Concept 13,14,15,16,17,18 Flashcards

(165 cards)

1
Q

Central dogma of gene expression?

A

Flow of genetic information: DNA → RNA → Protein

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2
Q

Coding proteins from DNA - 2 overall steps?

A

1) TRANSCRIPTION
Creating mRNA
In nucleus
3 steps = initiation, elongation, termination

2) TRANSLATION
mRNA used to make proteins
In cytoplasm
3 steps = initiation, elongation, termination

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3
Q

3 steps of transcription?

A

1) Initiation
2) Elongation
3) Termination

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4
Q

TRANSCRIPTION - imagination of what happens

A
  • DNA is double stranded
  • We only care about one strand
  • RNA polymerase zips it open, adds nucleotides
  • Creates mRNA
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5
Q

BASICS ON TRANSCRIPTION - What is the enzyme that synthesises RNA? Tell me about the enzyme 2 points

A

ANS = RNA POLYMERASE

DUAL FUNCTION
1) Unwinds the 2 strands of dna
2) Adds RNA nucleotides to the RNA strand

HOW IT WORKS
- Works in the 5-3 prime direction

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6
Q

BASICS ON TRANSCRIPTION - what are the 2 strands of DNA being used?

A

1) TEMPLATE STRAND OF DNA/NON CODING
- Used to make mRNA
- So will be complementary to mRNA
- 3’ to 5’ left to right

2) COMPLEMENTARY/CODING STRAND OF DNA
- Complementary = to the original template DNA
- Coding = it is the EXACT
- SAME as the mRNA strand made, BUT thymine will be replaced with uracil!
- 5’ to 3’ left to right

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7
Q

TSS

A

TSS: The section of DNA where RNA polymerase ONLY begins synthesizing RNA
transcriptional start sites

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8
Q

INITIATION - How does rna polymerase recognise transcriptional start sites? - SUMMARISED FOR EUK + PROK

A

TRANSCRIPTION FACTORS:

Prokaryotes = Sigma Factors

Eukaryotes = General Transcription Factors (GTFs)

Na vs Ye

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9
Q

INITIATION - How does rna polymerase recognise transcriptional start sites? PROK

A
  • σ Factor binds to RNAP
  • SO…σ guides RNAP to the promoter
  • Promoter → TSS → RNA polymerase can start performing!
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10
Q

INITIATION - what does the promoter consist of? 3

A

Promoter structure (LEFT TO RIGHT)
1) Tata box = GTF binding site
2) TSS
3) RNA polymerase binding site

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11
Q

INITIATION - How does rna polymerase recognise transcriptional start sites? EUK 4

A

FRAGILE - they bind to DNA strand, which ALLOWS them to bind together

1) Transcription preinitiation complex hovers around the promoter

2) GTF binds to TATA (promoter)

3) RNA polymerase binds to RNA polymerase binding site

4) This allows for
GTF + RNA Polymerase to bind - forms a HOLOENZYME

UPSTREAM = BEFORE (on the left)

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12
Q

Whole process of transcription

A

INITIATION
- RNA polymerase eventually will end up to the TSS

ELONGATION
- Here, RNA polymerase unzips the DNA strands into 1) Template 2) Complementary / Coding
- RNA polymerase adds nucleotides to form mRNA. It works in the 5’ to 3’ direction (LEFT TO RIGHT)
- It uses template DNA to make the mRNA
- During this process RNA transcript exits in the opposite direction of rna polymerase working direction

TERMINATION
- A termination sequence signals the end of the gene.
- This triggers the release of RNA polymerase and mRNA produced.
- Also causes restoration of DNA into 2 strands again

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13
Q

RNA polymerase in eukaryotes vs eukaryotes

A

Prokaryotes: Have ONE type of RNA polymerase.

Eukaryotes: Have THREE types of RNA polymerase
- RNA polymerase I
- RNA polymerase II
- RNA polymerase III

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14
Q

RNA polymerase in bacteria

A

5 subunits TOTAL

2 alpha subunits
1 Beta subunit
1 Beta prime subunit
1 Omega subunit
Each subunit has different functions

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15
Q

Rna polymerase I, II, III function

A

RNA polymerase I
- transcribes rRNA genes

Rna polymerase II
- transcribes all mRNA (codes for proteins) genes
- Has binding site for transcription factors (GTF)

Rna polymerase III - function
- transcribes tRNA genes

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16
Q

RNA polymerase in eukaryotes + prokaryotes - which is the most similar?

A
  • RNA Polymerase II is most similar to bacterial RNAP
    BUT similarities not related to mechanism of action
  • All eukaryotic RNA polymerases share similar features w/ each other + bacterial rna polymerase
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17
Q

Gene expression?

A

converting genes into proteins

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18
Q

Types of RNA? (4)

A
  • Genes (DNA!!!) can be transcribed/produce into various types of RNA:
  • mRNA (messenger RNA)
  • tRNA
  • rRNA
  • non-coding RNA (microRNA)
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19
Q

Which of the 3 types of RNA is used to make protein?

A

Only mRNA is used to make protein.

