genetics Flashcards
purines and pyrimidines
purines = AG (2 bonds, 2 rings). pyrimidines = CT (3 bonds, 1 ring)
telomeres
only in eukaryotes, reads TTAGGG…
stop codons
UAA, UGA, UAG
nucleotide structure
triphosphate on 5’ of sugar. deoxy on 2’. nitrogenous base on 1’. Free hydroxyl end on 3’.
point mutation
single substitution of NT. May result in missense, nonsense, or silent mutation.
frameshift mutation
very serious. NTs inserted or deleted not in multiple of 3
UV ray mutation
causes pyrimidines to fuse into dimer. Distorts helix backbone
X ray mutation
can break covalent bonds, such as break backbone
intrastrand and interstrand crosslinking
form of endogenous DNA damage
if transposon is put in intergenic region
no effect
if transposon put in coding region
mutation
mismatch repair pathway
during or soon after replication to correct a single mismatched bp. Identify parent strand by its methylation to correct daughter
NT excision repair
can occur anytime; replace the bad base with correct one
homologous recombination
must occur BEFORE replication, you use the other sister chromatid as a template to correct chromosomal DSBs
non homology end joining
can occur anytime; just use ligase to join broken ends of a chromosome (this is the option before S phase when there’s no sister chromatid as reference)
theta replication
occurs in prokaryotes’ circular DNA, beginning at a single Ori. proks have 5 DNA polymerases
DNA pol III
very fast. It is the main replicase enzyme. No repair function.
Also has 3’ to 5’ exonuclease activity (when it backs up a NT and lops it off if wrong. This is called the proofreading function that can ONLY occur during replication)
DNA pol I
slower than pol III. Like III, it has 3’ to 5’ exonuclease activity where it can proofread too. Unlike III, it can remove RNA primers in 5’ to 3’ direction. it performs excision repair
telomerase
extends telomeres (reverse transcriptase ability because it copies its RNA template to make DNA)
DNA pol II
backup for DNA pol III. Also possesses proofreading function and also has repair mechanisms.
DNA pol IV and V
quite error prone
hnRNA
heterogeneous nuclear RNA. Large pre-mRNAs that must be further processed before entering cytoplasm
siRNA
short interfering RNA. It is double stranded and exogenous, taken up by cells
miRNA
micro RNA, single stranded and endogenous
Compare prok and euk transcription
Prok: translation occurs simultaneously with transcription; no processing of mRNA, only 1 RNA pol.
No introns, no splicing.
Euk: translation occurs in cytoplasm; mRNA needs to be mature, 3 RNA pol types
Poly vs monocistronic
In prokaryotes, many proteins can come from 1 mRNA transcript
aminoacyl tRNA synthetase
matches tRNA to its amino acid. Takes 2 ATP.
Wobble theory
though the first 2 NTs of the codon pair correctly, the 3rd has some leeway, permitting the same tRNA to match with multiple codons that vary in the 3rd letter. This reduces number of tRNA types needed
Translation energy requirements
takes 4ATP per 1 amino acid
release factor
binds to stop codon to release growing peptide from ribosome
Shine-Dalgarno sequence
sequence in mRNA, upstream of AUG, that helps find and bind ribosome. ONLY PROKARYOTES
photoreactivation
visible light can recruit enzymes to repair pyrimidine dimer mutations formed by UV
gyrases
only exist in prokaryotes; they maintain the helix coil shape
splicing
hnRNA -> mRNA. Occurs in nucleus.
metacentric
p and q arms equal in length
submetacentric
p and q arms almost equal; q still longer
acrocentric
p arms VERY VERY short
Kozak sequence
sequence in eukaryotic mRNA (not prok) by which ribosomes can recognize it. They also recognize 5’ cap
telocentric
p arms shorter even than acrocentric; barely there
2 DNA strand types?
coding = sense template = antisense = the one being 'read' by RNA pol
heterochromatin
has more histones, very compact. mostly noncoding regions; euchromatin: more often transcribed
kinetochores
multi protein complexes that attach spindle fibers (of mitosis) to the centromeres of chromosomes
types of genomic variation
single nucleotide polymorphisms, copy-number variations, and tandem repeats (which are rich in heterochromatin, centromeres, telomeres)
SSBPs
bind to exposed DNA to prevent reannealing
nucleophile
the 3’ hydroxyl during replication is the nucleophile
ethidium bromide
a mutagen that inserts itself between bp (intercalating) thus causing errors in replication
inversion
chromosomal mutation where a segment is flipped
amplification
chromosomal mutation where segment is duplicated
translocation
chromosomal mutation where segment is moved to another chromosome altogether
transposons
all contain a gene coding for transposase (that has cut and paste activity)
IS element - simplest type; merely transposase flanked by repeats
Complex transposon - IS element followed by genes
Composite transposon - central region flanked by IS elements
hemizygous
when there is only one gene copy in a diploid organism. Quite dangerous, because having 2 copies protects from mutations
haploinsufficiency
diploid organism has only a single functional copy of a gene
ncRNA
non coding RNA includes tRNA and rRNA. Also a type call long ncRNAs that control basal transcription level by regulating initiation complex assembly. Also work on post transcriptional regulation and have a function in X-inactivation
rRNA
some rRNA serves a catalytic function, thus called RIBOZYMES
snRNA
associate with proteins to form snRNP which do splicing. They also regulate transcription factors and maintain telomeres
miRNA and siRNA
both bind specific mRNA to serve as post transcriptional regulation
piRNA
PIWI-interacting RNA are single stranded and short. they work with the PIWI protein class to prevent transposon movement
Pribnow box
a sequence in the bacterial promoter region (prok only) which is recognized by holoenzyme component of RNA pol
RNA pol I
makes most rRNA
RNA pol II
makes most hnRNA -> mRNA. Remember that transcription is MORE ERROR PRONE than replication
RNA pol III
makes tRNA, siRNA, miRNA, and certain rRNA
steps of translation
- amino acid + ATP –> aminoacyl AMP + PPi
- cleaving of PPi is extremely favored. this provides energy for tRNA loading (unfavourable).
- tRNA loading is where aminoacyl AMP and tRNA become aminoacyl-tRNA, with the AMP discarded
aminoacyl tRNA synthetase enzymes
AT LEAST one for each amino acid type
eIF proteins
essential to initiate translation. One binds the smaller ribosome subunit, another binds the 5’ mG cap of mRNA
cap-independent translation
long believed that euk could only translate start at the 5’ cap, sometimes they begin in the middle of the transcript
where does each process occur?
transcription, splicing, polyadenylation, 5’ cap adding = nucleus
translation = cytoplasm
lac operon
P region - promoter site on DNA
O region - operator site to which the lac repressor binds
Z gene - codes for beta galactosidase, which digests lactose
Y gene - codes for permease, so lactose may enter
A gene - transacetylase, not strictly required for lactose metabolism
crp gene - located elsewhere, codes for CAP, the glucose-dependent promoter protein
I gene - also elsewhere, codes for Lac repressor protein. The repressor typically sits on the O region, blocking transcription, till binding a lactose makes it fall off
trp operon
for making tryptophan
trpR gene - codes for repressor. The repressor binds trp when present and in turn turns the operon off
post transcriptional control
miRNAs and siRNAs can inactivate mRNA
cells also monitor quality of mRNA and degrade defective ones
mRNA is also transported to correct location in cell BEFORE translated
post translational modification
chaperones fold proteins
covalent modification (functional groups added, like sugars, phosphates, etc)
cleavage
formyl-methionine
only used by prok; euk have regular methionine
