Chapter 10: DNA Structure

X-Ray diffraction

Provides info about structures of molecules

Rosalind Franklin

An English chemist and X-Ray crystallographer who, despite rampant sexism, worked on DNA structure in early 1950s.

Nucleotides

Used as cellular energy and signaling factors

5-carbon sugar (ribose or deoxyribose)

Phosphate group/Pentose Sugars

Nitrogenous base ( A, C, T, G, U)

Purines

Made up of 2 aromatic rings

(A,G)

Pyrimidine

Made up of 1 aromatic ring

(C, U, T)

Nucleoside Monophosphate

Strands of DNA, and RNA (AMP, GMP, etc.)

Nucleoside Diphosphate

Energy storage by adding another phosphate group or energy release by cleaving extra group (ADP, GDP, etc.)

DNA Triphosphate

Energy release by cleaving phosphate group(s) (ATP, GTP, etc.)

DNA Helix

Made of polynucleotide chains

Sugar-Phosphate Backbone

The hydroxyl of a nucleotide sugar (deoxyribose) attaches to the phosphate of the next nucleotide

1’

Attaches to the nitrogenous base, important for base-pairing with other strand

2’

attaches to either -OH (ribose) or -H (deoxyribose), helps differentiate DNA vs. RNA

3’

attaches to the OH group, which attaches to (P) of the next nucleotide, important for sugar phosphate backbone.

4’

attaches to the 5’ carbon, important to form sugars cyclical structure

5’

attaches to phosphate group important for sugar phosphate backbone

Chargoff’s Rule

For a given species, you can identify the approximate percentage of each nucleotide

Double Helix

Two strands of DNA

Antiparallel

Each strand is the opposite direction of each other

3 components of nucleotides

Pentose Sugar, Nitrogenous Base, Phosphate Groups

Pentose Sugar

Ribose or Deoxyribose

Nitrogenous Base

DNA: A, C, T, G, and RNA: A, U, C, G

Phosphate Group

Mono, Di, Tri

Nucleobase

Nitrogenous base (e.g. adenine)

Nucleoside

Nitrogenous base + pentose sugar (e.g. adenosine)

Nucleotide

Nitrogenous base + sugar + phosphate (e.g. adenosine triphosphate)

A-DNA

Right-Handed Double Helix

Forms under low hydration conditions

2.3nm width, 11bp/turn

B-DNA

Right-Handed Double Helix

Common form under normal physiological conditions

2nm width, 10bp/turn

Z-DNA

Left-handed Double Helix

Forms under high salt conditions

1.8nm width, 12bp/turn

DNA Methylation

Methyl groups added to nucleotide bases

related to gene expression in Eukaryotes

Affects the three dimensional structure of DNA

DNA Replication

In order to ensure each cell has a copy of DNA, cells must make an extra replica of DNA every time the cell divides.

Conservative

The 2 original strands come back together after DNA is replicated

Dispersive

copies of DNA are hybrids of original and new DNA

Semi-Conservative

Newly replicated DNA will include 1 of the original strands

Unidirectional

1 Fork

Bidirectional

2 Fork

Theta Replication

Occurs in circular DNA

1 Ori, usually bidirectional

Is a type of replication common in E.Coli and other organisms possessing circular DNA

Rolling-Circle Replication

Occurs in plasmids

(Prokaryotes and Viruses)

1 Ori, unidirectional

Takes place in some viruses and in the F factor of E.Coli

Linear DNA Replication

occurs in Linear DNA (eukaryotes) multiple ori, usually unidirectional

Takes place in Eukaryotic chromosomes

DNA polymerase

Is enzyme that “reads” the template strand and incorporates complementary base pairs into new strand

Adds nucleotides to make new strand

SSBs (Single-Stranded Binding Proteins)

Stabilizes ssDNA (single-stranded DNA), prevent hydrogen bonds between complementary bases from reforming

dNTPs

Nucleotides needed to add to the new strand

Primers

Short stretch of RNA that allows DNA polymerase to short

Molecules that are required to create the discontinuous strand

Mismatch Pair

If there is still an error after proofreading, other enzymes can come in to repair errors

Nucleotide Excision Repair

(a type of mismatch pair)

Nuclease removes a segment of DNA

DNA pol adds correct dNTPs

DNA ligase glues fragments back together

Lagging Strand

DNA made discontinuously to maintain 5’ → 3’ direction

Ligase

“Glues” fragments back together (they are enzymes)

Primase

Creates short RNA fragments, called primers, to help start DNA replication

Okazaki Fragments

Short sequences of DNA that are created as the lagging strand is made and link together to form a single, connected copy of DNA

Topoisomerase

relieves tension from unwinding, separates hydrogen bonds between complementary on opposite strands (eukaryotes)

Gyrase

relieves tension from unwinding, separates hydrogen bonds between complementary bases on opposite strands (prokaryotes)

Helicase

Unwinds DNA (dsDNA → ssDNA)

Leading Strand

New copy of DNA created continuously in 5’→ 3’

DNA alpha

If this enzyme is removing primers/filling some gaps (eukaryotes)

DNA pol 1

If this enzyme is removing primers/filing some gaps (prokaryotes)

DNA pol delta

If this enzyme is synthesizing the lagging strand (eukaryotes)

DNA pol 3

If this enzyme is synthesizing the lagging strand (prokaryotes)

Mismatch pair

If there is still an error after proofreading, other enzymes can come into repair errors

Nucleotide Excision Repair

a type of mismatch pair

nuclease removes a segment of DNA

DNA polymerase adds correct dNTPs

DNA ligase glues fragments back together

DNA Pol 1

removes/replaces primers

DNA Pol 2

DNA repair, restarts replication

DNA Pol 3

Elongates DNA

DNA Pol 4 and DNA Pol 5

DNA Repair

DnaA

A protein that binds to start replication

DNA Pol alpha

initiation of DNA synthesis, DNA repair

DNA Pol delta

Lagging strand synthesis, DNA repair

DNA Pol epsilon

leading strand, synthesis

Telomerase

Is a enzyme that is responsible for the replication of chromosome ends

MCM (minichromosome maintenance)

proteins that restrict application to ONOE per cell cycle, S-Phase

Are binded by Cdc6 and Cdt1

Cdc6

Cell division cycle 6

Cdt1

Chromatin licensing & DNA replication factor 1