Genetics- Cormier Flashcards
What parts make up a nucleotide?
nitrogenous base, 5 carbon sugar, and a phosphate
Which NTs are purines?
Pure As Gold (2 rings)
-adenine and guanine
Which NTs are pyrimidines?
CUT the Py
-cytosine, thymine (DNA), uracil (RNA)
What is the difference between heterochromatin and euchromatin?
heterochromatin is wound tightly and not easily transcribed
euchromatin is easily and actively transcribed
How many pairs of chromosomes do humans have?
23 (homologous pair of 22 chromosomes and 1 pair of sex chromosomes)
What is ataxia?
disease, progressive deterioration of motor skills (1 normal and 1 aberrant chromosome 12 with extra piece from chromosome 4)
Do exons or introns become proteins?
exons, and only code about 1% of DNA
How is eukaryotic DNA organized?
histones (with lots of arginine and lysine) wrab DNA to make nucleosome which includes about 200 NT pairs of DNA
What are the names of histones involved in DNA organization?
2 H2A, 2 H2B, H3 and H4 are the histone core
-H1 is linker that joins DNA cores
What do HAT (histone acetyltransferase) enzymes do?
adds acetyl groups to histone tails, added charge loosens DNA to promote transcription
What do HDAC (histone de-acetyltransferase) enzymes do?
take acetyl groups off histone tails, silences DNA transcription and DNA compacts
How is eukaryotic DNA processed before leaving the nucleus?
5’ 7 methyl guanosine cap added, 3’ poly A tail, and introns spliced out
What subunits make up eukaryotic and prokaryotic ribosomes?
eukaryotic- 60S and 40S
prokaryotic- 50S and 30S
What size pieces of rRNA make up prokaryotic and eukaryotic ribosomes?
Prokaryotic (3 types): 5S, 23S, 16S
Eukaryotic (4 types): 5S, 5.8S, 18S, 28S
What are the distinguishing features of tRNA?
- attaches AA at 3’ end
- has 3’ to 5’ anti-codon
- cloverleaf structure
How does DNA replication work for prokaryotes?
DnaA binds at OriC (single point of origin)
-bidirectional replication (2 replication forks)
DnaB = helicase
DnaG = primase
DNA gyrase = like topoisomerase
In what direction is all DNA and RNA made?
always made in 5’ to 3’ direction (so template strand is read 3’ to 5’)
What are the main functions of Pol 1, Pol 2, and Pol 3? (prokaryotes)
Pol 1 = fill lagging strand gaps, remove RNA primer
Pol 2 = DNA repair
Pol 3 = DNA replication
Which parts of the cell cycle are part of interphase?
G1, S1, and G2 (M phase = mitosis, cell division)
What is the difference between topo1 and topo2?
topo1 = single strand breaks topo2 = double stranded break, target for cancer drugs
How does telomerase help the dividing cell?
adds back DNA at end of telomere where it’s lost during replication
-reverse transcriptase, adds 5 nucleotide repeating sequence
During transcription, what type of bond is formed between incoming nucleotides and complementary NTs on DNA template strand?
ester bonds
How do cis and trans regulatory sequences differ?
cis- same side of DNA strand
trans- act from afar
In bacteria, what binds to the promoter (TATA box) to associate the polymerase enzyme?
Sigma factor. It dissociates soon after transcription begins
In eukaryotes, what do pol 1, pol 2, and pol 3 usually transcribe?
Pol 1 = rRNA
Pol 2 = mRNA, miRNA, lincRNA
Pol 3 = small RNAs (tRNAs and 5S RNA)
How is transcription initiated in eukaryotes?
Pol 2 is main transcription factor
- TF2D binds TATA box and binds TF2A and TF2B
- other TFs and RNA pol assemble at promoter
- TF2H uses ATP to open double helix
What sequence is at each end of the intron for splicing?
5’ GU AG 3’ of intron gets spliced out
What structure forms as an intermediate in splicing?
lariat structure
What is the start codon, and what does it code?
methionine, AUG
What is “wobble”?
the 3rd BP on mRNA or 5’ side on tRNA can vary and still code same amino acid
Which end of the protein is made first and which end last?
