stem cells have a unique chromatin confiuration: - nuclues larger/smaller? - more/less relaxed chromatin formation? - distinctive pattern of histon tail ?

- larger - more relaxed, (less heterochromatin) - methylation

Molecular Biology MCQ Flashcards by Max Mordente

chromatin structure regulates gene expression by?

determining promoter accessibility

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? + ? =chromatin

DNA + Protein = Chromatin

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what are histones

small basic proteins with net positive charge to facilitate binding to DNA

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what are non-histones

often negatively charged, and though to vbind to positvely charged histones. Non histone content varies widley.

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what are the 4 core histones?

H2A, H2B, H3, H4

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? + ? = nucleosome

2 of each histone + DNA = nucleosome

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how many bp DNA is wrapped around the core histones in a nucleosome

147bp DNA

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2 of each core histone + DNA forms ‘beads on string’ (?nm chromatin fibers), compacts DNA approximately 6 fold

After this, H1 binds to linker DNA to condense further (?nm chromatin fibers), compacts DNA approximately 40 fold

10nm

30nm

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how many bp DNA wrapped around each nucleosome?

how many bp DNA wrapped around each linker region?

147bp
more variable, up to around 80bp

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DNA binding to to nucleosome must be ?

sequence independent and reversible

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how many hydrogen bonds are there between Histons and DNA?

Where are most of these?

are these base discriminatory?

~40H bonds

Phosphodiester backbone

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what does H1 do?

tightens DNA wrappng around chromosomes

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fomration of 30nm fibre also requires what?

core histone amino tails often ?

histone amino-terminal tails
modified

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histone tails =

absolutely critical for controlling/regulating the compaction of chromatin

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genes in 30nm fibre = more or less accessbile than genes in 10nm fibre

30nm = less accessible

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why is chromosome packaging important?

5 reasons

allows oragainsiation and compaction of genetic material
in eukaryotes, determines accessibility of DNA
way of switching gene expression on or off
involved in development, differentaition, and cellular response to envrionment
also epigenenetics

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why is it important to be able to regulate gene expression?

to achieve cellular differentiation
so cells can perfoorm different functions
during development
responding to envronmental change

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explain the basic principle of how chromatin structure influences wheter a gene is expressed

-if DNA is tightly compacted it cant be accessed by transcripton factors

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what the first mechanism responsible for regulation of chromatin structure

nucleosome/chromatin remodelling complexes

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how do nucleosome/chromatin remodelling complexes work?

What are the 2 mechansim by which they work?

bind to histones and translocate DNA relative to histones

a) sliding
b) transfer

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what the second and third mechanisms responsible for regulation of chromatin structure

nucleosome positioning

protein dependent mucleosome postiioning
DNA dependent nucleosome positioning

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what is the fourth mechanism responsible for regulation of chromatin structure

Histone tail modification and chromatin accessibility

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stem cells have a unique chromatin confiuration:

nuclues larger/smaller?
more/less relaxed chromatin formation?
distinctive pattern of histon tail ?

larger
more relaxed, (less heterochromatin)
methylation

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high levels of gene expression are associated with:

histone acetylation or de-acetylation

histone acetylation

as additon of negative acetyl group weakens postive charge of hsiton, weakening/loosening binding between histone and DNA

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what happens in DNA methylation? What does DNA methylation add?

- methyl group added to cytosine C5 - covalent modificaiton of DNA - adds info not encoded in DNA sequence

does DNA methylation interfere with DNA pairing?

-no

where is the the methyl group positioned in DNA methylation

- cytosine C5 - methyl group postioned in major groove of DNA

name the 6 functions of DNA methylation

- transcriptional gene silencing - chromatin compaction - x chromosome inactivation (females) - gene stability - genome defense - supression of homologous recombination between repeats

DNA methylation regulates gene expression. In mammalian cells, promoter DNA methylation switches transcription on/off? how does DNA methylation inhibit gene expression? (2 different ways)

- on 1) first level, transcription factors cannot bind to methylated DNA 2) second level, proteins that recognise methylated DNA (e.g. MeCP2) recruit nuclesome remodelling proteins and histone modifiers e.g. HDAC

DNA methylation at ?/? also regulates gene expression?

enhancers/insulators

Abberant DNA methylation and chromatin strucvture can lead to

cancer

what condition can occur when proteins that recognise methylated DNA do not work porperly?

Rett Syndrome

what causes Rett's syndrome? -what does MeCP2 do?

