Nucleic Acids: Carriers of Biological Information

Question 1

What is the central dogma?

Answer 1

DNA–>RNA–>protein

Question 2

Number of chromosomes (total and of each kind)

Answer 2

46 total
44 autosomes (22 pairs)
2 sex chromosomes (1 pair)

Question 3

Classes of RNA species in human cells

Answer 3

(3)
Structural RNAs
Regulatory RNAs
Information containing RNAs

Question 4

Structural RNAs

Answer 4

rRNA
tRNA
snRNA
snoRNA

Question 5

Information containing RNAs

Answer 5

mRNA

Question 6

Regulatory RNA

Answer 6

miRNA

siRNA

Question 7

Purines

Answer 7

Adenine and Guanine

two rings: imidazole and pyrimidine rings

Question 8

Pyrimidines

Answer 8

Cytosine, Uracil, Thymine

one ring

Question 9

Nucleoside

Answer 9

sugar (ribose or deoxyribose) + base (purine or pyrimidine)

Ex: adenosine, guanosine, thymidine, cytosine, uridine

Question 10

Nucleotide

Answer 10

base+sugar+phosphate group

Question 11

Deoxyribonucleotides

Answer 11

dAMP, dGMP, dTMP, dCMP

Question 12

Ribonucleotides

Answer 12

AMP, GMP, UMP, CMP

Question 13

Relative solubility of 5 components of nucleotides

Answer 13

pyrimidines>purines
nucleotides>nucleosides>bases

*Gout and Lesch-Nyhan disease: build of of purines of low solubility in tissues

Question 14

Nucleotide and deoxynucleotide residues in RNA and DNA are joined by _______ into strands with _______ polarity

Answer 14

phosphodiester linkages

5’–3’ polarity

Question 15

Nucleoside Di and Tri phosphates

Answer 15

base (purine/pyrimidine)+ sugar(ribose/deoxyribose)+ 2-3 phosphates (ADP, ATP, GDP, GTP, etc.)

Question 16

Phosphodiester bond

Answer 16

3’ OH attacks 5’ alpha phosphate; Leads to two alcohols esterically bound to molec of phosphoric acid (C-O-P-O-C)

Question 17

Chargaff’s Rule

Answer 17

DNA from any cell should have 1:1 ratio of purine and pyrimidine bases
%G=%C
%A=%T

Question 18

Avery, McCloud and McCarty

Answer 18

Experiment:
Live encapsulated virulent bacteria to mouse–>dies
Live nonencapsulated nonvirulent bacteria to mouse–>lives
Heat virulent bacteria (kill/denature)–>mouse lives
Denatured fatal bacteria into live nonvirulent bacteria–>mouse dies
Live nonvirulent bacteria mixed w/ DNA from virulent–>mouse dies
protein doesn’t transfer genetic info, DNA does

Question 19

Hershey and Chase

Answer 19

Bacteriaphage: radioactive label for DNA (exp 1) radio label for protein coat (exp 2)
Label showed in new bacteriaphages ONLY in exp 1–> DNA transfers genetic material, not protein

Question 20

Franklin and Wilkins

Answer 20

XR diffraction of DNA showing helical structure, 10 layer lines, 3.4 nm repeat

Question 21

B form DNA:

two strands intertwined in _____ helix

Answer 21

right handed

Question 22

DNA backbone are ____ to each other

Answer 22

anti-parallel

5’–>3’ and 3’–>5’

Question 23

Where is the sugar phosphate backbone? bases?

Answer 23

on outside of helix

stacked on inside

Question 24

How many steps for DNA to get back to same position?

Answer 24

10

Question 25

Major groove and minor groove lengths

Answer 25

Major: 22 A (proteins like tfs usually make contact w/ bases in major groove, easier to access) Minor: 12 A

Question 26

What are the two factors important to the stability of the DNA (overcome negative charge on each phosphate)?

Answer 26

1. ) Hydrogen bonds (A:T 2 H bonds, C:G 3 H bonds) | 2. ) Stacking energies (hydrophobic interactions)

Question 27

Factors affecting Tm.

Answer 27

1. Salt Concentration 2. pH extremes 3. Increases in DNA chain length (increase Tm) 4. Increasing GC content (increase Tm, 3 H bonds for GC)

Question 28

Why does salt concentration affect Tm?

Answer 28

High salt, higher Tm because positive charges stabilize negative charges on phosphate groups.

Question 29

Why do extremes of pH affect Tm?

