BIOCHEMISTRY

Question 1

Chromatin Structure to fit into the nucleus

Answer 1

Beads on a string. Histone octamer to form a nucleosome

Question 2

Gives positive and negative charges to DNA respectively

Answer 2

Phosphate (-) and Lysine and Arginine (+)

Question 3

Does mitochondria utilize histones?

Answer 3

No. They have their own which is circular

Question 4

Condensed, Transcriptionally inactive

Answer 4

Heterochromatin

Question 5

Example of heterochromatin

Answer 5

Barr Bodies

Question 6

Phase where DNA and histone synthesis occur?

Answer 6

S phase

Question 7

Less condensed chromatin, transcriptionally active, sterically accessible

Answer 7

Euchromatin

Question 8

Changes the expression of DNA segment without changing the sequence. Involved in genomic imprinting, x-chromosome inactivation, repression of transposable elements, aging, and carcinogenesis

Answer 8

DNA methylation

Question 9

Within what gene promoter region does methylation repress gene transcription?

Answer 9

CpG

Question 10

Usually causes reversible transcriptional suppression, but can also cause activation depending on location of methyl groups.

Answer 10

Histone methylation. (Histone Methylation Mostly Makes DNA Mute.

Question 11

Allows transcription and relaxes DNA coiling.

Answer 11

Histone Acetylation

Question 12

Components of nucleoside

Answer 12

Base + Deoxyribose (sugar)

Question 13

Components of Nucleotide

Answer 13

Base + Deoxyribose + phosphate

Question 14

Linkage of both nucleoside and nucleotide

Answer 14

3’-5’ phosphodiester bond

Question 15

Number of rings for purine and pyrimidine respectively

Answer 15

2 and 1

Question 16

Deamination of cytosine will form?

Answer 16

Uracil

Question 17

Deamination of adenine will form?

Answer 17

Hypoxanthine

Question 18

Deamination of guanine will form?

Answer 18

Xanthine

Question 19

Deamination of 5-methylcytosine will form?

Answer 19

Thymine

Question 20

Methylation of uracil makes what?

Answer 20

Thymine

Question 21

Of the two base pair bonds, A-T and G-C, which is stronger?

Answer 21

G-C (3>2), higher G-C content, higher melting temperature of DNA.

Question 22

Amino acids necessary for purine synthesis.

Answer 22

Glycine, Aspartate, Glutamine

Question 23

Inhibits both purine and pyrimidine synthesis by inhibiting ribonucleotide reductase

Answer 23

Hydroxyurea

Question 24

Inhibits purine synthesis by inhibiting de novo purine synthesis. Give its prodrug form also.

Answer 24

6-MP, 6-Mercaptourine (azathioprine)

Question 25

Inhibit purine synthesis by inhibiting inosine monophosphate dehydrogenase.

Answer 25

Mycophenolate and ribavirin

Question 26

Inhibits pyrimidine synthesis by inhibiting dihydroorotate dehydrogenase

Answer 26

Leflunomide

Question 27

Inhibits drihydrofolate reductase (lower deoxythymidine monophosphate/dTMP in humans, bacteria, and protozoa respectively

Answer 27

Methotrexate (MTX), Trimethoprim (TMP), pyrimethamine

Question 28

Where does CPS 1 usually occur?

Answer 28

Mitochondria (urea cycle)

Question 29

Where does CPS2 occur?

Answer 29

Cytosol

Question 30

Enzyme deficiency that is One of the major causes of autosomal recessive SCID. Higher dATP may cause lymphotoxicity.

Answer 30

Adenosine deaminase deficiency (ADA is required for degradation of adenosine and deoxyadenosine)

Question 31

Enzyme deficiency due to defective purine salvage due to absent HGPRT which converts hypoxanthine to IMP and guanine to GMP. Results in excess uric acid production and de novo purine synthesis. X-linked recessive

