molecular Flashcards
nucleosome
H2A, H2B, H3, H4 - two of each.
POSITIVELY CHARGED.
negative DNA loops twice around each octamer. octamer subunits are mainly LYS and ARG.
histone H1
ties nucleosome “beads” together.
ONLY histone that is not in nucleosome core.
HeteroChromatin
Highly Condensed.
transcriptionally inactive.
sterically inaccessible.
methylation
template strand CYTOSINE and ADENINE are methylated during DNA replication, allowing mismatch repair enzs to distinguish old and new strands
HYPERmethylation
inactivates DNA transcription
euchromatin
less condensed.
transcriptionally ACTIVE.
sterically accessible.
histone acetylation
relaxes DNA coiling,
allows for transcription.
deamination of what base makes uracil?
cytosine
guanine contains?
ketone
thymine contains?
methyl
which bonds are stronger?
G-C (3 H bonds)
vs. A-T (only 2 H bonds)
increased G-C content means..?
increased melting temp
AA needed for PURINE synth?
Glycine
Aspartate
Glutamine
nucleotides linked together by?
3’-5’ phosphodiester bonds
AA needed for pyrimidine synth?
aspartate
only other component is carbamoyl phosphate
purine process
- start with sugar + phosphate (PRPP).
2. add base.
pyrimidine process
- make temporary base (OROTIC ACID).
- add sugar + phos.
- modify base.
ribonucleotide reductase
convert ribonucleotides to deoxyribonucleotides
carbamoyl phosphate
2 uses:
- de novo pyrimidine synth.
- urea cycle.
if carbamoyl phosphate can’t be used for urea cycle…
due to deficiency of ornithine transcarbamoylase (OTC), carbamoyl phosphate ACCUMULATES and is converted to OROTIC ACID of pyrimidine pathway
orotic aciduria
auto recessive inability to convert orotic acid to UMP (de novo pyrimidine synth).
due to defect of:
- orotic acid phosphoribosyltransferase (adds PRPP).
- orotidine 5’-phosphate decarboxylase (removes CO2 to form UMP.
orotic aciduria FINDINGS
increased orotic acid in urine.
megaloblastic anemia.
failure to thrive.
orotic aciduria vs OTC deficiency
no hyperammonemia in orotic aciduria
TX of orotic aciduria
oral uridine
what is significant about megaloblastic anemia of orotic aciduria?
does NOT improve with admin of B12 or folic acid
adenosine deaminase
convert adenosine to inosine in purine salvage pathway
adenosine deaminase deficiency
excess ATP and dATP imbalance via feedback inhib of ribonucleotide reductase
= prevent DNA synth and thus, decrease lymphocyte count
adenosine deaminase deficiency causes what disease?
SCID:
B and T cells die off.
occurs in kids.
1st to be treated with experimental human gene therapy (retroviral vector).
Lesch Nyhan syndrome
defective purine salvage due to absent HGPRT.
results in excess uric acid prod and de novo purine synth.
X-linked recessive.
HGPRT
converts hypoxanthine to IMP,
guanine to GMP.
Lesch Nyhan syndrome FINDINGS
retardation. self mutilation. aggression. hyperuricemia. gout. choreoathetosis.
what is the only base that can be salvaged in Lesch Nyhan syndrome ?
adenine
genetic code feature: unambiguous
each codon specifies only ONE AA
genetic code feature: degenerate/redundant
more than 1 codon may code for SAME AA
genetic code feature: commaless, nonoverlapping
read from a fixed starting point as a continuous sequence of bases
AA that are NOT degenerate/redundant
methionine (AUG) and tryptophan (UGG) are encoded by only ONE codon
genetic code feature: universal
genetic code is conserved throughout evolution (except: mito DNA)
severity of DNA mutations
nonsense > missense > silent
what do frameshift mutations often result in?
truncated, nonfunctional protein
where does DNA replication begin in prokaryotes?
at consensus sequence of base pairs
where does DNA replication begin in eukaryotes?
multiple consensus points (origins of replication)
helicase
unwinds DNA template at replication fork
single-stranded binding proteins
prevent strands from reannealing
DNA topoisomerases
create nick in helix to relieve supercoils created during replication
DNA gyrase
PROKARYOTIC
topoisomerase II.
*inhibited by fluoroquinolones
primase
DDRP.
makes RNA primer on which DNA pol III can initiate replication.
DNA polymerase III
PROK ONLY.
- elongates leading strand by adding deoxynucleotides to the 3’ end (5’-3’ synth).
- elongates lagging strand until it reaches primer of preceding fragment.
- 3’-5’ exonuclease activity to proofread each added nucleotide.
DNA polymerase I
PROK ONLY.
- degrades RNA primer with 5’-3’ exonuclease.
- fills in gap with DNA (5’-3’ synth).
- proofreads with 3’-5’ exonuclease activity.
DNA ligase
seals
telomerase
adds DNA to 3’ end of chromosomes to avoid loss of genetic material with each duplication
nucleotide excision repair
single strand.
specific ENDONUCLEASES release oligonucleotide-containing damaged bases.