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20
Q

Location of transcription+translation in prokaryotes?

A

Transcription = cytoplasm
Translation = cytoplasm

  • Prokaryotes do not have membrane bound organelles
  • So…Transcription + translation occur simultaneously because there is no nucleus
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21
Q

Does RNA have to be processed in eukaryotes? How many types of processing 3

A

EUKARYOTES
- Required

3 MAIN processing
1) Removal (SPLICING) of introns
2) 5’ cap
3) 3’ poly A tail

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22
Q

mRNA name right after it is transcribed?

A

pre-mRNA

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23
Q

Does RNA have to be processed in prokaryotes?

A
  • Not required
  • There are no introns in prokaryotic mRNA
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24
Q

How is RNA processed in eukaryotes? - removal of introns

A

Process is called SPLICING

1) Removal of introns (don’t code for proteins)
2) Attaching together exons (code for proteins)

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25
How is RNA processed in eukaryotes? - 5’ end of molecule
- 5’ end of molecule BECOMES…5’ cap - A modified G nucleotide is added to the 5’ end via a triphosphate linkage
26
How is RNA processed in eukaryotes? - 3’ end of molecule
3’ end of molecule BECOMES…3’ tail - CLEAVAGE = A polyadenylation signal (e.g., AAUAAA) in the pre-mRNA 3’ end triggers cleavage of around 10–30 nucleotides downstream. - ADDITION = THEN, 150–250 adenine (A) nucleotides added to the 3′ end.
27
Why is RNA processed in eukaryotes? - 5’ cap
- 5’ cap helps SMALL SUBUNIT of ribosome attach to the mRNA - prevents mRNA from getting degraded
28
Why is RNA processed in eukaryotes? - 3’ tail
- Protects ends of transcript from degradation - 3’ tail signals that mRNA is ready to leave the nucleus
29
A particular eukaryotic protein is rendered non-functional. - This protein becoming non-functional results in longer mRNA products for many genes - explain
- mRNA products = referring to what we get AFTER processing pre-mRNA - longer mRNA products means that there must be an issue in PROCESSING - this is because processing = removal of introns + 5' cap + addition of polyA tail - so the protein must have been responsible for mRNA processing
30
How would your explanation change if it was also found that these longer mRNAs were - less stable (more rapidly degraded)? - not translated into polypeptide?
- we know there must be an issue with the processing of pre-mRNA - less stable points that the protein must have been involved in the addition of 5' cap OR polyA tail, as both are involved in stability - BUT since it can't be translated, this proves that the protein must be involved in adding the 5' cap - as this is required for mRNA to bind to the ribosomes
31
If there are 4 nucleotides, how is it possible to code for 20 amino acids?
- If 1 nucleotide codes for amino acids = there are 4 bases = 4 possible amino acids - If 2 nucleotides code for amino acids = 16 (4^2) possible amino acids - If 3 nucleotide code for amino acids = 64 (4^3) possible amino acids 3 nucleotides which code for 1 amino acid = CODON
32
Features of the genetic code 4
1) Degeneracy / Redundancy 2) Start codon 3) Stop codons 4) Universality
33
Features of the genetic code - degeneracy
- Codons SHOULD mean 64 amino acids - But we only have 20 amino acids BECAUSE… - Multiple codons can code for THE SAME amino acid Eg. leucine has six codons
34
Degeneracy - where does it often occur?
- Often occurs in the third position of the codon. Eg. UAA, UAC codes for the same amino acid
35
Features of the genetic code - universality
The genetic code is nearly universal across all life domains.
36
Start codon
- ONE START CODON = AUG Indicates where the open reading frame for translation begins.
37
Stop codon
THREE STOP CODONS = UAA, UAG, UGA - Signal the end of translation.
38
(tRNA) structure 3
1) 5’ to 3’ LEFT TO RIGHT 2) Loop in the middle = anticodon (3 nucleotides) 3) 3’ end = amino acid binding site ALWAYS CCA
39
(tRNA) structure - what is everything joined tgth by?
tRNA synthetase
40
(tRNA) when is it charged?
CHARGED when an amino acid is attached to the tRNA
41
How do we know what the amino acid of a tRNA molecule to form the polypeptide chain will be?
- Amino acid binding sites are the same…how about codon/anticodon? - YOU CANNOT infer the amino acid bound to the trna based on its anticodon/codon! No relationship - The amino acid is determined by smth else - So instead the mRNA sequence, which impacts the anticodon, and therefore the type of tRNA and what amino acid it happens to carry!
42
Messenger RNA (mRNA) role
Transcription → from template DNA strand, used to code for proteins
43
Transfer RNA (tRNA) role
Translation → carries the amino acids
44
Ribosomal RNA (rRNA) role A component of ribosomes.
A component of ribosomes
45
Possible advantages of degeneracy of the genetic code? 2
Eg. UAG and UAA code for the same protein 1) Mutation Buffering - If one base is changed, the amino acid coded for could still be the same! - Mutations likely do not alter the amino acid sequence, reducing harmful effects/loss of function 2) Efficient Translation - Allows multiple tRNAs with different anticodons to bind the same codon, speeding up protein synthesis
46
Open Reading Frame (ORF) - what is it?
