Chromatin and Genomes Flashcards
1
Q
Problems With Having a Large Genome
A
-have to compromise between saving space and storing DNA and keeping it selectively available for use
2
Q
DNA Structure Through Cell Phases
A
- DNA structure is dynamic
- accessibility of DNA varies through cell phases
- Metaphase Chromosomes have maximum condensation of DNA to facilitate amplification
- Interphase nucleus has the most spread out and accessible DNA for transcription
3
Q
Chromatin
A
- DNA and protein complexes
- allows genetic information to be stored and read
4
Q
Euchromatin
A
genetic region containing genes that are used ( e.g. for transcription), a region that is opened up extensively
5
Q
Heterochromatin
A
-genetic region containing genes that appear not to be use, highly condensed
6
Q
What direction is DNA read in?
A
5’ to 3’ on the top strand
7
Q
Pyrimadines
A
cytosine
thyamine
uracil
8
Q
Purines
A
andenine
guanine
9
Q
Nucleotide
A
pentose sugar
nitrogenous base
phosphate group
10
Q
Beads on a String
A
- After initial unpacking (dissolving in various ions)
- DNA appears as a strand with beads on it
- The ‘beads’ are nucleosomes
11
Q
Nucleosomes
A
- 2 loops of DNA wrapped around 8 histone molecules
- the octameric histone core is made up of 2xH2A, 2xH2B, 2xH3 and 2xH4
- H3 and H4 form heterodimers
- H2A and H2B form heterodimers
- histone protein tails stick out from the nucleosome complex allowing it to interact with the outside
- enzymes can interact with and modify the tails and other enzymes can detect these signals
12
Q
Condensed Chromatin Solenoid
A
-6 nucleosomes held together in a circle by six histone 1 molecules, one inbetween each pair of nucleosomes
13
Q
Protein Scaffold
A
- protein complexes on the inner side of the nuclear membrane
- attach to certain regions of chromatin
- forming a 3D network
14
Q
Levels of Chromatin Packing
A
- DNA double helix (2nm)
- nucleosomes (10nm)
- soleoids (30nm)
- attachment to protein scaffold and folding of the chain (loops 300nm long)
- metaphase chromosome (1400nm)
15
Q
Organisation and Territories
A
- interphase chromosomes have preferred positions in the nucleus
- genes have specific positions within interphase chromosomes called territories
- there is very limited intermingling of chromatin between chromosome territories
- if a gene is moved to a different chromosome it is often found that it doesn’t work
16
Q
Gene -> Phenotype
A
- chromatin
- DNA unpacking involving DNA demethylation and histone acetylation
- DNA
- transcription
- RNA with introns
- RNA processing
- mRNA
- transport out of nucleus
- translation
- polypeptide
17
Q
Which genes are found in condensed chromatin?
A
inactive genes
18
Q
Which genes are found in open chromatin?
A
active genes
19
Q
Opportunities for Gene Regulation
A
- local changes in accessibility of genes prevent certain proteins from being transcribed in certain cells
- chromosome packing correlates with gene expression
20
Q
What do genes do?
A
- genes don’t just code for proteins
- only ~1% of the human genome codes for proteins
- the other 99% is pseudogenes, non-functional copies of genes
- these regions are created when genes are transcribed to RNA but the RNA is then reverse transcribed to cDNA which is integrated into the genome
- at least 75% of the genome is transcribed but much of the function of these RNAs is unknown
21
Q
What are the two types of repetitive sequences?
