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Foundations of Medical Science > Molecular & Cell Genetics > Flashcards

Molecular & Cell Genetics Flashcards

1
Q

Metacentric

Submetacentric

Acrocentric

A

Metacentric:
Centromere in middle

Submetacentric:
Centromere towards the end of the chromosome

Acrocentric:
Centromere far closer to one end than the other

P=short
Q=long

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2
Q

Part of Y chromosome that determines maleness

A

SRY is the only region of the Y required for male development

Just below the PAR (pseudoautosomal region)

(Sex-determining region)

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3
Q

Euploid state

Aneuploid state

A

The complete chromosome set

An irregular number of chromosomes (caused by non-disjunction)

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4
Q

Trisomy’s that are born (not miscarried)

Autosomal

A

Chromosome 21:
Down syndrome

Chromosome 13:
Patau syndrome

Chromosome 18:
Edwards syndrome

(Small chromosomes so don’t contain many genes, so more likely to be born that other chromosomes)

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5
Q

Abnormal complement of sex chromosomes

A

XXY - Klinefelter syndrome (male)
X - Turner syndrome (female)
XYY - XYY syndrome (male)

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6
Q

Amniocentesis

A

Carried out weeks 15-20 of pregnancy

Only offered when combined test in 1st trimester indicates severe risk of developing condition (eg. Down’s syndrome)

Amniotic fluid removed, foetal cells isolated, dna extracted and Q-PCR for 13,18&21
(Done in 2 days for parents)

Then grown in medium for 2 weeks to definitively determine karyote

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7
Q

Composition of human genome

A

1.1% exon
4% regulatory regions (promoter/transcriptional terminators)
44% other sequences including introns (23%)

The repeated sequences is the rest:
45% transposon based repeats
6.6% heterochromatin

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8
Q

Transposon based repeats

Eg. Retrotransposable elements

A

Move randomly into other parts of genome (copy&paste mechanism)

LINES (long interspersed elements)
SINES (short interspersed elements)

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9
Q

Heterochromatin

A

Highly condensed DNA
So transcriptionally inactive
(RNA polymerase can’t have access to bases)

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10
Q

Non-coding RNA

A

Function:

  • message processing
    (snRNAs form complexes with proteins to form snRNPs required for splicing pre-mRNAs)
  • de-coding mRNA
    (Compose the ribosome and tRNAs)
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11
Q

Long ncRNAs

A

Most have unknown function

Xist controls mammlian X inactivation (on X chromosome)

Inactivation happens by condensing DNA into heterochromatin so can’t be transcribed
(Doesn’t happen in other X chromosome)

X-linked recessive disorder that reveal X inactivation:

  • anhidrotic ectodermal dysplasia
  • red green colour blindness
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12
Q

miRNA (ncRNA example)

A

Regulate expression of specific genes

miRNA transcribed to give hairpin loop, can bind to itself

Nuclease removed capping&adenylation, RNA enters cytoplasm

One strand degraded, other miRNA strand can base pair with a mRNA that encodes a protein
(ribosome can’t translate)
(Levels of corresponding protein will drop)

Either:

  • translational repression
  • deadenylation rendering mRNA unstable

Mutations in miRNA genes can implicate disease

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13
Q

Mitochondrial genome

A

Encodes 13 polypeptides plus rRNA and tRNA

No introns or repetitive DNA

Mitochondrial cytopathies:
- organs most affected are those that use a lot of energy
Example:
- MELAS
- LHON
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14
Q

Autosomal recessive

A

CFTR on chromosome 7

Mutant allele lacking 508th codon (normally)

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15
Q

Autosomal dominant

A

Huntington disease
Mutation at HD locus
More repeats of CAG (causes longer polyglutamine tract, causes protein aggregation)

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16
Q

X-linked recessive

A

Haemophilia A

Males inherit X from mothers

Occurs more frequently in males because only have one X

If fathers affected, all daughters will be carriers of the disease

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17
Q

Multifactorial trait

A

Polygenic (controlled by genes at more than one locus) & affected by environment

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18
Q

Disorders showing multifactorial traits

A

Cardiovascular disease

Diabetes mellitus

Obesity

Mental illness

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19
Q

Nucleic acid composition

A

Either:
Deoxyribose:
H at 2’ position on sugar ring

Ribose:
OH at 2’ position on sugar ring

AND

Phosphate

Nitrogenous base:
Purines = guanine, adenine
Pyrimidines = cytosine, thymine
(No thymine in RNA, it’s uracil)

