patrick (L11) Flashcards by myriam Unknown

organelles within the cell that contain dna

nucleu
mitochondria
chloroplasts (in plant cells)

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size of human genome

Human genome has 3.2 Gb of bases
A lot of genome information in our cells is not gene encoding

dna per human cell is 2m long, and the nucleus diameter is 10 micrometers –> so the helix is packaged by histones and further packaged into chromosomes

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structure of chromatin

euakryotic chroomosomes are approximately equal amounts of dna andprotein
protein both packages dna and regulates gene expression
major protein component of chromatin are histones

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state of the chromatin in interphase stage

10% active euchromatin - transcribed
80% inactive euchromatin - not transcribed
10% heterochromatin - condensed and not transcribed

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difference between heterochromatin and echromatin during interphase

euchromatin decondenses during interphase - most expressed sequences

heterochromatin remains condensed, few expressed sequences

heterochromatin contains elements essential to chromosome stability and inheritance

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structure and function of histones

small (10-13kD)
basic and highly conserved
form a solenoid structure with dna wound around the core of the histone protein
nucleosome contains two molecules of each H2A, H2B, H3 and H4 (and one H1)

Histones have a positive charge because the dna has a negative charge (for attraction)

the handshake conformation is formed from the interaction between H3-H4 tetramer and 2 H2A-H2B dimers
HISTONES HAVE IMPORTANT N-TERMINAL ENDS

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nucleosomes

the packaged state of DNA wound around 8 histone proteins
1st stage - dna wrapped around hsitone protein (10nm fibre)
2nd stage - additional compact packaging that is condensed (30nm fibre)

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DNA PACKAGING MECHANISM

LOOK AT L11 S13

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histone modification

histones are modified at their tails
N terminal is 19 to 39 residues long
H2A and B also C terminus

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core histone tails’ modifications

acetylation
methylation
phosphorylation
ubiquitylation
--> HISTONE CODE?

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histone code

The amino acids are found on histone tails
Depending on what amino acids we find there, they can be acetylated methylated phosphorylated or ubiquitylated
Depending on how the histone trails were modified, then the chromosome is more or less pegged
it’s called a code because we can predict which proteins are modified and how
We now have a dataset to tell us which modification will open or close the dna to allow or prevent transcription

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Sir proteins function and modification

Sir proteins sit on the histones and aggregate to each other to package the dna very very tightly

hypoacetylation leads to Sir protein binding and closed chromatin

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non-histone proteins

equal abundance than histones
mostly unknown
include transcription and replication factors
high mobility group HMG proteins implicated in global regulation of transcription

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chromosome regions

telomere
origin of replication
kinetochore proteins
centromere
origin of replication
telomere

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ORIGINS OF REPLICATION MECHANISM

L11 S23-24

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yeast’s centromeres

We have a sequence specific dna binding protein that is part of the kinetochore complex which binds to the microtubulins
pulls the 2 chromatids in separate ways
(LOOK AT DIAGRAM IN L11 S26)

organisation of human centromere

more complex mechanism than yeast (obvy)

fundamental importance in chromosome partitioning, site of kinetochore assembly
contain nucleosomes with variant histone protein
assembled on long regions of highly repetitive dna

LOOK AT DIAGRAM IN L11 S27

telomere sequences

they are repetitive
vary in size and repeat number
vertebrate sequence is TTAGGG repeated over several kb
yeast telomeres are several hundred base pairs long

eukaryotic problem of telomere replication

dna synthesis always goes 5’ to 3’ BUT dna is read 3’ to 5’
so RNA primer near the end of the chromosome on the lagging strand cant be replaced with dna since dna polymerase must add to a primer sequence

in replication, primer is reoved and gaps are filled by dna ligase
So the ends of the chromosome with each replication will be shortened because the primer sequence could not be replicated

telomerase

Telomerases use the overhang to generate additional dna (blue nucleotide sequence) used to generate more dna on the overhang and the synthesis regestrates the DNA sequence
This gives us enough space for the telomerase to bind to the dna

LOOK AT DIAGRAM OF MECHANISM L11 S30

telomere rejuvenation

We can take differentiated cells and convert them to embryonic stem cells again
with this conversion the machinery adds a lot of telomeres to this once differentiated cell nuclei - this is telomere rejuvenation
All of our cells can revert to younger cells
We can supress proteins involved in protecting these telomeres to stop the production of telomeres for them to shrink even faster

PREMATURE AGEING
WERNER SYNDROME

what does eukaryotic dna code for?

genes that encode proteins
non coding dna
repetitive dna

explain the different genome sizes

as genomes get larger, an increasing proportion of the dna is non coding and repetitive

human genes STATS

in gene dense regions - 1 gene per 20kb
in gene poor regions 1 gene per 200kb
average gene size (including introns) - 10 to 15 kb, but varies hugely
2 copies of each gene is called alleles

eukaryotic genomes contain families of related genes

protein coding genes have relatives with which they share common ancestry genes exist in families and super families within a genome, families can be disperses or clustered maintenance of clusters implies functional coordination --> If they sit in the same cluster of a chromosome, then we may think that they be function-related and work together so if we have a gene family then that means that they originated from the same gene in the beginning

the globiin gene family

example of the creation of new genes by duplication during evolution ``` ancestral globin gene DUPLICATION into 2 globin genes DIVERGENCE into hemoglobin gene and myoglobin gene due to mutations in different places ```

human globin gene clusters - 2 types

alpha cluster, chromosome 16 (40kb) beta cluster, chromosome 11 (30kb) During evolution in human genome, we have the development of different protein genes (alpha beta etc of the same protei )

developmental changes in globin expression as humans grow up

Level of Hg gene can be found in different developmental stages In pregnancy, the alpha chain is up and stays up throughout its lifetime The gamma chain stays up in the fetal blood but decreases again after birth, instead, the beta chain increases Adult Hg is composed of alpha and beta chains but fetal is only alpha and gamma This is because fetal Hg has a greater affinity to oxygen this shows why the variation of gene families helps the development and evolution of complex species like us

eukaryotic genomes can be characterised by reassociation kinetics

this is a measure to predict the number of genes per genome (pregenome sequencing era) 1. highly repetitive dna - high copy number sequences, repetitive very short sequences (<100bp) 2. moderately repetitive dna - moderate short sequences (repeated 10 to 10 000 times in genomes) like histones, ribosomal genes and transposons 3. non repetitive dna - unique sequences, genes, gene families (repetitive DNA sequences were once thought to be junk DNA but it actually a source of generating new genes)

composition of human genome

trasnposons, genes, repeated sequences, unique sequences only 19% of our genome encodes proteins (is genes) a lot of our genome consists of inactive viral DNA which may also contributes to the evolution transposons are DNA elements that can cleave genes and move them around or insert or delete LOOK AT DIAGRAM L11 S43

who discovered the first evidence for eukaryotic transposable elements from maize?

barbara mcclintock studied corn colours change in pigmentation during development, variegation results in sector of tissue with altered phenotype proposed due to rearrangement of genome unstable alleles all of these corn variations come from the same homozygous parent so they should show the same colours Barbara realised that it is because parts of the DNA sequences move around to change gene expression

patrick (L11) Flashcards

eukaryotic genome organisation