(Dr. Heinemann) (Unit C) Topic 14

Question 1

Purines

Answer 1

• 2 rings
• Adenine (A) and Guanine (G)

Question 2

Pyrimidines

Answer 2

• 1 ring
• Cytosine (C), Thymine (T), Uracil (U)

Question 3

What are purines and pyrimidines?

Answer 3

Nitrogenous bases

Question 4

What are the two major categories of nitrogenous bases?

Answer 4

1. Purines
2. Pyrimidines

Question 5

What shapes are nitrogenous bases?

Answer 5

• Flat
• Hydrogen bonding groups on the outside

Question 6

What types of bonds links nitrogenous bases together?

Answer 6

N-Glycosidic Bonds

Question 7

2 major types of nucleic acids in humans

Answer 7

1. Ribonucleic
2. Deoxyribonucleic

Question 8

Function:

DNA

Answer 8

• Holds genetic material

Question 9

Function:

RNA

Answer 9

• Template from which proteins are produced (mRNA)
• Ribosome formation (rRNA)
• Catalyzing protein synthesis (rRNA)
• Carrying amino acids to growing peptide chain (tRNA)
• Gene regulation
• mRNA splicing
• Telomere maintenance

Question 10

What are ribonucleotide/deoxyribonucleotide monomers comprised of?

Answer 10

• A monosaccharide
• A nitrogenous base
• A phosphate

Question 11

What is the difference between Uracil and Thymine?

Answer 11

Uracil lacks a methyl group

Question 12

Where are purines/pyrimidines joined to monosaccharides?

Answer 12

Joined to the anomeric (1’) carbon of ribose/deoxyribose
* Via N-Glycosidic Bond

Question 13

Nucleoside

Answer 13

Nitrogenous base joined to a sugar

Question 14

List:

The 5 common nucleosides

Answer 14

• Adenosine
• Guanosine
• Cytidine
• Thymidine
• Uridine

Question 15

Where do phosphates attach to on a nitrogenous base?

Answer 15

Attached to the 5’ position of ribose/deoxyribose

Question 16

What is the bond between phosphate and nitrogenous bases known as?

Answer 16

Phosphoester linkage

Question 17

Nucleotide

Answer 17

Has 3 groups:
* A nitrogenous base
* A sugar
* A phosphate group

Question 18

What is the notation of nucleotides?

Answer 18

1. Nitrogenous base
2. Number of phosphates

E.x. ADP (Adenosine Diphosphate)

• Sometimes deoxyribonucleotides will begin with a “d” (e.x. dTTP)

Question 19

Polynucleotide structure

Answer 19

Phosphate group at 5’ carbon on one pentose, forms phosphoester bond with hydroxyl group at the 3’ position of another pentose

Question 20

How are 5’ and 3’ ends determined in a polynucleotide?

Answer 20

• 5’ free carbon (not attached to anything) is 5’ end
• 3’ free carbon (not attached to anything) is 3’ end

Question 21

How are polynucleotides conventionally written?

Answer 21

5’ to 3’

Question 22

Oligonucleotides

Answer 22

“Short” (up to 200 base pairs)

Question 23

True or False:

Double helices are usually right handed

Answer 23

True

Question 24

What types of interactions between bases stabilize the double helix?

Answer 24

1. Base stacking
2. Base pairing

Question 25

Base stacking

Answer 25

As bases are planar aromatic rings, they can stack on top of each other and tstasbilize via interactions (London forces)

Question 26

Base pairing

Answer 26

Hydrogen bonding between chemical groups on edges of ring structure

Question 27

What are the different types of base pairings?

Answer 27

* C and G: 3 bonds * A and T: 2 bonds

Question 28

What form of double helices do DNA usually form?

Answer 28

B-DNA double helix

Question 29

What are certain features of B-DNA double helices?

Answer 29

1. Narrow (2 nm or 20 angstroms wide) 2. Long (1 human chromosome is 245 million base pairs) 3. Distance between consecutive bases is around 0.34 nm

Question 30

What are the two grooves in the sugarphosphate backbones known as?

Answer 30

* Major groove * Minor groove

Question 31

Major groove

Answer 31

The wider groove in B-DNA double helices

Question 32

Minor groove

Answer 32

The narrower groove in B-DNA double helices

Question 33

5 differences between RNA and DNA

Answer 33

1. Ribose vs. Deoxyribose 2. Uracil vs. Thymine 3. Shorter (few thousand nucleotides, usually) 4. Single stranded (folds into cocmplex 3D structures 5. More likely to chemically modify nitrogenous bases

Question 34

What can modified bases in RNA do?

Answer 34

Influence the secondary and tertiary structure of RNA

Question 35

Tm

Answer 35

The melting temperature * Temperature at which 50% of a specific dsDNA has become single stranded

Question 36

What types of factors determines the Tm?

Answer 36

* Intrinsic factors * Extrinsic factors

Question 37

Intrinsic factors that affect Tm

Answer 37

1. A:T / G:C ratio: More GC content, the higher Tm 2. Length: Longer means higher Tm 3. Degree of complementarity: Imperfect matches have lower Tm

Question 38

Extrinsic factors that affect Tm

Answer 38

1. Salt concentration: Increasing salt concentration increases Tm 2. Organic solent concentration: Lowers Tm (reduces base stacking interactions) 3. Hydrogen bonding compounds: Urea decreases Tm 4. pH: Extreme pH decreases the Tm | (these do not need to be memorized, except for pH)

Question 39

How is melting temperature approximated?

Answer 39

* 2 degrees Celsius for every AT * 4 degrees Celsius for every GC

Question 40

Chromatin

Answer 40

Organizes and packages DNA

Question 41

Histones structure

Answer 41

* Fewer than 200 amino acids * Many lysine and arginine residues

Question 42

Nucleosome core particle

Answer 42

Wrapped DNA and histone core proteins