Chap 5/6 Flashcards
central dogma (and exception)
DNA -> RNA -> protein
Retroviruses use RNA to make DNA (reverse trasncription)
which nitrogenous bases match to each other
A-T
C-G
molecular structure of nucleotides
ribose sugar with a nitrogenous base attached to 1’ carbon and and phosphate group attached to 5’ carbon
nucleoside structure
ribose sugar with nitrogenous base attached to 1’ carbon
which nitrogenous bases are purines
adenine and guanine
which nitrogenous bases are pyrimidines
thymine, cytosine, and uracil
phosphodiester bond
forms between the 3’ hydroxyl group of one sugar and the 5’ phosphate of the next
hydrogen bonds in DNA
hold the two nitrogenous bases together; keep the DNA double-stranded structure together
number of hydrogen bonds between A-T and C-G
A-T: 2
C-G: 3
DNA synthesis direction
5’ to 3” direction
phosphodiester bond formed at the 3’ hydroxyl end of the growing DNa chain with the incoming 5’ phosphate group
handedness of the DNA double helix
right-handed
the lowest level of chromosome organization (2 parts):
nucleosome (core particle and linker DNA)
nucleosome core particle
consists of 8 histones and DNA wrapped around them
linker DNA
connects nucleosome cores
how can the nucleosome core particle be released from chromatin in test tube solution
nuclease digests the linker DNA but cannot attack the DNA wrapped around the nucleosome core
how can the DNA be releases from the histone octamer (nucleosome core particle dissociation)
high salt breaks ionic bonds
levels of chromosome packing
DNA double helix -> beads on a string chromatin -> chromatin fiber of packed nucleosomes -> chromatin fiber folded into loops -> assembles into mitotic chromosome
how does the beads on a string chromatin fold to become packed nucleosomes (fiber)
linker histone (H1) associates with linker DNA and pulls nucleosomes together into fiber
other involved proteins in chromosome packing
loop forming clamps, cohesins, condensins
chromatin remodeling complexes
use ATP to change the position of DNA wrapped around histones by loosening nucleosomal DNA and pushing it along histone core to expose DNA to other proteins
de-condense chromatin
euchromatin
regions of relaxed (less condensed) chromatin
more accessible for gene expression
heterochromatin
regions that contain more histones and are more condensed and less accessible
silent genes are more condensed
includes centromere and telomeres
epigenetic regulations of histones
chemical modifications on specific locations (amino acids) at the N-terminal of histones affect gene expression
ex: acetylation, methylation, phosphorylation
acetylation of lysine (k) effects
loosens chromatin structure - increases accessibility
carbon on the deoxyribose sugar where new where new deoxyribonucleotide will attach
3’
carbon that differs on ribose sugar in RNA and DNA
carbon 2’
has H attached in DNA
has OH group in RNA
semiconservative model
every daughter helix is comprised of one conserved parent strand (template) and one newly synthesized strand
where are DNA bases added to deoxyribose sugar
where OH group is on 1’ carbon
what provides the energy for DNA polymerase to form phosphodiester bond along growing DNA chain
hydrolysis of nucleoside triphosphate into nucleoside monophosphate (releases pyrophosphate)
how does DNA polymerase proofread and correct errors
contains two catalytic domains: P and E
P: polymerization
E: Editing
why does DNA polymerase have to move in the 5’ to 3’ direction
if it moved 3’ to 5’ it could not proofread and still continue forward because it wouldn’t have the energy provided to form phosphodiester bond
DNA helicase
unwinds the DNA double helix by breaking H bonds
replication initiator proteins
recognize and bind to origin of replication
why are many origins of replication A-T rich regions
A-T bases connected by 2 H bonds (not 3 like C-G)
number of replication origins in bacteria and humans
bacteria have 1
humans have many per chromosome
Replication forks
2 y-shaped junctions that extend both direction from origin of replication
place where DNA synthesis occurs
where does the replication machinery assemble and start its movement
replication forks (2- one for each direction)
Okazaki fragments
the successive separate small fragments of DNA that is made on the lagging strand
