Structure Of The Human Genome

Question 1

General distribution of genome

Answer 1

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

45% intermediate repeat

10% highly repetitive

Question 2

Gene

Answer 2

DNA sequence that contributes to phenotype of organism

Code for proteins or functional RNA molecules

Question 3

Trans acting

Answer 3

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

Question 4

Gene layout

Answer 4

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

Question 5

Post transcriptional modifications

Answer 5

5’ cap added immediately

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

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

Question 6

Development of gene families

Answer 6

By duplication and divergence events

Question 7

Pseudo genes

Answer 7

Arise from loss of function after duplication

Question 8

Spacers in between genes may have a ____

Answer 8

Sequence independent function

Question 9

Intermediate repeated sequence likely formed by ___

Answer 9

Transposition

Question 10

Types of repeated DNA elements

Answer 10

LINEs long interspersed elements

SINEs short interspersed elements

LTR retrotransposons (long terminal repeat)

DNA transposons

Question 11

LINEs

Answer 11

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

Question 12

SINEs

Answer 12

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

Question 13

3 SINE families in human genom

Answer 13

Alu (10% of genome)

MIR

MIR3

Question 14

LTRs

Answer 14

Very similar to virus, just lacking envelope sequence

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

Occupy 8% of genome

Question 15

DNA TRansposons

Answer 15

Encode for transposonase
Cut and paste
Copy doesn’t increase

Question 16

Highly repetitive DNA

Answer 16

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

Question 17

Minisatellites

Answer 17

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

Question 18

Microsatelites

Answer 18

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

Likely arise by slippage during replication

Question 19

Telomeres

Answer 19

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

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

Question 20

G-bands

Answer 20

Associate with low GC content

Visualized with Giesma stain

Question 21

FISH

Answer 21

Fluorescent in situ hybridization

Can map chromosomal origin of a clone- important in mapping

Useful in karyotypes - painting

Question 22

Histones

Answer 22

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

Question 23

Giamsa stain protocols

Answer 23

Capture cells in prometaphase

Fix cells

Gentle digestion

Giamsa stain binds to AT rich regions

Question 24

Why isn’t sequencing a good method for determining size

Answer 24

Repeat areas are shortened by incorrect overlap

Question 25

Method for genome size determination

Answer 25

Feulgen stain: Isolate nuclei and fix slide Stain DNA Image quantifies density Converts density to pg (1pg = 1 Gbp) Or flow cytometry

Question 26

Reassociation test protocols

Answer 26

Extract DNA Shear DNA to 400 bp Boil in salty buffer to dissociate Monitor over time More small particle = higher concentration = faster reassociation

Question 27

Human genome is CpG ____

Answer 27

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

Question 28

Reason for CpG islands

Answer 28

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

Question 29

Ensembl stats

Answer 29

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

Question 30

Duplication leads to _____

Answer 30

Gene families

Question 31

Unequal crossing over leads to ____

Answer 31

Clustered gene duplication Ex: his tone 1 cluster on chromosome 6

Question 32

Interchromosomal crossovers can lead to ___

Answer 32

Segmental duplications More common in high repeat areas (subtelomeric and pericentromeric)

Question 33

Non-processed pseudo genes

Answer 33

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

Question 34

Processed pseudogenes

Answer 34

Have no promoters or introns Could be located anywhere Formed by retrotransposition

Question 35

Intermediate repeats

Answer 35

Interspersed throughout genome by jumping

Question 36

Common human retrogenes

Answer 36

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

Question 37

Retrotransposons or rna transposons

Answer 37

Copy and paste | Increase in number

Question 38

Alpha satellites

Answer 38

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

Question 39

Beta satellites

Answer 39

Mostly near telomeres

Question 40

Qualities of genetic markers

Answer 40

Sequence is known and location is known May be polymorphic Can be used for determining parentage, identifying individuals, quantifying diversity in population linking/mapping

Question 41

Diseases caused by micro satellite repeat expansion

Answer 41

Huntington’s CAG Myotonic dystrophy CTG Fragile X CGG Repeated RNA SEEMS TO TRAP MACHINARY PREVENTING MRNA PROCESSING