in order to initiate transcription
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15
Q

Action of RNA polymerase

A
  • Catalyses assembly of ribonucleotides, which form c.b.p. w template
  • Catalyses formation of phosphodiester bonds between the free 5’ phosphate group of the incoming nucleotide and the free 3’ OH group of the growing RNA polynucleotide chain
  • RNA is synthesised in 5’ to 3’ direction via c.b.p with DNA template
  • Simultaneous transcription occurs from the same DNA template strand
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16
Q

What are General Transcription Factors? (GTF)

A

General Transcription Factor is a protein required for RNA polymerase to bind to promoter and initiate transcription

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17
Q

Role of General Transcription Factors

A

GTF assists in:

  • Positioning RNA polymerase correctly at the promoter and assists in binding it to the promoter
  • Separate the 2 strands of DNA to allow transcription to begin
  • Release RNA polymerase from the promoter
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18
Q

3 main stages of transcription

A
  1. Initiation
  2. Elongation
  3. Termination
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19
Q

3 main processes all pre-mRNA transcripts have to undergo before becoming functional

A
  1. Addition of 5’ methylguanosine cap
  2. addition of 3’ poly(A) tail
  3. RNA splicing
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20
Q

Function of 5’ methylguanosine cap

A
  • protects mRNA from degradation by nucleases (which cleave phosphodiester bonds) from the 5’ end during its transport from the nucleus to the cytoplasm
  • signals the 5’ end of the mRNA serving as the assembly point to recruit the small subunit of the ribosome for translation to begin
  • distinguishes the mRNA from other types of RNA
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21
Q

Function of 3’ poly (A) tail

A
  • protects the mRNA from degradation by nucleases, thus making mRNA a more stable template for trnslation in the cytoplasm
  • facilitates the export of mRNA out of the nucleus via nuclear pores
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22
Q

eukaryotic genes contain

A

coding sequences (exons) and non-coding sequences (introns & regulatory sequences)

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23
Q

exons

A

have protein coding sequences which contain codons, which are translated to form polypeptides

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24
Q

regulatory sequences

A

are the
1. promoter
2. 5’ and 3’ untranslated regions (UTR)
which can affect the rate of gene expression

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25
Q

introns

A

are non-coding sequences inserted between exons and eukaryotic genes. introns may contain regulatory sequence

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26
Q

5 components of mature mRNA

A
  1. 5’ cap
  2. 5’ UTR
  3. protein coding region
  4. 3’ UTR
  5. 3’ poly (A) tail
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27
Q

spliceosome structure

A
  • large complex consisting of several small nuclear ribonucleoproteins (snRNPs)
  • Each snRNP contains small nuclear RNAs (snRNAs) and a set of proteins
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28
Q

when does RNA splicing occur

A

RNA splicing occurs after the release of pre-mRNA from RNA polymerase

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29
Q

simplified description of RNA splicing

A

Introns are removed while exons are spliced (joined tgt) to form mature mRNA (process requires hydrolysis of ATP)

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30
Q

Define translation

A

the process in which a polypeptide chain is synthesised by ribosomes using genetic information encoded in an mRNA template

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31
Q

6 components of translation machinery

A
  1. Mature messenger RNA (template)
  2. transfer RNA (tRNA)
  3. amino acids (monomers)
  4. aminoacyl-tRNA synthetase (enzyme)
  5. ribosome (ribosomal proteins + rRNA)
  6. translation factors (initiation, elongation & termination)
32
Q

why does mature messenger RNA (mRNA) have a short lifespan

A

it is a single-stranded RNA which exists for a relatively short time because it is continuously being synthesised and degraded

33
Q

mRNA is obtained after

A

pre-mRNA undergoes post-transcriptional modifications

34
Q

function of mature mRNA

A
  • acts as a template for translation;
  • recruits small ribosomal subunit;
  • determines start and termination of translation using start (AUG) and stop codons
  • serves as an intermediate that carries the copy of DNA sequence information that encodes proteins
35
Q

what does the protein-coding region of mRNA consist of

A

consists of a series of codons representing the amino acid sequence of the polypeptide

