DNA and Chromosomes: Company

* Chapter 5
DNA and Chromosomes
Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton &

Company
Chapter Topics
THE STRUCTURE OF DNA

THE STRUCTURE OF EUKARYOTIC CHROMOSOMES
THE REGULATION OF CHROMOSOME STRUCTURE
Essential Cell Biology, Fifth Edition

Copyright © 2019 W. W. Norton & Company
The Structure of DNA
A DNA Molecule Consists of Two Complementary Chains
of Nucleotides
A DNA Molecule Consists of Two Complementary Chains of Nucleotides
Two strands of the DNA double helix are held together by H-bonds between
complementary base pairs
G and C (triple H bond) and A and T (double bond)
Two antiparallel chains oriented in opposing directions
Remember – structural polarity  5’ phosphate and 3’-hydroxyl
Right-handed helix with 10 bases per turn = coiling creates two grooves (major and
minor) Essential Cell Biology, Fifth Edition
The Structure of DNA Provides a Mechanism for Heredity
The exact correspondence between the 4-letter DNA alphabet and the 20 amino acid alphabet of
proteins – GENETIC CODE – is not obvious from the DNA structure
It took >10 years of experiments after the structure of DNA became defined to decipher this
We will soon discuss process of (1) TRANSCRIPTION (DNA to RNA) and (2) TRANSLATION
(RNA to PROTEIN)
The Structure of Eukaryotic
Chromosomes
Eukaryotic DNA Is Packaged into Multiple Chromosomes
 Isolated from cell undergoing
nuclear division/mitosis
 DNA is condensed
 Chromosome Painting 
chromosomes exposed to
ssDNA molecules conjugated
to fluorescent dyes
 HUMAN CELLS  contains 2 meters of DNA but cell nucleus is 5-8um in diameter
 Human DNA distributed into 23 or 24 different types of chromosomes
 These chromosomes are associated with proteins that fold and pack the fine DNA threads into compact structure =
CHROMATIN
 HUMAN CELLS  contain 2 copies of each chromosome (maternal and paternal – homologous chromosomes)
 3.2 X 109 nucleotide pairs of DNA in human chromosome set = HUMAN GENOME

Chromosomes
Chromosomes Organize and Carry Genetic Information
 A GENE = segment of dsDNA containing instructions for

producing a specific RNA or PROTEIN molecule
 Coding region can be found on either DNA strand (see orange

segments)
 Most RNAs are translated into PROTEINS while other RNAs are
the final product
 RNA have diverse functions as well – structural, catalytic, gene

regulatory roles
 In humans – total number of genes = 24,000
 GENES are interspersed amidst NON-CODING DNA
 Genome size to complexity of organism

 EXCEPTIONS
 i.e., Amoeba genomic is 60 times larger than humans
Chromosomes
Specialized DNA Sequences Are Required for DNA
Replication and Chromosome Segregation
 Cell Cycle: Interphase (G0, S, and G1) & Mitosis (Nuclear division)
 Interphase = DNA is duplicated/replicated
 Mitosis = DNA is segregated into daughter cells
 Remember the Mitotic Spindle which pulls the condensed chromosomes to each end of cell…….

Chromosomes
Specialized DNA Sequences Are Required for DNA
Replication and Chromosome Segregation
 Each chromosome = multiple ORIGINS OF REPLICATION

 Two TELOMERES = ends of each chromosomes as a protective cap
 One CENTROMERE = holds duplicated chromosomes together until they are pulled apart in Mitosis
Chromosomes
Interphase Chromosomes Are Not Randomly Distributed
Within the Nucleus
Interphase chromosomes are undergoing:

 Dynamic rearrangements
 Occupation of a specific region of nucleus
 Specific attachment to NUCLEAR ENVELOPE/NUCEAR LAMINA
This might hinder tangling of DNA…..
NUCLEOLUS  example of chromosomal organization

 rRNAs combine with proteins form = RIBOSOMES
Chromosomes
*Nucleosomes Are the Basic Units of Eukaryotic Chromosome
Structure
DNA binding Proteins:

 HISTONES
 NON-HISTONE (chromatin associated)
Both protein classes + DNA = CHROMATIN
 NUCLEOSOME = chromatin packing by histones
 8 HISTONE MOLECULES (abundant in positively

charged amino acids) on which DNA is wrapped
 Histone tails at N-terminus can be covalently
modified
 See figure for details
Chromosomes
Chromosome Packing Occurs on Multiple Levels

The Regulation of Chromosome
Structure
Changes in Nucleosome Structure Allow Access to DNA
 ATP-dependent CHROMATIN REMODELING COMPLEXES -  HISTONE MODIFYING ENZYMES

changes DNA position around nucleosomes  i.e., acetyl (Ac), phosphates (P), methyl groups (M)
 This can enable DNA to be more or less accessible  Affects packing of chromatin fiber
 Acetylation – looses chromatin structure
 Modification enable protein protein interactions
* Chapter 6
DNA Replication and Repair
Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton &

