Molecular Biochemistry

Question 1

Components of a nucleoside

Answer 1

base and (deoxy)ribose

Question 2

Components of a nucleotide

Answer 2

base, (deoxy)ribose, and phosphate

Question 3

Side of a nucleotide chain which has the triphosphate

Answer 3

5’ end

Question 4

Side of a nucleotide chain which has the hydroxyl

Answer 4

3’ end

Question 5

Four important deamination reactions in nucleotides

Answer 5

1) cytosine -> uracil
2) adenine -> hypoxanthine
3) guanine -> xanthine
4) 5-methylcytosine -> thymine

Question 6

Amino acids necessary for purine synthesis (3)

Answer 6

Glycine, aspartate, and glutamine

Mnemonic: “Cats PURr until they GAG”

Question 7

Function of Leflunomide

Answer 7

Inhibits dihydroorotate

Question 8

Function of Methotrexate (also trimethoprim and pyrimethamine)

Answer 8

Inhibit dihydrofolate reductase

Question 9

Function of 5-fluorouracil (5-FU)

Answer 9

Form 5-F-dUMP, which inhibits thymidilate synthase (dec. in dTMP)

Question 10

Function of 6-mercaptopurine

Answer 10

inhibit de novo purine synthesis

Question 11

Function of hydroxyurea

Answer 11

Inhibits ribonucleotide reductase (purine and pyrimidine synthesis)

Question 12

One of the major causes of autosomal recessive SCID (severe combined immunodeficiency). The deficient enzyme is required for degradation of adenosine and deoxyadenosine

Answer 12

Adenosine Deaminase Deficiency

Question 13

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

Answer 13

Lesch-Nyhan syndrome

Question 14

Lesch-Nyhan Syndrome symptoms and HGPRT mnemonic

Answer 14

Hyperurecimia, Gout, Pissed off (aggression, self-mutilation), Retardation, dysTonia

Question 15

Genetic code feature: each codon specifies only 1 amino acid

Answer 15

Unamibigious

Question 16

Genetic code feature: Most amino acids are coded by multiple codons

Answer 16

Degenerate / Redundant

Question 17

Codons that differ in the 3rd base, may code for the same tRNA/amino acid.

Answer 17

Wobble

Question 18

Genetic code feature: read from a fixed starting point as a continuous sequence of bases

Answer 18

Nonoverlapping

Question 19

Genetic code feature: genetic code is conserved throughout evolution

Answer 19

Universal

Question 20

What sort of nitrogenous bases would be heavily present in the origin of replication?

Answer 20

AT-rich sequences

Question 21

Create a single or double stradned brea in the DNA helix to add or remove supercoils

Answer 21

DNA topoisomerases

Question 22

Reverse transcriptase that adds DNA (TTAGGG) to 3’ ends of chromosomes to avoid loss of genetic material with every duplication

Answer 22

Telomerase

Question 23

Subtype of point mutation: purine to purine or pyrimidine to pyrimidine

Answer 23

Transition

Question 24

Subtype of point mutation: purine to pyrimidine or vice versa

Answer 24

Transversion

Question 25

Nucleotide substitution but codes for the same amino acid; often base change in 3rd position of the codon

Answer 25

Silent mutation

Question 26

Nucleotide substitution resulting in changed amnio acid

Answer 26

Missense mutation

Question 27

Nucleotide substitution resulting in premature stop codon. Usually results in a nonfunctional protein

Answer 27

Nonsense mutation

Question 28

Deletion or insertion of a number of nucleotides not divisible by 3, resulting in a misreading of all nucleotides downstream.

Answer 28

Framshift mutation

Question 29

Mutation at a splice site, retained intron in the mRNA, protein with impaired or altered function.

Answer 29

Splice site mutation

Question 30

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

Answer 30

Nucleotide excision repair

Question 31

Inability to repair DNA pyrimidine dimers caused by UV exposure. Dry skin, extreme light sensitivity, skin cancer. Defect of exinucleases in nucleotide excision repairs

Answer 31

Xeroderma pigmentosum

Question 32

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.

Answer 32

Base excision repair

Question 33

Which type of DNA repair is critical in repair of spontaneous/toxic deamination?

Answer 33

Base excision repair

Question 34

Newly synthesized strand is recognized, mismatched, nucleotides are removed, and the gap is filled and resealed. Occurs predominantly in S phase of cell cycle

Answer 34

Mismatch repair

Question 35

What process is defective in Lynch syndrome, also known as hereditary nonpolyposis colorectal cancer (HNPCC)

Answer 35

DNA mismatch repair

Question 36

Brings together 2 ends of DNA fragment to repair double-stranded breaks. No requirement for homology. Some DNA might be lost.

Answer 36

Nonhomologous end joining

Question 37

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

Answer 37

Homologous recombination

Question 38

What process is defective in breast/ovarian cancers with BRCA1 mutation?

Answer 38

Homologous recombination

Question 39

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)

Answer 39

Promoter

Question 40

DNA locus where activator regulatory proteins bind, increase expression of a gene on the same chromosome

Answer 40

Enhancer

Question 41

DNA locus where repressor regulatory proteins bind, decreasing expression of a gene on the same chromosome

Answer 41

Silencer

Question 42

_____ and _____ may be located close to, far from, or even within the gene whose expression they regulate

Answer 42

Enhancers and silencers

Question 43

What is preprocessed mRNA called? (First aid uses a different term then we did)

Answer 43

heterogeneous nuclear RNA (hnRNA)

Question 44

What is the cap added in 5' end mRNA processing?

Answer 44

7-methylguanosine

Question 45

What is added on the 3' end of processed mRNA?

Answer 45

polyadenylation / poly A tail

Question 46

What is a good way to remember how RNA polymerases are numbered?

Answer 46

They're numbered in the order they're used. I - rRNA, II - mRNA, III - tRNA

Question 47

Product(s) of RNA Polymerase I

Answer 47

rRNA

Question 48

Product(s) of RNA Polymerase II

Answer 48

mRNA and snRNA

Question 49

Product(s) of RNA Polymerase III

Answer 49

5s rRNA, tRNA

Question 50

Small noncoding RNA molecules that posttranscriptionally regulate gene expression by targeting the 3' untranslated region of specific mRNAs for degradation or translational repression.

Answer 50

microRNAs (miRNAs)

Question 51

What's on the 3' end of a tRNA

Answer 51

CCA acceptor stem for covalent binding to amino acids

Question 52

Function of the T arm on tRNA, which features a TΨC sequence

Answer 52

Tethers the tRNA molecule to the ribosome

Question 53

Arm of tRNA which is used in recognizion by the correct aminoacyl-tRNA synthetase

Answer 53

D-arm

Question 54

What charges tRNA with the correct amino acid

Answer 54

Aminoacyl-tRNA synthetase

Question 55

What are the triphosphate nucleotides used for charging tRNA and then translocation, respectively?

Answer 55

ATP and GTP

Question 56

Sites of a ribosome

Answer 56

A Site: incoming aminoacyl-tRNA P Site: accomodates growing peptide E Site: holds empty tRNA as it exits