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20
Q

Nucleoside

A

Sugar & base

Via glycosidic bond

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21
Q

dAMP
dADP
dATP

A

deoxyadenosine 5’ monophosphate

deoxyadenosine 5’ diphosphate

deoxydenosine 5’ triphosphate

22
Q

What nucleotides are the building blocks of DNA

A

nucleotide triphosphates

Eg. dATP

23
Q

Polynucleotide link of nucleotides

A

Catalysed by DNA polymerase

Makes covalent bond between the OH of the sugar and the phosphate group attached to the five prime carbon of the next nucleotide

Forms phosphodiester bond

(Liberates inorganic pyrophosphate)

24
Q

Eukaryotic cell cycle

A

G1:
If signal, cell replicates cellular components
If no signal, cell enters quiescent Go phase

S:
Phase that replicates the DNA

G2:
Preparing for mitosis

Mitosis:
Cell division

25
At the replication fork of semi-conservative replication
DNA helicase binds and unwinds DNA SSB (single strand binding) proteins prevent immediate re-formation of double helix Above replication fork, Topoisomerase breaks a phosphodiester bond on one of the parental strand, providing a degree of freedom (prevents positive supercoiling) DNA polymerase only synthesizes DNA in the 5 to 3’ direction (all polymerases) Leading strand and lagging strand (synthesised in pieces/Okazaki fragments) In order for DNA polymerase to add nucleotides, an RNA primer strand needs to be synthesized (by primase) creating a 5’ to 3’ and then DNA polymerase can add to it Joining Okazaki fragments: RNA primer on new strand degraded by exonuclease leaving a gap, DNA polymerase continues synthesis across gap. DNA ligase replaces the missing phosphodiester bond between the fragments To make strand go in same direction, lagging strand loop is formed so net direction of synthesis is the same
26
Checking for mutations
DNA polymerases possess a 3’-5’ exonuclease which can remove incorrect bases
27
End replication paradox
RNA primer removed at each very end of strand Telomeres form at ends catalysed by telomerase (has portable RNA template) Hundreds of copies of 5’ TTAGGG 3’ (In humans) Once born, telomerase is switched off With every division, telomeres get shorter
28
Point mutations
Silent mutation: AA doesn’t change Missense mutation: AA does change Nonsense mutation: AA codon to stop codon
29
Indel mutations
Small scale insertions/deletions If multiple of 3: reading frame maintained but pp changed If not: frameshift Non-native DNA sequence followed by premature stop codon So mal-functioning polypeptide and truncated polypeptide May not affect if in non-coding region
30
Spontaneous mutations
Errors in DNA replication (Which escape proofreading & repair mechanisms) ``` Replication slippage (Gain repeat=reverse, Loss repeat=forward) ``` Deamination
31
Induced mutations
Physical: Ionising radiation = causes single or double strand breaks UV = thymine dimers (incorrect bases inserted opposite) Chemical: Nitrous acid = cytosine to uracil Alkylating agents = guanine modification Free radicals = strand breaks and base modify
32
DNA damage repair
Direct repair: Removing the chemical entity that has changed the nucleotide base Nucleotide excision repair: Removal of damaged region (helicase action) followed by re-synthesis Homologous recombination: Repairs double strand breaks - after break, exonuclease removes a few bases leaving protruding ends, Rad51 bind to single strands which invaded homologous intact duplex (normal duplicate from S phase), donor strand used as template for repair (Needs Rad51 in eukaryote)
33
Decondensing of chromosomes
- Nucleosome sliding (away from eachother) | - DNA pulled away from nucleosome
34
DNA vs RNA structure
Deoxyribose has H where ribose has OH on 2’ carbon
35
Transcription
Initiation: Sigma factor protein binds to ‘boxes’ either end of promoter region to align RNA polymerase at transcription start site Elongation: RNA polymerase unwinds DNA, synthesizes mRNA by adding complementary nucleotides (no primer needed), speed 50nt/sec Termination: Rho independent termination: G-C rich stem loop, detachment from DNA template Rho dependent termination: Behind RNA, unwinds DNA-RNA duplex, when RNA polymerase slows down (often when lots of C&G sequences) rho catches up and pulls it away from template
