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monomer of DNA
nucleic acid
what direction does DNA go in
5’→ 3’
runs antiparallel and are complimentary
bacteria
single stranded
circular DNA molecule
no nucleus (all prokaryotes)
eukaryotes
long
double stranded
DNA is packed into chromosomes
how many pairs of chromosomes do humans have?
23 pairs
43 individual
23rd set is the sex chromosome
what are the 4 phases of the cell cycle?
G1
S phase - DNA replication
G2
Mitosis- Cell divides
what does interphase look like?
has long thin tangled threads of DNA
cannot see clearly w/ a light microscope
where the cell is preparing to duplicate
includes G1, S, and G2 phases
G1 phase
cell grows physically larger
copies organelles
makes the molecular building blocks it will need in later steps
S phase
cell synthesizes a complete copy of the DNA in its nucleus
duplicates a microtubule-organizing structure called the centrosome
centrosomes help separate DNA during M phase
G2 phase
the cell grows more
makes proteins and organelles
begins to reorganize its contents in preparation for mitosis
phase ends when mitosis begins.
M phase
cell divides its copied DNA and cytoplasm to make two new cells
involves two processes: mitosis and cytokinesis
cytokineses in animals needs cleavage furrow to split, plants needs cell plate
mitotic chromosome
the “X” shape
only happens during division
interphase nucleolus
contains dense DNA for ribosomal RNA
centromere
where 2-sister chromatids connect after replication
telomere
ends of chromosome
replication origins
duplication on DNA begins here
there can be multiple of them on the chromosome
dye to identify DNA
Hoechst stain: attaches directly to DNA
way to identify human chromosomes
FISH (DNA hybridization)
“painting” chromosomes a dif color
karyotype
displays full set of chromosomes labeled with numbers
A-T banding
shows A-T rich regions
is a specific banding pattern for each chromosome
red knobs are genes that code for large ribosomal RNA
translocations
can lead to cancer
shown by karyotypes
how does all the DNA fit into the cell?
chromatin aids w/ folding and packing
contains DNA repair proteins
nucleosome
beadlike structural unit composed of a short length of DNA wrapped around 8 histone molecules to form chromatin
histones are positively charged and DNA backbone is negative
in interphase the chromatin are tightly packed
when they are unpacked they are nucleosomes
how is the chromatin structure?
structure is labile or constantly changing and flexible
chromatin remodeling complexes
use ATP hydrolysis to change position of DNA wrapped around nucleosomes
can loosen or tighten DNA
if DNA is too tightly coiled what happens?
it can turn off the expression
heterochromatin
closed
tightly packed
highly condensed form of interphase chromatin
euchromatin
open
more extended
what does a cell use to communicate opening and closing of DNA?
histone tails which can make reversible modifications
epigenetics
modifications on the DNA can happen from the environment
can be inherited as well
acetylation
open, increase gene expression
methylation
close, decrease gene expression
epigenetic inheritance
ability to inherit chromatin structure helps cells “remember” whether a gene was active in the parent cell
how long does copying the human genome take? how many mistakes?
8 hours
only one or two mistakes!
what acts as a template for its own duplication?
DNA
one side is template and one is complementary strand
5’ → 3’
semi-conservative
DNA replication is this
1 old strand and 1 new strand
where is DNA first opened?
origin of replication is where DNA is first opened
eukaryotes have many origins
bacteria has 1 origin
where are A-T rich regions typically found?
at the origins of replication bc they are easier to break apart
replisome
has all the proteins needed for copying the DNA
DNA helicase
separates and opens DNA strands so proteins and enzymes have access to genetic material
uses ATP hydrolysis to do open double helix
DNA polymerase
synthesizes new DNA using an old strand as a template only in 5’→3’
primase
a RNA polymerase that generates a short length of RNA or a primer
provides base-paired 3’ OH end as a starting point for DNA polymerase
nuclease
breaks apart the RNA primer
repair polymerase
replaces RNA w/ DNA
DNA ligase
acts as a “glue”
joins 5’ phosphate of new DNA to 3’ hydroxyl end of the next
what happens when DNA polymerase makes a mistake
the proofreading subunit corrects it bc mistakes can cause distortion
single stranded binding protein
binds to single-stranded DNA and keeps the strand straight
what do topoisomerase I and II do?
resolve tension and tangled DNA
topo 1 is for single stranded, makes a “nick”
topo 2 is for double stranded coiling, breaks and untangles
telomerase
reaches end of DNA where there is a gap due to RNA primers
extends the strand and allows another primer and DNA polymerase synthesizes
mutation
permanent change in the DNA
many mutations can lead to cancer
how does mismatch repair work?
the DNA mismatch repair proteins bind and remove the strand and DNA polymerase and ligase come and fix it
only happens if DNA polymerase doesn’t catch its own mistake
what are the types of base damage?
depurination- leads to a base loss in guanine and adenine
deamination- leads to a base change in cytosine, uracil, and thymine
what does UV radiation cause in thymine?
thymine dimers- where two thymines covalently attach to each other instead of their corresponding base pairs
excision repair
base nucleotide and single strand repair work this way
nuclease cleaves covalent bonds that join damaged base, repair DNA polymerase fills in gap from 3’ hydroxyl, DNA ligase seals nick
what are the two types of double stranded break repairs?
