Molecular Biology MCQ Flashcards
chromatin structure regulates gene expression by?
determining promoter accessibility
? + ? =chromatin
DNA + Protein = Chromatin
what are histones
small basic proteins with net positive charge to facilitate binding to DNA
what are non-histones
often negatively charged, and though to vbind to positvely charged histones. Non histone content varies widley.
what are the 4 core histones?
H2A, H2B, H3, H4
? + ? = nucleosome
2 of each histone + DNA = nucleosome
how many bp DNA is wrapped around the core histones in a nucleosome
147bp DNA
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
how many bp DNA wrapped around each nucleosome?
how many bp DNA wrapped around each linker region?
- 147bp
- more variable, up to around 80bp
DNA binding to to nucleosome must be ?
sequence independent and reversible
how many hydrogen bonds are there between Histons and DNA?
Where are most of these?
are these base discriminatory?
~40H bonds
Phosphodiester backbone
No
what does H1 do?
tightens DNA wrappng around chromosomes
fomration of 30nm fibre also requires what?
core histone amino tails often ?
- histone amino-terminal tails
- modified
histone tails =
absolutely critical for controlling/regulating the compaction of chromatin
genes in 30nm fibre = more or less accessbile than genes in 10nm fibre
30nm = less accessible
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
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
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
what the first mechanism responsible for regulation of chromatin structure
nucleosome/chromatin remodelling complexes
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
what the second and third mechanisms responsible for regulation of chromatin structure
nucleosome positioning
- protein dependent mucleosome postiioning
- DNA dependent nucleosome positioning
what is the fourth mechanism responsible for regulation of chromatin structure
Histone tail modification and chromatin accessibility
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
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
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.