Translation is from N-terminus to C- terminus (corresponds with 5’ to 3’)
What is the order of ribosome assembly on mRNA for eukaryotes?
initiator tRNA first loads on small ribosomal subunit with euk initiation factors
- small subunit scans mRNA for AUG
- IFs dissociate and large subunit binds
What are the 3 ribosomal sites?
E (exit)
P (where growing peptide chain attaches)
A (where tRNA binds codon)
How does translation initiate in prokaryotes?
at Shine Dalgarno sequence, small ribosomal subunit binds
What does the antibiotic tetracycline do?
blocks binding of amino-acyl tRNA to A site of ribosome
targets bacteria
What does the antibiotic streptomycin do?
prevents transition from translation initiation to chain elongation
targets bacteria
What does the antibiotic chloramphenicol do?
blocks peptidyl transferase reaction on ribosome
-targets bacteria
What does the antibiotic erythromycin do?
binds in exit channel of ribosome and inhibits elongation of peptide chain
-targets bacteria
What does the antibiotic rifamycin do?
prevents RNA synthesis by binding RNA polymerase
-targets bacteria
What does the release of glucocorticoids signal to the body?
released during starvation
signal liver to produce glucose from AAs
How is gene expression regulated?
transcriptional control, RNA processing, RNA transport and localization, translational control, mRNA degradation, protein activity control
What are homeodomain proteins?
key regulators of animal development, subclass of helix turn helix motif
What are the 2 regulatory parts in the lac operon?
to be on, lactose is broken into allolactose which binds to remove repressor
- when no glucose, cAMP binds CAP to remove
- lac operon is OFF if glucose is present
What is epigenetics?
heritable (meiosis, mitosis), reversible changes in genome that regulate gene expression
In mammal females, how is one X chromosome turned “off”?
inactivated by XIC (X inactivation center) and XIST (X inactivation specific transcript)
-association of XIST RNA with X chromosome is correlated with condensation
What addition signals imprinting? What does it do?
add methyl group to cytosine in CG sequence on 5th carbon which causes chromatin condensation
-methylation is inherited in progeny DNA
If it is a maternally imprinted gene, will either of the mom’s gametes be functional?
No, will imprint both genes so all children will have a maternally imprinted gene.
-if son gets maternally imprinted gene, will NOT pass along imprinted gene to children
What HIV protein transports unspliced HIV mRNA from nucleus to cytoplasm?
Rev
In low iron conditions, how does body respond?
Shut off ferritin product by inhibiting translation from IRE-BP in 5’UTR
-express transferrin receptor to uptake iron into cell
What is Werner Syndrome?
premature aging, caused by genome instability (affects accessory DNA helicase for replication)
Where is benzo[a]prene found?
the carcinogen produced by cigarette smoke
-only becomes carcinogenic when oxidized in cells
What does cytosine de-aminate to ?
uracil
What does 5-methyl Cytosine deaminate to?
thymine (usually missed by proofreading)
How are thymine dimers created?
from UV light, binding of adjacent pyrimidine bases
What is the process in strand directed mis-match repair?
in euk and prok: MutS binds to mismatched BP, MutL scans nearby DNA for nick (new strand) then MutL triggers degradation
Bacteria: no nicks so MutH nicks unmethylated DNA
What is the process in base excision repair (BER)?
endonuclease and phosphodiesterase remove sugar base, DNA pol adds new nucleotides, ligase seals nick
What is the process for nucleotide excision repair (NER)?
bigger problem: DNA helicase unwinds DNA, DNA pol adds NTs, DNA ligase seals back up
What are the 2 solutions for double stranded breaks?
1) nonhomologous end joining- chop off jagged, ligate ends together, lose NTs, Ku protein
2) homologous end joining- more effective and difficult, use homologous chromosomes and recombination mechanisms
What genes are involved in recombination in prok and eukaryotes?
Euk: Rad 51 and proteins ATM, Brca1, Brca2
Prok: RecA
Where is p53 protein important?
at G1 checkpoint before cell division