what does DNA polymerase require to bind and start synthesizing DNA
a base paired (double stranded) end
Primase function
RNA polymerase that makes RNA primer for DNA polymerase to bind to (using DNA single strand template ) - 5’ to 3’ direction
What base does RNA polymerase use that’s different from DNA polymerase
U instead of T, U base pairs with A
primers required on leading and lagging strands
leading strand: 1
lagging strand: multiple
Nucleases function in DNA synthesis
removes RNA primers
Repair polymerase function in DNA synthesis
synthesizes DNA where primers have been removed, uses ends of Okazaki fragments to bind to
DNA ligase function in DNA synthesis
joins 5’ phosphate and 3’ hydroxyl of fragments by catalyzing formation of phosphodiester bond to create continuous strand
which DNA synthesis enzymes use ATP
DNA ligase, helicase, clamp loader, and primase
why do chromosomes become shorter when DNA is replicated
the leading strand is synthesized to the end, but when the primer on the end of the lagging strand is removed, repair DNA polymerase cannot attach and replace RNA at the end of the strand
telomeres
long repetitive nucleotide sequences that are added to the end of every chromosome which allow the lagging strand to be completed by DNA polymerase
telomerase
adds additional telomere repeats to the template strand and keeps telomeres long enough
carries short RNA template whose sequence is complementary to the DNA telomere sequence
single strand DNA binding proteins
binds to the single stranded DNA to prevent it from reforming base pairs
sliding protein clamps
hold the DNA polymerase on the leading and lagging strands facilitating its sliding
DNA topoisomerase
relives the tension that builds up in front of replication fork by temporary nicks (single or double stranded)
ways that DNA tension is relived when unwinding
DNA
how does UV radiation damage DNA
two adjacent thymine bases become covalently attached forming a thymine dimer
how are thymine dimers removed and corrected, and how does it affect replication
nucleotide excision pair
stalls replication machinery
spontaneous DNA damage (2)
depurination and deamination
depurination
loss of purine base (A or G) from DNA
will cause deletion (and frame shift mutation) if left unrepaired
deamination
loss of amino group from cytosine to form uracil
will cause base pair change (point mutation) if left unrepaired
if replication errors are unrepaired how does this effect further replication
error strand produces double strand with permanent mutation which can cause diseases
what is DNA redundancy
more than one codon codes for the same amino acid (silent mutation)
sickle cell anemia point mutation
single nucleotide change of beta globin gene > abnormal hemoglobin
what must a person inherit to develop sickle cell anemia
two copies of mutant beta globin gene
deamination and depurination are repaired by what mechanism
base excision repair mechanism
base excision repair mechanism steps
- identification of the damaged base
- excision of the nucleotide
- resynthesis by DNA polymerase
- ligation by DNA ligase
excision in DNA repair
damage is cut out by nuclease specific for type of DNA damage
which enzyme restores original sequence in gap after excision cuts it out in base excision repair
repair DNA polymerase
DNA ligase function in DNA repair
seals the nick left in the backbone of repaired strand
nonhomologous end joining
mechanism to repair double strand breaks
two broken ends are brought together by enzymes and rejoined rejoined by ligation
results in short deletions, quick but could cause gene disfunction
homologous recombination repair
mechanism that repairs double strand breaks with no loss of genetic information
uses other newly replicated double strand as template-must happen while two copies are near each other
steps in homologous recombination
- d.s. break in one newly replicated DNA
- nucleases digests more DNA in 5’ direction on each strand (opposite directions)
- damaged DNA crosses over and DNA is synthesized using undamaged DNA as the template
- invading strand released and DNA synthesis continues using complementary strands as template + ligation
is what other situation is homologous recombination used
meiosis- paired chromosomes from parents align and cross over to cause genetic variation