Thinking in the context of TRANSLATION - Region of DNA or mRNA that can be TRANSLATED into a protein - this is therefore read by RNA POLYMERASE / ribosome
47
Open Reading Frame (ORF) - 3 conditions
1) Start codon: Begins with AUG 2) Stop codon: Ends with UAA, UAG, or UGA 3) Length: The sequence between start and stop codons is a multiple of three (triplets = codons). / Length must be divisible by three
48
Open Reading Frame (ORF) - what is it read by?
RIBOSOMES, during TRANSLATION 1) Bind to the 5′ end of mRNA 2) Scan the mRNA in the 5′→3′ direction for the start codon (AUG). 3) Decode codons (triplets) into amino acids using tRNAs. 4) Stops at the stop codon
49
Open Reading Frame (ORF) - 3 possible ways the ORF can be read
Each strand can be read in three possible ways - Rmb AUG is the start codon!! - How it is read depends on whether the coding sequence is read from the first, second, or third nucleotide. 1) Frame 1: Start at 1st nucleotide AUG CCG AUG UAG → Met-Pro-Met-Stop (valid, will produce functional protein). 2) Frame 2: Start at 2nd nucleotide UGU CGA UGU → Cys-Arg-Cys (no stop codon → invalid protein). 3) Frame 3: Start at 3rd nucleotide GCC GAU GUA → Ala-Asp-Val (no stop codon → invalid protein). **only the one starting with ATG will be translated. so...these are reading frames , but the REAL potential reading frames (esp when exam qs ask), is based on where the start codon is found
50
You are given mRNA, 2 strands of DNA. Translate the sequence to provide an amino acid sequence. How would you do this?
- Look at mRNA!!!! (not dna) - Look for start codon (AUG)
51
We are shown 2 strands of DNA. One is labelled 5’ to 3’, the other is labelled 3’ to 5’. Which one is the coding/complementary or template strand? 2 approaches.
1) We know rna polymerase works in the 5’ to 3’ direction, hence template must be 3’ to 5’ (bottom) 2) We know mRNA must be 5’ to 3’, hence top is coding/complementary
52
Effect of translation in the incorrect reading frame? (ie. frame 2 or 3)
SITUATION 1 - No stop codon → ribosomes translate the entire mRNA (GOES TO THE VERY END) → doesn’t stop until the very end of mRNA → long, useless protein. SITUATION 2 - Introduce a new stop codon → Translation stops early → creates a truncated prote
53
You are given 2 strands of DNA. Identify the longest open reading frame - how will you do this? - unlike the 3 possible open reading frames, we want to find the REAL reading frame. Top is 5’ to 3’ , bottom is 3’ to 5’
- ORF = what can be TRANSLATED into a protein - Protein is made using mRNA - Rmb mRNA is read by ribosomes in the 5’ to 3’ direction!!! (translation) BUT… - There are TWO strands of DNA - Rmb EITHER one of them can be used for TRANSLATION / TEMPLATE - It is only ONCE you decide which strand you use, then you will set the strands as template or coding Just make sure to read it in the 5’ to 3’ direction!!! AND… - Reading frames always start from a START CODON (in this case it is ATG) SO… - Read top strand from 5’ to 3’ (LEFT TO RIGHT) - Top = template - Bottom = coding - Read bottom strand from 5’ to 3’ (RIGHT TO LEFT)
54
Ribosomes - structure + what it is made up of
- A large subunit - A small subunit Both subunits are made of: - rRNA (catalyzes the peptide bond formation between amino acids.) - Ribosomal proteins
55
Large subunit - structure 3
FROM LEFT TO RIGHT E site: Exit site P site: Peptidyl site A site: Aminoacyl site Each site is a binding site for tRNA
56
Does it matter which direction mRNA is read by the ribosome?
YES!!! - mRNA is read by the ribosome in the 5'→3' direction - absolutely matters because this ensures proper protein synthesis.
57
Translation initiation - euk + prok
SMALL subunit of the ribosome has to bind to something in the mRNA - Euk = 5’ cap - Prok = Shine-Dalgarno sequence - Once binded, it will move along the mRNA to find AUG (start codon) - Once it finds AUG, the LARGE SUBUNIT will bind to the small subunit. A complete ribosome will be formed!
58
Translation - eukaryotes - 3 OVERALL steps
1) Initiation - Small subunit 2) Elongation - Large subunit - Moving 3) Termination
59
Translation - eukaryotes - initiation 3
SMALL SUBUNIT 1) Small subunit binds to 5’ cap 2) Small subunit will move along mRNA until it finds AUG (start codon) 3) Once on AUG, the large subunit will bind to the small subunit
60
Translation - eukaryotes - elongation 3
LARGE SUBUNIT 1) The first tRNA molecule will bind to P site (tRNA anticodon will be complementary to the codon AUG. Carry Met amino acid) 2) Next tRNA molecule binds to the A site 3) Bond forms between amino acids on P and A site 4) Amino acid chain will sit on the tRNA on the A site MOVING 5) Ribosome moves from left to right 6) So first tRNA molecule sits on E site, second tRNA molecule sits on P site 7) tRNA will leave. Above there is 2 beads in the amino acid chain 8) New tRNA molecule will enter the A site
61
Translation - eukaryotes - termination 3
- Ribosomes reaches a STOP CODON - BUT…there is no tRNA that recognizes/binds to a stop codon. - Protein called RELEASE FACTOR enters the A site - No peptide bond is formed - So when the previous tRNA moves from the P site to the E site, the entire peptide is released
62
Translation - what will be the first amino acid of the amino acid sequence?
- Initiator tRNA will bind to AUG codon - This tRNA will be charged with methionine
63