Answer 31

Lesch-Nyhan Syndrome

Question 32

Common findings of Lesch-Nyhan Syndrome

Answer 32

``` Hyperuricemia Gout Pissed off(aggression, self-mutilation) Retardation (intellectual disability) Dystonia ```

Question 33

Clinical feature of hyperuricemia in the laboratory

Answer 33

Orange sand (sodium urate crystals) in diaper

Question 34

Treatment for Lesch-Nyhan Syndrome

Answer 34

Allopurinol or febuxostat

Question 35

Genetic code feature where each codon specifies only 1 amino acid

Answer 35

Unambiguous

Question 36

Genetic code feature where most amino acids are coded by multiple codons.

Answer 36

Degenerate/redundant

Question 37

Codons that differ in 3rd position may code for the same tRNA/amino acid. Specific base pairing is usually required only in the first 2 nucleotide positions of mRNA codon

Answer 37

Wobble/Wobble theory

Question 38

Genetic code feature where the DNA is read from a fixed starting point as a continuous sequence of bases

Answer 38

Commaless, nonoverlapping (except in some viruses)

Question 39

Genetic code features where the genetic code is conserved throughout evolution (except in humans-mitochondria)

Answer 39

Universal

Question 40

Semiconservative, involves both continuous and discontinuous (Okazaki fragments) synthesis and occurs in 5’-3’ direction

Answer 40

Eukaryotic DNA replication

Question 41

Particular consensus sequence of base pairs in genome where DNA replication begins. May be single (prokaryotes) or multiple (eukaryotes)

Answer 41

Origin of replication

Question 42

Found in promotors and origins of replication

Answer 42

AT-rich sequences (TATA box regions)

Question 43

Y-shaped region along DNA template where leading and lagging strands are synthesized

Answer 43

Replication form

Question 44

Unwinds DNA template at replication fork

Answer 44

Helicase

Question 45

Prevents strands from reannealing

Answer 45

Single-stranded binding proteins

Question 46

Create a single- or double-stranded break in the helix to add or remove supercoils

Answer 46

DNA topoisomerase

Question 47

Makes an RNA primer on which DNA polymerase III can initiate replication

Answer 47

Primase

Question 48

In eukaryotes: _________ inhibit topoisomerase I, while _______ inhibit topoisomerase II

Answer 48

Irinotecan/topotecan | Etoposide/teniposide

Question 49

In prokaryotes, _______ inhibit TOP II (DNA gyrase) and TOP IV

Answer 49

Fluoroquinolones

Question 50

Used by prokaryotes only. Elongates leading strand by adding deoxynucleotides to the 3’ end. Elongates lagging strand until it reaches primer of preceding fragment

Answer 50

DNA polymerase III

Question 51

Proofreads each added nucleotide

Answer 51

3’-5’ exonuclease

Question 52

Drugs blocking DNA replication often have a _______ thereby preventing addition of the next nucleotide (“chain termination”h

Answer 52

Modified 3’OH

Question 53

Prokaryotic only. Degrades RNA primer; replaces it with DNA. Same functions as DNA polymerase III, also excises RNA primer with 5’-3’ exonuclease

Answer 53

DNA polymerase I

Question 54

Catalyzes the formation of a phosphodiester bond within a strand of double-stranded DNA (joins Okazaki fragments)

Answer 54

DNA ligase

Question 55

Eukaryotes only. A reverse transcriptase (RNA-dependent DNA polymerase) that adds DNA TO 3’ ends of chromosomes to avoid loss of genetic material with every duplication

Answer 55

Telomerase

Question 56

Sequence of telomerase

Answer 56

TTAGGG

Question 57

Purine-purine or pyrimidine-pyrimidine

Answer 57

Transition

Question 58

Purine-pyrimidine or pyrimidine-purine

Answer 58

Transversion

Question 59

Nucleotide substitution but codes for same/synonymous amino acid; often base change in 3rd position of codon (tRNA wobble)

Answer 59

Silent Mutation

Question 60

Nucleotide substitution resulting in changed amino acid (conservative if new amino acid is similar in chemical structure). Ex. Sickle cell disease (substitution of glutamic acid with valine)

Answer 60

Missense mutation

Question 61

Nucleotide substitution resulting in early stop codon (UAA, UAG, UGA). Usually results in non-functional protein

Answer 61

Nonsense mutation

Question 62

Deletion or insertion of a number of a number of nucleotides not divisible by 3, resulting in misreading of all nucleotides downstream. Function may be disrupted or altered. Ex. (Duchenne muscular dystrophy, Tay-Sachs disease)

Answer 62

Frameshift mutation

Question 63

Retained intron in the mRNA; protein with impaired or altered function. Rare cause of cancers, dementia, epilepsy, some types of B-thalassemia

Answer 63

Splice site mutation

Question 64

Classic example of genetic response to an environmental change. Seen in the activity of E.coli in culture. Low glucose-high adenylate cyclase activity-high generation of cAMP from ATP- activation of catabolite activator protein (CAP)- increased transcription. High lactose-unbinds repressor protein from repressor/operator site-increased transcription

Answer 64

Lac operon gene activation