DNA

Question 1

DNA is a polymer of ________ and stands for __________?

Answer 1

Nucleotides, deoxyribonucleic acid

Question 2

List the three components of DNA and what they are responsible for

Answer 2

phosphate backbone - acidity, stabilization
deoxyribose sugar (5 carbons = pentose monosaccharide) (carbohydrate) - stability, as the sugar can’t undergo alkaline hydrolysis
nitrogenous base - purine or pyrimidine containing nitrogen. The sequence of the bases determines genetic code.

Question 3

Nucleoside?

Answer 3

Pentose sugar + nitrogenous base

Question 4

Nucleotide?

Answer 4

Phosphate + pentose sugar + nitrogenous base

Question 5

State the structural difference between DNA and RNA’s ribose sugars

Answer 5

DNA will NOT have a hydroxyl group on the 2nd carbon hence deoxy, will also have thymine as a base.
RNA will have this hydroxyl, will have uracil as a base.

Question 6

Purines

Answer 6

2 ringed structure of a nitrogenous base. Adenine and guanine.

Question 7

Pyrimidines

Answer 7

1 ring structure of a nitrogenous base. Cytosine and thymine.

Question 8

DNA helix properties

Answer 8

Double stranded, hydrophobic bases in center, hydrophilic phosphate heads on outside. Hydrophobic bases interact with hydrogen bonds.

Question 9

DNA: ______ (base) always pairs with ________ (base) via 2 hydrogen bonds

Answer 9

Adenine + thymine

Question 10

DNA: ______ (base) always pairs with ________ (base) via 3 hydrogen bonds

Answer 10

cytosine + guanine

Question 11

RNA: ______ (base) always pairs with ________ (base) via 2 hydrogen bonds

Answer 11

Adenine + uracil

Question 12

Chargaff’s Rules

Answer 12

Purines : Pyrimidines = 1:1 (A+G = C+T)

Percent composition w/in purines and pyrimidines should be same: (purines: %A = %G and pyrimidines: %T = %C)

Question 13

When attached to a ribose sugar, what happens to the base names?

Answer 13

Add suffix “-osine” (purine) or suffix “-idine”

Question 14

When attached to a deoxyribose sugar, what happens to the base names?

Answer 14

The prefix “deoxy-“ is added to the nucleoside

Question 15

DNA replication is semi-conservative, explain.

Answer 15

Each strand unzips and acts as a template for a new strand. For each strand unzipped a new strand will be synthesized.

Question 16

Define the terms bidirectional and anti-parallel

Answer 16

Bidirectional: DNA replication originates at a specific site within the DNA (origin) and creates a replication bubble (the DNA is replicated in both directions) of two replication forks
Anti-parallel: 5’ phosphate is always opposite the 3’ hydroxyl

Question 17

Helicase

Answer 17

Enzyme that breaks the hydrogen bonds between nitrogenous bases of the template DNA. Unwinds the DNA.

Question 18

Topoisomerase

Answer 18

Works ahead of the replication fork to combat torsional forces by hacking and cleaving the DNA preventing supercoiling. If topoisomerase did not do this, the coiling would be too tight for polymerase to act.

Question 19

Single-stranded binding proteins!

Answer 19

After helicase breaks the hydrogen bonds the SSBPs bind to the strands to prevent annealing, to stabilize and maintain the single-stranded DNA template.

Question 20

Primase

Answer 20

Lays down complementary RNA primers which are used in the process of extending the DNA. DNA cannot be created from nothing so primers are needed.

Question 21

What bond links the phosphates of the 5th carbon of the deoxyribose sugar to the following nucleotide? (think, building up!)

Answer 21

Phosphodiester bond links the phosphate backbone together. Phosphates on the 5th carbon are linked to where the 3’ hydroxyl used to be. Phosphodiester bonds are created by the addition of the 5’ phosphate of a dNTP molecule to the 3’ hydroxyl group.

Question 22

Replication occurs in what direction?`

Answer 22

5’ to 3’.

Question 23

Replication from the RNA primer can occur as the helicase unwinds the DNA CONTINUOUSLY on which strand? Which enzyme replicates this strand?

Answer 23

Leading strand is replicated by DNA Polymerase 3 in E. coli

Question 24

On which strand are multiple primers necessary for replication? What are the fragments of replicated DNA called and which enzyme synthesizes them?

Answer 24

Lagging strand is replicated by DNA Polymerase 1 in E coli. The fragments of synthesized DNA are called Okazaki fragments

Question 25

In a replication bubble, the leading and lagging strands are switched for the two opposite replication forks. Why is this possible?

Answer 25

Helicase travels in opposite directions.

Question 26

How are RNA primers degraded?

Answer 26

Enzymatically degraded by RNases, endonucleases, or the proofreading function of DNA Pol 1.

Question 27

What are RNA primers replaced with and how are the replaced?

Answer 27

Replaced with new complementary DNA BASES by extending the Okazaki fragments using DNA Pol.

Question 28

DNA ligase

Answer 28

Repairs the phosphate backbone through the use of a phosphodiester bond at the nick

Question 29

Why does a lack of an Okazaki fragment for extension at the end of the chromosome create issues? What is this term known as?

Answer 29

Creates an overhang of single-stranded DNA which will be lost in one of the daughter cells because the other template strand will miss this information during further replication. Known as chromosome shortening.

Question 30

What are the functions of telomeres?

Answer 30

Prevent chromosome shortening. A repetitive nucleotide sequence is added in tandem (called a telomere) and provides a disposable buffer at the ends of chromosomes.

Question 31

What process causes telomere shortening? Which enzyme can replenish telomeres and how does it accomplish this?

Answer 31

Cell division. Telomerase can replenish telomeres using it’s own RNA template for the replication and extension of telomeres.

Question 32

Telomere shortening is thought to be the cause of what?

Answer 32

Senescence (cellular ageing) where cells have a limit to the number of times they can divide.