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Biology 3/4 > Gene expression/Protein synthesis > Flashcards

Gene expression/Protein synthesis Flashcards

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1
Q

The stages of gene expression for eukaryotic organisms are:

A
  1. Transcription
  2. RNA processing
  3. Translation
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2
Q

Explain why DNA needs to make a single stranded copy

A

DNA cannot leave the nucleus as it is too large
cellular structures that build proteins are outside the nucleus

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3
Q

Compare structure of mRNA and DNA

A

mRNA: single stranded, Uracil, ribose sugar
DNA: double stranded, Thymine, deoxyribose sugar
Both contain phosphate and nitrogenous bases

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4
Q

Outline the process of transcription

A

Initiation:
- RNA polymerase binds to promoter region of the DNA template strand.
- separates the DNA strands to expose nitrogenous bases
Elongation:
- RNA polymerase moves along the DNA template strand in a 3’ to 5’ direction, catalysing the joining of complementary RNA nucleotides which are added to the 3’ end of mRNA and attach to each other via condensation reactions
Termination:
- when RNA polymerase reaches a terminator region, it detaches from DNA, releasing the pre-mRNA.
- DNA strands pair via complementary base pairing and recoil (due to hydrogen bonds)

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5
Q

What are monomers?

A

atoms or mall moleucles that bond together to form more complex structures (nucleotide, amino acid)

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6
Q

What are polymers?

A

large molecule made up of repeating subunits (monomers)

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7
Q

DNA polymers:

A

DNA
- double helix
- strands run antiparallel to each other
- two strands are connected through hydrogen bonds between complementary base pairs

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8
Q

RNA polymer (structure and types):

A
  • single stranded
  • messenger RNA
  • transfer RNA
  • ribosomal RNA
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9
Q

Protein monomer:

A
  • amino acid
  • central carbon with hydrogen attached
  • amine group (NH2)
  • carboxyl group (COOH)
  • variable R group
  • 20 different amino acids (20 R groups)
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10
Q

Name and summarise the reaction that creates bonds that join nucleotides together to create mRNA

A
  • condensation reactions
  • pentose sugar of one nucleotide interacts with phohsphate of another nucleotide
  • creates a phosodiester bond (covalent), eliminating a water
  • nucelotides added to 3’ end
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11
Q

Condensation polymerisation for amino acids (protein monomer)

A
  • carobxyl group of one amino acid and amine group of another amino acid interact, creating a peptide link
  • a water molecule is released
  • forms the polymer (polypeptide)
  • ATP is needed
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12
Q

When do amino acids become proteins?

A

Chains of amino acids (polypetpides) become proteins when they fold into
a functional shape

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13
Q

Primary structure

A
  • order of amino acids
  • joined together by peptide bonds (covalent- strong)
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14
Q

Secondary structure

A
  • 3 different folds can occur depending on the R groups
  • Formation of alpha helices (e.g. wool)
  • beta pleated sheets (e.g. silk)
  • random coils (folding)
  • hydrogen bonding (Weaker than covalent)
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15
Q

Tertiary structure

A
  • formation of irregular 3D structure (single poplypeptide chain)
  • many proteins are functional at this level
  • various types of bonding between the variable R groups
  • e..g myoglobin
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16
Q

Quaternary structure

A
  • multiple polypeptide chains combining (it may be multiple of the same polypeptide chain).
  • various types of bonding between R groups
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17
Q

Prokaryote vs Eukaryote DNA

A

Prokaryote: single circular chromsome and plasmid DNA
Eukaryote: linear chromosomes (humans- 46)

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18
Q

Eukaryote gene structure

A

Promoter:
- positioned at the front of a gene
- particular nucleotide sequence (TATAAA…)
- location where enzyme RNA polymerase binds and initiates beginning of gene expression

Exons- regions of DNA that contain information for making a protein

Introns- sections of DNA (no info for making a protein), removed in the process of gene expression

Terminator:
- positioned at the end of a gene
- RNA polymerase detaches at this region
- represents specific nucleotide sequence

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19
Q

Prokaryotic gene structure

A

Organised into operons:
- genes with similar functions are grouped together for efficiency
- under the control of a single promoter

  • Promoter
  • Operator: after promoter, before genes, represents specific nucleotide sequence, repressor proteins can bind to regulate gene expression
  • no introns
  • terminator
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20
Q

RNA processing

A
  • production of mature mRNA from pre mRNA
  • occurs in the nucleus
  • only occurs in eukaryotes

Process:
1. Capping: Addition of the 5’ methyl cap (modified guanine nucleotide added to 5’ end)
- protection from degradation and enzyme attack to the 5’ end
- contributes to its stability
- assist in ribosome binding in translation (as ribosome first binds to 5’cap)

  1. Addition of the poly-A tail to the 3’ end (AAAAA…)
    - contributes to stability
    - facilitate mRNA export from the nucleus
  2. Splicing (removing introns and joining exons)
    - done by spliceosomes

https://www.youtube.com/watch?v=m2lOf3ker9M&ab_channel=PeterCavnar

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21
Q

What do mRNA vaccines do?

