DNA structure and replication

Question 1

Deoxyribonucleic Acid (DNA)

Answer 1

Double-helix structure with deoxyribose-phosphate backbone, smallest unit of inheritance
Pic is RNA, the only difference is the OH group on the 2’ carbon
1’: DNA base
2’: H (why it is called deoxy..)
3’: Hydroxyl group: OH
4’: H
5’: Triphosphate group

Question 2

Leading Strand

Answer 2

3′ to 5′ template strand during DNA replication where the new DNA strand is synthesized continuously

Question 3

Primase

Answer 3

Enzyme that makes RNA primers during DNA replication, primers are necessary for DNA synthesis but not for RNA synthesis

Question 4

Why are RNA primers necessary for DNA replication?

Answer 4

These primers serve as starting points for DNA synthesis by providing a free 3’-OH group to which DNA polymerase can add nucleotides.

Question 5

DNA bases

Answer 5

Purine: Adenine; Guanine
Pyrimidine: Cytocine, Thymine
Pairs: A/T; G/C

Question 6

Deoxyribose

Answer 6

The sugar present in DNA

Question 7

DNA bases

Answer 7

Purine: Adenine; Guanine
Pyrimidine: Cytosine, Thymine; Uracil
Pairs: A/T; G/C

Question 8

Ligase

Answer 8

Enzyme that joins adjacent Okazaki fragments by forming a phosphodiester bond between the 3’ OH and the 5’ phosphate of adjacent Okazaki fragments

Question 9

phosphodiester

Answer 9

A phosphodiester bond is a chemical bond that links nucleotides together in nucleic acids such as DNA and RNA. It forms between the phosphate group of one nucleotide and the hydroxyl group of the sugar molecule in the adjacent nucleotide.

The formation of a phosphodiester bond occurs through a dehydration reaction, where a molecule of water is removed and the phosphate group of one nucleotide reacts with the hydroxyl group of another nucleotide. This results in the formation of a covalent bond between the phosphate group and the sugar molecule of the adjacent nucleotide.

Question 10

Chargaff’s Rule

Answer 10

In any DNA molecule, number of adenines equals the number of thymines, and the number of guanines equals the number of cytosines.

Question 11

Pyrimidine

Answer 11

One-ringed nitrogenous base: Cytosine, Thymine; Uracil (Pyrimidine base that replaces Thymine in RNA)

Question 12

DNA Polymerase I (Kornberg’s polymerase)

Answer 12

A type of DNA polymerase that fills in nucleotides between Okazaki fragments and corrects mistakes in the nucleotide sequence

Question 13

Purine

Answer 13

Two-ringed nitrogenous base; Adenine; Guanine

Question 14

Topoisomerase

Answer 14

Enzyme that regulates DNA supercoiling during biological processes like DNA replication by altering the conformation of DNA

Question 15

Polymerase

Answer 15

Enzyme that synthesizes polymers of nucleic acids during the synthesis of nucleic acids

Question 16

Okazaki Fragments

Answer 16

Short DNA fragments synthesized on the lagging strand during DNA replication

Question 17

Lagging Strand

Answer 17

5′ to 3′ template strand during DNA replication where the new DNA strand is synthesized discontinuously

Question 18

Nucleotide

Answer 18

Building block of DNA and RNA, made up of a nitrogenous base, a pentose sugar (deoxyribose in DNA, ribose in RNA), and a phosphate group

Question 19

Exonuclease

Answer 19

Enzyme that removes one or a few nucleotides from the end of a nucleic acid molecule

Question 20

What bonds are holding the complementary base pairs?

Answer 20

Hydrogen bond

Question 21

Why is DNA always synthesized in 5’ to 3’ direction?

Answer 21

Bacause the triphosphate group is highly reactive. If it is 3’ to 5’, risks the whole chain break off

Question 22

Nucleotide

Answer 22

Building block of DNA and RNA, made up of a nitrogenous base, a pentose sugar (deoxyribose in DNA, ribose in RNA), and a phosphate group
dATP
dGTP
dCTP
dTTP

Question 23

DNA replication process

Answer 23

Topoisomerase –> RNA primase –> RNA primer –> DNA polymerase –> Ligase –>

Question 24

Origin of replication

Answer 24

The origin of replication (ORI) is a specific sequence of DNA where the process of DNA replication is initiated. This is the site where the replication machinery, consisting of enzymes and other proteins, binds to and begins the process of unwinding the DNA double helix and copying the genetic material.

In prokaryotes, such as bacteria, the ORI is typically a relatively short sequence of DNA that is rich in adenine-thymine (AT) base pairs, since these base pairs are easier to separate than the guanine-cytosine (GC) base pairs. The ORI usually contains several binding sites for the proteins that initiate and regulate DNA replication.

In eukaryotes, the ORI is more complex and can be several hundred to several thousand base pairs long. The eukaryotic ORI contains multiple binding sites for initiator proteins and other factors that regulate DNA replication. In addition, the eukaryotic ORI is often flanked by regions of DNA that contain regulatory sequences, which help to control when and how frequently DNA replication occurs.