DNA Structure And Replication

Question 1

Polymer composed of nucleotide building blocks

Chemical basis of hereditary and is grouped into genes, which are the fundamental units of genetic information

Doxynucleotides covalently linked by 3’5’-phosphodiester bonds:

• DeoxyAdenylate
• DeoxyGuanylate
• DeoxyCytidylate
• Thymidylate

Double helix structure with major and minor grooves

Contained in the cytoplasm of prokaryotes and in the nucleas of eukaryotes

Answer 1

DNA (deoxyribonucleic acid)

Question 2

DNA structure

Answer 2

3’5’ Phosphodiester bonds

• 5’-OH group attached to 3’-OH group
• strands have directionality
• bonds are cleaved hydrolytically by chemicals or hydrolyzed enzymatically by exonucleasesmor endonucleases

Question 3

Strands run into opposite directions

Answer 3

Antiparallel strands

Question 4

Held together by hydrogen bonds and hydrophobic interactions

Adenine to thymine

Guanine to cytosine

Answer 4

Complementary base pairing

Question 5

Chargall’s Rules

Answer 5

In any sample of dsDNA, the amount of adenine equals the amount of THYMINE, the amount of guanine equals the amount of CYTOSINE

the total amount of PURINES equals the total amount of pyrimidines

Question 6

Temperature at which one half of the helical structure is lost (denaturation)

Under appropriate conditions, renaturation (annealing) may occur

Answer 6

Melting temperature

Question 7

Structural forms of the double helix

Answer 7

B-DNA

A-DNA

Z-DNA

Question 8

Right-handed helix with ID residues per 360* turn of the helix

Answer 8

B-DNA

Question 9

Moderately dehydrated B form, also right-handed with about 11 base pairs per turn

Answer 9

A-DNA

Question 10

Left-handed helix that contains about 12 base pairs per turn, naturally in regions of alternating purines and pyrimidines

Answer 10

Z-DNA

Question 11

Five classes of small, positively charged proteins that form ionic bonds with negatively charged DNA

2 each of histones H2A, H2B, H3 and H4 form a structural core around which DNA is wrapped creating a nucleosome

The DNA connecting the nucleosome is called LINKER DNA, and is bound to histone H1

High in ARGININE and LYSINE

Answer 11

HISTONES

Question 12

Further packing of DNA due to hydrophobic interactions and in association with other non-histone proteins compacts it into chromatin

Answer 12

HETEOCHROMATIN

EUCHROMATIN

Question 13

Densely packed and transcriptionally inactive chromatin during interphase, observed by electron microscopy

Answer 13

Heterochromatin

Question 14

Transcriptionally active chromatin that stains less densely

Answer 14

Euchromatin

Question 15

Also called nucleofilament

Nucleosomes that are packed more tightly

Organized into loops that are anchored by a nuclear scaffold containing several proteins

Answer 15

Polynucleosome

Question 16

Properties of DNA

Answer 16

1. Coding regions are often interrupted by intervening sequences
2. More than half of the DNA in eukaryotic organisms is in unique or nonrepetitive sequences
3. At least 30% of the genome consists of repetitive sequences 1% of cellular DNA is in mitochondria
   - each strand serves as a template for complementary daughter strand
   - each strand becomes part of the daughter strand

Question 17

Prokaryotic DNA synthesis

Answer 17

Begins at the origin of replication (one in prokaryotes, multiple in eukaryotes), a short sequence composed almost exclusively of AT base pairs

Strands are separated locally, forming two replication forks

Replication of double stranded DNA is bidirectional

STEP 1: DNA A PROTEIN
- group of proteins that recognize the origin of replication

STEP 2: HELICASE
- unwind the double helix ahead of the advancing replication fork

STEP 3: SINGLE-STRANDED DNA-BINDING PROTEINS
- maintain the separation of the parental strands

STEP 4: DNA TOPOISOMERASES

• remove supercoils that interfere with the further unwinding of the double helix
• two types: TYPE I - SWIVELASE (cleaves one strand); TYPE II - GYRASE (cleaves both strands, target of quinolone antibiotics)

STEP 5: PRIMASE
- synthesize short stretches of RNA called primers, needed by DNA polymerase to begin in DNA chain elongation

STEP 6: DNA POLYMERASE II

• catalyzes chain elongation, using 5’-deoxyribonucleic triphosphate substrates
• proofreads the newly synthezied DNA using its 3’–> 5’ exonuclease activity
• DNA polymerases are only able to read the template in the 3’ –> 5’ direction and synthesize in the 5’–> 3’ direction
• thus, DNA is synthezised in the opposite direction in both strands: leading strand, lagging strand (with formation of Okazaki fragments)

STEP 7: DNA POLYMERASE I
- removes RNA primers using its 5’–> 3’ exonuclease activity, and fills in the resulting gaps

STEP 8: LIGASE
- seals the nicks between Okazaki fragments and catalyzes the final phospholipid ester linkage

Question 18

Central dogma

Answer 18

Replication

Transcription

Translation