A

contain instructions for cells to make proteins that mimics the virus so the immune system can be trained

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22
Q

What is the point of the nucleus?

A

To protect the DNA as if the DNA is damaged, every cell produced could be affected

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23
Q

Why is thymine replaced with Uracil?

A
  • Thymine has a mtheyl group which makes it more stable in DNA
  • RNA is more transient (while DNA stores genetic information over a long period of time), doesn’t need the stability
  • Uracil is synthesised and broken down more easily, more energy efficient
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24
Q

Describe a codon and where they are found

A

3 nucleotides found on the m-RNA

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25
Q

Explain role of ribosomal RNA

A
  • assists in bringing RNA to correct site
  • rRNA in the small subunit helps align the tRNA anticodons with the appropriate mRNA codons
  • catalyses protein synthesis by forming peptide bonds between amino acids
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26
Q

Outline process of translation

A
  1. Initiation
    - small subunit of the ribosome attaches to mRNA (at 5’ cap in eukaryotes)
    - ribosome moves along mRNA until it reaches a start codon (AUG- methionine)
    - initiator tRNA binds to start codon
    - large subunit joins
  2. ELongation
    - tRNA molecule with an anticodon complementary to the codon of mRNA will bind via complementary base pairing.
    - amino acids added to growing peptide chain
    - the ribosome moves down the mRNA sequence, allowing complementary tRNAs carrying specific amino acids to bind.
    - Amino acids are attached to each other via condensation reactions.
    Termination:
    - When a stop codon is reached, the ribosome detaches, releasing the mRNA and polypeptide chain.
27
Q

why do tRNA come to ribosomes?

A

attracted by hydrogen bonds of complementary base pairs

28
Q

Describe structure of transfer RNA

A
  • coiled or folded version of RNA
  • amino acid site at one end
  • anticodon at the other end
29
Q

explain relationship between codons and anticodons

A

anticodons are complementary to codons so they can bind together.

30
Q

describe how translation is terminated

A

Stop codon signals end of amino acid sequence
ribosome releases amino acid chain and separates into 2 pieces

31
Q

explain why product of translation is a polypetptide chain, not a functional protein

A

Translation produces a polypeptide chain which is a linear sequence of amino acids. TO become a functional protein, it needs to undergo further folding into its specific 3D shape.

32
Q

what can the genetic code be described as?

A

degenerate/redunant- multiple codons for the same amino acid
- minimises the impact of mutations
(A change in a DNA sequence may result in the same amino acid.)

33
Q

polymerisation

A

the process of bonding monomer molecules in a chemical reaction to form polymer chains

34
Q

The genetic code is described as:

A

degenerate/redundant
- each amino acid can be coded for by multiple codons
- minimises impact of mutations
- mutations may result in same amino acid

universal
- same across all organisms

35
Q

Genome vs proteome

A

Genome: all the genetic material in a cell/organism (about 20000-25000 genes)

Proteome: all the proteins that (or can be) exoressed by a cell, tissue or organism
- much larger and more complex than genome (over 1 000 000 proteins)

36
Q

What makes the proteome more complex and larger than the genome?

A
  • alternative splicing
  • occurs during splicing (RNA processing)
  • some exons removed/rearranged
  • different arrangement of exons leads ro differenent mRNA sequences, amino acid order, polypeptides and proteins
37
Q

Directionality of mRNA:

A

read up: 3’ to 5’
write down: 5’ to 3’
mRNA is ANTIPARALLEL to template strand

38
Q

what is the 3’ end?

A

the hydroxyl end of the sugar, associated with the 3rd carbon of the sugar

39
Q

how are the nitrogenous bases bonded?

A

A and T bond with 2 hydrogen
bonds
C and G bond with 3 hydrogen bonds

40
Q

structure of dna

A

Double helix combines iwth histones as it condenses into chromosomes, forming nucleosomes

40
Q

what is splicing done by?

A

spliceosomes,
recognise specific base sequences at the
ends of the introns: GU at the 5′end and AG at the 3′
end.

41
Q

Structure of gene: (general)

A

Coding region:
- contains the coded information for making a polypetide chain
Flanking region:
- region on either side of coding region
- before the start of the coding region it’s the upstream region
- after the end of the coding region it’s the downstream region

42
Q

Structure of coding region of a gene:

A
  • segement of DNA that includes DNA template strand (always starts with TAC) and some distance away there is (ACT, ATT, ATC)
  • made up of exons (contain the instrcutions for protein synthesis)
  • exons separated by introns
43
Q

Promoter region:

A
  • region of DNA on the template strand located in upstream region
  • TATA box (rich in As and Ts)
  • location where RNA polymerase and transcription factors bind to initiate transcription
  • site for proteins called transcription factors can bind and regulate gene expression
  • upstream sequences are found in all organisms
  • if altered by mutations, activity of the coding region may reduce or become inactive, can affect final protein produced (e.g. thalassaemia)
  • upstream region has segments of DNA to which regulators (such as proteins and hormones) can attach to regulate rate of transcription
44
Q

What is the leader region?