36
Q

describe untranslated regions of mRNA

A

consists of additional sequence at the 5’ end known as the 5’ UTRand downstream of the stop codon, known as the 3’ UTR (contains polyadenylation signal)

37
Q

each codon within coding region of mRNA

A

represents as amino acid in corresponding amino acid sequence in protein

38
Q

main function of tRNA (transfer RNA)

A
  • serves as an adaptor molecule in the translation of an mRNA molecule sequence into the amino acid sequence in a polypeptide
  • brings in specific amino acid sequences corresponding to the sequence of codons in mRNA
39
Q

5 properties of tRNA

A
  • small RNA molecule consisting of about 80 nucleotides
  • ability of the anti-codon to base pair with an mRNA codon
  • specific base pairing with ribosomes
  • binds to a specific amino acid determined by the anticodon sequence
  • a tRNA with an amino acid bound to it is known as aminoacyl-tRNA
40
Q

all tRNAs have common

A

secondary and tertiary structures

41
Q

secondary structure of tRNA

A
  • 2D cloverleaf shape, held by complementary base-pairing within the single-stranded molecule
  • 3 loops
  • on one of the loops, 3 unpaired bases form an anticodon, the triplet base that binds to a specific mRN codon via c.b.p (via hydrogen bonds)
  • 3’ end (CCA stem) of a tRNA molecule attached to a specific amino acid via an ester linkage
42
Q

Tertiary structure of tRNA

A

twisting and folding into a compact 3D conformation of the specific amino acid and anticodon sequence of the tRNA

43
Q

Characteristics of ribosomes

A
  • a large ribonucleoprotein complex comprised of ribosomal proteins and ribosomal RNA (rRNA)
  • bacteria ribosomes are 70S while eukaryotic ribsomes are 80S
44
Q

Structure of ribosomes

A
  • small 40S subunit: contains an mRNA binding site
  • Large 60S subunit has 3 binding sites for tRNA:

Aminoacyl-tRNA site (A)
holds the incoming tRNA carrying the next amino acid to be added

P site (Peptidyl-tRNA site)
holds the tRNA carrying the growing polypeptide chain
E site (exit site)
site of release of deacylated tRNA (no more aa attached)
45
Q

3 functions of ribosomes

A
  1. provides an environment for the specific recognition between a codon of mRNA and an anticodon of tRNA
  2. holds the tRNA and mRNA in close proximity and positions the new amino acid for addition to the growing polypeptide
  3. rRNA in the large ribosomal subunit has peptifyl transferase activity, catalyzes the formation of peptide bonds between amino acids
46
Q

3 types of translation factors

A

initiation
elongation
release

47
Q

initiation translation factor

A

required for assembly of mRNA, first tRNA and ribosomal subunits

48
Q

elongation translation factors

A

required for synthesis of polypeptide chains

49
Q

release translation factors

A

required for recognition of stop codon and disassembly of translation machinery

50
Q

what form of energy do translation factors use

A

some translation factors use GTP as an energy source to carry out their functions. GTP is an alternate energy source to ATP and is used in specific reactions

51
Q

account for tRNA’s ability to act as an adaptor

A
  • anticodon can determine specific amino acid attached to 3’ CCA stem
  • anticodon can undergo complementray base pairing with mRNA codon
52
Q

polyribosomes

A
  • ribosomes that aggregate in clusters
  • simultaneous translation of polypeptides from the same mRNA strand
  • increases the rate of translation
53
Q

rRNA

A
  • has peptidyl-transferase enzymatic activity which form peptide bonds
  • component of large and small ribosomal subunits; complexes with ribosomal proteins
  • reads mRNA in the 5’ to 3’ direction, searches for start codon
  • aligns mRNA such that it pairs with tRNA in close proximity
54
Q

function of post-translational modification in eukaryotic cells

A

to allow the newly translated polypeptide chain to coil and fold in a precise manner to assume the unique 3D conformation of a protein in the lumen of the rER cytoplasm, so that protein can function

