bio130 test 1 Flashcards
prokaryote doesn’t have but eukaryote does (main thing)
nucleus
eukaryotes are ___ celled
single or multi
prokaryotes are ___ celled
single
plants have but animals dont (3)
cell wall, vacuole, chloroplast
ectosymbiosis
a form of symbiotic behav in which an organism lives on the surface of another organism
bacterium model organism
e coli
eukaryote model organism
yeast
plant model organism
arabidopsis
tractability
ease of manipulation/modification of an organism
animal model organisms
worms, flies, fish, mice
genome
all genetic material in a cell or organism
transcriptome
all RNA/RNA sequences in a cell or organism
proteome
all proteins/protein sequences in a cell or organism
interactome
all protein-protein interactions
metabolome
all small molecule metabolites in the cell/organism
phenome
all the phenotypes of the cell/org.
why is DNA stable
its structure
nucleotide is comprised..
nitrogenous base, 5C sugar, 1+ phosphate group
phosphate is attached to __ carbon and base is attached to __ carbon of the carbon chain
5’, 1’
phosphate is attached to __ end and the sugar is at the __ end of DNA molec
5’, 3’
pyrimidine = ___ ring
1 ring
purine = ___ ring
2 rings
pyrimidines:
C U T
purines:
G A
uracil replaces __
thymine
nucleoside
base + sugar
DNA is synthesized from…
dNTP
dNTP aka..
deoxyribonucleoside triphosphate
RNA is synthesized from…
NTP
NTP/rNTP aka
ribonucleoside triphosphate
examples of dNTP
dATP, dGTP, ..
bond b/w nucleotides
phosphodiester bonds
A-T = __ H bonds
2H bonds
C-G = ___ H bonds
3H bonds
how do van der waals forces keep dna together
van der waals act b/w bases
how do hydrophobic interactions contribute to the structure of dna
bases are hydrophobic = ‘inside’, sugars = outside
protein contact is typically at the… (DNA)
major groove
primary protein struc referes to..
AA seq
2ndary protein struc refers to…
local folding
tertiary protein struc refers to…
long range folding
quaternary protein struc is when
there’s >1 polypeptide chain
how are peptide bonds formed (chemically)
condensation rxn bw OH (carboxyl group) and H (amino group)
what forms peptide bonds (organelle)
ribosomes
what are AAs called after peptide bonds have been formed
residues
backbone of a polypeptide chain is…
everything except for the R groups (N-C-C-N-C-C…)
amino end aka…
N terminus
what stabilizes alpha helices?
H bond b/w carbonyl atom and amide hydrogen - 4 AA apart. NOT R GROUPS
alpha helix vs DNA helix - R groups
alpha R groups face out, DNA base pairs face in
super secondary structures
2 secondary structures interact with each other in some way?? that doesnt count as tertiary… e.g. amphipathic helix
amphipathic helix
when R groups on 1 side are hydrophobic and on the other side are hydrophilic -> 2 alpha helices coil around e/o
how are beta sheets stabilized
more H bonds b/w carbonyl oxygen and amide group hydrogen
2 types of beta sheets
anti parallel vs parallel OR beta sheet made w 1 vs multiple polypeptide chains1
types of AA (chemical properties)
acidic, basic, uncharged polar, nonpolar
parts of an AA
alpha carbon, H, amino group, carboxyl group, R group
CYSTEINE?!?!
draw the structure
CH3–CH2–SH
what happens to cysteine in oxidation conditions
H removed from SH– and it forms covalent disulphide bonds
how strong are covalent disulphide bonds
VERY strong!
reduction conditions in the cell ?
cytosol
oxidation conditions in the context of the cell?
ER and outside of the cell (ECM)
what is the role of cysteine in protein
helps proteins hold their shape (like a brace)
chaperone proteins
proteins that help tertiary structures fold
what connects protein domains
intrinsically disordered sequences
what are protein domains
semi-independent areas of a protein that do diff things
what are proteinfamilies
proteins w similar AA seq.s and tertiary struc.s
methods to study proteins (purification)
purified w electrophoresis, affinity chromatography
multiprotein complexes
many proteins work together
molecular machine
all proteins work together for a particular function
hemoglobin structure (subunits)
has 4 subunits where each subunit is a separate polypeptide but counts as 1 protein :D
multiple polypeptides = multiple proteins?