A
  • upstream of some genes
  • prokaryotes (usually small), eukaryotes (can be larger)
  • plays a role in controlling when and how gene is expressed
  • contain sections called attenuators (in prokaryotes)
  • involved in attenuation (process of gene regulation)
  • attentuation involves formation of hairpin loops, stalling and detachment of the ribosome and thus RNA polymerase when the genes do not need to be transcribed and translated.
45
Q

Operator region

A
  • in an operon, between promoter and the gene being transcribed in prokaryotes
  • binding site for repressor proteins
  • when a repressor binds to the operator, prevents RNA polymerase binding to the promoter
  • transcription cannot be initiated
46
Q

Distinguish between introns and exons

A

Introns are interfering sections of DNA that are transcribed
but not translated, and are thus non-coding. Exons are
sections of DNA that are coding and are translated into the
final polypeptide product in the ribosome.

  • introns are thought to have regulatory functions
47
Q

What would happen to a protein if introns were not removed?

A
  • polypeptide formed would be
    different
  • The addition of extra amino acids will change the protein
    produced.
  • inclusion of extra nucleotides may
    change the reading frame within the exons, affecting the amino acids that are translated.
48
Q

regulatory vs structural gene

A

The regulatory gene codes for proteins that control the action of other genes. (e.g. DNA binding proteins, signalling molecules bind to receptors on the cell surface)
Structural genes code for proteins that contribbute to the structure or functioning of the organism

49
Q

Explain how the expression of a single gene can lead to the production of different proteins.

A
  • alternative splicing
  • post transcriptional modifications (addition of 5’ methly cap, poly-A tail, splicing)
  • different nucleotide sequences/mRNA sequences code for a
    different protein (e.g. mutations)
  • post-translational changes to the protein, such as alternative folding (even with same amino acid sequence, different folding can effect function of protein)
50
Q

Tryptophan:

A
  • amino acid that E.coli ingests from its enviroment or makes itself using enzymes
  • these enymes are encoded by 5 genes
  • since making tryptophan requires energy, the enzymes are only produced when tryptophan is not present
  • genes that synthesise them are only active when required and controlled by the trp operon
51
Q

trp operon:

A
  • contains 5 structural genes that encode for the enzymes that synthesis Tryptophan
    genes: (trpA, trpB, trpC, trpD and trpE.)
  • upstream promoter
  • operator sequence (regulates transcription when tryptophan is in low abundance)
  • operator partially overlaps with the promoter
  • leader (contains trpL gene which encodes a leader peptide and attenuator section to regulate transcription)

(check this!!!- I think it’s not actually within the operon) regulatory gene (encodes a repressor which, when active, binds to DNA and decreases rate of transcription)

52
Q

operon:

A

group of linked structural genes with a common promoter and operator that is transcribed in a single unit (only prokaryotes)
- expression of operons is controlled by regulator genes that produce repressor proteins.

53
Q

what happens when tryptophan is present and absent?

A

Present:
- tryptophan binds to the repressor protein, causing a change in shape, allowing it to be active
- allows repressor to bind at the operator
- RNA polymerase unable to bind to promotor
- operon is off

Absence:
- repressor unable to bind to operator
- RNA polymerase can bind to promoter and start transcription of structural genes

54
Q

regulation through attentuation:

A
  • relies on leader region
  • prevents transcription from being completed
55
Q

How is the structure of an operon different to eukaryotic genes?

A
  • operon contains a common promoter and operator
  • eukaryotic genes, no operator, instead a longer upstream region where regulation can occur.
56
Q

Transcription factors what is it?

A

proteins that directly influence the process of transcription by binding to specific regions of DNA to regulate gene expression

57
Q

In what two ways is gene regulation in eukaryotes different from gene regulation in prokaryotes?

A
  • In prokaryotes: repressor proteins bind to operator
  • In Eukaryotes: no operator, so they bind to upstream region
  • Prokaryotes: gene regulation occurs only at a transcriptional level
  • Eukaryotes: occuers at a transcriptional, post-transcriptional (RNA processing), translational level and through epigenetic factors
  • Prokaryotes: only in cytosol
  • Eukaryotes: cytosol and other locations s.a nucleus
58
Q

what does condensation polymerisation mean?

A

condensation- water is released
polymerisation- monomers being bonded together to form a polymer

59
Q

forces that maintain the tertiary structure of proteins are:

A
  • hydrogen bonds (Weak attractions between a hydrogen atom and an electronegative atom.)
  • ionic attractions being charged R groups
    (Attractions between oppositely charged R group)
  • interactions between hydrophobic R groups in the protein interior
    (Nonpolar R groups, tend to avoid water and cluster together in the protein’s interior.)
  • covalent disulfide cross links. (strongest bond, between the sulfur atoms of two cysteine amino acids)
60
Q

What is the basic formula of an amino acid molecule?

A

H2NCHRCOOH

61
Q

How is a peptide bond formed?

A
  • covalent bond between carboxyl group of one amino acid and amino group of adjacent amino acid
  • occurs through condensation polymerisation
  • ATP is added and water is released
62
Q
A

Biology 3/4 (2 decks)

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