Flashcards in FA - Biochemistry - Molecular Deck (95):
What is the charge of histones?
In what amino acids are histones rich?
Lysine + Arginine
To what does H1 bind?
To the nucleosome and to "linker DNA" --> Stabilizing chromatin fiber.
What is the only histone NOT in the nucleosome core?
Which are the histones of the nucleosome core?
H2A, H2B, H3, H4 (each x2).
What is heterochromatin?
1. Condensed, appears darker on EM.
2. Transcriptionally inactive, sterically inaccessible.
HeteroChromatin = Highly Condensed
What happens in DNA methylation?
1. Template strand cytosine and adenine are methylated in DNA replication --> Allows mismatch repair enzymes to distinguish between old and new strands in prokaryotes.
2. DNA methylation at CpG islands represses transcription.
Methylation Makes DNA Mute.
What happens in histone methylation?
Usually represses DNA transcription - BUT can activate it in some cases depending on methylation location.
Histone Methylation Mostly Makes DNA Mute.
What happens in histone acetylation?
Relaxes DNA coiling --> allowing for transcription.
Histone Acetylation makes DNA Active
Which are the purines?
A, G - 2 rings.
PURe As Gold
Which are the pyrimidines?
C, U, T - 1 ring.
CUT the PY (pie)
Which nucleotide has a methyl?
Thymine - MeTHYl.
What does deamination of cytosine make?
What is the meaning of more G-C content?
More 3-H bonds --> More powerful bonding --> Higher melting temperature of DNA.
Which are the amino acids necessary for purine synthesis?
What is a nucleoside?
NucleoSide = base + (deoxy)ribose (Sugar)
What is a nucleotide?
NucleoTide = base + (deoxy)ribose + PhosphaTe.
Linked by 3'-5' phosphodiester bond.
What does the de novo purine synthesis involve?
1. Start with sugar + phosphatee (PRPP)
2. Add base
What does the de novo pyrimidine synthesis involve?
1. Make temporary base (orotic acids)
2. Add sugar + phosphate (PRPP)
3. Modify base
Ribonucleotides or deoxyribonucleotides are synthesized first?
Ribonucleotides --> Converted to deoxyribonucleotides by ribonucleotide REDUCTASE.
In which 2 metabolic pathways is Carbamoyl phosphate involved?
1. De novo pyrimidine synthesis
2. Urea cycle
What is the action of leflunomide?
Inhibits dihydroorotate dehydrogenase.
What is the mechanism of Mycophenolate and rivabirin?
Inhibit IMP dehydrogenase.
What is the mechanism of hydroxyurea?
Inhibits ribonucleotide reductase.
What is the mechanism of 6-mercaptopurine (6-MP) and its prodrug azathioprine?
Inhibit de novo purine synthesis.
What is the mechanism of 5-fluorouracil (5-FU)?
Forms 5-F-dUMP ==> Inhibits thymidylate synthase --> DOWN dTMP.
What is the mechanism of methotrexate (MTX), trimethoprim (TMP), and pyrimethamine?
Inhibit dihydrofolate reductase (DOWN dTMP) in humans, bacteria, and protozoa, RESPECTIVELY.
What happens in adenosine deaminase deficiency?
ADA is required for degradation of adenosine + deoxyadenosine.
==> In ADA def. ==> Incr. dATP ==> Toxicity in lymphocytes.
What is adenosine deaminase deficiency?
One of the major causes of AR SCID.
What happens in Lesch-Nyhan syndrome?
Defective purine salvage due to ABSENT HGPRT, which converts hypoxanthine to IMP and guanine to GMP.
--> Excess uric acid production and de novo purine synthesis.
What is the inheritance pattern of Lesch-Nyhan syndrome?
What are the findings in Lesch-Nyhan syndrome?
1. Intellectual disability
4. Hyperuricemia ==> ORANGE SAND IN DIAPER [Sodium urate crystals].
What is the mnemonic for the findings in Lesch-Nyhan syndrome?
Pissed off (aggression, self-mutilation)
Retardation (intellectual disability)
What is the treatment for Lesch-Nyhan syndrome?
2. Febuxostat (2nd line)
Genetic code is unambiguous?