Describe the life journey of a tRNA during the process of translation. Make sure your account is from the perspective of the tRNA and includes the steps before, during and after it encounters the ribosome. (Variation- describe the journey of a small ribosomal subunit) 6 marks
KEY POINTS TO CONSIDER 1) tRNA is produced by transcription of the tRNA gene. done by RNA polymerase III 2) tRNA is charged with an amino acid. occurs on the 3' acceptor sequence 3) tRNA binds to the A site (only the 1st time the initiator tRNA binds to the P site) 4) it binds as its anticodon is COMPLEMENTARY to the CODON of the mRNA!!! 5) amino acid is added to the carboxyl end of the growing polypeptide chain via a peptide bond on the 3' end (A site) 6) tRNA moved down to the P site 7) tRNA exits the ribosome, recycled and charged with the same amino acid
64
What might happen if there is not a stop codon in the mRNA of a bacterial gene? Explain. (3 marks
EXPLAIN MEANS STATE THE OBVIOUS, IMPACTS, CAUSES ETC. - DETAILED 1) STATE THE OBVIOUS = translation's termination will be affected 2) EXPLAIN = the ribosome will continue translating until it reaches the end of the mRNA 3) IMPACTS = longer polypeptide will be non0functional -> wastes cellular resources
65
The eukaryotic 80s ribosome is divided into large and small subunits - specify
Large subunit (60S ribosome) Small subunit (40S ribosome):
66
What does the table of codons represent?
- these codons (3 amino acids) show the AMINO ACID that will be produced. - these codons are on mRNA!!!!! - These codons have to be read in the 5' to 3' direction
67
does the anticodon of tRNA impact the amino acid it is charged with?
NO!! - the amino acid binds to tRNA according to its shape, NOT based on its anticodon
68
A mutant is found where Tyrosine (Tyr) residues are incorrectly incorporated in proteins in place of Serine (Ser). Explain how this could be caused by a mutation in a tRNA that affects the anticodon sequence? 6 marks
UNDERSTANDING: - understand that in the amino acid sequence, Ser should be there, but Tyr is now there - trna holding Tyr is mutated - mutation in anticodon does NOT mean a diff amino acid carried. what it DOES mean is that the anticodon will bind to a different CODON on the mRNA sequence!!! SO... - tRNA charged with Tyr has an anticodon that has mutated. most likely SINGLE POINT MUTATION - this anticodon will now bind to a CODON on the mRNA that is complimentary to the codon CODING for serine, not tyr - this explains why Tyr replaces Ser GETTING THE EXTRA MARKS: - figuring out what the new anticodon for Tyr could be! - mRNA codons that code for serine (get from table) = UCU, UCC, UCA, UCG, AGU, AGC (5' to 3') - so....new anticodon will bind to 5' to 3' UCU. hence mutated anticodon should be 3' to 5' AGA -> so original anticodon must be AUA - new anticodon will bind to 5' to 3' UCC. Hence mutated anticodon will be 3' to 5' AGG -> so original anticodon must be AUG, underwent single point mutation
69
Are genes expressed all the time? - factors
NO - This is REGULATED - Only expressed when protein is needed - Time of development, environmental conditions, cell type
70
How is gene expression regulated?
- Transcription activated only at certain times - mRNA processing can be impacted at different times - mRNA produced can be stable, or degraded over time - Translation efficiency may be changed, based on whether the protein is needed or not
71
Genome instability
- increased tendency for DNA mutations and other genetic changes (eg. insertions, deletions , or changes in chromosome number)
72
What causes genome instability 3
It happens when these systems are not working properly: - repair DNA - check for errors - control cell division ALL THIS DUE TO DNA DAMAGE --> MEANS DNA CANNOT BE REPAIRED/REPLICATED ACCURATELY
73
Impact of genome instability 3
1) cell degenerates/dies 2) cell loses its normal function 3) cell develops cancer --> uncontrolled cel growth
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Mutation impacts 3
1) Beneficial: Provides advantages for selection. 2) Neutral: No detectable change in phenotype. 3) Deleterious: alters cell function (of the protein) Most mutations don't show obvious phenotypes.
75
2 types of mutations:
1) Spontaneous (de novo) = Occur with no outside influence. 2) Induced mutations
76
Endogenous DNA damage
alterations in DNA structure caused by internal cellular processes rather than external environmental factors.
77
Spontaneous mutations - examples 3
1) Deamination 2) Transposons 3) Depurination (hydrolysis)
78
Deamination
- Removal of an amino group (NH2) from a nucleotide. - Cytosine becomes uracil. - overtime will become a C-->T mutation
79
Depurination
- Hydrolysis of nucleotide - Specifically cutting the bond between PENTYL SUGAR + DEOXYRIBOSE
80
Transposons
- GENES that code for enzymes needed for movement. - A transposon will COPY itself - Then it will PASTE itself into a new POSITION of the genome.
81
Impacts of transposons?
Protein-coding sequence could be interrupted If it lands within a gene, it can cause functional problems.
82
Induced Mutations - what is it caused by? 4
Caused by external agents (MUTAGENS ). 1) Nitrous acid: Deamination 2) Cigarette smoke (benzopyrene) 3) Radiation (X-rays, gamma rays): 4) Ultraviolet radiation (sun)
83
How does 4 mutagens cause mutation?
1) NITROUS ACID = deamination 2) BENZOPYRENE = add chemical group to guanine 3) X-RAY RADIATION = break DNA’s sugar phosphate backbone 4) UV = impact covalent bonds between adjacent thymine bases