NO (counterexample: hemoglobin)
what is the genome
all hereditary material
what is the genome made of and what does that depend on
DNA: living things and some viruses
RNA: some viruses
num base pairs in human genome
3B
why does any given individual have 6B base pairs
3B from e/ genome and 1 genome from e/ parent
how many protein coding genes in human genome (for 23 pairs of chromosomes)
20k protein coding genes
genome size is not related to ___
complexity, organism size, # of genes
what % of human genome codes protein
less than 1%
what % of human genome is repetitive DNA
~50%
a type of repetitive DNA
mobile genetic elements
mobile genetic elements - types?
retrotransposons, DNA-only transposons
what are mobile genetic elements aka transposons
elements that can ctrl x, ctrl c, ctrl v themselves in/out of the genome
what are types of mobile genetic elements, specifically based on length and found in human genome?
LINEs, SINEs
num b.p.s in SINEs
less than 500
what does LINE stand for
Long Interspersed Nuclear Elements
what is the main role of nonrepetitive DNA that is not in introns or exons
determines which + how many RNAs get transcribed and in which cells
types of unique DNA
nonrepetitive DNA not in introns or exons, introns, protein-coding exons
types of DNA packaging (prok vs euk)
prokaryotic nucleoid, eukaryotic nucleus
FISH, CPH, chromatin, histones, interphase
this is not a real card
fish is .. and it does..
fluorescence in situ hybridization, a diagnostic technique to detect presence of a specific sequence
how does fish work
probe DNA (antiparallel, complementary) labelled w dye, denatured w sample, cooled and ideally probe bound to dna now
what is cph
chromosome painting hybridization - colour chromosomes
what is chromatin
single long dna molec + extra proteins
when does chromosome duplication begin
interphase
where does chromsome duplication begin (a part of the cell)
centromeres
how is chromatin organized (how’s it wrapped)
wrapped around histone octamers, 1.66 times per octamer
what is dna not wrapped around histones called and how long is it
linker DNA, 80 bp
how long is dna wrapped around e/ histone
~147bp
how long is dna (per nucleosome)
~200 bp
what is a histone octamer made of
8 proteins: 2 H2A, 2 H2B, 2 H3, 2 H4
charge of histone octamer
positive
role of linker histone (H1)
clips the DNA on, not actually in the octamer
nucleosome core particle =
core histones + DNA wrapped around them
role of sequence specific clamp proteins and cohesins
hold tgt loops of interphase chromosome - involved in cell division
as cells enter mitosis, what happens to cohesins
condensins replace them to form double loops of chromatin (compact chromosome)
does chromatin packaging require atp
yes
2 forms of chromatin? (condensity)
heterochromatin (highly condensed), euchromatin (less condensed)
most chromatin is in what form
30nm fiber (heterochromatin)
quiescent
euchromatin that’s not being actively transcribed and thus genes are not being expressed
beads on a string is what type of chromatin
euchromatin
constitutive chromatin is
chromatin that is always heterochromatin
facultative chromatin is
chromatin that is not always heterochromatin but sometimes is
when is gene expression expressed? (chromatin)
only active euchromatin
where is heterochromatin always found (part of cell ish)
meiotic + mitotic chromosomes, centromere, telomere
what happens when a specific gene is being expressed
chromatin shifted to allow RNA polymerase to transcribe it and that specific area is made less condensed
interphase chromosomes are in ___ regions of the nucleus
distinct/discrete
types of DNA synthesis + explain (this is the theory…)
conservative (old theory, 1 daughter cell gets all new DNA and 1 gets all parental DNA), nonconservative
general process of DNA synthesis - what is used to build and what protein does that
dNTPs added to parental strands from 5’-3’ by DNA polymerase
direction of DNA synthesis vs direction of reading template strand
5’ to 3’ vs 3’ to 5’
dna replication for eukaryotes and bacteria is _____ growth from __ starting point aka the ____
bidirectional growth, 1 starting point, origin of replication
origin of replication is made of.. and why?