55
Q

3 main types of post-translational modifications

A
  1. attaching it to biochemical functional groups
  2. Structural changes
  3. proteolytic cleavage
56
Q

adding biochemical functional groups

A
  1. glycolysation- addition of oligosaccharides to protein to form glycoproteins
  2. reversible phosphorylation of threonine, serine nd and tyrosine
  3. attaching ubiquitin (protein molecule) - marks protein for proteolysis by proteosome. at least 4 ubiquitin must be attached before proteolysis can take place
  4. addition of signal peptides
57
Q

structural changes

A

eg addition of disulfide bonds

58
Q

proteolytic cleavage

A

refers to cleaving of amino acid sequences from the protein (eg insulin)

59
Q

selective degradation of proteins allows for

A

control of the length of time in which a protein can function

60
Q

why is selective degradation of protein important

A

this regulation allows a cell to:

  1. adjust the kinds and amounts of proteins in response to changes in the environment
  2. maintain the proteins in working order
61
Q

How does the DNA base sequence affect primary structure of proteins

A

DNA base sequence of a gene is translated into amino acid sequence of polypeptide. hence it determines the primary structure of proteins

62
Q

what is the genetic code

A

it is a list of codons of mRNA/ sequence of triplet bases in the non-template strand of DNA. it consists of information in the form of 3 nucleotide bases (codons of mRNA), each codon corresponding to an amino acid in the encoded protein

63
Q

why is the genetic code comprised of triplet codes

A

only a triplet code contains enough combinations to code for the 20 different amino acids, 4^3=64 different codons

64
Q

acronym for features of genetic code

A

Triplet
Universal
Non-overlapping
Degenerate

code

65
Q

how many codons code for amino acids

A

61 codons code for amino acids, including start codon (AUG). the 3 stop codon (UAG, UGA, UAA) serve as termination signals of polypeptide synthesis

66
Q

how is codon written

A

codon is written as it appears on mRNA

67
Q

triplet code feature

A

each mRNA codon that specifies an amino acid in the polypeptide chain consists of 3 nucleotide bases

68
Q

linear code feature

A

each mRNA codon is always read in the 5’ to 3’ direction

69
Q

universal code feature

A

same code is used by almost all organisms

70
Q

continuous and non-overlapping

A
  • codon read as a triplet in 5’ to 3’ direction

- nucleotides in the mRNA are read continuously as successive groups of 3 nucleotides without skipping any nucleotides

71
Q

degenerate but unambiguous

A
  • a single amino acid is coded by more than 1 different codon
  • only methionine (AUG) and tryptophan (UGG) are coded by a single codon each
  • every codon codes for only one amino acid, thus it is unambiguous
  • most amino acids are encoded by degenerate codons that differ in the 3rd position of the codon. mutations can arise in this position of the codon without altering amino acid sequences (silent mutations)
72
Q

wobble base phenomenon

A
  • a single tRNA can recognize 2 or more degenerate codons in some cases
  • wobble is the violation of the usual rules of base pairing at the 3rd nucelotide
  • this occurs because base-pairing at the 3rd base is not so specific (due to degenerate codons, some polypeptides have the same amino acid sequence)
73
Q

start codon

A
  • AUG, codes for methionine

- defines the first amino acid and the reading frame

74
Q

stop codon

A
  • UAA, UGA, UAG mark the end of protein synthesis
  • not translated and do not code for any amino acid
  • there is no tRNA with the anticodon complementary to these 3 bases
75
Q

polypeptides of proteins destined for the endomembrane system/ secretion are marked by

A

signal peptide

76
Q

signal peptide

A
  • targets polypeptides to ER
  • sequence of about 20 amino acids near N-terminal of p.p is recognised as it emerges from ribosome by protein- RNA complex known as Signal Recognition Particle (SRP)
77
Q

signal recognition particle

A
  • functions as an adaptor that brings the ribosomes to a receptor protein built into ER membrane
  • polypeptide synthesis continues there and growing polypeptide snakes across the ER membrane into cisternal space via a protein pore

A Level Biology (1 decks)

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