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Human Molecular Genetics > Structure Of The Human Genome > Flashcards

Structure Of The Human Genome Flashcards

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1
Q

General distribution of genome

A

45% single sequence DNA (unique/contains gene coding regions)

45% intermediate repeat

10% highly repetitive

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2
Q

Gene

A

DNA sequence that contributes to phenotype of organism

Code for proteins or functional RNA molecules

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3
Q

Trans acting

A

Factors encoded by another gene, translated in cytoplasm and brought back into nucleus

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4
Q

Gene layout

A 
Promoter (200 bp upstream)
Tata box (30 bp upstream)
Transcription start site
Coding region
Transcription stop site

Enhancers, may be located upstream, downstream or mid gene

Silencers: opposite of enhancer

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5
Q

Post transcriptional modifications

A

5’ cap added immediately

Cleavage ~ 30 bp downstream of AAUAAA > addition of 100-200 As

Splicing by splicosome
Intron = 5’ GT————AG 3’

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6
Q

Development of gene families

A

By duplication and divergence events

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7
Q

Pseudo genes

A

Arise from loss of function after duplication

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8
Q

Spacers in between genes may have a ____

A

Sequence independent function

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9
Q

Intermediate repeated sequence likely formed by ___

A

Transposition

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10
Q

Types of repeated DNA elements

A

LINEs long interspersed elements

SINEs short interspersed elements

LTR retrotransposons (long terminal repeat)

DNA transposons

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11
Q

LINEs

A

6-8 kB

Contain promoter for RNA POL 2, an ORF for protein similar to reverse transcriptase, and an ORF for an endonuclease for re-insertion

Because mRNA is copied from 3’ end, pol often doesn’t reach 5’ end therefore ‘functional’ LINE isn’t formed

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12
Q

SINEs

A

300-400 bp

Most were originally tRNA transcripts

Do not encode any proteins

Have promoter for pol 3

have similar 3’ sequence to LINEs so can be retrotransposed

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13
Q

3 SINE families in human genom

A

Alu (10% of genome)

MIR

MIR3

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14
Q

LTRs

A

Very similar to virus, just lacking envelope sequence

Encode for: reverse transcriptase, protease, RNAse H, and integrase

Occupy 8% of genome

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15
Q

DNA TRansposons

A

Encode for transposonase
Cut and paste
Copy doesn’t increase

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16
Q

Highly repetitive DNA

A

More dense than other DNA > forms bands in chromosomes aka satellites

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17
Q

Minisatellites

A

10-100 bp repeats in tandem arrays = 0.5-40 kb

Often occur near telomeres - limits use in mapping

Loci can be hypervariable - used in forensics

18
Q

Microsatelites

A

2-4 bp repeats
Number of repeats varies - valuable genetic marker (more uniform distribution)

Likely arise by slippage during replication

19
Q

Telomeres

A

Tandem repeats
Overhanging 3’ end (may fold back on itself)

Telomere is dissolved after ~ 50 cell cycles in eukaryotes - active telomerase can extend this

20
Q

G-bands

A

Associate with low GC content

Visualized with Giesma stain

21
Q

FISH

A

Fluorescent in situ hybridization

Can map chromosomal origin of a clone- important in mapping

Useful in karyotypes - painting

22
Q

Histones

A

Octamer
2 (H2A + H2B + H3 + H4)
With H1 between ‘beads’

23
Q

Giamsa stain protocols

A

Capture cells in prometaphase

Fix cells

Gentle digestion

Giamsa stain binds to AT rich regions

24
Q

Why isn’t sequencing a good method for determining size

A

Repeat areas are shortened by incorrect overlap

25
Q

Method for genome size determination

A

Feulgen stain:

Isolate nuclei and fix slide
Stain DNA
Image quantifies density
Converts density to pg (1pg = 1 Gbp)

Or flow cytometry

26
Q

Reassociation test protocols

A

Extract DNA
Shear DNA to 400 bp
Boil in salty buffer to dissociate
Monitor over time

More small particle = higher concentration = faster reassociation

27
Q

Human genome is CpG ____

A

Poor
Only 40%
Higher in gene rich areas (~50%)

28
Q

Reason for CpG islands

A

Selection will maintain CG in gene coding regions by keeping them methylated

Outside of genes they undergo deaminatipn > change to uracil > 50/50 chance of being ‘fixed’ correctly

29
Q

Ensembl stats

A

~ 20,000 coding genes
14,000 pseudogenes
200,000 gene transcripts

30
Q

Duplication leads to _____

A

Gene families

31
Q

Unequal crossing over leads to ____

A

Clustered gene duplication

Ex: his tone 1 cluster on chromosome 6

32
Q

Interchromosomal crossovers can lead to ___

A

Segmental duplications

More common in high repeat areas (subtelomeric and pericentromeric)

33
Q

Non-processed pseudo genes

A

Usually found side by side

Usually duplicated in tandem with original gene (may contain promoter)

Copied at genomic level therefore contains introns and is Collen non processed

34
Q

Processed pseudogenes

A

Have no promoters or introns

Could be located anywhere

Formed by retrotransposition

35
Q

Intermediate repeats

A

Interspersed throughout genome by jumping

36
Q

Common human retrogenes

A

Escape from X to autosomal so genes can continue to be transcribed during replication (escaping prolonged condensed state)

37
Q

Retrotransposons or rna transposons

A

Copy and paste

Increase in number

38
Q

Alpha satellites

A

Bind to CenA (centromeric histone) have function in centromere kinetochore attachment

39
Q

Beta satellites

A

Mostly near telomeres

40
Q

Qualities of genetic markers

A

Sequence is known and location is known

May be polymorphic

Can be used for determining parentage, identifying individuals, quantifying diversity in population linking/mapping

41
Q

Diseases caused by micro satellite repeat expansion

A

Huntington’s CAG

Myotonic dystrophy CTG

Fragile X CGG

Repeated RNA SEEMS TO TRAP MACHINARY PREVENTING MRNA PROCESSING

Human Molecular Genetics (3 decks)

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