Biochemistry-Molecular Flashcards
How does DNA exist?
In a condensed, chromatin form in order to fit in the nucleus. Negatively charged DNA loops twice around positively carged histone octamers to form nucleosomes
What AAs are histones rich in?
lysine and arginine
What makes up the histone octamers?
(H2A, H2B, H3, and H4) x2
and H1 links them
DNA and histone synthesis occurs during what phase?
S
What is heterochromatin?
condensed, appears darker on EM
Transcriptionally inactive, sterically inaccessible
What is euchromatin?
less condensed, appears lighter
transcriptionally active, and sterically accessible
Describe DNA methylation
Template strand cytosine and adenine are methylated in DNA replication, which allows mismatch repair enzymes to distinguish between old and new strand in prokaryotes.
DNA methylation at CpG islands repressed transcription
Describe Histone methylation
Usuallu reveribly represses DNA trnscription, but can activate it in some cases (acetylation usually relaxes DNA coiling to allow for transcription)
Describe the nucleotides
PURines (A,G)- 2 rings PUR As Gold
PYrimidines (C,T,U)- 1 ring CUT the PY (pie)
More about nucleotides
Thymine has a methyl (found in DNA)
Deamination of cytosine makes uracil (found in RNA)
G-C bonds (3H) stronger than A-T bonds (2H). Higher G-C content= higher melting temp of DNA
What AAs are needed for purine synthesis?
Glycine
Aspartate
Glutamine
What is the difference between a nucleoside and a nucleotide?
nucleoside= base + deoxyribose (sugar)
nucleotide= based + deoxyribose + phosphate; linked by 3’-5’ phosphodiester bonds
What are the initial steps of pyrimidine base production?
1) Gutamate + CO2 (add 2 ATP and via carbamoyl phosphate syntthetase II) produces carbamoyl phosphate
2) carbamoyl phosphate + aspartate = orotic acid via dihydrooratate dehydrogenase
What drug blocks the conversion of carbamoyl phosphate + aspartate = orotic acid via dihydrooratate dehydrogenase?
leflunomide
What are the next steps in pyrimidine synthesis?
3) orotic acid + PRPP (from Ribose 5-P using PRPP synthetase) = UMP and then UDP
4) UDP converted to either CTP or dUDP via ribonucleotide reductase
What drug inhibits the conversion of UDP to dUDP via ribonucleotide reductase?
Hydroxyurea
What happens to dUDP in pyrimidine synthesis?
5) converted to dUMP
6) dUMP is converted to dTMP via thmidylate synthase by oxidizing N5N10- methylene THF to DHF (DHF is then made back into THF via dihydrofolate reductase)
What drug blocks thymidylate synthase?
5-FU
What drug blocks dihydrofolate reductase?
Methotrexate, Trimethoprim, pyrimethamine
How are purines made?
1) convert PRPP to IMP (6-MP, azathioprine (prodrug of 6-MP) blocks)
2) IMP to AMP or GMP via IMP dehydrogenase
What drug blocks conversion of IMP to GMP via IMP dehydrogenase?
mycophenolate, ribavirin
What other pathway besides de novo pyrimidine synthesis is carbamoyl phosphate involved in?
urea cycle
Purine salvage pathway- note that you can convert Adenosine to inosine using adenosine deaminase
What drugs inhibit the conversion of hypoxathine to xanthine and xanthine to uric acid?
allopurinol and Febuxostat
What does adenosine deaminase deficiency cause?
Excess ATP and dATP imbalances nucleotide pools via feedback inhibition of ribonucleotide reductase, which prevents DNA synthesis and thus, decreases lymphocyte counts (one of the major causes of AR SCID)
What is Lesch-Nyhan syndrome?
Defective purine salvage due to absent HGPT which converts hypoxanthine to IMP and guanine to GMP resulting in excess uric acid production and de novo purine synthesis
What is the MOA of Lesch-Nyhan syndrome?
X-linked recessive
How does Lesch-Nyhan syndrome present?
intellectual disability
self-mutilation
aggression
hyperuricemia
gout
dystonia
How is Lesch-Nyhan syndrome tx?
allopurinol or febuxostat
Genetic code features
Unambiguus- each codon specifies only 1 AA
Degenerate/Redundant- most AAs are coded by multiple codons (exceptions: methionine and tryptophan are encoded y only 1 codon, AUG and UGG, respectively)
Commaless, nonoverlapping- read from a fixed starting pt as a continuous sequence of bases
Universal- genetic code is conserved throughout evolution (except in mitochondria)
Describe the origin of replication of DNA
particular consensus sequence of base pairs in genome where DNA replication begins. May be single (prokaryotes) or multiple (eukaryotes)
What is the replication fork in DNA replication?
