CSF (week 4) Flashcards
describe the 3 steps of transcription
initiation; in which Polymerase II binds to the promoter region.
elongation; in which polymerase moves down the gene reading DNA
termination; polymerase detaches at the terminator region
what are initiation factors, and one example of them?
things that aid in the initiation of transcription, there are many but important example is TATA box, which is usually ~25 NT upstream from area of transcription starting
what is formed from RNA polymerase II and other transcription factors prior to transcription beginning?
a transcription initiation complex
template strand is read from _’ to _’ direction?
3’ to 5’
the resulting RNA strand is made in _’ to _’ direction?
5’ to 3’.
in elongation, DNA is unwound by ______, how many nucleotides at a time?
helices enzyme, 10-20 nts
how are adjacent NTs held together?
phosphodiester bonds
what signals the end of transcription (termination)?
polyadenylation signal
why is there less precision (fidelity) in transcription as opposed to DNA replication?
because transcription occurs many times for each individual gene. if one protein e.g is a bit messed up, consequences are much lower than if the recipe for it (DNA) is messed up.
what is the order of mRNA processing?
capping, tailing, splicing
what does capping consist of
a modified guanine nucleotide cap is added to the 5’ end
what is a spliceosome made of
proteins and small RNAs (called sRNA)
is an exon kept or removed in processed RNA
kept
describe an UTR
untranslated region. RNA sequences at the 3’ and 5’ end of mRNA that are transcribed but not translated, important in other ways e.g initiation and regulation.
what does splicing consist of
at the spliceosome in the nucleus, introns are removed from the RNA and exons are joined together to form mature mRNA
what is an important concept for protein synthesis that occurs during splicing?
alternative splicing. one section of mRNA could be spliced many different ways, allowing for one DNA/pre mRNA sequence to code for many different potential protein products.
what does tailing consist of
a poly-A (series of adenine nucleotides) tail is added to the 3’ end of the RNA
two types of bonds involved in translation
hydrogen bonding of the tRNA anti-codons to mRNA codons, peptide bonding between adjacent peptides as they are brought to the PP chain by tRNA
name and describe the purpose for each ‘site’ in a ribosome
A - site for next tRNA to be read to dock
P - site for currently read tRNA
E - exit site for read tRNA
describe the initiation step of translation
initiation; (small unit) of ribosome with Met tRNA bound to it binds to the 5’ capped end of mRNA. small unit scans downstream for AUG start codon. large ribosomal unit binds on top, completing translation initiation complex.
what is the purpose and structure of a poly-A tail
it is made up of 50-250 adenine nucleotides. thought to be important for stabilising the fragile RNA and exporting it out of the nucleus for translation.
what binds to the ribosome first - tRNA or mRNA?
the tRNA anti-codon, always carrying Met amino acid
describe the elongation phase of translation
codon recognition, in which complimentary tRNA anti-codons bind mRNA codons bringing AAs with them.
peptide bonding, in which the large ribosomal subunit triggers peptide bonds to form between AAs.
translocation, in which tRNA shuffles/moves down sites, releasing the read tRNA from the E site.
what is required in all 3 steps of translation?
GTP
describe the termination phase of translation
ribosome reaches a stop codon. a release factor binds to the A site in place of tRNA, causing the bond between peptide and tRNA in P-site to be hydrolysed, and finished PP chain is released. remaining components at ribosome dissociate, require hydrolysis of GTP.
what happens to used ribosomal units?
they are reused
why is gene expression controlled? (long answer)
to achieve the right things (proteins typically) in the right place at the right time. e.g more frequent and widespread transcription housekeeping genes, and less of hyper-specific genes, which may only be transcribed in response to stimuli.
what aspect of an amino acid differentiates it and determines its function?
the R’ side group
what does the ‘primary structure’ refer to
the base form of the completed polypeptide chain - before folding and modification
what are polypeptide bonds?
strong covalent bonds
what direction is RNA read in?
5’ to 3’
what are the C and N terminus, and what end of the mRNA are they each on?
N = amino end = 5’
C = carboxyl end = 3’
when does a primary structure begin to form a secondary structure?
immediately after leaving the ribosome
where would a protein be translated if it is destined to be in a vesicle?
ate a fixed ribosome in the RER, as vesicle = endomembrane system
describe how a protein would be directed to the RER if it needs to be translated there?
a signal peptide on the N terminus will be bound by an SRP floating in the cytosol. this directs the ribosome and PP chain to the RER, docks to an SRP receptor in the RER membrane, allowing translation of PP chain to be completed into the RER
where do all proteins begin translation?
free ribosomes in the cytosol
what are post-translational modifications, where do they take place?
modifications to a folded protein that are necessary to allow it to function/activate it. occur at area appropriate to where they will function, e.f phosphorylation in the cytosol.
what might a post-translational modification do
- regulate activity
- affect interactaction w other molecules
- determine protein location
what happens in G1 phase
cellular activities, organelles are duplicated for division
what happens in S phase
DNA is replicated
what does a signal-cleaving enzyme do
cut off the signal peptide on a polypeptide chain after it has been directed to the RER
what happens in G2 phase
preparation for division, e.g gathering of reactants, production of related proteins, replication of centrosomes.
