Topic 2.1 - Genome, chromsome and genes

Genome (def)

totality of genetic information belonging to a cell or an organism -> DNA or RNA carries this information

Chromosome set

one copy of each unique chromosome

Types of genomes found in a person

DNA in nucleus, DNA in mitochondria, DNA of bacterial chromosome, RNA of influenza virus

C-value (def)

genome size in kilobases

C-paradox

genome size (C-value) does not always correlate with an organism’s complexity or number of protein-coding genes

C-paradox example

humans = 3,200Mb

barley = 5,000Mb

C-paradox cause

genes are packed tightly in bacterial and yeast genomes

human genes only comprise a small fraction of the whole → most is intergenic DNA, DNA transposons and intronic DNA

Gene (def)

region of DNA that is transcribed as a single unit and carries information for a discrete hereditary characteristic

usually corresponds to a single protein or a single functional RNA

polycistronic gene (def)

gene that produces multiple different polypeptides

Untranslated regions - UTR (def)

regions before the start codon and after the stop codon that are transcribed but not translated

Purposes of UTRs (3)

5’ UTR: initiating translation → binding sites for ribosomes and regulatory proteins

3’ UTR: mRNA stability

both contain sequences that bind regulatory proteins and microRNAs which can enhance or silence gene expression

unprocessed pseudogenes (def)

nonfunctional segments of DNA that resemble functional genes but have lost their protein-coding ability due to mutations

unprocessed pseudogenes - origin

from gene duplication or transposition

unprocessed pseudogenes - impact of mutations

mutations in duplicated gene are not under selection as there’s still a functioning gene

processed pseudogenes (def)

nonfunctional DNA sequences created when cellular mRNA is reverse-transcribed and inserted back into the genome

processed pseudogenes - structure

no introns

3’ poly A tail

flanking direct repeats

gene fragments (def)

nonfunctional genes broken up by chromosomal rearrangements

composition of human genome (2)

genes and gene-related sequences → genes, introns and gene-related sequences

intergenic DNA → transposons and other intergen regions

composition of human genome - gene-related sequences (2)

pseudogenes

gene fragments

composition of human genome - transposons (4)

LINES

SINES
LTR elements

DNA transposons

composition of human genome - other intergenic regions (2)

satellite DNA
various

Tandem repeats (def)

repeated end-to-end copies of DNA sequences

tandem repeats - types (2)

microsatellites → very short DNA sequences of 10-150bp (Short tandem repeats or simple sequence repeats)

minisatellites → short DNA sequences of 100-20,000bp

transposons (def)

parasitic genetic elements that can move around the genome

transposons - haemophilia cause

insertion of retrotransposon L1 into factor IX gene

transposons - muscular dystrophy cause

insertion of L1 into Dystrophin gene

types of transposition (2)

conservative → transposons excised form its original position and inserts at a new locations (often leaves characteristic mark)

replicative → transposon inserts at a new location but the original copy remains

types of transposition - examples (2)

conservative → DNA transposons

replicative → retrotransposons

DNA transposons - enzyme name and role

transposase involved in movement of DNA transposon

DNA transposition steps (4)

1. transposase gene is transcribed and translated to make the transposase protein

2. transposase enzyme binds to inverted terminal repeats

3. transposase catalyses excision of the transposon from its original site

4. transposase catalyses insertion of the transposon into a new site

transposase - ITR and TSD (def)

ITR = inverted terminal repeat → palindromic sequence involved in movement

TSD = target site duplication → genomic sequence duplicated during insertion (characteristic mark left behind)

retrotransposons - enzyme

reverse transcriptase (rvt)

elements that code for reverse transcriptase (2)

LINE → long interspaced element

LTR retrotransposition → long terminal repeat like a retrovirus (eg. HIV)

SINE → short interspaced element does not encode

reverse transcription steps (5)

1. retrotransposon that encodes rvt is transcribed

2. translation creates rvt

3. rvt synthesises reverse strand in DNA using RNA as template

4. 2nd DNA strand is prodced

5. retrotransposon inserts into new chromosomal position

nucleosomes (structure)

beads of DNA wrapped ~1.7 times around an octomer of histone proteins

method of histone binding to DNA

ionic bonding

DNA = negatively charged phosphate groups

histones = positively charged lysine and arganine residues

histone structure (5)

1 H1

2 H2a

2 H2b

2 H3

2 H4

histone structure - role of H1 histone

H1 histone contacts both DNA and histone octamer → facilitates further compaction into fibres

forms of chromatin (2)

euchromatin → open and accessible to other molecules for transcription

heterochromatin → highly compacted and generally not transcribed

where is heterochromatin commonly found

in regions of chromosomes like the centromeres and telomeres where there are few genes

histone tails - role in chromatin structure

chemically modified by acetylation or methylation of lysine residues and phosphorylation of serine or threonine residues to alter compactness

histone modification - acetylation

reduces positive charge → reduced attraction to DNA → loosens chromatin and associated with active gene expression

histone modification - methylation

disrupts transcription by RNA polymerase

types of heterochromatin (2)

facultative → can switch between open and condensed states to regulate genes

constitutive → always in condensed state

histone modification states (3)

H3K4me

H3K9me

H3K27me

histone modification states - H3K4me (5)

H3 lysine 4 methylation

recruits chromatin-remodelling complexes and transcription machinery

active locus → gene expression

associated with euchromatin

found near promoter

histone modification states - H3K9me (4)