Y-shaped region along dNA where the leading and lagging strands are made
What does helicase do?
unwinds DNA template at the replication forks (single-stranded binding proteins prevent the strands from reannealing)
What do DNA topoisomerases do?
create single or double stranded DNA breaks to add or remove supercoils (fluoroquinolones inhibit prokaryotic enzymes topo II (DNA gyrase) and topo IV)
What does primase do?
Makes an RNA primer on which DNA polymerase III can initiate replication
Describe DNA polymerase III
Prokaryotic only. Elongates the leading strand by adding deoxynucleotides to the 3’ end and elongates the lagging strand until itreaches the primer of the preceding fragment
so, DNA polymerase III has 5’-3’ activity and proofreads with 3’-5’ exonuclease
Describe DNA polymerase I
Prokaryotic only. Degrades RNA primer and replaces it with DNA
Has same function as DNA polymerase III but also excises RNA primer with 5’-3’ exonuclease
What does DNA ligase do?
catalyzes the formation of a phosphodiester bond with a strand of double-stranded DNA (i.e. joins Okazaki fragments)
What is telomerase?
An RNA-dependent DNA polymerase that adds DNA to 3’ ends of chromosomes to avoid loss of genetic material with every duplication (eukaryotes only)
Severity of damage in DNA mutation types
silent < missense < nonsense < frameshift
What is a ‘transition’ mutation? Transverse?
Transition- purine to 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?
when nucleotide substitution codes for the same AA; often the result of a base change in the 3rd position
What is a missense mutation?
substitution causes a new AA to be inserted (e.g. valine for glutamic acid in SCD)
Describe the Lac operon
Glucose is the preferred metabolic substrate in E. Coli but when it is absent and lactose is available, the lac operon is activated to switch to lactose use.
How does the shift from glucose to lactose use in E. Coli occur?
Low glucose increases adenylyl cyclase actvity to increase generation of cAMP from ATP which activates catabolite activator protein (CAP) to induce transcription of Lac Z, Y, and A (glucose inhibits adenylyl cyclase normally)
Similarly, high lactose unbinds a repressor protein (Lacl) from the repressor/operator site to induce transcription
So you need both low glucose AND high lactose for this mechanism to occur (in other words, just having low glucose wont produce more lactose)
How does nucleotide excision repair occur?
specific endonucleasaes release the oligonucleotides containing damaged based; DNA polymerase and ligase fill and reseal the gap, respectively.
Occurs in G1 phase
Nucleotide excision repair is defective in what disease?
Xeroderma pigmentosum, which prevents repair of pyrimidine dimers because of UV light exposure
How does base excision repair occur?
Base specific glycosylase removes altered based and creates an AP site (apurinie/apyrimidinic)\
One or more nucleotides are removed by AP-endonuclease, which cleaves the 5’ end. Lyase cleaves the 3’ end. DNA polymerase-B fils the gap and DNA ligase seals it.
Occurs throughout the cell cycle
How does mismatch repair occur?
Newly synthesized strand is recognized, nucleotides are removed, and the gap is filled and sealed
Occurs mostly in G2
Mismatch repair is defective in what disease?
Hereditary nonpolypopis colorectal cancer
What is nonhomoglous end joining?
Brings together 2 ends of DNA fragments to repair double-strand breaks. No requirement for homology. Some DNA may be lost
Nonhomoglous end joining is mutated in what diseases?
ataxia telangiectasia and Fanconi anemia
DNA/RNA?protein synthesis direction
DNA and RNA are both synthesized 5’-3’. The 5’ end of the incoming nucleotide bears the triphosphate (energy source for bonds)
Protein synthesis is N-terminus to C-terminus
What is the mRNA start codon?
AUG (or rarely GUG)
In eukaryotes, codes for methionine, which may be removed before translation is complete
In prokaryotes, codes for N-formylmethionine (fMet)
What does fMet do in prokaryotes?
neutrophil chemotaxis
What are the mRNA stop codons?
UGA, UAA, and UAG
Parts of a eukaryotic gene
Enhancer- Promoter (TATA box)- start of transcription- Introns/Exons- Termination Signals
What is the promoter region?
region where RNA polymerase II and multiple other transcription factors bind to DNA upstream from the gene locus (AT-rich sequence with TATA and CAAT boxes)
Pormoter mutation commonly results in a dramatic decrease in the level of gene transcription
What is the enhancer region?