84
Germline vs. Somatic Mutations - 2 differences
1) WHICH CELLS DOES IT OCCUR? - SOMATIC = Occurs in cells that undergo mitosis - GERMLINE = Occurs in specialised reproductive cells that give rise to gametes 2) IMPACT? - SOMATIC = LOW IMPACT = Mutation only passed to daughter cells produced via mitosis -> mutation only present in the organism in which they occur - GERMLINE = WIDESPREAD IMPACT = Mutation passed to gametes, which can be passed to the next generation
85
Germline vs. Somatic Mutations - similarity
- mutations can have little to no effect on the organism - mutations can have positive or negative effects
86
Small vs large mutations
SMALL - mutations affect either one or a few nucleotides LARGE - mutations impact chromosome regions or entire chromosome structures
87
single base mutations - examples
- substitutions - insertions deletions
88
Single base mutations - when does it have an impact?
- depends on if mutation occurs in important regulatory genes (eg. promoters) - depends if they change the polypeptide sequence of protein coding genes
89
large chromosomal mutations - impact?
- more likely to have a negative effect on the organism - affects more genes due to size involved + result in chromosomal imbalance
90
Progeny
offspring
91
Impact of mutations? 3
genome instability, cell death, or cancers.
92
DNA repair mechanisms: 3
1) Base Excision Repair - replacing wrong bases w/ the right ones 2) Nucleotide Excision Repair - cut out big chunks of wrong dna, replace it with correct section 3) Mismatch Repair (mismatch caused by DNA polymerase)
93
QUESTION 27: Base excision, nucleotide excision and mismatch repair are strategies the cell uses to correct certain DNA mutations. Which of the following enables these repair mechanisms to occur accurately?
DNA is double stranded, and the complementary strand can be used as a template for repair.
94
Why is DNA good for repair?
- Has 2 strands - Complementary strand + template strand - So contains 2 copies of genetic info - So if one of the strands are damaged, complementary strand can be used as a guide for restoration - INCREASES the ACCURACY of dna repair mechanisms
95
Deleterious mutation
= a genetic alteration that disrupts gene function, leading to harmful effects on an organism's fitness, survival, or health. These mutations can: Disrupt Protein Function: - Cause loss of protein production (e.g., null mutations). - Generate non-functional proteins (e.g., misfolded enzymes). - Create proteins that interfere with normal cellular processes (e.g., dominant-negative mutations).Germline vs. Somatic Mutations
96
Is reading frame and open reading frame (ORF) the same thing?
NO!!!! READING FRAME - All possible ways to SPLIT DNA INTO CODONS - The "reading frame" is how you split it into 3-letter codons (e.g., ATG-CCG-TAA vs. TGC-CGT-AAT). OPEN READING FRAME - Section of DNA that CAN code for a protein/be translated
97
Key idea when an exam question asks you to translate a dna sequence/mRNA? 2
1) Go in 5' to 3' direction (mRNA is in this direction as this is how rna polymerase works) 2) Look for START CODON (ATG in dna, AUG in mRNA)
98
Synonymous Mutations
- SILENT - NO CHANGE in the AMINO ACID of the product - Amino acid sequence is still the same Eg. AUG and ACG will code for the same amino acid
99
Non-Synonymous Mutations
- Change in the AMINO ACID of the product - BUT this shouldn’t change the entire POLYPEPTIDE - Hence nonsense mutations (truncated proteins) is NOT considered a non-synonymous mutation, as it changes the ENTIRE protein, stuffs it up, not just a few amino acids
100
Missense mutation
- Change in ONE SINGLE NUCLEOTIDE (not amino acid like non-synonymous) - MUST be a SUBSTITUTION - Amino acid sequence changes by ONE amino acid Eg. Gln, Pro Ala → Gln, Arg, Ala
101
Missense mutation 2 POSSIBLE IMPACTS
1) Protein GAINS a new function 2) Protein has a LOSS of function
102
Nonsense mutation
- Changes a functional codon to a STOP codon IMPACT - truncates the protein (shorter) → non-functional protein
103
Frameshift mutation 3
- Insert/delete nucleotides that are NOT divisible by 3 - This should cause the amino acid sequence to COMPLETELY change - Because…insertion/deletion changes your READING FRAME (ie. how you SPLIT your sequence into codons/3 bases)
104
Can a single nucleotide insertion cause a frameshift mutation?
YES!! The reading frame (ie. HOW you read the triplets) would TOTALLY change
105
Can a nonsense mutation be a frameshift mutation?
YES!! - It just totally depends on HOW the nonsense mutation came about (ie. how was the stop codon introduced) - SUBSTITUTION - then the reading frame wouldn’t have changed OR - INSERTION - although at the insertion point a stop codon was introduced and the protein is truncated, if you look AFTER the mutation point, you will find that the reading frame completely shifts!
106
If a mutation occurs within the coding sequence of a gene, would an insertion of 6 nucleotides or an insertion of 2 nucleotides, or a deletion of 8 nucleotides be least likely to be a frameshift mutation?