36
RNA polymerases in eukaryotes
RNA pol I: rRNA RNA pol II: mRNA, snRNA RNA pol III: 5S rRNA, tRNA
37
Eukaryotic co-transcriptional processing
Capping: 7 - methylguanosine cap at 5’ end Protects transcript from degradation/role in translation Polyadenylation: Multiple adenosine residues added to 3’ end of mRNA Protects transcript from degradation/role in translation Splicing: Spliceosome removes introns
38
The genetic code
All proteins start with Methionine (AUG) 3 stop codons: UAA UAG UGA
39
tRNA
20 types Contains unusual bases CCA - OH sequence at 3’ end to amino acid (Ester linkage) Anticodon on other end - first 2 letters in codon are the same but 3rd base can vary
40
Joining tRNA to AA
Specific aminoacyl-tRNA-synthetase joins them together via hydrolysis of ATP
41
Prokaryote ribosome
70S complex Made up of rRNA and proteins Large subunit (50S) ``` Small subunit (30S) - 16S rRNA & others ``` Sites: A-site = amino acid site P-site = polypeptide firmed E-site = exit site for tRNA
42
Prokaryotic translation: initiation
Initiation factors IF1 and IF3 bind the 30S subunit Complex binds to mRNA First AA fMet in complex with IF2-GTP enters the P site 16S rRNA binds to Shine-Dalgarno sequence (5’) in the mRNA to line up fMet-tRNA with AUG start codon Large 50S subunit binds (accompanied by hydrolysis of GTP) GDP + Pi + all IFs released (1,2,3)
43
Prokaryotic translation: elongation
Next aminoacyl tRNA binds to elongation factor EF-Tu GTP, and enters A site in ribosome If anticodon of tRNA is complementary to the codon, then hydrolysis of GTP -> EF-Tu GDP + Pi are released Peptidyl transferase process: Protein is synthesized by ‘lifting’ the incomplete polypeptide, and placing the new AA underneath (The free -NH2 of incoming AA attacks carbonyls carbon of previous AA to form the peptide bond) Translocation of ribosome occurs with hydrolysis of the GTP bound to EF-G A site is now free
44
Prokaryotic translation: termination
Stop codon (UAA, UAG, UGA) on mRNA presented in A site Release factor (RF1 or RF2) mimics shape of tRNA Release factor enters A site with H2O molecule Peptide is hydrolysed from the final tRNA using H2O molecule Ribosome dissembles requiring a ribosomal recycling factor and IF3
45
Restriction enzymes sites & recombinant DNA
Different restriction enzymes recognise different nucleotide sequences Sequence forms a palindrome (reads same on both strands) Enzymes leave sticky or blunt ends Plasmid cut using same enzyme so have complementary cohesive ends DNA ligase joins fragment and plasmid together to form recombinant DNA molecule
46
cDNA
DNA copy of mRNA produced using an reverse transcriptase
47
cDNA cloning
Isolate mRNA ``` Add oligo(dT) primer (pairs with polyA tail) ``` Add reverse transcriptase & synthesis continues (Extends from T’s) Partially digest RNA with RNase H Add DNA polymerase, transcription, DNA ligase seals gap ``` To add to plasmid: Add EcoRI restriction sites either side Protect these sites using EcoRI methylase Cut sites at two ends and plasmid cDNA inserted ```
48
DNA sequencing
Reaction components: - DNA template - primer - DNA polymerase - dNTPs (dATP, dCTP, dGTP, dTTP) - small amounts of ddNTPs with flurochromes (don’t have -OH on 3’ carbon)
49
Steps of PCR | repeat
Denaturation: Reaction heated to 95°C to denature the DNA into single strands Primer annealing: Reaction temp reduced to 45-68°C to allow primers to hybridise to their complementary sequences in the target DNA Primer extension: Reaction temp raised to 72°C to allow Taq polymerase to synthesize DNA
50
Polymorphisms
SNPs: Single base substitution Closely located SNPs could be correlated (SNP1&2 are in linkage disequilibrium) Tandem repeat polymorphisms: Repetition of short stretches of sequence Used in forensics - hungtingtons (CAG>40) & motor neurone disease (GGGGCC~100) Structural variation: Segment of DNA that can be adenylate in some chromosomes or present in multiple tandem copies
51
Haplotype
Series of SNP alleles along a single chromosome

Foundations of Medical Science (2 decks)

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