Each codon specifies only 1 amino acid.
Genetic codon is degenerate/redundant?
Most amino acids are codes by multiple codons.
EXCEPT: Methionine + Tryptophan --> AUG, UGG, respectively.
Genetic code is commaless, overlapping?
Read from a fixed starting point as a continuous sequence of bases.
Exception --> Some viruses.
What is the role of the single-stranded binding proteins?
Prevent strands from reannealing.
What is the role of DNA topoisomerases?
Create a single- or double-stranded break in the helix to add or remove supercoils.
What is the mechanism of fluoroquinolones?
Inhibit DNA gyrase (prokaryotic topoisomerase II).
Is there DNA pol III in eukaryotic cells?
NO - Only prokaryotic cells.
What exonuclease activity does DNA pol III have?
3'-5' exonuclease activity.
Is there DNA pol I in eukaryotic cells?
NO - Only prokaryotic cells.
What is the role of the DNA pol I in prokaryotic cells?
Degrades RNA primer - replaces it with DNA.
What is the difference between DNA pol I and DNA pol III?
Same functions BUT --> Also excises RNA primer with 5'-3' exonuclease.
What is the telomerase?
An RNA-dependent DNA polymerase that adds DNA to 3' ends of chromosomes to avoid loss of genetic material with every duplication.
Put the mutations of DNA according to severity of damage?
Silent << missense < nonsense < frameshift.
For POINT (silent, missense, and nonsense) mutations, what happens in transition and what happens in transversion?
Transition --> Purine to purine or pyrimidine to pyrimidine.
Transversion --> Purine to pyrimidine or pyrimidine to purine.
What happens in silent mutation?
Nucleotide substitution but codes for same (synonymous) amino acid --> Often base change in 3rd position of codon (tRNA wobble).
What happens in missense mutation?
Nucleotide substitution resulting in changed amino acid (called conservative if new amino acid is similar in chemical structure)
--> Sickle cell anemia (GLUTAMIC ACID WITH VALINE).
What happens in nonsense mutation?
Nucleotide substitution resulting in early stop codon ==> Usually results in nonfunctional protein.
STOP THE NONSENSE!
Mention 2 examples of frameshift mutation?
1. Duchenne muscular atrophy.
What is the role of the nucleotide excision repair?
1. Specific endonucleases release the oligonucleotide-containing damaged bases --> DNA pol and ligase fill and reseal the gap, respectively.
2. Repairs bulky helix-distorting lesions.
3. Occurs in G1 phase of cell cycle.
In which condition is nucleotide excision repair defective?
Defective in xeroderma pigmentosum, which prevents repair of pyrimidine dimers because of UV exposure.
What is the function of base excision repair?
1. Base-specific glycosylase recognizes altered base and creates AP site (apurinic/apyrimidinic).
2. One or more nucleotides are removed by AP-endonuclease, which cleaves the 5'-end.
3. Lyase cleaves the 3'-end.
4. DNA polymerase-β fills the gap and DNA ligase seals it.
5. OCCURS THROUGHOUT THE CELL CYCLE.
What is the importance of base excision repair?
Important in repair of spontaneous/toxic deamination.
What is the function of mismatch repair?
Newly synthesized strand is recognized, mismatched nucleotides are removed, and the gap is filled and resealed.
==> Occurs predominantly in G2 phase of cell cycle.
In which condition is mismatch repair defective?
What is the function of non homologous end joining?
1. Brings together 2 ends of DNA fragments to repair double-stranded breaks.
2. No requirement for homology.
3. Some DNA may be LOST.
In which conditions is non homologous end joining mutated?
1. Ataxia telangiectasia.
2. Fanconi anemia.
What is the target of the 3' hydroxyl attack?
The triphosphate bond.
What is a rare mRNA start codon?
AUG in prokaryotes codes for which amino acid?
==> STIMULATES NEUTROPHILIC CHEMOTAXIS.
What is the promoter?
Site where RNA pol II + multiple other transcription factors bind to DNA upstream from gene locus (AT-rich upstream sequence with TATA and CAAT boxes).
What is the result of promoter mutation?
Dramatic decrease in level of gene transcription.
What is the enhancer?
Stretch of DNA that alters gene expression by binding transcription factors.