DNA pol fills gap, ligase reseals.
xeroderma pigmentosum
endonuclease deficiency.
UV light causes THYMINE DIMER formation.
UV endonuclease needed to excise dimer.
deficiency = inability to repair.
features of XP
photosensitivity.
poikiloderma.
hyperpigmentation.
increased risk for skin cancer.
base excision repair
single strand.
specific GLYCOSYLASES recognize and remove damaged bases.
AP endonuclease cuts DNA at apurinic or apyrimidinic site, empty sugar removed.
gap filled and resealed.
base excision repair is important for?
repair of spontaneous or toxic deamination
mismatch repair
single strand.
unmethylated, newly synthesized string is recognized. EXONUCLEASE removes mismatched nucleotides.
gap filled and resealed.
mutated mismatch repair
HNPCC: hereditary nonpolyposis colorectal cancer
nonhomologous end joining
double strand repair.
brings 2 ends of DNA fragments together.
homology not required.
mutated nonhomologous end joining
ataxia telangiectasia
rRNA
made by EUK RNA pol I.
most abundant type.
“Rampant”
mRNA
made by EUK RNA pol II.
longest type.
“Massive”
tRNA
made by EUK RNA pol III.
smallest type.
“Tiny”
mRNA start codon
AUG:
codes for methionine in EUK.
formyl-methionine (f-Met) in PROK.
*starts PROTEIN synth.
mRNA stop codons
UGA
UAA
UAG
promoter
site where RNA pol and multiple other TFs bind DNA upstream of gene locus.
AT-rich sequence with TATA and CAAT boxes.
mutated promoter
dramatic decrease in amount of gene transcribed
enhancer
stretch of DNA that alters gene expression by binding transcription factors
silencer
site where negative regulators (repressors) bind
where are enhancers and silencers located?
anywhere….
close to, far from, or even within the gene whose expression is being regulated
RNA polymerases
no proofreading.
can initiate chains.
PROK RNA pol
only 1 type. multisubunit complex.
makes all 3 kinds of RNA.
which EUK RNA pol opens DNA at promoter site?
RNA pol II
what toxin can inhibit RNA pol II?
alpha-amanitin (amatoxin) in death cap mushrooms - stops mRNA synth.
cause liver failure if ingested.
hnRNA
heterogeneous nuclear RNA (initial transcript) - must be processed before it can leave nucleus
RNA processing
- 5’ cap (7-methylguanosine).
- 3’ polyadenylation (200 A’s).
- splicing of introns.
= mRNA
Abs to spliceosomal snRNP
lupus
lac operon: allolactose
inhibits repressor
lac operon: glucose
inhibits activator
exons
contain actual genetic info coding for protein
introns
intervening noncoding segments of DNA
alternative splicing
combines diff exons to make unique proteins in different tissues
ex: beta thal (abn splicing)
tRNA structure
75-90 nucleotides.
secondary structure: cloverleaf.
tRNA 3’ aminoacyl end
contains CCA and high #chemically modified bases.
AA covalently binds to 3’OH of CCA tail.
“Can Carry Amino acids”
tRNA charging
aminoacyl-tRNA synthetase (uses ATP) examines AA before and after it binds to tRNA
what happens if AA-tRNA bond is incorrect?
bond is hydrolyzed
where does energy for peptide bond formation come from?
AA-tRNA bond
what blocks attachment of aminoacyl-tRNA to ribosome?
tetracyclines - bind 30S subunit
tRNA wobble
accurate base pairing only required for FIRST 2 nucleotide positions of codon.
3rd WOBBLE position can code for same tRNA/amino acid.
protein synth: initiation
activated by GTP hydrolysis.
initiation factors help.
initiation factors (eIFs)
help assemble 40S subunit with initiator tRNA.
released when mRNA and ribosomal subunit assemble with complex.
EUK ribosomal subunits
40S + 60S = 80S (Even)
PROK ribosomal subunits
30S + 50S = 70S
protein synth: elongation
- charged tRNA binds A site.
- ribosomal rRNA (RIBOZYME) catalyzes peptide bond formation, transferring growing polypeptide TO CURRENT AA in A site.
- ribosome advances 3 nucleotides toward 3’ of mRNA, moving growing peptidyl RNA to P site (translocation).
protein synth: termination
stop codon recognized by RELEASE FACTOR.
completed protein released from ribosome.
posttranslational modification: trimming
remove N or C-terminal PROpeptides from zymogens to create mature proteins
posttranslational modification: covalent alterations
phosphorylation,
glycosylation,
hydroxylation
posttranslational modification: proteasomal degradation
attachment of UBIQUITIN to defective proteins to tag them for breakdown
aminoglycosides
bind 30S and inhibit formation of INITIATION COMPLEX.
cause misreading of mRNA.
chloramphenicol
inhibit peptidyltransferase (ribosomal rRNA/ribozyme), AKA peptide bond formation.
binds 50S.
macrolides
block translocation (A to P site)- prevent release of uncharged tRNA after it has donated its AA
