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Foundations of Medical Science > Molecular & Cell Genetics > Flashcards

Molecular & Cell Genetics Flashcards

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USMLE® Step 1 flashcards Biology 101 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
Q

At the replication fork of semi-conservative replication

A

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
Q

Checking for mutations

A

DNA polymerases possess a 3’-5’ exonuclease which can remove incorrect bases

27
Q

End replication paradox

A

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
Q

Point mutations

A

Silent mutation:
AA doesn’t change

Missense mutation:
AA does change

Nonsense mutation:
AA codon to stop codon

29
Q

Indel mutations

A

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
Q

Spontaneous mutations

A

Errors in DNA replication
(Which escape proofreading & repair mechanisms)

Replication slippage
(Gain repeat=reverse, Loss repeat=forward)

Deamination

31
Q

Induced mutations

A

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
Q

DNA damage repair

A

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
Q

Decondensing of chromosomes

A
  • Nucleosome sliding (away from eachother)

- DNA pulled away from nucleosome

34
Q

DNA vs RNA structure

A

Deoxyribose has H where ribose has OH on 2’ carbon

35
Q

Transcription

A

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
Q

RNA polymerases in eukaryotes

A

RNA pol I: rRNA
RNA pol II: mRNA, snRNA
RNA pol III: 5S rRNA, tRNA

37
Q

Eukaryotic co-transcriptional processing

A

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
Q

The genetic code

A

All proteins start with Methionine (AUG)

3 stop codons:
UAA
UAG
UGA

39
Q

tRNA

A

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
Q

Joining tRNA to AA

A

Specific aminoacyl-tRNA-synthetase joins them together via hydrolysis of ATP

41
Q

Prokaryote ribosome

A

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
Q

Prokaryotic translation: initiation

A

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
Q

Prokaryotic translation: elongation

A

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
Q

Prokaryotic translation: termination

A

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
Q

Restriction enzymes sites & recombinant DNA

A

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
Q

cDNA

A

DNA copy of mRNA produced using an reverse transcriptase

47
Q

cDNA cloning

A

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
Q

DNA sequencing

A

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
Q

Steps of PCR

repeat

A

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
Q

Polymorphisms

A

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
Q

Haplotype

A

Series of SNP alleles along a single chromosome

Foundations of Medical Science (2 decks)

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