ANS = INSERTION OF 6 NUCLEOTIDES - Genetic code read in multiples of 3s (ie. codons) - Eg. insert 6 nucleotides. You will have 2 more amino acids. - BUT the rest of the amino acid sequence will remain the same - ie. READING FRAME will stay the same - So things like removing 9, adding 6 etc. will less likely be a frameshift mutation - If you are adding/removing something not of a multiple of 3, then you would COMPLETELY change the entire order of amino acid sequence - The other 3 - after the mutation, the reading frame would totally change (IE. THE CODONS)
107
When does a mutation cause loss of the entire protein?
- Talking about the ENTIRE amino acid sequence - No more ATG (which creates the START CODON) - NOT a mutation that results in a stop codon in the middle of the sequence, as there is still one/few amino acids before it
108
What would happen if DNA was perfectly stable - ie. no mutation?
This means we would have never evolved!
109
Frameshift mutation - does it belong to nonsynonymous mutation?
- Nonsynonymous is the change in AMINO ACIDS - not a whole polypeptide (which is what frameshift mutation does)
110
Point mutations
- Any SINGLE nucleotide change - Could be substitutions, insertions, deletion (indel)
111
Size of mutation 2
1) SMALL MUTATIONS - point mutation - insertion - deletion 2) LARGE MUTATIONS
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Large mutation 3
1) GENE DUPLICATION - an entire gene is copy + pasted (so you have 2x of the same gene) 2) INVERSION - change the order of a whole gene so its backwards 3) GENOME DUPLICATION - double the no. of chromosomes in an individual
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A eukaryotic gene that is 1,440 base pairs long codes for a polypeptide that is 192 amino acids long. How many base pairs code for the polypeptide (including the STOP codon)?
FIRST QUESTION - 1 amino acid = 3 nucleotides - so..192 amino acids --> 192 x 3 = 576 nucleotides + STOP codon = 579 nucleotides/bases ON THE MRNA - now finding this on the DNA - but since they ask base pairs no need to multiply by 2
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Discuss the discrepancy between the gene length and the coding sequence of the gene. ie. gene has 1440 base pairs, polypeptide only has 576 nucleotides/base pairs
GENE = BEFORE TRANSCRIPTION + TRANSLATION, MAKE SURE TO TRACK THE WHOLE PROGRESS FROM DNA -> MRNA 1) TRANSCRIPTION - some part of the mRNA will be removed as they are introns 2) TRANSLATION - some parts of the mRNA will not be translated (as it comes before/after the START/STOP codon)
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Describe the life journey of a tRNA during the process of translation. Make sure your account is from the perspective of the tRNA and includes the steps before, during and after it encounters the ribosome. (Variation- describe the journey of a small ribosomal subunit) 6 marks
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Genome - what cells do not contain this?
- This is found in each CELL - Each cell (except red blood cells and gametes) contains a full copy of this genome
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2 types of genetic variations in a population?
1) SNP - Difference in a SINGLE base 2) CNV - Difference in whole sections of DNA
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What Is a SNP?
- A SNP is when ONE base (A,T,C,G) are different between individuals in a population OR within cells in a single organism - Caused by SINGLE BASE SUBSTITUTIONS -> Eg. C in dna sequence may be T in somebody else - BUT To be classified as a SNP, the variant must occur in ≥1% of the population / cells in an organism -> Eg. out of 100 people, everyone mostly have a C, but more than 1 person will have a T
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CNV - GENETIC VARIATION IN THE POPULATION
- Your DNA has extra or is missing certain genes. - Within the population, you can increase/decrease the “copy number” of a gene -> Eg. Some individuals may have multiple copies of a gene or none at all Why It Matters: - Extra Copies: Might make you better at something (e.g., digesting starch). - Missing Copies: Could cause problems (e.g., disease). Example:- Some people have extra copies of a "starch-digesting gene" because their ancestors ate lots of potatoes/rice, while others don’t
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Diploid:
Ie. 2 alleles - Carry 2 copies of every gene
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Allele definition
- Alleles: Different versions of the SAME gene - They are basically MUTATIONS of each other
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TYPES OF GENOTYPES 3
1) Homozygous: When the two alleles are the same (BB or bb). 2) Heterozygous: When the two alleles are different (Bb). 3) Hemizygous: Organism has only one allele
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Example of hemizygous genotype
- Sex chromosomes vs autosomes -> Eg. female is XX, carry diff versions of the SAME X gene, alleles could be homozygous OR heterozygous -> Eg. male is XY, the genes are totally different, therefore only have one allele for the X chromosome gene
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Pure breeding
Homozygous for the trait of interest (coat color).Homozygous for the trait of interest (coat color)
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Can we identify Dominant and recessive alleles? How?
Through GENETIC CROSSES EXAMPLE = Crossing a pure-breeding black-haired dog (BB) with a pure-breeding brown-haired dog (bb). - F1 Generation: All pups are black-haired (Bb). This indicates that the black coat trait is dominant to the brown coat trait, which is recessive.
