Biochemistry - Molecular Flashcards
What is the structure of chromatin?
“Beads on a string”
Negative DNA wrapped around a positively charged histone octamer –> forms a nucleosome
What phase does DNA and histone synthesis occur?
S phase
Which type of chromatin is condensed and which is less condensed b/t heterochromatin and euchromatin?
Heterochromatin - highly condensed, transcriptionally inactive
Euchromatin - less condensed, transcriptionally active
At what site does DNA methylation occur?
What is a result of DNA methylation?
CpG islands
Methylated CpG islands repress transcription
“CpG Methylation Makes DNA Mute”
Histone methylation
Histone Methylation Mostly Makes DNA Mute
What effect does histone acetylation have on DNA?
Relaxes DNA coiling –> allows transcription
Histone Acetylation makes DNA Active
What are the 2 purines? How many rings do they have?
Adenine, Guanine (PURe As Gold)
2 rings
What are the 3 pyrimidines? How many rings do they have?
Cytosine, Thymine, Uracil (CUT the PY (pie))
1 ring
What structure is uracil found in?
What structure is thymine found in?
DNA vs. RNA
RNA
DNA
What side group does thymine have?
A methyl group
Thymine has a methyl.
What amino acids are necessary for purine synthesis?
GAG
Glycine
Aspartate
Glutamine
NucleoSide = base (deoxy)ribose
Attached to a SUGAR
NucleoTide = base (deoxy)ribose + phosphaTe
Linked by 3’-5’ phosphodiester bond
Which two metabolic pathways is carbamoyl phosphate involved in?
pyrimidine synthesis
urea cycle
What enzyme does the following drug inhibit in nucleotide synthesis?
- Leflunomide
- Mycophenolate, Ribavirin
- Hydroxyurea
- 6-Mercaptopurine (MP) and its prodrug Azathioprine
- 5-Fluorouracil (5-FU)
- Methotrexate (MTX), Trimethoprim (TMP), and pyrimethamine
- dihydroorotate dehydrogenase
- IMP dehydrogenase
- ribonucleotide reductase
- de novo purine synthesis
- thymidylate synthase
- dihydrofolate reductase
Purine Salvage Deficiencies
What disease results from a deficiency in adenosine deaminase?
What is its genetic inheritance pattern?
What molecular findings will you see?
SCID
Autosomal recessive
Excess ATP and dATP –> prevents DNA synthesis –> decreases lymphocyte count
Purine Salvage Deficiencies
What disease results from a deficiency in HGPRT?
What is its genetic inheritance pattern?
What molecular findings will you see?
What physical findings will you see?
What is the treatment?
Lesch-Nyhan Syndrome
X-linked recessive
Overproduction of purines and accumulation of uric acid
Hypersegmented neutrophils*
Intellectual disability, gout, dystonia
Tx: allopurinol or febuxostat (2nd line)
Hyperuricemia Gout Pissed off (aggression, self-mutilation e.g. biting nails) Retardation (intellectual disability) DysTonia (spasticity)
Which two codons are encoded only by 1 codon (AUG and UGG, respectively)?
Methionine and tryptophan
What type of DNA replication occurs in both prokaryotes and eukaryotes?
Semi-conservative DNA replication
How many origins of replication does a prokaryote have? Eukaryote?
1) single
2) multiple
What is the function of a helicase enzyme?
unwinds DNA
What is the function of a single-stranded binding protein?
prevent strands from reannealing
What is the function of a DNA topoisomerase?
What drug class inhibits DNA gyrase (prokaryotic topoisomerase II)?
- Create a single or double stranded break in the helix to add or remove supercoils
- Fluoroquinolones
What is the function of a primase?
make an RNA primer on which DNA polymerase III can initiate replication
What two polymerases are present in prokaryotes only?
DNA polymerase I and II
In what direction is DNA made?
5’ –> 3’
What is the function of DNA polymerase I?
Degrades RNA primer –> replaces it w/ DNA
What is the function of DNA ligase?
Joins Okazaki fragments together on lagging strand
What is the function of telomerase?
RNA dependent DNA polymerase that adds DNA to 3’ ends of chromosomes to avoid loss of genetic material w/ every duplication
What is the order of severity of mutations in DNA from least to most?
silent «_space;missense < nonsense < frameshift
For silent, missense, and nonsense mutations, what are the changes made to the DNA?
Transition: purine –> purine (e.g. A to G) or pyrimidine to pyrimidine (e.g. C to T)
Transversion: purine to pyrimidine (e.g. A to T) or vice versa
What is a silent mutation?
nucleotide substitution but codes for same amino acid
*often base change in 3rd position of codon (tRNA wobble)
What is a missense mutation?
nucleotide substitution –> changed amino acid (conservative if similar in chemical structure)
*Sickle Cell Disease
What is a nonsense mutation?
nucleotide substitution –> early STOP codon
STOP the NONSENSE!
