molecular genetics Flashcards
central dogma
DNA –> RNA –> protein
- transcription and translation
hershey-chase experiment
radiolabeled sulfur and phosphorus to distinguish where genetic info was (protein vs nucleic acids)
- result was radiolabeled phoshporus which is in dna not protein
reverse transcriptase
allows dna to be transcribed from rna
- retroviruses
- special kind of dna polymerase that operates with rna template
codon
3 dna nucleotides that code for an amino acid
4^3 = 64 combinations
degeneracy
multiple codons can make the same amino acid
- increase resistance to error
wobble position
provide protection against mutation in the final nucleotide of a codon. most codons are defined by the first two nucleotides
stop codons
UGA, UAG, UAA
start codon
AUG (met)
watson and crick model of dna
dna is a double helix of antiparallel strands with a sugar phsophate backbone
- complimentary basepairing
- interior stabilized by h bonds between bases and hydrophobic interactions between stacked bases
base stacking
arrangement of nucleotide nitrogenous bases that allow for hydrophobic interactions`
compliementary dna strands
are complimentary and antiparallel (be aware of directionality when looking at question wording)
how is dna organized in eukaryotes
linear chromosomes in the nucleus
autosomes
22 chromosomes in humans that are somatic cells and have two copies each. 1 maternal and 1 paternal
sex chromosomes
two each
female XX
male XY
how is the massive content of dna squeezed into chromosomes
histones and chromatin
histones
proteins that are wound around dna with subproteins: h1 h2A h2B H3 H4
core: two dimers ofh2a and h2b and a tetramer of h4 and h3
h1: linking unit
nucleosomes
dna-histone complex
- beads on a string
chromatin
structure formed by nucleosomes (dna and histones)
euchromatin
loose configuration that allows dna to be easily transcribed
- during interphase (allows for transcription)
heterochromatin
tighly coiled dense form of chromatin that is visible during CELL DIVISION
how do histones and dna interact
charge driven interactions
- histones are positive and dna is negative
acetylation of histones
reduce their positive charge, and loosen binding on dna allowing for an increase in dna transcription
semiconservative replication
dna replication where end product is 1 original strand and one new strand
meselson-stahl experiment
experiment that distinguished between old and new dna
they grew radioactive N in e. coli and traced it
- found that dna is semi-conservative
orgin of replication
start of dna replication
- one place in prok
- multiple in euk
helicase
unwinds dna for transcription
- seperates the strands
single stranded binding proteins
keep the strands seperated
primase
short rna primer with a free 3’ oh that is used to start dna synthesis
dna polymerase
reads dna from 3-5 and synthesizes from 5-3
dna gyrase/ topoisomerase
alliviates supercoiling created by helicase
ligase
links okazaki fragments on the lagging strand
DNA polymerase direction
can only add in the 5’ to 3’ direction and read in the 3’ to 5’
lagging strand
made into short sequences by dna polymerase that must be ligated together by ligase
dna polymerase 1
prokaryotic dna polymerase that assists with okazaki fragments
- removes rna primer through excision repair
dna polymerase 2
primary eukaryotic dna polymerase involved with repair
dna polymerase 3
primary eukaryotic polymerase for dna replication
dna polymerase alpha
initiates synthesis in replication in both strands
dna polymerase delta
takes over from dna polymerase alpha amd adds dna after the rna primer is removed
dna polymerase epsilon
extension of leading strand and dna repair
dna polymerase beta
dna repair
dna polymerase gamma
replicates miDNA
telomerase
extends telomeres at the end of eukaryotic chromosomes
what are telomeres
repeating sequences at the end of the chromosome that cope with the fact that dna polymerase can’t replicate the end of a chromosome
what kind of cells is telomerase active in
stem and cancer (not somatic)
transcription
transcribe dna to rna in the nucleus. results in mrna
rna polymerase
enzyme that synthesizes pre-mrna during transcription
- synthesizes in the 5’ to 3’ direction
promotor region
where rna polymerase binds to dna to begin transcription with the assitance of transcription factors
TATA box
most important promotor in eukaryotes
template strand for rna synthesis
antisense strand
sense strand
the non - template strand that corresponds to the codons on the mRNA molecule
requirements for dna polymerase
- always need a template
- they add in the 5-3 ‘ direction
- they cannot start from scratch (need primer)
rna polymerase 2
default rna polymerase that synthesizes hn RNA (precursor to mRNA)
hnRNA (heterogeneous nuclear)
precursor to mRNA that must undergo post-transcriptional modification
1. poly a tail
2. 5’ cap
3. splicing
RNA polymerase 1
synthesizes ribosomal rna in nucleolous
rna polymerase 3
synthesizes trna and rRNA
does post transcriptional modification of rna occur in prokaryotes?