regions that are A-T rich (not random areas though, specific sequences) b/c A-T = 2 H bonds vs C-G = 3 H bonds
what recognizes the origin of replication
initiator proteins that bind to the DNA
euk vs bacteria OOR
euk have multiple, bacteria have 1
primosome =
helicase + primase
replisome is…
molecular machine that’s the whole dna duplication process
(dna synthesis) what happens after OOR is recognized
initiator proteins bind, and it + helicase-loading protein help the helicase bind
(dna synthesis) what happens after helicase binds
helicase unwinds DNA
2 types of helicase? (their function not their name)
DNA repair, unwinds 5’-3’ along the lagging strand template
(dna synthesis) what happens after helicases unzip
single strand binding proteins bind to keep the strangs separated to prevent DNA from sticking to itself
hair pins?
caused by DNA H-bonding to itself
(dna synthesis) what happens after SSBs bind
primer and primase do their thing
what is bound primer and what’s special about it
short seq of nt w free 3’ OH that lets the DNA polymerase begin
what does primase do
synthesises an RNA primer from 5’-3’ (same direction as DNAP)
(dna synthesis) what happens after primase
DNA polymerase uses dNTPs to synthesize new strand from 5’-3’
what is a necessary part of DNA polymerase (another helper protein!)
sliding clamp prevents DNAP from flying off
(dna synthesis) what happens after DNA polymerase
nick sealing of okazaki fragments with nucleases
how is nick sealing done
DNA ligase seals the fragments by removing the leading strand primer, DNAP fills in the gaps left by the primer and ligase creates a phosphodiester bonds b/w unbonded fragments
supercoiling happens when
DNA is unwound and wants to spin due to torsional strain
how is supercoiling fixed
topoisomerase cuts a little break in DNA, lets it spin, then re-seals it
eukaryote specific dna replication problem? (think.. not circular dna..)
primase is bad at putting the primer at the end of a lagging strand and a removed primer cannot be re-filled
how is primase being bad (dna replication issue) solved?
telomerase
how does telomerase work
RNA temp[ate sticks to parental strand, extends parental strand (repetitions of template), generates G-rich ends (template C-rich), DNAP alpha then synthesizes that piece
where is telomerase less abundant (and why is this a problem)
somatic cells -> aging
why is lots of telomerase bad
cancer
what happens when dna polymerase screws up - how is it fixed? (2 methods)
3’-5’ exonuclease (backspace) and strand-directed mismatch repair
what does 3’-5’ exonuclease do
removes a wrongly put nucleotide during DNA synthesis at the E site
2 sites of DNAP
P and E site (synthesis site and proofreading/editing site)
2 proteins of strand directed mismatch repair in eukaryotes
MutS and MutL
what does MutS do
is a strand directed mismatch repair protein that identifies and binds to an issue
what does MutL do
is a strand directed mismatch repair protein that scans DNA, works w sliding clamp and MutS, identifies nicks and cuts out the area with the problem
what happens after MutL cuts out a problem area
DNAP repairs it
how is strand directed mismatch repair diff for prok vs euk
prok don’t detect nicks, they detect unmethylated adenines
what does UV radiation do to DNA
causes pyrimidine dimers
pyrimidine dimers are when
2 pyrimidines in a row covalently bind
how are pyrimidine dimers fixed
NER
2 types of spontaneous dna dmg
depurination
deamination
depurination is when
h2o hits purine and removes it (dna dmg)
deamination happens when
h2o hits cytosine and deaminates it, cytosine turns into uracil (dna dmg)
how is spontaneous dna dmg (depurination, deamination) fixed
BER
what is BER and how does it work
base excision repair, fixes 1 nt at a time
what is NER and how does it work
nt excision repair, fixes multiple nt at a time
how is a double stranded break repaired (2 methods)
non homologous end joining (NHEJ) or homologous recombination (HR)
molecular definition of a gene
segments of DNA that are transcribed into RNA
what RNA is not translated? (example)
mRNA
transcription and translation ____ start at the same site
DO NOT
non template strand aka the ___ strand
sense
template strand aka the ____ strand
antisense
(transcription in bacteria) RNA is made ___ to DNA and in _’ to _’
antiparallel and complementary, 5’ to 3’
what does it mean to be made in 5’-3’
add onto 3’ end of newly synthesized strand, the template is read 3’-5’
ssDNA stands for
single strand DNA
diff b/w RNA and DNA polymeras? (related to how they begin doing their thing)
RNA polymerase doesn’t require a primer!