H3 lysine 9 methylation

inactive locus

associated with constitutive heterochromatin

broad regions

histone modification states - H3K27me (4)

H3 lysine 27 methylation

inactive locus → gene silencing

associated with facultative heterochromatin

spread over gene → centromeres, telomeres, repetitive sequences

Histone modification - acetylation v methylation

acetylation directly reduces histone-DNA attraction → opens chromatin

methylation indirectly works via protein recruitment

telomere (def)

protective cap on ends of linear chromosomes

centromeres (def)

point of attachment for microtubules during mitosis

eukaryotic origin of replication

have multiple on each linear chromosome

AT-rich → easier to separate the two DNA strands because only 2 hydrogen bonds compared tot hat of CG

eukaryotic origin of replication - histone modification

H4K20me2 marks chromatin regions → origin recognition complex binds

origin recognition complex - DNA replication steps

1. ORC binds to the origin via H4K20me2 recognition

2. ORC recruits DNA helicase enzyme → binds to ORC to complete pre-replicative complex

3. after S phase begins, S-Cdk phosphorylates many targets associated with DNA synthesis

4. DNA polymerase is loaded → two replication forks head off in opposite directions

DNA-replication steps - what targets are phosphorylation by S-Cdk

helicase → activated and melts AT rich area

ORC → deactivated to prevent recruitment of another helicase and synthesis of another DNA copy before next cell cycle

DNA replication - cause of telomere shortening

no primer for okazaki fragment at last part of chromosome on lagging strand can be created

single-stranded overhand removed by exonuclease

each cell cycle shortens chromosome

telomeres - structure

consists of tandem repeats of the sequence GGGTTA and proteins

3’ overhand forms t-loop to exchange with strands → proteins hold structure together

chromosomes lacking telomeres

unstable and may be susceptible to chromosomal rearrangements → fusion

telomerase - purpose

ribonucleoprotein that elongates telomere sequences

telomerase - structure

RNA portion has sequence complementary to telomere repeat GGGTTA

protein component (TERT) has reverse transcriptase activity

telomerase - steps to elongate telomere (5)

1. Telomerase binds to 3' flanking end of telomere that is complementary to telomerase RNA

2. Bases added to 3' overhanging strand using RNA as template by TERT reverse transcriptase

3. Telomerase relocates

4. Repeat of second step

5. DNA polymerase complements lagging strand

consequence of loss of telomeres - DNA replication

causes cellular senescence → cells stop dividing

telomere length correlates with age

Werner syndrome - telomeres

mutations to WRN (protein invovled in telomere CAP structure) causes shorter telomeres and premature ageing

centric region of centromere

consists of tandem repeats of 171bp sequence → alpha-satellite repeat

pericentric regions flank the centric region → often rich in LINEs and SINEs

chromosomal abberations (def)

changes in structure or number of chromosomes resulting in missing, extra or irregualr DNA segments

reciprocal translocations not usually an issue assuming translocation doesn’t occur within a gene → all genes still there and not duplicated

chromosomal aberrations - cause

can be issues with centromeres and translocations due to inappropriate crossing-over during meiosis

chromosomal aberrations - down syndrome cause (3)

extra third copy of chromosome 21

most cases due to meiotic non-disjunction → failure of homologous chromosomes or sister chromatids to separate during meiosis

2-3% due to Robertsonian translocation

chromosomal aberrations - down syndrome characteristics (3)

physical growth delays

characteristic facial features

mild/ moderate intellectual disability

chromosomal aberrations - Robertsonian translocation

two chromosomes joining at the centromere region

can occur between acrocentric chromosomes → most common between 13 and 14

chromosomal aberrations - Robertsonian translocation (effect)

short arm of acrocentric chromosomes do not contain any essential genes but contain tRNA and rRNA present in multiple copies

if crossing over occurs at centromere, chromosomes join and short arm lost → not much of an issue

can lead to trisomy in offspring

chromosomal aberrations - acrocentric chromosomes (5 chromosomes)

chromosomes in which centromere is located close to the end of the chromosome

13, 14, 15, 21, 22

mRNA role

codes for proteins

rRNA role

forms basic structure of ribosome and catalyses protein synthesis

tRNA role

central to protein synthesis as adaptors between mRNA and amino acids

snRNA role

function in variety of nuclear processes including splicing of pre-mRNA

RNA polymerase of prokaryotes

single RNA polymerase

RNA polymerase of prokaryotes - structure

core enzyme responsible for polymerase composed of 5 subunits → alpha1, alpha2, beta, beta', omega

sigma factor only needed to initiate transcription

core enzyme + sigma factor = holoenzyme

RNA polymerase of eukaryotes (3)

RNA pol I → rRNA

RNA pol II → mRNA

RNA pol III → tRNA

Prokaryotic transcription initiation (4)

1. Sigma factor binds to sigma binding sites in promotor region of DNA via complementary base pairing

2. Once bound, sigma factor recruits core enzyme to form holoenzyme

3. Core enzyme separates DNA strands and begins transcription of the template strand

4. Sigma factor is released

C terminal domain of RNA pol (structure)

consists of 52 tandem repeats of 7 amino acid motif

serine at positions 2 and 5 → can be phosphorylated by kinase

protein conservation meaning

same amino acids will produce similar if not sam proteins in all species

amino acid wobble position

usually third position in a codon

last position can be any nucleotide but gives same amino acid if first two are the same

ribosome subunits (2)

large 60s and small 40s to form 80s ribosome