DNA Intro

Question 1

What is heterochromatin and euchromatin?

Answer 1

Heterochromatin - (solenoid) tightly wound around histones - darker patches - genes not expressed
Euchromatin - loosely wound DNA - lighter patches - genes expressed

Question 2

What are the 3 opponents of a nucleotide

Answer 2

Sugar, phosphate, base

Question 3

What’s the difference between the major groove and minor groove?

Answer 3

The strand backbones are closer together on one side of the helix than on the other. The major groove occurs where the backbones are far apart, the minor groove occurs where they are close together. The grooves twist around the molecule on opposite sides

Question 4

How much DNA is in one cell?

Answer 4

DNA width is 2nm but the total length is 2m per cell

Question 5

Define histone

Answer 5

Histones are a family of basic proteins that associate with DNA in the nucleus and help condense it into chromatin. Nuclear DNA does not appear in free linear strands; it is highly condensed and wrapped around histones in order to fit inside of the nucleus and take part in the formation of chromosomes.

Question 6

How does DNA bind to histones?

Answer 6

Histones are basic proteins, and their positive charges allow them to associate with DNA, which is negatively charged. Some histones function as spools for the thread-like DNA to wrap around.

Question 7

What is a nucleosome?

Answer 7

Under the microscope in its extended form, chromatin looks like beads on a string. The beads are called nucleosomes. Each nucleosome is made of DNA wrapped around eight histone proteins that function like a spool and are called a histone octamer. Each histone octamer is composed of two copies each of the histone proteins H2A, H2B, H3, and H4. The chain of nucleosomes is then wrapped into a 30 nm spiral called a solenoid, where additional H1 histone proteins are associated with each nucleosome to maintain the chromosome structure.

Question 8

Describe genes

Answer 8

What?
  Genes carry the code for proteins
Where?
  Genes have a chromosomal location
How many?
  Humans have about 25,000 genes
  Fruitfly has about 15,000 genes
  E.coli has about 4,500 genes

Question 9

What is a genome?

Answer 9

What?
  Genome is the entire DNA sequence
  Human Genome is 24 chromosomes
  (22 plus 2 sex chromosomes X and Y)
Genes are on the same chromosome on the same location in each individual

Question 10

How many chromosomes in the human genome

Answer 10

22 autosomal

2 sex chromosomes

Question 11

What is a nucleic acid?

Answer 11

Nucleic acids are ‘polynucleotides’ = linear polymers of nucleotides

Question 12

What’s the difference between a nucleotide and a nucleoside?

Answer 12

A nucleoside consists of a nitrogenous base covalently attached to a sugar (ribose or deoxyribose) but without the phosphate group. A nucleotide consists of a nitrogenous base, a sugar (ribose or deoxyribose) and one to three phosphate groups

Question 13

What’s the difference between ribose and 2-deoxyribose?

Answer 13

2-deoxyribose has a H on C2 rather than OH

Question 14

What charge does a phosphate group. Have

Answer 14

-ve

Question 15

What are the 2 types of nitrogenous base?

Answer 15

Purine (2 C ring) - A and G

Pyrimidine (1 C ring) C T and U

Question 16

Give an example of a ribonucleotide

Answer 16

AMP

Question 17

Give an example of a deoxyribonucleotide

Answer 17

dAMP

Question 18

Name each nucleotide/nucleoside of ATCGU using nucleic acid nomenclature

Answer 18

Base
Nucleoside  Nucleotide
Adenine (A) Guanine (G) Uracil (U) Cytosine (C)
Adenosine Guanosine Uridine Cytidine
Adenosine monophosphate (AMP) 
Guanosine monophosphate (GMP) 
Uridine monophosphate (UMP) 
Cytidine monophosphate (CMP)

In DNA:
Base
Nucleoside  Nucleotide
Adenine (A) Guanine (G) Thymine (T) Cytosine (C)
Deoxyadenosine Deoxyguanosine Deoxythymidine Deoxycytidine
Deoxyadenosine monophosphate (dAMP) 
Deoxyguanosine monophosphate (dGMP) 
Deoxythymidine monophosphate (dTMP) 
Deoxycytidine monophosphate (dCMP)

Question 19

What type of bonds join nucleotides?

Answer 19

Phosphodiester

Question 20

What are the 2 ends of the chain

Answer 20

5’ P

3’ OH

Question 21

How do base pairs bond?

Answer 21

A-T (2 H bonds)
C-G (3 H bonds)
A-U (2 H bonds)

Question 22

What measures the length of a bond?

Answer 22

Angstroms

Question 23

How do DNA strands run in relation to each other

Answer 23

Antiparallel

Question 24

What is the convention of reading dna strands

Answer 24

5’ to 3’ left to right unless otherwise stated

Question 25

What is an equation to explain DNA replication

Answer 25

(dNMP)n + dNTP —-> (dNMP)n+1 + PPi

D = dna
N = any
M = mono
P = phosphate
T = tri

Question 26

Describe the model or dna replication

Answer 26

• separation of DNA strands
• stepwise reaction
• reaction driven by pyrophosphate hydrolysis
• chain growth is directional, from 5’ to 3’

Question 27

Describe dna replication in prokaryotes

Answer 27

Initiation
• Recognition of origin of replication
• Requires recruitment of DNA polymerase plus other specific proteins
• Requires a ‘kick-start’ by primase (as DNA polymerase can only extend a 3’end)

Elongation 
•  Moving replication forks 
• Helicase unwinds double helix 
• DNA polymerase extends 3’ ends only leading to leading strand (continuous), lagging strand (discontinuous) and Okazaki fragments
• DNA ligase joins fragments

Termination
When two facing replication forks meet and DNA ligase joins the final fragments