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Short answers that could be in exam Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

Define the central dogma of molecular biology

A

Unidirectional flow of information:

DNA -> RNA -> protein

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2
Q

Explain the differences between an F+ strain of E.coli, an Hfr strain and an F’ strain

A

F+ cells contain the fertility plasmid in an episomal form
Hfr cells contain the fertility plasmid integrated into the chromosome
F’ cells contain the fertility plasmid episomally but also a fragment of the cellular DNA

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3
Q

Name 3 variants of the E.coli sigma(σ) protein and the class of genes they each regulate

A

Sigma70/sigma D - housekeeping, most general genes
Sigma38/sigma S - general stress response genes
Sigma19/sigma Fecl - iron regulation/transport/uptake genes

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4
Q

Describe the concserved sequences found in the majority of E.coli promoters that the general sigma (σ70) subunit can recognise

A

The -35 box and the -10 box (TATA box)

Both separated by 17bp

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5
Q

Explain how the attenuator functions to regulate transcription of the E.coli trp operon

A

Transcription of leader attenuator between trpO operator and trpE coding sequence contains 2 palindromic sequences followed by polyT region in leader form polyU region in RNA2
Folds into 2 structures because of palindromes - one is a terminator of transcription and one is not - allowing transcription to proceed

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6
Q

Briefly define the following term: a) Promoter

A

Region near the transcription start site which promotes assembly of polymerase

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7
Q

Briefly define the following term: b) Transcription start site

A

Region where polymerase starts to copy into RNA

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8
Q

Briefly define the following term: c) polyA signal

A

Sequence in the RNA recognised by the RNA cleavage complex

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9
Q

Briefly define the following term: d) Enhancer

A

DNA element that can increase the rate of transcription from a gene

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10
Q

Briefly define the following term: e) Abortive transcript

A

RNA produced when polymerase initiates but does not proceed to full elongation

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11
Q

What are the proteins found in or associated with the E.coli core RNA polymerase structure?

A 
Alpha = enzyme assembly
Beta = nucleotide binding
Beta-prime = template binding
Omega = aids b' folding & assembly
Delta = regulator
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12
Q

Where would you typically find a TATA box? What proteins bind to a TATA box?

A

In the promoter of eukaryotic genes

It binds to general transcription factors

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13
Q

What is meant by the term global regulation?

A

Global regulation acts simultaneously at multiple promoters in a genome to co-ordinate their simultaneous transcription

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14
Q

What is meant by the term constitutive transcription?

A

Constitutive transcription describes the continuous expression of housekeeping genes

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15
Q

What is trans-splicing?

A

A form of RNA processing in which multiple pre-mRNAs are spliced to form a single fusion transcript

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16
Q

What two subunits make up the cap-binding complex?

A

eIF4E and eIF4G

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17
Q

Explain what is meant by the term “end replication problem” and it’s significance to our chromosomes. How do telomeres reduce the problem?

A

Mechanism of DNA replication means that the lagging strand can’t be copied right to the end
Because RNA primer which primes lagging strand synthesis is degraded
This means each round of replication shortens the chromosome
Telomeres are repetitive regions which can be extended at the end of the chromosome so we can afford to lose some and there is a mechanism for lengthening them in appropriate cells

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18
Q

Name 3 mechanisms by which bacteria, viruses or plasmids may be replicated

A

Bi-directional or theta
Rolling circle
Strand displacement

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19
Q

A mutation changes the DNA sequence in such a way that the spliceosome cannot remove an intron. What effect will this have on transcription and translation of the gene?

A

Transcription: no change/normal as introns are retained in pre-mRNA
Translation: causes a problem as it will lead to intron retention in the mature mRNA which will disrupt the translation of mRNA into protein

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20
Q

Name 3 common promoter motifs found associated with eukaryotic protein coding genes. (4 possible answers)

A

TATA box
GC box
Octamer box
CAAT box

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21
Q

What does the term “tRNA charging” mean?

What enzyme mediates tRNA charging?

A

The linking of an amino acid to the correct tRNA molecule

Mediated by aminoacyl tRNA synthesases

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22
Q

Define the term “degenerate code” in the context of the genetic code

A

More than one codon can code for the same amino acid
Each amino acid can be coded for by different triplets
First 2 triplets of amino acid normally fixed but 3rd position can vary

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23
Q

Define the term “wobble hypothesis” in the context of the genetic code

A

3rd base of the codon binds to 1st position of the anticodon on tRNA
Curved structure of the anticodon means the pairing is looser at the site
Allows some wobble
G and U bases are more wobbly than C and A

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24
Q

Which ribosome subunit is the smallest?

A

30S

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25
Q

Where is the Kozak sequence found and what is it for?