Answer 29

Extreme pH affects the ionization states of the groups on the bases which provide/accept H bonds

Question 30

Major covalent modification of human DNA?

Answer 30

Covalent methylation of cytosine at 5' C in CpG sequences. | Add methyl group, repress transcription, silence gene.

Question 31

Methylation of adenine

Answer 31

In bacteria like E. coli, methylation of adenine helps DNA repair enzymes identify older strands of DNA, which are used as a reference for repairing damage during DNA replication.

Question 32

De-amination of bases

Answer 32

Exposure to nitrous acid precursors can cause loss of amine group from base. 5mC:G can be changed to T:G w/ deamination. Leads to T:G mismatch. Mismatch can be fixed, but T has 50% chance of remaining. MAJOR CAUSE OF MUTATION.

Question 33

Depurination

Answer 33

Remove purine (base) from sugar (break beta glycosyl bond linkage). After depurination, backbone is sensitive to breakage.

Question 34

Oxidative damage

Answer 34

-OH (reactive oxygen free radical) from mitochondria can damage DNA, -OH groups on bases disrupt structure

Question 35

UV light damage

Answer 35

UV light can cause adjacent thymine to covalently bond to one another. (kink in DNA)

Question 36

Base alkylation and examples

Answer 36

Reaction of alkylating agents forms large covalent adducts to DNA, can cause issues w/ replication and transcription. Ex: Carcinogens, benzene, dimethylnitrosamine, nitrogen mustard, dimethylsulfate, [Cisplatin-->cancer drug, similar mech]

Question 37

Ex of intercalation

Answer 37

doxorubicin (chemotherapeutic agent), actinomycin D (natural)

Question 38

What do etoposide and camptothecin do?

Answer 38

chemotherapeutics that target topoisomerases which are needed to relax DNA supercoiling. (Drugs interfere, thus leaving breaks in DNA that can't be repaired)

Question 39

Linear vs circular DNA locations

Answer 39

linear: in nuclear chromosome circular: mitochondria only

Question 40

Underwound DNA produces _______

Answer 40

negative supercoils, decreased twist

Question 41

Overwound DNA produces_____

Answer 41

positive supercoils, increased twist

Question 42

What do topoisomerases do?

Answer 42

They "relax" supercoiling by breaking the DNA backbone. | Needed for DNA replication.

Question 43

DNA polymerization

Answer 43

DNA is added 5' to 3'. 3' OH nuclophilic attack of 5' alpha phosphate.

Question 44

Nucleoside analogues

Answer 44

Used to be antiviral drugs that halt viral DNA replication. On 3' C, there is not and OH group, there is N=N=N (Azide) or Hydrogen. No nucleophilic attack of phosphate, so replication stops. (AZT, ddl-->HIV treatment)

Question 45

DNA and RNA similarities

Answer 45

2 pyrimidines, 2 purines 5C sugar, phosphate group, base Sugar-phosphate backbone Adenine, Guanine, Cytosine

Question 46

DNA and RNA Differences

Answer 46

Uracil vs. Thymine Single strand vs. Double strand Ribose vs Deoxyribose sugar DNA more stable than RNA DNA codes for RNA, RNA codes for protein RNA has enzymatic function too, DNA is info storage Diff protein interactions (RNA pol vs DNA pol) RNA has greater flexibility, structural capacity almost to protein level

Question 47

Why is RNA unstable?

Answer 47

3' OH can act as a nucleophile and attack nearby phosphate, thereby destabilizing the backbone. (RNA more susceptible to hydrolysis.)

Question 48

Puromycin

Answer 48

An antibiotic that mimics the 3' acceptor end of tRNA that is charged with an aa. It can bind in the ribosome and covalently attach to growing poplypeptide chain, thus stopping translation. Steptomyces makes it, and also has enzyme to stop it.

Question 49

RNA hairpin folds using ______ connections

Answer 49

AU, GU, GC base pairs

Question 50

Information containing RNAs do what?

Answer 50

mRNA: translated into proteins

Question 51

Structural RNAs do what?

Answer 51

tRNA, rRNA, snRNA (small nuclear RNA). tRNA and rRNA form machinery to convert mRNA into protein (rRNA provides peptidyl transferase activity) (tRNA transfers amino acid to growing chain at ribosomal site of protein synth) snRNA splices mRNA from longer initial forms rRNA is a ribozyme (has enzymatic activity)

Question 52

Regulatory RNAs do what?

Answer 52

use base-pairing and interaction w/ proteins to up or down regulate cellular processes like transcrip and translation (microRNAs, small interfering RNAs)