A
- tandem repetitive sequences
- dispersed repetitive sequences
22
Q
Cell Response to Repetitiveness in the Genome
A
- cells can sense repetitiveness
- repetitive regions are often condensed to prevent expression
23
Q
Tandem Repetitive Sequences
A
- repeats aligned at one locus
- e.g. telomeres, centromeres
24
Q
Dispersed Repetitive Sequences
A
- regions that are repeated but the repeats are spread throughout the genome
- e.g. transposons, retrotransposons
25
Transposable Elements
- DNA elements that can migrate or amplify
| - usually controlled by chromatin condensation
26
Retrotransposable Elements
- DNA elements that can migrate or amplify via RNA
| - usually controlled by chromatin condensation
27
Transposons
- a transposon is a sequence of DNA that has repeats at the start and end of the sequence
- the repeats at the start and end may be inverted
- a transposon is able to migrate from its existing site to a target site
- transposons accumulate in the genome over the organisms lifetime
28
Retrotransposons
- the same as a transposon but migrates using RNA
- retrotransposon is transcribed to RNA
- RNA is reverse transcribed to cDNA
- this cDNA copy is inserted at a target site elsewhere in the genome
- we accumulate more retrotransposons than transposons as retrotransposons replicate each time they migrate
- a retrovirus that has lost its gag and env regions
29
Long Terminal Repeat
- LTR
| - signals for genome to try and inactivate retroviruses when they integrate into the genome
30
Retrovirus
- sequence of DNA inserted into our genome by a virus
- consists of a long tandem repeat at each end, and three coding regions, gag, pol and env
- gag codes for 2 capsid proteins
- pol encodes a multi function protein with reverse transcriptase function, proteinase and integrase activity
- env encodes envelope proteins that allow the virus to interact with host cells
31
Retroposon
- retrovirus that has lost its long terminal repeats and only has short ones
- SINEs (short interspersed elements) are retroposons without reverse transcriptase, ~100-400bp
- LINEs (long interspersed elements) are retroposons that have reverse transcriptase, ~6kbp
32
DNA Replication
- many origins of replication long the DNA strand where polymerase can start synthesis of a second strand
- all of these regions are joined up until only the ends of the strands are left
- on the top strand (5' to 3') the polymerase can just continue until it falls off
- but on the bottom strand the polymerse has to start at the end of the strand as it can only go 5' to 3'
- the polymerase has to have a primer it sits on before beginning replication so there is always a region right at the end of the strand that it cant synthesise
- telomerase carries a dhort RNA primer which it uses as a template to synthesise cDNA using reverse transcriptase
- this cDNA sequence is attached to the end of the chromosome one nucleotide at a time
33
Telomeres
- more than 1000 tandem repeats of the same short sequence (TTAGGG in humans) at the end of every chromosome
- there is a special enzyme, telomerase that can maintain and replicate these ends
- telomerase is functional in embryonic stem cells and cancer cells but not in most somatic cells
- this means that telomeres (and also chromosomes) shrink with every replication
34
Centromere
- part of the chromosome to which the spindle attaches
- highly condensed sequence
- centromeres don't share a common sequence, the only requirement is that the sequence is highly repetitive
- 240kbp - several Mbp long
- each chromosome has 1 centromere
35
Making a Centromere
- the centromere is just the most condensed region on a chromosome, wherever that happens to be
- by removing some repeats from the current centromere and moving them elsewhere to make another region the most repetitive, it is possible to move the centromere
36
Interphase
- Growth 1
- Synthesis
- Growth 2
37
Miotic Phase
Mitosis
| Cytokinesis
38
Chromosome Duplication
-produces two sister chromatids joined together at their centromeres
39
Mitosis
| Stages
- Prophase
- Prometaphase
- Metaphase
- Anaphase
- Telophase
40
Mitosis
| Prophase
- chromatin condenses
| - spindle forms
41
Mitosis
| Prometaphase
- spindle poles reach fixed positions
| - nuclear envelope breaks down
42
Mitosis
| Metaphase
-alignment of sister chromatids on the metaphase plate
43
Mitosis