A

Consensus sequence surrounding the initiation codon (AUG) in mRNA
Sequence is recognised by pre-initiation complex to initiate translation

26
Q

What happens in the elongation phase of translation?

A

Positioning of the next amino acids into the A (aminoacyl) site
Guided by tRNA
Peptide bond forms between amino acids, releasing uncharged tRNA
mRNA shifted to free up A site

27
Q

Define the term “codon bias”

A

Difference in the relative occurrence of the different synonymous codons for the same amino acids

28
Q

What is the difference between a silent mutation, a missense mutation, and an nonsense mutation?
Which is likely to be more deleterious?

A

Silent - no change in amino acid sequence (synonymous)
Missense - change to amino acid sequence (non-synonymous)
Nonsense - introduction of premature STOP codon in amino acid sequence
Nonsense most likely to be pathogenic as they will truncate protein. But this can depend on the position of the induced STOP (near start or end of protein?)

29
Q

Give three examples of causes of spontaneous mutations and the types of DNA damage they cause in DNA

A

Tautomeric shifts - mispairing (replication error)
DNA slippage - insert/deletion in repetitive regions
Double strand breaks - if during replication can lead to translocations

30
Q

Give three examples of causes of induced mutations and describe the types of damage they cause in DNA

A

Radiation - UV causes formation of thymidine dimers.
Oxidative damage - by-product of metabolism but also can be caused by radiation. Can cause breaks in DNA (DSBs lead to translocation) and modified bases which cause mispairing
Chemicals - acridines (intercalacting agents) can cause DNA polymerase to mistake them for an extra base and cause insertion of an extra base

31
Q

Briefly describe three ways to measure DNA damage in cells

A

Comet assay - semipermeabilise cells embedded in agarose, run gel - broken DNA escapes the nucleus and when stained makes it look like a comet
Karyotype analysis - visualise chromosomes and look for aberrations
yH2AZ visualisation - forms foci in nuclei where damage occurs

32
Q

How are most spontaneous mutations caused by replication errors fixed? Briefly describe the process

A

DNA polymerase has proofreading capabilities
Proofreading enzyme recognises the mistake
Exonuclease removes incorrect nucleotides
Polymerase copies the region again

33
Q

Briefly describe the mismatch repair process in bacteria

A

MutS recognises mismatched bases or loops from deletions/insertions caused by replication slippage
MutL binds to the MutS and stabilises the complex
This activates MutH which locates the nearest unmethylated GATC and makes a nick
uvrD unwinds the helix
Exonuclease degrades the DNA and DNA polymerase III replaces it

34
Q

Name two mechanisms that cells can use to fix double strand breaks in DNA

A

Homologous recombination

Non-homologous end joining

35
Q

What is ‘G-banding’ and how can it be used to assess the integrity of the genome?

A

Giemsa staining and proteolytic removal of protiens to give light and dark bands
Chromosomes have defined staining patterns so karyotype can be assessed, chromosomes counted and translocations spotted

36
Q

What is spectral ‘karyotyping’?

Briefly describe the principle and what it can be used to tell us about the state of a person’s genome

A

A multiplex FISH method in which each chromosome is labelled a different colour
It allows use to quickly look at the chromosome complement (total number of each chromosome) and aberrations in the chromosomes

37
Q

What is a Barr body?

A

A condensed X chromosome in the cells of a healthy female

38
Q

Briefly describe the structure of a nucleosome.
Give an example of a chromatin modification, where it is placed on the nucleosome and what effect it has on gene expression

A

Has a core octomer of histones - 2X(H2A, H2B, H3 and H4)
Approx 145bp of DNA wraps around the octomer
H1 can connect the nucleosomes
The nucleosome is like a flat disk with histone tails protruding above and below which are highly mobile and can be modified
H3K27me which is repressive (condenses chromatin)

39
Q

What effect does DNA methylation at he promoter have on the expression of a gene?

A

Represses it

40
Q

What are the main five histone proteins found in chromatin?

A 
H1
H2A
H2B
H3
H4
41
Q

What is the difference between euchromatin and heterochromatin?
Which type of chromatin do active genes tend to reside as?

A

Euchromatin has permissive chromatin marks and is condensed. Form that active genes tend to be in
Heterochromatin is highly condensed and contains repressive chromatin marks

42
Q

Give one example of how histone methylation can repress gene expression and one example of how it can activate gene expression

A

Repressive - H3K27me represses by condensing chromatin

Activating - H3K4me (found at promoter and helps recruit polymerase) activated by methylation

43
Q

What is the ‘histone code hypothesis’?

