Biochemistry

Question 1

Heterochromatin

Answer 1

Condensed, appears darker on EM. Transcriptionally inactive, sterically inaccessible.

HeteroChromatin = Highly Condensed.  
Barr bodies (inactive X chromosomes) are heterochromatin .

Question 2

Euchromatin

Answer 2

Less condensed, appears lighter on EM. Transcriptionally active, sterically accessible.

Eu = true
“truly transcribed”

Question 3

DNA methylation

Answer 3

Template strand cytosine and adenine are methylated in DNA replication, which allows mismatch repair enzymes to distinguish between old and new strands in prokaryotes

DNA methylation at CpG islands represses transcription.

CpG Methylation Makes DNA Mute

Question 4

Histone methylation

Answer 4

Usually reversibly represses DNA transcription, but can activate it in some cases depending on methylation location.

Histone Methylation Mostly Makes DNA Mute.

Question 5

Histone acetylation

Answer 5

Relaxes DNA coiling, allowing for transcription.

Histone Acetylation makes DNA Active.

Question 6

NucleoSide

Answer 6

base + (deoxy)ribose (Sugar)

Question 7

NucleoTide

Answer 7

base + (deoxy)ribose + phosphaTe

linked by 3’-5’ phosphodiester bond

Question 8

PURines

Answer 8

2 rings
PURe As Gold
Adenine
Guanine

GAG - amino acids necessary for purine synthesis:
Glycine
Aspartate
Glutamine

Question 9

PYrimidines

Answer 9

1 ring
CUT the PY (pie)
Cytosine, Uracil, Thymine (Thymine has a methyl)

Deamination of cytosine makes uracil
Uracil in RNA; Thymine in DNA

Question 10

Hydrogen bonding between DNA bp

Answer 10

G-C bond (3 H bonds) stronger than A-T bond (2 H bonds).

Higher G-C content —> Higher melting temp of DNA

Question 11

De novo synthesis

Answer 11

refers to the synthesis of complex molecules from simple molecules such as sugars and amino acids, as opposed to recycling after partial degradation

Ex: nucleotides are not needed in the diet as they can be constructed from small precursor molecules such as formate and aspartate.

Various immunosuppressive, antineoplastic, and antibiotic drugs function by interfering with nucleotide synthesis

Question 12

Leflunomide

Answer 12

Disrupt pyrimidine synthesis

Inhibits dihydroorotate dehygrogenase

Question 13

Methotrexate (MTX)

Answer 13

Disrupt pyrimidine synthesis

inhibit dihydrofolate reductase (decreases [dTMP]) in humans

Question 14

Trimethoprim (TMP)

Answer 14

Disrupt pyrimidine synthesis

inhibit dihydrofolate reductase (decreases [dTMP]) in bacteria

Question 15

Pyrimethamine

Answer 15

Disrupt pyrimidine synthesis

inhibit dihydrofolate reductase (decreases [dTMP]) in protozoa

Question 16

5-fluorouracil (5-FU)

Answer 16

Disrupt pyrimidine synthesis

forms 5-F-dUMP, which inhibits thymidylate synthase (decreases dTMP)

dTMP = deoxythymidine monophosphate

Question 17

6-mercaptopurine (6-MP) and its prodrug azathioprine

Answer 17

Disrupt purine synthesis

inhibit de novo purine synthesis

Question 18

Mycophenolate

Answer 18

Disrupt purine synthesis

inhibit inosine monophosphate dehydrogenase

Question 19

Ribavirin

Answer 19

Disrupt purine synthesis

inhibit inosine monophosphate dehydrogenase

Question 20

Hydroxyurea

Answer 20

Disrupts purine and pyrimidine synthesis

inhibits ribonucleotide reductase

Question 21

Adenosine deaminase deficiency

Answer 21

ADA is required for degradation of adenosine and deoxyadenosine.

In ADA deficiency,
increased dATP –> toxicity in lymphocytes

One of the major causes of autosomal recessive SCID

Question 22

Lesch-Nyhan syndrome

Answer 22

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

Findings: intellectual disability, self-mutilation, aggression, hyperuricemia (orange “sand” [sodium urate crystals] in diaper), gout, dystonia.

HGPRT:
   Hyperuricemia 
   Gout
   Pissed off (aggression, self-multilation)
   Retardation (intellectual disability)
   DysTonia

Question 23

Unambigous

Answer 23

Genetic code features

Each codon specifies only 1 amino acid

Question 24

Degenerate/redundant

Answer 24

Genetic code features

Most amino acids are coded by multiple codons

Exceptions: methionine and tryptophan encoded by only 1 codon (AUG and UGG, respectively)

Question 25

Commaless, nonoverlapping

Answer 25

Genetic code features

Read from a fixed starting point as a continuous sequence of bases

Exceptions: some viruses

Question 26

Universal

Answer 26

Genetic code features

Genetic code is conserved throughout evolution.
Exception in humans: mitochondria

Question 27

DNA replication

Answer 27

Eukaryotic DNA replication is more complex than the prokaryotic process but uses many enzymes analogous to those listed below. In both prokaryotes and eukaryotes, DNA replication is semiconservative and involves both continuous and discontinous (Okazaki fragment) synthesis

Question 28

Origin of replication

Answer 28

Particular consensus sequence of base pairs in genome where DNA replication begins.

May be single (prokaryotes) or multiple (eukaryotes)

AT-rich sequences are found in promoters and origins of replication

Question 29

Replication fork

Answer 29

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

Question 30

Single-stranded binding proteins

Answer 30

Prevent strands from reannealing

Question 31

Helicase

Answer 31

Unwinds DNA template at replication fork

Question 32

DNA topoisomerases

Answer 32

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

Topoisomerase inhibitors:
fluoroquinolones - prokaryotic topoisomerase II [DNA
gyrase] and topoisomerase IV
etoposide/teniposide - eukaryotic topoisomerase II

Question 33

Primase

Answer 33

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