What is interesting to remember about enhancers?
Enhancers/Silencers may be located close to, far from, or even within (in an intron) the gene whose expression it regulates.
What is a silencer?
Site where negative regulators (repressors) bind.
What is the role of RNA pol I in eukaryotes?
Makes rRNA --> Most numerous RNA, rumbant!
What is the role of RNA pol II in eukaryotes?
Makes mRNA --> Largest RNA, massive!
What is the role of RNA pol III?
Makes tRNA --> Smallest RNA, tiny!
Do RNA polymerases in eukaryotes have any proofreading function?
1. Can initiate chains.
2. RNA pol II opens DNA at promoter site.
In what way are the RNA polymerases numbered in eukaryotes?
I, II, and III are numbered as their products are used in protein synthesis.
What is the role of a-amanitin, found in Amanita phalloides (death cap mushrooms)?
Inhibits RNA polymerase II --> Causes severe hepatotoxicity if ingested.
What is hnRNA?
Initial transcript is called heterogeneous nuclear RNA (hnRNA) --> hnRNA is then modified and becomes mRNA.
Mention the processes that occur in the nucleus following transcription?
1. Capping of 5' end (addition of 7-methylguanosine cap).
2. Polyadenylation of 3' end (200 A's).
3. Splicing out of introns
Capped, tailed, and spliced transcript ==> mRNA.
What happens to mRNA after its transport into the cytosol?
1. mRNA quality control occurs at cytoplasmic processing bodies (P-bodies).
2. P-bodies contain exonucleases, decapping enzymes, and microRNAs.
3. mRNAs may be stored here for future translation.
Does Poly-A polymerase require a template?
AAUAAA = POLYADENYLATION SIGNAL.
What are the steps of splicing of pre-mRNA?
1. Primary transcript combines with small nuclear ribonucleoproteins (snRNPs) and other proteins to form spliceosome.
2. Lariat-shaped (looped) intermediate is generated.
3. Lariat is released to precisely remove intron and join 2 exons.
What are the anti-Smith antibodies?
Antibodies to spliceosomal snRNPs (Anti-Smith antibodies) are highly specific for SLE.
With what are the anti-U1 RNP antibodies highly associated?
With mixed connective tissue disease.
How many nucleotides does the tRNA have?
What do all tRNAs, both eukaryotic and prokaryotic, have at 3' end?
1. CCA + high percentage of chemically modified bases.
2. Amino acid is covalently bound to the 3' end of the tRNA.
CCA --> Can Carry Amino acids.
What is the T-arm of tRNA?
Contains the TΨC (ribothymidine, pseudouridine, cytidine) sequence necessary for tRNA-ribosome binding.
What is the D-arm of tRNA?
Contains dihydrouridine residues necessary for tRNA recognition by the correct aminoacyl-tRNA synthetase.
What is the acceptor stem of tRNA?
The 3'-CCA is the amino acid acceptor site.
What is the tRNA wobble?
Accurate base pairing is required only in the first 2 nucleotide portions of an mRNA codon, so codons differing in the 3rd "wobble" position may code for the same tRNA/amino acid (as a result of degeneracy of genetic code).
What initiates the protein synthesis?
Initiated by GTP hydrolysis --> Initiation factors (eukaryotic IFs) 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 steps of elongation in protein synthesis?
1. Aminoacyl-tRNA binds to A site (EXCEPT for initiator methionine).
2. rRNA ("ribozyme") catalyzes peptide bond formation, transfers growing polypeptide to amino acid in A site.
3. Ribosome advances 3 nucleotides toward 3' end of mRNA, moving peptidyl tRNA to P site (translocation).
What is the mnemonic for the elongation in protein synthesis?
Think of "going APE":
A site --> Incoming Aminoacyl-tRNA.
P site --> accomodates growing Peptide.
E site --> holds Empty tRNA as it Exits.
How is stop codon recognized?
By release factor.
==> Complete polypeptide is released from ribosome.
Mention 2 posttranslational modifications:
2. Covalent alterations
What happens in trimming?
Removal of N- or C-terminal propeptides from zymogen to generate mature protein (e.g., trypsinogen to trypsin).
What are the covalent alterations?