Stretch of DNA that alters gene expression by binding trnscription factors
Enhancers and silencers may be located close to, far from, or even within (in an intron) the gene
What is a silencer?
site where negative regulators (repressors) bind
What RNA polymerases do Eukaryotes have?
I (makes rRNA)
II (makes mRNA, larged RNA; opens DN at promoter sites)
III (makes tRNA, smallest)
No proofreading function, but can initiate chains.
What is a-amanitin?
Found in Amanita phaloides, (death cap mushrooms) this inhibits RNA polymerase II and causes severe hepatotoxicity if ingested
How many RNA polymerases do prokaryotes have?
1 polymerases (multisubunit complex) makes all 3 kinds of RNA
Rifampin inhibits RNA polymerase in prokaryotes
RNA processing (eukaryotes)
The initial transcript is called heterogeneous nucleus RNA (hnRHA). hnRHA is then modified and becomes mRNA.
The following processes occur in the nucleus following transcription:
Capping of 5’ end (addition of 7-methylguanosine cap)
Polyadenylation of 3’ end (200 A’s)
Splicing out of introns
Capped, tailed, and spliced transcript is called mRNA
What happens to newly made mRNA?
transported out of the nucleus into the cytosol, where it is translated.
mRNA quality control occurs at cytoplasmic P-bodies, which contain exonucleases, decapping enzymes, and microRNAs
How does splicing of pre-mRNA occur?
1) Primary transcript combines with small nuclear ribonucleoproteins (snRNPs) and other proteins to form spliceosomes
2) Lariat-shaped (looped) intermediate is formed
3) Lariat is released to precisely remove intron and join 2 exons
Abs to spiceosomal snRNPs (anti-Smith bodies) are highly specific for what disease?
SLE
Anti-U1 RNP Abs are highly specific for what disease?
Mixed CT Disease
Describe exons and introns
Exons contain the actual genetic info coding for proteins and introns are intervening noncoding segments
Different exons are frequently combined by alternative splicing to produce a larger number of unique proteins
Describe the structure of tRNA
75-90 nucleotides with a 2ndary structure of a cloverleaf form, anticodon end/loop is opposite the 3’ aminoacyl end.
All tRNAs, eukaryotic and prokaryotics, have CCA at the 3’ end along with a high percentage of chemically modified bases
The incoming AA is covalently bound to the 3’ end of the tRNA
What does the t-arm of tRNA do?
contains the TyC (thymine, pseudouracil, and cytosine) sequence needed for tRNA-ribosome binding
What does the D-arm of tRNA do?
contains the dihydrouracil residues necessary for tRNA recognition by the correct aminoacyl-tRNA synthetase
NOTE: The acceptor stem contains the 5’-CCA’-3’
Describe tRNA charging
Aminoacyl tRNA synthetase (uses ATP) scrutinizes AAs before and after it binds to tRNA. If correct, the bond is hydrolyzed.
The AA-tRNA bond has energy for formation of peptide bond.
What is ‘wobble’?
Accurate base pairing is usually required only in the first 2 nucleotide positions of an mRNA codon, so codons differing in the 3rd wobble position may code for the same tRNA/AA
What are the 3 steps of protein synthesis?
Initiation
Elongation
Termination
Describe protein Initiation
Initiated by GTP hydrolysis; initiation factors help assemble the 40S ribosomal subunit with the initiatory tRNA and are released when the mRNA and the ribosomal 60S subunit assemble with the complex
What are the subunits of eukaryotic ribosomes?
40S + 60S - 80S
What are the subunits of prokaryotic ribosomes?
30S + 50S - 70S
Describe elongation protein synthesis
1) Aminoacyl-tRNA binds to the A site (except for the intitiator methionine)
2) rRNA (“ribozyme”) catalyzes the peptide bond formation, transfers growing polypeptide to AA in the A site
3) Ribosome advances 3 nucleotides toward the 3’ end of the mRNA, moving peptidyl tRNA to P site (translocation)
Describe termination protein synthesis
Stop codon is recognized by release factor and the complete polypeptide is released from the ribosome
What posttranslational modifications occur to proteins?
1) Trimming: removal or N- or C-terminal propeptides from zygomen to generate mature protein
2) Covalent alterations including: Phosphorylation, glycoylation, hydroxylation, methylation, acetylation, and ubiquitination
What are Chaperone proteins?
Intracellular proteins involved in facilitating and/or maintaining protein folding.