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3 types of allele interactions
1) DOMINANT + RECESSIVE 🐶 = black, brown dogs 2) INCOMPLETE DOMINANCE 🌸 = red, white, pink flowers 3) CODOMINANCE 🐔 = black + white feathers
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Dominant + recessive
DOG EXAMPLE… - Dominant allele → codes for a enzyme that results in black pigment - Recessive allele → MUTATED dominant gene. Changes function of enzyme, so black pigment can no longer be produced PHENOTYPE - Dominant + recessive allele → black pigment overrides the brown pigment → because black pigment is produced in LARGER QUANTITIES
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Incomplete dominance
FLOWER EXAMPLE - Red allele (R) → red flower - White allele (W) → white flower PHENOTYPE - RR → red flower → high level of pigment → 2 red allele doses - WW → white flower → no level of pigment → no red allele dose - RW → pink flower → intermediate pigment → 1 red allele dose - We call this a DOSAGE EFFECT - ie. because NEITHER allele is dominant
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Incomplete dominance - definition
- When the heterozygote displays an INTERMEDIATE PHENOTYPE between the two homozygous phenotypes. - The phenotype will be a blend of both parents. - Neither allele is dominant or recessive.
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Codominance - definition
Wjhen both traits are expressed in the heterozygote. The heterozygote's phenotype shows both traits evident in homozygous individuals.
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Codominance
CHICKEN EXAMPLE - Black allele → black feathers - White allele → white feathers PHENOTYPE - BW → black AND white feathers (not grey) - BECAUSE…Black and white pigments are DISTINCT, SEPARATE, produced in different cells, and also not in equal quantities
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Another Example of codominance?
ABO blood groups in humans. You will be AB blood type You won’t be a mixture of A+B
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What does it mean if organisms have different sexual life cycles?
Mature form = original form of the organism HUMANS/PLANTS = mature form is diploid. Next generation is haploid FUNGI = mature form is haploid. Diploid is a brief state
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Homologous chromosomeS / homologous pair of chromosomes - what can it NOT be
Cannot be sister chromatids They are basically just replicated versions of each other!
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What does 2N=2 mean?
2N Diploid Means there are 2 alleles (Eg. Aa) This means there are 2 SETS of CHROMOSOMES in total in a CELL =2? Means there is a total of 2 CHROMOSOMES in a cell (ie. 1 homologous pair) For example, humans would be 2n = 46
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Which cells do mitosis/meiosis?
Mitosis = somatic cells (all non-reproductive cells) Meiosis = germline cells (reproductive cells)
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Mitosis use? 3
1) Cell growth (of the cell itself!) 2) Tissue repair 3) Cell proliferation = increase in no. of cells
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Meiosis use?
- Producing gametes Used in sexual reproduction
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First theories of inheritance? -
BLENDING MODEL THEORY - Offspring are a blend of the parents phenotype Eg. red flower + white flower = pink flower offspring - REAL LIFE - Eg. continuous variables, height over time in families
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First theories of inheritance? - HOW was it disproved?
PROVED TO BE FALSE!!! - Disproved by Mendel pea experiment - only found 2 phenotypes Eg. bred yellow + green plants together BASICALLY DID A MONOHYBRID CROSS, THE 2 STEPS
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Law of segregation, Mendel 2 observations
MONOHYBRID CROSS OBSERVATIONS: 1) Noticed one phenotype disappeared in the F1 generation 2) 3:1 green to yellow in F2 generation
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Law of segregation, Mendel 4 - ie. what was assumed through observations?
BASIC QUALITIES OF ALLELES 1) Each individual has 2 alleles for each gene 2) Each allele comes from each parent 3) These alleles separate so each gamete has 1 allele - So that when gametes fuse, we have 2 alleles again! RANDOM SEGREGATION 4) As random segregation of alleles, parents are EQUALLY LIKELY to pass on a dominant/recessive allele
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When is a punnett square not needed?
When both parents are homozygous + are told all offspring are black - Therefore all offspring must be Bb
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If an organism is homozygous aa what gametes will it produce? // If an organism is heterozygous Aa what gametes will it produce?
Remember each gamete will have ONE ALLELE So 4 gametes all will have a // Remember each gamete will have ONE ALLELE 2 gamete cells will have A (2xA) 2 gamete cells will have a (2xa)
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Different ways to determine sex/gender in different organisms? - JUST THE POINTS 5
1) ENVIRONMENT 2) DIPLOID OR HAPLOID 3) XY SYSTEM 4) RATIO OF X CHROMOSOMES TO AUTOSOMES 5) ZW SYSTEM