A

The hypothesis that different patterns of epigenetic marks are interpreted by a specific set of proteins
These ‘interpret’ the epigentic code by altering chromatin structure and recruiting appropriate sets of proteins to activate or repress gene expression

44
Q

What is Xist?

Briefly describe how it mediates ‘dosage compensation’ in humans

A

Xist is a long non-coding RNA encoded by a gene on the X chromosome
Dosage compensation is the process by which gene from a sex chromosome is altered to equalise gene expression between the sexes
Xist is expressed from the inactive X, where it interacts with the PRC2 complex and recruits it to methylate H3K27
This causes repression of gene expression and condensation of the entire chromosome

45
Q

Define the term imprinting

Give an example of an imprinted gene

A

Imprinting is when a gene, on an autosomal chromosome, is normally expressed from one allele
Such as: NDN

46
Q

Give three examples of how deregulated epigentic mechanisms can lead to disease

A

Mutations in MeCP2 (DNA-methyl binding protein) causes Rett syndrome
Mutation to Ataxin gene (HAT) causes spinocerebellar ataxia type 7 (SCA7)
Mutations in genes involved in regulating chromatin structure an genetics like EZH2 often seen in cancer

47
Q

What are chromatin territories?

A

Discreet and separate (no overlapping) regions of the nucleus that each chromosome occupies

48
Q

Define three key characteristics of an enancer

A

Can enhance transcription of the gene from a long distance away
Can be upstream, downstream or even in the gene
Can be in either orientation relative to the gene (in the same direction or facing the other way)

49
Q

When a dihybrid cross is performed to observe the segregation of two dominant genes the ratio of phenotypes for F2 generations, what would a 9:3:3:1 ration of phenotypes tell us about the relative positions of the genes?
What about if this ratio is distorted?

A

9:3:3:1 - genes are segregating independently (they are on different chromosomes)
Distorted ratio - they are on the same chromsome

50
Q

What does ‘incomplete penetrance’ mean in the context of genetics?

A

An individual could have the allele associated with a trait (e.g. a mutation causing a disease)
But not exhibit the phenotype (e.g. they have the mutation but don’t get the disease)

51
Q

Give two examples of how bioinformatics approaches can be used to analyse gene function

A

Use BLAST - find similarity to other genes of known function

Use bioinformatics - find functional domains of known function

52
Q

Define the acronyms:
‘SNPs’
‘INDELs’

A

SNPs - Single nucleotide polymorphisms

INDELs - Insertions/deletions

53
Q

Briefly describe how a genome wide association study can be used to identify parts of the genome that may contribute to complex conditions such as heart disesae

A

Take DNA from two large populations of unrelated individuals - 1 with the disease and 1 without
Extract DNA and analyse using SNP microarray which will detect SNP variants across the whole genome
Analyse and identify SNPs that are more frequently associated with the disease

54
Q

Why is the ‘Sanger sequencing’ method also called the ‘chain termination’ method?

A

During procedure the polymerase copies the template, extending the chains of millions of copies of the template as it does so
In the reaction there is a certain proportion of each ddNTP
The ddNTP is missing hydroxyl group and so the chain terminates whenever it is incorporated
Looking at the pattern of bands tells us the location of the bases

55
Q

Briefly describe the principle of shotgun sequencing - how can it be used to obtain the sequences of large genomes?

A

Break up the genome into lots of smaller pieces
Clone on and sequence the small pieces
Use bioinformatics to overlap the sequences and build up the geneome

56
Q

Give a specific example oh how genetic testing can inform treatment choice

A

Ace inhibitors more effective in D/D genotype in ACE gene

57
Q

What is the difference between a forward genetic screen and a reverse genetic screen?

A

Forward screen - start with a phenotype and try to discover what gene is linked to it
Reverse screen - start with a gene and look at the effect of modifying it on the phenotype

58
Q

What are induced pluripotent stem cells and how can they be generated?

A

Stem cells produced from differentiated cells like skin fibroblasts
Reprogramming done by forced expression of various genes (SOX2, Oct4, klf4)
They can then be induced to differentiate down various pathways

59
Q

Name four potential benefits of pharmacogenomics

A

Better drug dosages
Fewer side effects
First time success
More effective medicine

60
Q

Define the term transcriptomics and name four methods that can be used to quantify RNA levels

A 
Transcriptomics is the measure of RNA species in a cell
Possible ways to measure RNA:
RT-PCR
Northern blotting
Microarrays
RNA-seq
RNA-FISH
61
Q

Give an example of a non-coding RNA

And briefly describe the molecular mechanism by which it is able to affect gene function

A

Xist

Encoded on X chromosome and represses inactive X chromosome by recruiting PRC2 to methylate chromatin

Molecular Biology & Genetics (8 decks)

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