- mutation in gene encoding MeCP2 (X-linked) - MeCP2 recognises methylated DNA -\> inhibits gene expression of target genes

define gene expression

process by which genetic info is used to make a gene product

1 genome encodes multiple cellular phenotypes how?

via differential gene expression

A cell selects which proteins it needs to make and how much by?

expressing different genes at different rates

what are the 6 stages of eukaryotic gene expression 1+2 = in nucleus 3-6 = in cytosol

1) transcriptional control (transcriptional regulation) 2) RNA processing control (post-transcriptional regulation) 3) RNA transport and localisation control 4) translational control 5) mRNA degradation control 6) Protein activity control

In transcription, whcih direction are ribonuceotides added one by one to replicate the DNA template strand

5' to 3'

what are the 4 nirogen bases in RNA

adenine, cytosine, uracil and guanine

what is the enzyme that makes a mRNA copy of DNA in eukaryotic cells

RNA polymerase II

synthesis of RNA from DNA occurs in which direction?

5' to 3' on the template strand

what would the sequence of the RNA strand transcribed from the DNA template CAGGCT be?

GUCCGA

Which of the following mRNA transcripts is the reverse complement of the DNA sequence 5’-CAGGCT-3’?

5’-AGCCUG-3’

what are trnscription factors

DNA binding proteins that control gene expression by binding to specific DNA sequences within a gene promoter region.

what are the 2 types of transcroption factors?

general (basal) transcription factors specific transcripton factors

what are General (basal) transcription factors?

required to help RNA polymerase attach to promoter region

what are specific transcription factors for?

can activate (turn up) or repress (turn down) transcription of particular genes

name 4 types of DNA binding protein

- homeodomain - zinc finger - leucine zipper - helix-loop-helix; HLH

whats TFIID

- largest of the general transcription factors - first factor required

what dpes TBP do?

binds to DNA using TATA box to postion TFIID near the transcription initiation site

describe 3 mechanisms by which repressors can work

a) competitive DNA binding b) masking hte activation surface c) direct interaction with the general transcription factors

insulators block?

activation by enhancers (activators)

which part(s) of a eukaryotic gene are transcribed?

exons and introns

General transcription factors bind to which type of DNA sequence?

Promoters

Transcriptional activator proteins bind to regions near a eukaryotic gene and allow

RNA polymerase to transcribe a gene.

Transcriptional repressors do what?

A.decrease gene expression levels through binding to silencers

Muscle cells are different to nerve cells mainly because

A.They express different genes

what is mature mRNA

mRNA after processing

what are the 2 functions of the 5' cap

- protects endof mRNA from degradation by nucleus - helps position mRNA correctly on ribosomes during protein synthesis

what does 3'polyadenylation (addition of polyA tail) do?

- Stabilises mRNA and prevents degradation - Allows mRNA to be exported from nucleus for translation - polyA tails can be added at alternative sites, to produce different transcripts from same gene

a gene must start and finish with an?

exon

what happens to introns post transcription

removed from primary transcript

what needs to happen to the exons and introns to make 'mature' mRNA

introns need to be spliced out and exons stuck together

important parts on the intron whcih allow the cell to know which bits to chop out are what?

donor site (GU) opposite end = acceptor site (AG)

splicing out mRNA is catalysed by?

spliceosome

spiceosome ocmposed of ?

snRNA (small nuclear RNAs) associated with proteins =small nuclear ribonucleoprotiens (snRNPs)

RNA polymerase II enables what?

simultaneous transcripton and porcessing of mRNA

what does alternative splicing allow?

one gene to encode multiple different proteins

what does alternative spllicing involve?

joining together of exons (and sometimes introns) in different combinations

what does alternative splicing increase?

vastly increases the coding potential of the genome

alternative splicing and what else can both be used to produce multiple different transcripts from the same gene

poly A tailing

what else can genes have that can be used to include different exons at the start of transript

alternative promoters

in tumour cells, what can happen in alternative pre-mRNA splicing to allow experession of particular mRNA transcripts that facilitate cancer?

- process can be 'highjacked' - mutations in cancer cells can also affect splicing

what 3 things happen in the processing of pre-mRNA

1) 5' capping 2) splicing 3) 3' polyadenylation

A eukaryotic primary RNA (pre-mRNA) transcript must be processed before it can ?

leave the nucleus

Pre-mRNA processing involves the?

addition of a 5’ cap, a poly A tail and splicing to remove introns and join exons together

Alternative poly adenylation (polyA) sites can enable?

different transcripts to be produced from same gene

Splicing is catalysed by the spliceosome, a complex of snRNAs and proteins. SR and hnRNP proteins also help?

identify exons and introns.

Alternative splicing and use of alternative promoters can result in

multiple different transcripts being produced from the same gene.