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Different ways to determine sex/gender in different organisms?
1) ENVIRONMENT Eg. higher temps = male 2) DIPLOID OR HAPLOID Diploid = female, haploid = male 3) XY SYSTEM XX in humans = female XY in humans = male 4) RATIO OF X CHROMOSOMES TO AUTOSOMES Eg. for every 2 X chromosomes = 1 autosome 5) ZW SYSTEM ZZ = male ZW = female
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What do sex chromosomes carry?
Some genes related to gender BUT NOTE: Can also carry genes for physical traits, inherited diseases etc.
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Sex chromosomes in gametes?
Egg cell = 1 X chromosome Sperm cell = either ONE X or Y chromosome (meiosis, parent cell = XY) So…fertilisation determines gender
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If an insect parent had a genotype of XO, what would its gametes be?
WORKS IN THE SAME WAY AS HUMANS - GAMETES WOULD HAVE 1 OF THE 2 ALLELES // BETWEEN 4 DAUGHTER CELLS So… 2 gametes = X, 2 gametes = O
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How to generate heterozygous individuals?
Pure breeding Cross 2 individuals which are homozygous (F1) F2 = all heterozygous individuals
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How do we know if an allele is complete dominance or incomplete dominance - monohybrid cross?
CROSS OFFSPRING IN THE F1 GENERATION (IE. BOTH PARENTS ARE HETEROZYGOUS) Complete dominance = 3:1 ratio in offspring Incomplete dominance = 1:2:1 ratio in offspring
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Back cross?
Used to determine if an individual of dominant phenotype is heterozygous or homozygous (Bb or BB) This individual will cross with one of their parents (homozygous) BB or bb Recessive homozygous is good This is because recessive homozygous parent will always give a b allele. So this will DIRECTLY reveal what the parent is giving, B or b, which tells us if it is homozygous or heterozygous If dominant homozygous, we can’t directly tell If complete dominance, 1:1 ratio of offspring If incomplete dominance, 1:2:1 ratio of offspring
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What is a lethal allele?
Allele that causes death of the organism Contains a gene that is essential for survival
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Dominant lethal allele? Homozygous + heterozygous?
- Homozygous and heterozygous both die - Therefore never identified in populations as the offspring die immediately
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Dominant lethal allele? EXCEPTION?
Huntington’s disease - Dominant lethal allele always present since birth, BUT DO NOT DIE IN THE WOMB - BUT only express/show disease past the age of 40 - So will pass the lethal allele to their offspring + be transmitted
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When does recessive lethal allele cause death?
Homozygous = result in death Heterozygous = does not result in death
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Recessive lethal allele - example?
Agouti - Gene in mice - Will determine coat colour - BUT certain mutations of alleles will be LETHAL A = grey, AY = yellow AY = dominant allele for fur colour AY = recessive lethal allele
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How to test if the yellow mice used as parents are heterozygous?
- Do a test cross - Get a grey mice (known recessive) - And then get your yellow mice - Use the yellow mice that produces offspring that are half yellow, half grey (1:1)
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Is the probability calculated for a trait to occur in an offspring accurate? Ie. will it be actually seen in real life (empirical results) WHY NOT?
- NOT NECESSARILY Eg. you calculated 0.14% for a child to have the disease. BUT maybe all kids in the family will have the disease, which is 100% // - Small numbers (eg. one family) tends to give very different results - The more families you look at, the average result will get CLOSER AND CLOSER to the theoretical probability
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Pleiotropy
OPPOSITE OF POLYGENIC TRAIT - Single gene affects 2 or more phenotypic traits that seem unrelated
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Pleiotropy - example in humans
SOX10 gene causes WS4 syndrome WS4 syndrome includes: - White forelock - Different coloured eyes - Areas of unpigmented skin - Lack of nerve components in the large intestine impacted bowel function - Hearing issues
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Pleiotropy - why does it arise?
- SOX10 gene expresses proteins used in EARLY DEVELOPMENT Eg. products needed in pigment cells, certain nerve tissues, future ear
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How do we know the likelihood of crossing over?
DISTANCE!! - The further the distance between 2 gene loci ON THE SAME CHROMOSOME, the higher the likelihood of crossing over + recombination
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Distance of 2 linked genes on the same chromosome? - units?
Distance is calculated in % However each 1% = 1 map unit = 1 centimorgan (cM)
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Genetic map?
- diagram that shows the relative positions of genes on a chromosome - Created based on how frequently they are inherited together