| Anaphase
-separation of sister chromatids by spindle
44
Mitosis
| Telophase
- one copy of each chromatid at each pole
| - reformation of the nuclear envelope
45
Nuclear Envelope During Mitosis
- in metaphase phosphorylation of lamins occurs leading to the break down of the nuclear envelope
- in anaphase dephosphorylation of the lamins occurs leading to reformation of the scaffold
- in early telophase fragments of the nuclear envelope start collecting around the DNA
- in late telophase the fragments fuse reforming the nuclear envelope
46
Lamins
- major architectural proteins lining the inside of the nuclear membrane
- provides mechanical stability and platform for binding of proteins and chromatin
47
Cell Division
| Plants vs Animals
- animals - cleavage furrow
| - plants - cell plate formation
48
Bacterial DNA Replication
- only one chromosome, a single loop of DNA
- one origin of replication
- bacterial binary fission
49
Nucleoid
the place in a bacterial cell where the DNA is held
50
Control of Cell Division
| Contact Inhibition
- cells divide until they come into contact with another cell
- then division stops
51
Contact Inhibition
| Healthy Cells vs Cancer Cells
- when normal cells are grown in a petri dish, they grow until a monolayer is formed
- a one cell thick layer across the bottom of the dish
- when cancer cells are grown in the petri dish, they keep growing forming many layers
52
Cancer
- uncontrolled growth of cells normally regulated
| - loss of cell cycle control
53
Susceptibility to Cancer
- one defective copy of an autosomal gene does not normally have consequences as there is a normal copy on the other chromosome
- but if the normal gene is lost or inactivated then the only source of information is the mutant
- mutations that increase susceptibility to cancer are acquired considerably after fertilisation i.e. in somatic cells
- low frequency, 1 in 10^8
54
BRCA1 and Breast Cancer
- on mutant allele gives a 60% chance of breast cancer by the age of 50
- normal alleles give a 2% chance of breast cancer by the age of 50
- BRAC1 is probably involved in DNA repair
55
Purpose of Recombination
- increased genetic diversity
- repair damage
- control gene expression
56
Recombination and Crossing Over
- in prophase sister chromatids cross over at points called chiasmata
- they exchange genetic information
57
Mutation
| Definition
-permanent change in a gene
58
What are the types of mutation?
- point mutations
| - insertions / deletions
59
Common Mutagens
- free radicals in oxygen
- cigarette smoke
- 5-fluororaol
- x rays
- UV rays
- cisplatin
60
Repair of Errors
- proof reading by exonucleases during replication
- reversal of damage
- repair of damage
61
Sickle Cell Anaemia
- caused by a single mutation
- an individual with two sickled copies is unlikely to survive
- but a carrier is more likely to survive malaria
- so the sickle allele persists
62
Sexual Life Cycle
alternation of haploid and diploid stages
63
At what life cycle stage do higher eukaryotes replicate by mitosis?
diploid stages
64
When in their life cycle are animals haploid?
only during sexual stages
65
Lower Eukaryote Life Cycles and Replication
- some lower eukaryotes only multiply during haploid stages of life cycle
- spend much of life cycle as haploid
- e.g. most fungi, some algae, protozoa
66
When in their life cycle do plants replicate?
during both haploid and diploid stages
67
Bacteria Asexual Reproduction
- very rapid
- clonal
- not good for diversity
68
Benefits of Sexual Reprouction
- competitive advantage in an unpredictable environment
- if parent produces many offspring with a wide variety of gene combinations then there is a better chance that at least one of the offspring having the assortment of features necessary for survival
- spread and sharing of beneficial mutations is possible
69
Meiosis 1
| Purpose
-reduces diploid cell to two haploid cells with duplicated chromosomes
70
Synapsis
pairing of two homologous chromosomes
71
What are the two types of cell death?
- Necrosis
| - apoptosis / programed cell death
72
Necrosis
-premature death of cells due to injury, toxins, inflammation or infection with cell lysis and release of intracellular content
73
Apoptosis
- aka programed cell death
- suicide activation
- DNA fragmentation
- cytoplasm shrinkage
- membrane changes without lysis or damage to neighbouring cells