what phases does interphase consist of
G1, S, G2 (all except M)
what is a germline cell, what doesn’t occur at them?
gametic cells and the stem cells they develop form. no mitosis.
what is a tetrad
4 chromosomes (2 homologous pairs of sister chromatids)
what happens in prophase (meiosis and mitosis!)
chromosomes condense, spindle fibres form, nuclear envelope disintegrates (in late prophase). synapsis and crossing over in meoisis I.
what is checked at G1 checkpoint? what is following action?
is cell undamaged
does it have correct size and nutrition
are appropriate signals present.
no -> go to G0. yes -> continue.
what is checked at M checkpoint?
what happens in metaphase (meiosis and mitosis!)
chromosomes line up at central plate, spindle fibres attach to centromeres. independent assortment in meiosis I
what is G0?
like a ‘pause’ state - a resting active state of no further division for cells who exit cell cycle after G1 checkpoint. can be a temporary or permanent state, neurons for example stay here forever.
what happens in telephase
nuclear envelopes reform around each new set of DNA
what happens in anaphase (meiosis and mitosis!)
spindle fibres pull apart:
sister chromatids (in mitosis and meiosis II)
homologous pairs of chromatids (in meiosis I)
what do different spindle fibres do in anaphase?
some shorten pulling the chromatids, ad some lengthen to push apart/separate the two cells for division
what are spindles fibres made of?
tubulin microtubules
what is crossing over
homologous chromosomes exchange some genetic material at points called chiasmata after synapsis in meiosis I
what does M checkpoint do/check
avoid improper chromosome division by checking that spindle fibre attachment is appropriate.
what are kinetochores
protein complexes at centrosomes for connection of kinetochore (shortening/separating) microtubules
what is the cleavage furrow
contractile indentation allowing cells to separate in telophase/cytokinesis
what are the three sources of variation in gametes/humans?
- crossing over
- independent assortment
- fusing of gametes
a mutation on which end of the DNA strand is more likely to have effect?
3’ end of DNA, therefore 5’ end of mRNA
what is a reason that mutations may not have an effect?
because we have two copies of DNA for each gene, 1 from each parent. if only one is mutated, the non-mutated gene products produced may be sufficient for function.
what area of the body would a mutation in a somatic cell affect?
only the individual cell at first, and then broadening to local effects as all cells originating from mutated cell will have the mutated DNA.
what type of mutation can cause a frameshift, why are these significant?
insertions/deletions. every codon/AA downstream of the mutation is affected.
when would a ‘truncated protein’ arise, what types of mutations?
if translation was stopped (early stop codon coded for) early due to a mutation.
- nonsense
- frameshift
- mutation affecting ribosome, spliceosome, etc.
what is sickle cell anemia, what are its consequences?
recessive inherited disorder resulting from mutation, causing abnormally shaped red blood cells which are inflexible and weak. leads to blockages in capillaries and reduced blood/oxygen supply.
when would an indel not cause a frameshift?
if 3 (or multiple of 3) bases were inserted/ deleted.
why is G2 checkpoint so important?
because it can stop a damaged cell from dividing
explain an MPF and its components
maturation promoting factor. consists of a cyclin and CDK. initiates mitosis/key to G2 checkpoint.
cyclins are proteins fluctuating as needed throughout the cell cycle.
CDKs are cyclin dependent kinases, which are activated when bound to a
how does an MPF initiate mitosis
phosphorylates other proteins initiating mitosis
which components of an MPF are reused/not reused
cyclin ISN’T reused, is degraded and remade each cycle. CDKs are reused, can be activated and deactivated as needed.
‘stop’ molecules normally: (sometimes known as…)
keep cell proliferation in check. (brakes)
‘go’ molecules normally:
stimulate cell proliferation. (accelerator)
what could happen if a mutation arose in a stop/go molecule?
G2 checkpoint won’t work
-> cell cycle proceeds where it shouldn’t
-> uncontrolled cell growth
-> tumor
two manners of mutation acquisition, and respective outreach:
genetic - inherited from parents, or de novo, meaning mutation in egg/zygote. affects all cells, as all cells arise from fused gametes.
acquired - somatic cell during life is mutated due to exposure to mutagens. affect local cells, as only ones arising from the mutated cell will have the mutated DNA.
what is a proto-oncogene
a go gene which stimulates cell division. if mutated, could cause cancer.
what is Ras, how does it function, how could it cause cancer
it is a GTPase enzyme involved in cell signalling to trigger cell division. if mutated, could over-activate signalling pathway, overactivate transcription factor causing over expression of protein and uncontrolled cell division.
what is tumor suppressor gene
normally keep cell proliferation in check (stop molecules/brake) if mutated, could cause cancer.
what is gene p53, what does it do, how could it cause cancer
a tumor suppressor gene that controls growth of damaged cells by repairing damaged DNA, or halting cycle and signalling apoptosis if DNA is damaged beyond repair. if mutated p53 gene, p53 protein is also mutated, therefore there is no control over damaged cells replicating.
does cancer result from one mutation; why or why not.
no.
typically requires a compounding series of mutations to create a malignant cell.
what is the name of the molecule that reloads amino acids to tRNA in the cytoplasm?
aminoacyl-tRNA synthetase
