Molecular Biochemistry Flashcards
Components of a nucleoside
base and (deoxy)ribose
Components of a nucleotide
base, (deoxy)ribose, and phosphate
Side of a nucleotide chain which has the triphosphate
5’ end
Side of a nucleotide chain which has the hydroxyl
3’ end
Four important deamination reactions in nucleotides
1) cytosine -> uracil
2) adenine -> hypoxanthine
3) guanine -> xanthine
4) 5-methylcytosine -> thymine
Amino acids necessary for purine synthesis (3)
Glycine, aspartate, and glutamine
Mnemonic: “Cats PURr until they GAG”
Function of Leflunomide
Inhibits dihydroorotate
Function of Methotrexate (also trimethoprim and pyrimethamine)
Inhibit dihydrofolate reductase
Function of 5-fluorouracil (5-FU)
Form 5-F-dUMP, which inhibits thymidilate synthase (dec. in dTMP)
Function of 6-mercaptopurine
inhibit de novo purine synthesis
Function of hydroxyurea
Inhibits ribonucleotide reductase (purine and pyrimidine synthesis)
One of the major causes of autosomal recessive SCID (severe combined immunodeficiency). The deficient enzyme is required for degradation of adenosine and deoxyadenosine
Adenosine Deaminase Deficiency
Defective purine salvage due to absent HGPRT which converts hypoxanthine to IMP and guanine to GMP. Excess uric acid and de novo purine synthesis. X-linked recessive
Lesch-Nyhan syndrome
Lesch-Nyhan Syndrome symptoms and HGPRT mnemonic
Hyperurecimia, Gout, Pissed off (aggression, self-mutilation), Retardation, dysTonia
Genetic code feature: each codon specifies only 1 amino acid
Unamibigious
Genetic code feature: Most amino acids are coded by multiple codons
Degenerate / Redundant
Codons that differ in the 3rd base, may code for the same tRNA/amino acid.
Wobble
Genetic code feature: read from a fixed starting point as a continuous sequence of bases
Nonoverlapping
Genetic code feature: genetic code is conserved throughout evolution
Universal
What sort of nitrogenous bases would be heavily present in the origin of replication?
AT-rich sequences
Create a single or double stradned brea in the DNA helix to add or remove supercoils
DNA topoisomerases
Reverse transcriptase that adds DNA (TTAGGG) to 3’ ends of chromosomes to avoid loss of genetic material with every duplication
Telomerase
Subtype of point mutation: purine to purine or pyrimidine to pyrimidine
Transition
Subtype of point mutation: purine to pyrimidine or vice versa
Transversion
Nucleotide substitution but codes for the same amino acid; often base change in 3rd position of the codon
Silent mutation
Nucleotide substitution resulting in changed amnio acid
Missense mutation
Nucleotide substitution resulting in premature stop codon. Usually results in a nonfunctional protein
Nonsense mutation
Deletion or insertion of a number of nucleotides not divisible by 3, resulting in a misreading of all nucleotides downstream.
Framshift mutation
Mutation at a splice site, retained intron in the mRNA, protein with impaired or altered function.
Splice site mutation
Specific endonucleases release the oligonucleotides containing damaged bases; DNA polymerase and ligase fill and reseal the gap, respectively. Repairs bulky helix-distorting lesions. Occurs in G1 phase of cell cycle
Nucleotide excision repair
Inability to repair DNA pyrimidine dimers caused by UV exposure. Dry skin, extreme light sensitivity, skin cancer. Defect of exinucleases in nucleotide excision repairs
Xeroderma pigmentosum
Base-specific glycosylase removes altered base and creates AP site (apurinic/apyrimidinic). One or more nucleotides are removed by AP-Endonuclease, which cleaves the 5’ end. Lyase cleaves the 3’ end. DNA polymerase-beta fills the gap and DNA ligase seals it. Occurs throughout the cell cycle.
Base excision repair
Which type of DNA repair is critical in repair of spontaneous/toxic deamination?
Base excision repair
Newly synthesized strand is recognized, mismatched, nucleotides are removed, and the gap is filled and resealed. Occurs predominantly in S phase of cell cycle
Mismatch repair
What process is defective in Lynch syndrome, also known as hereditary nonpolyposis colorectal cancer (HNPCC)
DNA mismatch repair
Brings together 2 ends of DNA fragment to repair double-stranded breaks. No requirement for homology. Some DNA might be lost.
Nonhomologous end joining
Requires two homologous DNA duplexes. A strand from the damaged dsDNA is repaired using a complementary strand from the intact homologous dsDNA template. Restores duplexes accurately without loss of nucleotides
Homologous recombination
What process is defective in breast/ovarian cancers with BRCA1 mutation?
Homologous recombination
Site where RNA polymerase II and multiple other transcription factors bind to DNA upstream from gene locus (AT-rich upstream sequence with TATA and CAAT box)
Promoter
DNA locus where activator regulatory proteins bind, increase expression of a gene on the same chromosome
Enhancer
DNA locus where repressor regulatory proteins bind, decreasing expression of a gene on the same chromosome
Silencer
_____ and _____ may be located close to, far from, or even within the gene whose expression they regulate
Enhancers and silencers
What is preprocessed mRNA called? (First aid uses a different term then we did)
heterogeneous nuclear RNA (hnRNA)
What is the cap added in 5’ end mRNA processing?
7-methylguanosine
What is added on the 3’ end of processed mRNA?
polyadenylation / poly A tail
What is a good way to remember how RNA polymerases are numbered?
They’re numbered in the order they’re used. I - rRNA, II - mRNA, III - tRNA
Product(s) of RNA Polymerase I
rRNA
Product(s) of RNA Polymerase II
mRNA and snRNA
Product(s) of RNA Polymerase III
5s rRNA, tRNA
Small noncoding RNA molecules that posttranscriptionally regulate gene expression by targeting the 3’ untranslated region of specific mRNAs for degradation or translational repression.
microRNAs (miRNAs)
What’s on the 3’ end of a tRNA
CCA acceptor stem for covalent binding to amino acids
Function of the T arm on tRNA, which features a TΨC sequence
Tethers the tRNA molecule to the ribosome
Arm of tRNA which is used in recognizion by the correct aminoacyl-tRNA synthetase
D-arm
What charges tRNA with the correct amino acid
Aminoacyl-tRNA synthetase
What are the triphosphate nucleotides used for charging tRNA and then translocation, respectively?
ATP and GTP
Sites of a ribosome
A Site: incoming aminoacyl-tRNA
P Site: accomodates growing peptide
E Site: holds empty tRNA as it exits