non-homologous end joining- alters original DNA by deletions or insertions, is fast and easy to do
homologous recombination repair- is more complicated and less frequent but is precise, slow and difficult to do
what is a popular disease that defective DNA repair will lead to?
cancer is the main one
werner syndrome
aging 2x as fast as a normal person
BRCA ½ defects
tumor suppressor proteins
what tells DNA when there’s damage?
cell signaling and ATM kinase which senses damage and amplifies the signal to the cell
structure of RNA
single stranded most of the time
has a ribose sugar
AUGC (AU connected by 2 H-bonds same as AT)
unstable and temporary
has an OH group
messenger RNA (mRNA)
codes for proteins
ribosomal RNA (rRNA)
forms the core of the ribosomes structure and catalyzes protein synthesis
microRNAs (miRNAs)
regulates gene expression
transfer RNA (tRNA)
adaptors between mRNA and amino acids during protein synthesis
transcription
DNA → RNA
opening and unwinding small portion of DNA to expose bases
template strand used for complementary base pairing
correct base is added and linked to RNA chain by RNA polymerase
RNA polymerase II
makes RNA
no primer sequence is needed
no proofreading
makes mistakes but it’s okay because it’s temporary
promoter
is the start sequence on the DNA
terminator
stop sequence on the DNA
how many RNA polymerase do eukaryotes have?
3- RNA poly I, II, III and they need accessory proteins
RNA polymerase II
all protein coding genes, miRNA genes, and other non-coding RNAs
general transcription factors (GTFS)
basal transcription factors; needed for transcription to occur
eukaryotic GTFS (5)
TFIIA and B help bind TBP (TATA binding protein) to the TATA box
TFIID is a complex that contains TBP
TFIIE helps melt or break bonds
TFIIH has helicase activity to unwind DNA
transcription initiation complex
general transcription factors + RNA polymerase II
order of the GTFs will vary based on the promoter or point of regulation
release of RNA polymerase II from the DNA needs dephosphorylation
RNA capping and polydenylation
done before the mRNA moves to the cytoplasm
poly-A tail is a series of Adenines at the 3’ end
5’ cap is specially altered nucleotide end to 5’ end of mRNA
eukaryotic mRNA contains non-coding regions
introns- non coding intervening sequences so they never code for amino acids
exons- expressed sequences code for the proteins
UTR- untranslated regions are important for gene expression
splicing
removal of introns
spliceosome
RNA splicing carried out by RNA molecules
snRNPs form the core of it and carry out RNA splicing
removes introns from pre-RNA to create mature mRNA
how are introns removed?
special sequences are recognized by snRNPs which cleave the RNA at exon-intron borders and covalently link the exon sequences together
alternative splicing
greater protein diversity
exons from the same gene are joined in different combinations, leading to different, but related, mRNA transcripts
increases the coding potential of the human genome bc there are more options of proteins that can be made
where are mature mRNAs transported to, to be translated?
cytoplasm
what marks the mature mRNA that allows recognition that they have been spliced?
poly A tail and 5’ cap
once recognized it moves on out of the nucleus
the start codon
AUG or methionine
how many reading frames is RNA translated into protein?
3 reading frames based on where it starts, but only one encodes the actual message
what process are ribosomes responsible for?
translation and making proteins by reading the order of amino acids and linking them together
what sites and subunits are made up of the ribosome?
A, P, E
large and small ribosomal subunit
what do the 3 sites in the ribsome do?
A site- accepts new tRNA
P site- at the peptide site, takes amino acids off the 2 RNAs to add to the polypeptide chain
E- ribosome exits and tRNA leaves
where on the tRNA is the mRNA code?
3’ end holds the amino acid
what recognizes the amino acid sequence on the mRNA?
anticodons
what covalently couples amino acids to the acceptor arm of the tRNA?
aminoacyl tRNA synthetase
produces a high energy bond between tRNA and amino acid
this charge is used later to link amino acid to the polypeptide chain
where do the ribosomes first start translating?
at the AUG closest to the 5’ end of mRNA
what are the stop codons?
UAA, UAG, UGA
release factors bind to stop codon (protein that allows for the termination by recognizing the stop codon)
do not code for any amino acids
polyribosome
more protein molecules can be made in a given time
what do antibiotics and other drugs block?
protein synthesis
differentiation
process by which a non-specialized cell becomes specialized (can perform specific tasks)
cloning
can take only one cell from cow and experiment to make a calf
that one cell contained all the info to clone
housekeeping proteins
common to all cells
differential gene expression
allows for variation in size, shape, behavior, and function of differentiated cells
cells can change gene expression in response to env. using signaling cascades- phosphorylation turns proteins on/off
3 main points where gene expression is regulated?
transcriptional control: when a given gene is transcribed and how often
mRNA degradation control: selectively degrade certain mRNA molecules
protein degradation control: selectively activating/inactivating proteins
transcriptional control
controlling when a gene is transcribed and how much
starts w chromatin remodeling to open up the gene, histones attach to tails- happens before eukaryotic transcription