no, only eukaryotic rna experiences poly A tail addition, 5’ cap, and spliciing
why does prokaryotic rna not undergo post transcriptional modification?
transcription and translation occur simultaneously so there is no time for modification
3’ poly A tail
string of 250 adenine nucleotides to the 3’ end of the hnRNA
- protects mrna from rapid degredation in the cytosol
- speed of mrna degredation depends on length of the poly A tail
5’ cap
7-methylguanylate triphosphate cap on the 5’ end of the hnRNA
- prevents premature degredation and prepares the RNA complex for export from the nucleus
splicing
noncoding (introns) are removed and exons (coding sequences) are left in the RNA and ligated together
- exons exit the nucleus
- exons can be alternatively spliced leading to protein variation
-carried out by the spliceosome and protein complexes –> snRNPs
alternative splicing
various combinations of exons produced by the splicosome that allows for large variation in protein produces
small nuclear ribonuclear proteins (snRNPs)
spliceosome + small nuclear RNAs and protein complexes
translation
process where mRNA is translated into a protein via ribosomes
where does translation take place
cytosol in both eukaryotes and prokaryotes
tRNA
small RNA molecule with a hairpin structure that translates between codons and amino acids
- contains anticodon
anticodon
complementary sequence to the mRNA codon
aminoacyl tRNA synthetases
charge tRNA with its amino acid by attatching the c terminus of the amino acid to the 3’ end of the tRNA molecule
- requires 2 atp to charge a tRNA and power the formation of the peptide bond
is protein synthesis endergonic or exergonic
endergonic
- energy consuming
large subunit of euk ribosome and prok
60s and 50s
small subunit of euk ribosome and prok
40s and 30s
overall ribosome for euk and prok
70 and 80s
function of small ribosomal unit
read the RNA
initiation
initiator trna binds to the start codon aug and the ribosome is assembled
initial amino acid in eukaryotes
methionine
initial amino acid in prokaryotes
N-formylmethionine
elongation
ribosome reads mRNA from 5’ to 3’ and synthesizes the polypeptide from N to C terminus
a site
contains the next aminoacyl-tRNA complex
p site
peptide bond is formed between growing peptide and incoming amino acid
e site
trna is no longer charged and detaches from the mrna
termination
stop codon (UGA, UAA, UAG) causes release factors to trigger ribosome disassembly and releases the peptide
post translational modifications
- phosphorylation
- glycosylation
- protein folding
- formation of quartenary structure
kinases
add phosphates
phosphotases
remove phosphates
chaperone proteins
assist in protein folding
cleavage
cleaving prehormones before they can become active
point mutation
one nucleotide base is wrong
silent mutation
missense mutation where the amino acid does not change
conservative mutation
a type of missense mutation where there is a new amino acid with similar properties
non-conservative mutation
missense mutation where amino acid change is large
nonsense mutation
premature stop codon
frameshift mutation
add/delete amino acid and codons downstream are altered
chromosomal deletion
missing a large part of a chromosome
chromosomal duplication
adding extra to chromosome
inversion
segment is reversed , usually harmless
translocation
genes switch places
insertion
move between chronosomes
transopons
non-coding genetic info that can move between chromosomes
anueploidy
too few or too many sets of chromosomes resulting from nondisjunction during cell division
monosomy
1 copy of chromosome
trisomy
3 copies of a chromosome
DNA excision repair
3’ to 5’ endonculease activity
Mutagens
Agents that damage dna, usually carcinogens
Base excision repair
Small scale errors like mismatched pairs
Nucleotide excision repair
Larger lesions of dna, thymine dimers
Which interphase checkpoint protects against anueploidy
M phase checkpoint