what’s specific to bacterial transcription? (specirfic protein)
sigma factor
purpose of sigma factor (2 main ones)
binds to RNAP and finds the promoter region. synthesizes a few short seq.s until RNAP gets ahold of itself and begins synthesis
other names for RNAP
RNA core enzyme, RNA polymerase,
RNAP holoenzyme =
RNA core enzyme + sigma factor
translation starts at AUG and transcription starts…
anywhere
when talking about the promotor sequence, what does + and - refer to
+ = in the direction of the transcription , upstream
- = before the transcription, downstream
promotor consensus sequence
most common sequences used for recognition
are promoter sequences transcribed
NO!!!
in bacteria, how are different promotor sequences recognized
by diff sigma factors
how does bacterial transcription stop (full process)
RNAP hits the terminator sequence, transcribes it, then the hairpin bs happens
hairpin mech?? (bacterial transcription)
abundance of G’s and C’s bond to each other, eventually snaps the newly synthesized strand off
in ___, translation and transcription are coupled
prokaryotes but not eukaryotes
___ are absent in eukaryotic finally processed mRNA
introns
list out parts of processed mRNA from 5’ to 3’
5’ cap, 5’ UTR, coding sequence, 3’ UTR, poly-A tail
num of RNAP in bacteria vs eukaryotic
1 vs 3
types of RNAP in eukaryotes and their purposes
RNAP I: most of them
RNAP II: protein coding genes (mRNAs)
RNAP III: tRNAs
which RNAP is similar to bacterial RNAP
RNAP II, similar but larger b/c of a special domain
what’s special about RNAP II
special domain! CTD! (carboxyl terminal domain)
eukaryotic equivalent of sigma factor
transcription factors (TFxD)
diff b/w euk and prok promoter regions for transcription
euk: more variable, can have multiple elements
where is the promoter region for prokaryotes usually (number range)
-10,35
what are elements
specific locations that are recognized by specific transcription factors to help position RNAPs
promoter region corresponding to RNAP II?
TATA box
TBP?
TATA-binding protein is a subunit of TFIID that binds to the minor groove of DNA
how does TFII work
TBP binds and bends the DNA, then TFIIH (helicase) separates the DNA strands and phosphorylates CTD, then RNAPII does its thing
activator proteins?
activate transcription idk
what IS CTD???
a stretch of 7 amino acids that is required for transcription to begin. Ser at its tail is phosphorylated to get RNAPII activated
eukaryotic mRNA processing process
add 5’ cap, remove introns, process and polyadenylate 3’ tail
purpose of 5’ cap
protect RNA from exonucleases
why can’t exonuclease cut up 5’ cap
has like 3 phosphates or something
prok mRNA doesn’t have ___
introns
how are introns removed
spliceosome recognizes intron-exon boundary, 2’ OH on adenine attacks the boundary to form a lariat/loop. spliceosome cuts out the intron and joins the exons together
important part of spliceosomes
snRNPs = snRNA + proteins
exon junction complex
a protein added near where the introns used to be after splicing - relevant to quality control (transcription)
snRNPs are…
small nuclear ribonucleoproteins that are building blocks of the spliceosome
does the spliceosome cut out the same areas for every cell, why or why not
no b/c it has a diff function (ie brain mRNA and muscle mRNA are cut at diff points)
what does poly A tail do
protect from 3’-5’ exonuclease
1st step of making poly A tail
cleavage signal/sequence (AAUAAA) recognized by 3’ end processing proteins (CPSF)
how do poly a tail???
AAUAAA, CPSF + CsTF (cleave), PAP=poly-A polymerase (+AAAAAAA), PABP=poly-A-binding protein (stabilize)
where is mRNA translated
cytoplasm
genetic code is read ‘-’
5’ - 3’
translation goes from _’ to _’
5’-3’
where does translation start
5’ most AUG
effects of mutations (all types - 6)
nucleotide-pair substitution (silent, missense, nonsense), frameshift (nucleotide-pair deletion, nucleotide pair insertion)
tRNA structure - key points (# nt, shape, how is it transcribed, special features?)
~80 nt long, clover shape, transcribed 5’-3’, modified bases
where does AA attach to tRNA
AA attaches to 3’ end
anticodon?
