Unit 2: 8

Question 0

What is the sense strand?

Answer 0

The sense strand carries the coded genetic information

Question 1

Discuss the central dogma of molecular biology

Answer 1

DNA->RNA-> Protein
genetic info is stored in the DNA - most common form is double stranded DNA composed of two antiparellel strands linked through complementary base pairing - Chargaff’s rule (A with T and C with G)

Question 2

What is the anti-sense strand?

Answer 2

The anti sense strand consists of a complementary sequence of bases oriented in the opposite direction

Question 3

From where is genetic information transcribed?

Answer 3

the anti-sense strand serves as the template for synthesis of the messenger RNA (mRNA) with the same base sequence 5’-3’ as the sense strand of the double helical DNA except that uracil replaces thymine (T)

Question 4

in what direction if messenger RNA translated into a sequence of amino acids ?

Answer 4

From N-terminus to C- terminus -read from 5’-3’

Question 5

define gene

Answer 5

a unique sequence of DNA that provides the complete instructions to make a functional product called a protein

Question 6

Nucleotide

Answer 6

sugar, phosphate, base

Question 7

Nucleoside

Answer 7

just sugar and base - side = simple so missing phosphate just sugar and bas

Question 8

what kind of bond links nucleotides

Answer 8

phosphodiester

Question 9

what is the directionality of the polymeric chain?

Answer 9

5’-3’

Question 10

pyrimidine bases

Answer 10

C, T and U

contain a flat plannar 6 member ring with two nitrogens- the bond between the pyrimidines and the sugar-phosphate is between position 1 on the pentose sugar to position 1 (-N) in the pyrimidine

Question 11

purines

Answer 11

A and G - a flat plannar 6 member ring fused to a 5 member ring with two nitrogens each -the bond between the purines and the sugar-phosphate is from position 1 on the pentose sugar to position 9 (-N) of the purine

Question 12

Modified bases in DNA

Answer 12

5 methyl cytosine -influences packaging of chromosomal DNA important for X chromosome inactivation.
-5 hyroxymethylcytosine ; may regulate gene expression by inducing DNA demethylation, found at high level in the CNS

Question 13

Modified bases in RNA

Answer 13

• hypoxanthine: found in the anticodon of tRNA, also used in purine biosynthesis
• pseudouracil: found in tRNAs
• N6-methyladenosine: found in mRNAs and may affect gene expression and splicing

Question 14

adenine phosphoribosyltransferase

Answer 14

a salvage enzyme that recovers purine bases

catalyzes the formation of adenylate
adenine + PRPP -> adenylate + PPi (pyrophosphate)

Question 15

Hypoxanthine-guanine phosphoribosyltransferase (HGPRT)

Answer 15

a salvage enzyme that recovers purines -catalyzes the formation of guanylate as well as inosinate (IMP) a precursor of guanylate and adenylate

guanine + PPRP -> adenylate + PPi
Hypoxanthine + PPRP -> inosinate + PPi

Question 16

Gout

Answer 16

• impaired excretion or overproduction of uric acid
• uric acid crystals precipitate into joints (Gouty arthritis), kidneys, ureters (stones)
• lead impairs uric acid excretion -lead poisoning from pewter drinking goblets
• Xanthine oxidase inhibitors inhibit the production of uric acid, and treat gout
• Allopurinol treatment: hypoxanthine analog that binds to Xanthine Oxidase to decrease uric acid production

Question 17

Lesch- Nyhan syndrome

Answer 17

• rare inherited disorder caused by deficiency of the enzyme HGPRT
• causes increased level of hypoxanthine and guanine (lead to increased degradation to uric acid)
• also causes accumulation of PRPP and stimulates production of purine nucleotides (and thereby increases their degradation)
• causes gout like symptoms, but also neurological symptoms: spasticity, aggressiveness and self-mutalation
• first neuropsychiatric abnormality that was attributed to a single enzyme

Question 18

Cellular functions of nucleotides

Answer 18

• building blocks for nucleic acid polymers, DNA and RNA
• energy carriers ATP and GTP
• important components of coenzymes; FAD, NAD(P)+ and co-enzyme A
• precursors for second messengers: cAMP, cGMP
• activated intermediates in many biosynthetic pathways: eg S-adenosylmethionine (SAM) as methyl donor

Question 19

Structural features of the B DNA double helix

Answer 19

1. Right handed helx
2. The plane of the base is perpendicular to the S-P backbone
3. One turn of the helix equals 10.5 base pairs (34 Angstroms or 3.4 nm)
4. The twisting of the helix forms major and minor grooves

Question 20

What factors influence the helix conformation of DNA?

Answer 20

1. certain sequences of bases
2. salt conditions
3. base modifications
4. conditions of relative humidity

Question 21

A- DNA

Answer 21

a. Right handed
b. 1 bp repeating unit
c. 11 bp/turn
d. 28 Angstroms

-most likely found in dehydrated living cells -NDA-RNA hybrid or dsRNA

Question 22

z- DNA

Answer 22

a. left- handed strand
b. 2 bp repeating unit
c. 12 bp/turn
d. 45 Angstroms

-not favorable however alternating purine-pyrimidine sequence (esp poly(dGC)2, negative supercoiling or high salt and some cations can induce z- DNA conformation

Question 23

Hoogsteen base pairs

Answer 23

1% of the time cells are in this transient state where the purine base flip from their normal anti conformation to a syn conformation and form a different set of hydrogen bonds with their pyrimidine partners

Question 24

Tm of DNA

Answer 24

the temperature at which one half of the DNA molecule has melted

Question 25

Name the factors that influence the Tm of a given DNA molecule

Answer 25

1. G and C content of DNA -because there are three hydrogen bonds stronger and harder to break 2. Ionic strength- Tm is proportional to the salt concentration, high salt concentration (excess NaCl in solution stabilizes double stranded DNA by binding to negatively charged phosphates in backbone and decreasing repulsion between chains 3. pH: Tm is inversely proportional to the pH. High concentrations of OH denature DNA by forming hydrogen bonds with bases thereby stabilizing single stranded DNA 4. Other Reagents: reagents that can form hydrogen bonds with bases (and thus stabilize the single-stranded DNA) decrease Tm

Question 26

Hybridization of DNA

Answer 26

when single stranded DNA bound to a surface, such as nylon or a glass microchip, can still renature with a complementary DNA or RNA sequence

Question 27

High stringency

Answer 27

at or close to the Tm- only perfect matches can form

Question 28

Low stringency

Answer 28

below the Tm -under conditions that stabilize the double helix (high salt or low temp) imperfect bases can form