What is a frameshift mutation?
Deletion or insertion of a number of nucleotides not divisible by 3 –> misreading of all nucleotides downstream –> truncation or non-functional protein
e.g. Duchenne Muscular Dystrophy
What is nucleotide excision repair (NER)?
Is it a single or double strand repair?
Specific endonucleases release the oligonucleotide-containing damaged bases
DNA polymerase and ligase fill and reseal the gap
Repairs bulky helix-distorting lesions
Single strand repair
What disease arises from a defect in nucleotide excision repair (NER)?
Xeroderma pigmentosum
What is base excision repair?
For what is BER especially important for repairing?
Base-specific glycosylase recognizes altered base –> DNA polymerase-beta fills the gap –> DNA ligase seals it
Important in repair of spontaneous/toxic deamination
What is mismatch repair (MMR)?
Newly synthesized strand is recognized –> mismatched nucleotides removed –> gap filled and resealed
What disease arises from a defect in MMR?
Hereditary Nonpolyposis Colorectal Cancer (HNPCC)
What is non homologous end joining?
Bringing together 2 ends of DNA fragments to repair double-stranded breaks
No requirement for homology
What disease arises from a defect in non homologous end joining?
Ataxia telangiectasia
DNA and RNA are both synthesized in what direction?
5’ –> 3’ direction
mRNA is read in what direction?
5’ –> 3’ direction
What mRNA codon starts protein synthesis
AUG
What are the mRNA stop codons?
UGA = U Go Away UAA = U Are Away UAG = U Are Gone
What does a promoter do?
Site where RNA polymerase and multiple other TFs bind to DNA upstream from gene locus (TATA box)
What happens if there is a mutation in the promoter?
Dramatic decrease in level of gene transcription
What is the function of enhancers and silencers?
Enhancers - stretch of DNA that alters gene expression by binding transcription factors
Silencers - site where negative regulators (repressors) bind
What kind of mRNA does RNA polymerase I make?
rRNA (most numerous RNA, rampant)
What kind of mRNA does RNA polymerase II make?
mRNA (largest RNA, massive)
What kind of mRNA does RNA polymerase III make?
tRNA (smallest RNA, tiny)
What is the process for making heterogenous nuclear RNA (hnRNA) into mRNA?
- capping of 5’ end (addition of 7-methylguanosine cap)
- polyadenylation of 3’ end (~200 A’s)
- splicing out of introns
Where in the cell is mRNA translated?
cytosol
What are the 3 steps to splicing pre-mRNA?
- primary transcript contains small nuclear ribonucleoproteins (snRNPs) to form spliceosome
- Lariat-shaped loop is made
- Lariat is released to remove INTRONS and join 2 exons
Abs to spliceosomal snRNPs are associated with which disease? What are they also called?
Anti-Smith Abs
Associated with SLE
Anti-U1 RNP Abs are highly associated with which disease?
mixed connective tissue disease
What is the fate of introns? Exons?
Introns are intervening sequences and say in the nucleus (introns are spliced OUT!)
Exons exit and are expressed.
Abnormal splicing variants are implicated in what diseases?
Oncogenesis and genetic disorders (e.g. beta-thalassemia)
What ensures accuracy of amino acid selection with tRNA?
- aminoacyl-tRNA synthetase
2. binding of charged tRNA to the codon
What is the tRNA wobble?
Accurate base pairing only required in first 2 nucleotide positions of an mRNA codon so codons differing in 3rd “wobble” position
What are the 3 stages of protein synthesis?
- Initiation
- Elongation
- Termination
Describe the process of initiation…
Initiated by GTP hydrolysis
Initiation factors help assemble the 40S ribosomal subunit with the initiator tRNA and are released when the mRNA and the ribosomal 60S subunit assemble with the complex
What are the subunits from eukaryotes and prokaryotes?
Eukaryotes: 40S + 60S –> 80S (EVEN)
PrOkaryotes: 30S + 50S –> 70S (ODD)
What is the order for elongation of a synthesizing protein?
Think of “going APE”
A site = incoming Aminoacyl-tRNA
P site = accommodates growing Peptide
E site = holds Empty tRNA as it Exits
What causes termination of protein synthesis?
stop codon is recognized by a release factor
What are some post translational modifications?
trimming
covalent alterations
What does a chaperone protein do?
intracellular protein involved in facilitating and/or maintaining protein folding