3 bp area where where tRNA binds to mRNA. note that it is antiparalle and complementary to the mRNA
anticodon = 5’-3’ GAA then mRNA is 3’-5’ ____ and you should look up ___ on the genetic code table
CUU, UUC
1 anticodon per ___
codon in the genetic code table (kinda, multiple codons can bind to the same anticodon though), tRNA
diff b/w euk and prok wobble pos.
euk is less flexible
wobble position is…
the 5’ position of the anticodon where other bases can attach (not strict)
how is accuracy ensured during translation
aminoacyl-tRNA-synthetase recognizes AA and puts it on the proper tRNA
how many types of aminoacyl-tRNA-synthetase are there and why
20 types, 1 per AA
how does aminoacyl-tRNA-synthetase identify a match
identifies the anticodon, identifies the n.t. seq of the acceptor, identifies n.t. on other parts of the tRNA
aminoacyl-tRNA-synthetase correction mech
hydrolytic editing
what are ribosome subunits made of
large and small subunits made of ribosomal proteins and rRNA molecules
ribosome sites and purpose
A site (aminoacyl), P site (peptidyl site, peptide bond formed b/w AA in P and E sites), E site (exit site)
where are ribosomes located
ER and cytosol
purpose of ribosomes in the ER
make proteins that are secreted or go to lumen of some organelles
how is peptide bond made during translation and what enzyme is involved
catalyzed by peptidyl transferase activity of the rRNA, can be done b/w of the high energy bond b/w tRNA and AA
ribozyme
RNA molecule that possesses catalytic activity
what is an EF and why is an EF??
elongation factor, quality control and efficiency
how do EFs do quality control
check the aminoacyl tRNA site to make sure that it’s the right AA. sticks to tRNA and will take away the tRNA if the pairing is wrong
EF types (prok vs euk)
EF-Tu for prok and EF1/EF1A for euk
EF and GTP interaction
EF + GTP bring tRNA to the rRNA, if it’s the right base pairing then GTP will hydrolyze to GDP and EF will get released
euk vs prok in how many proteins mRNA can code for
euk: 1 mRNA codes for 1 protein
prok: 1 mRNA can code for multiple proteins
polycistronic mRNA
when 1 mRNA can code for multiple proteins (prok)
diff b/w euk and prok mRNA (as it relates to translation)
has non coding regions b/w coding regions called ribosome-binding sites aka Shine-Dalgarno sequences that tell the ribosome where to start binding
which EFs help with elongation
EF-G (prok) and EF2 (euk)
how do EFs help with elongation
“pulls” the small subunit of RNA so that it’s immeidately ready to accept the next AA to speed up elongation
at which site is the initiator tRNA positioned?
P site
beginning of translation in prok (general process)
initiation bg w shine-dalgarno seq, initoation factors position small subunits, tRNA binds to initiator codon, large ribosomal subunit binds
beginning of translation in euk (general process)
small subunit, large subunit and initiation factors are alr together and bind to mRNA, then they jsut go ! starts with Met in the P site
translation termination? process
at the stop codon, a diff non-tRNA protein (translation release factor) binds to the A site and initiates dissociation of ribosome and termination of polypeptide chain
e.g. post translational modifications
phosphorylation, glycosylation
ubiquitin
a small protein that covalently attaches to proteins targeted for degradation
how does protein degradation work
ubiquitin does its thing then the proteins are directed to the proteasome where they are degraded by proteases
methods to study proteins (AA sequencing)
mass spectrometry
methods to study proteins (precise 3D struc)
x-ray crystallography, NMR, cryo-electron microscopy
proteins in the same family have similar…
structural domains
how is the tertiary structure of a protein held together (what forces)
hydrophobic interactions, covalent disulphide bonds, non covalent bonds
where are amphipathic alpha helices/coiled coils found
alpha-keratin of skin and hair, myosin of muscle cells
subunits of hemoglobin
2 alpha, 2 beta
nucleosome is made up of…
nucleosome core particle (histone octamer + wrapped DNA) + linker DNA + H1
proteomics
large scale study of proteins
histones are proteins rich in…
lysine and arginine
charge of histone and why
positive to neutralize negative charge of DNA
how do euchromatin and heterochromatin interchange
RNAP modulates the reversible switching of the 2