Company
Chapter Topics
*DNA REPLICATION
*DNA REPAIR
DNA Replication
Base-Pairing Enables DNA Replication
 Each strand (S or S’) serves as TEMPLATE for replication

1. Separation of strands
2. Each separated strand serves as template for producing new partner
strand
 DNA Replication is SEMI-CONSERVATIVE = each daughter dsDNA

contains 1 OLD and 1 NEW Strand
 Replication will be performed (copying of billion of nucleotide pairs) with

incredible speed and accuracy = performed by REPLICATION MACHINE

DNA Replication
Base-Pairing Enables DNA Replication

DNA Replication
DNA Synthesis Begins at Replication Origins
 dsDNA - very stable
 In lab can separate strands by boiling
 HOW DOES THIS HAPPEN IN OUR LIVING
CELLS?
 Begins by:
***INITIATOR PROTEINS that bind to specific
DNA sequences = REPLICATION ORIGINS
- it breaks H-bonds between bases
- in bacteria/yeast, it spans ~100 bp
- A-T rich
- Bacteria have 1 replication origin
- Human ~10,000 origins (220/ chromosome
This process attracts other proteins involved in

the DNA replication process…..

DNA Replication
Two Replication Forks Form at Each Replication Origin
 Y-shaped junctions = REPLICATION FORKS

 2 for each replication origin
 Replication machine moves along the DNA – opening up the two strands of dsDNA
 Each strand used as a template to make new daughter strands
 BIDIRECTIONAL- moving in opposite directions
 RATE = 1000 nucleotides per second in bacteria
 RATE = 100 nucleotides per second in humans
DNA Replication
DNA Polymerase Synthesizes DNA Using a Parental Strand
as a Template
Recall – Phosphodiester bonds (3’ - OH to 5’-phosphate); energy from incoming deoxyribonucleotide

- DNA Polymerase moves along the template
- Its structure determined by X-Ray Crystallography – it stays associated with DNA
DNA Replication
The Replication Fork Is Asymmetrical
LEADING STRAND
LAGGING STRAND
- DNA Polymerase moves ONLY 5’-to- 3’

- Backstitching Manoever – DISCONTINOUS STRAND – small pieces made at a time
OKAZAKI FRAGMENTS
DNA Replication
DNA Polymerase Is Self-correcting E-coli DNA Polymerase
(P) (E)
1 error every 107 nucleotide pairs
 DNA Polymerase carefully monitors  When it does make a mistake

base-pairing between nucleoside (rare), it can correct it
triphosphate and template strand  PROOFREADING ACTIVITY
 If correct, enzyme undergoes a small  Occurs at same time as DNA
structural change to catalyze synthesis
nucleotide-addition reaction

DNA Replication
DNA Polymerase Is Self-correcting

DNA Replication
Short Lengths of RNA Act as Primers for DNA Synthesis
HOW DOES DNA POLYMERASE (III)
BEGIN A NEW STRAND – ABSENCE
OF BASE_PAIRED END…….???
 RNA PRIMERS MUST BE

GENERATED
1. Synthesized by RNA Polymerase =

PRIMASE (No Proofreading activity)
2. It makes RNA (NOT DNA)
3. In 5’-to-3’ direction
4. ~10 nucleotides
5. Needs 2 nucleoside triphosphates
without the requirement of a based-
paried 3’-end
6. It uses RIBONUCLEOSIDE
TRIPHOSPHATES
7. Provides starting point for DNA
POLYMERASE
 Need 1 RNA primer on LEADING

STRAND
 Need RNA primers CONTINUOUSLY
on LAGGING STRAND at regular
intervals (~200 nucleotides)
 Previous RNA primer removed by
NUCLEASES & replaced by DNA
REPAIR POLYMERASE (I)
 Sealed with DNA LIGASE – creates
PHOSPHODIESTER BOND between
2 fragments (needs energy from ATP)
CLAMP LOADER (NEEDS
DNA Replication ATP) &
SLIDING CLAMP
Proteins at a Replication Fork Cooperate to Form a
Replication Machine
Need to pry
apart the DNA –
HOW?
DNA
HELICASES –
uses ATP as energy to
move forward
SINGLE
STRANDED
BINDING
PROTEINS –
keeps apart the DNA to
keep them from
reforming base pairs
and in an elongated
form for efficiency
DNA Replication
Replication Machine
 DNA TOPOISOMERASE – relieves TENSION from the excess TWISTIN

 Produces a transient SINGLE-STRANDED NICK in DNA BACKBONE AND
THEN RESEALS NICK BEFORE FALLING OFF DNA
DNA Replication
Replication Machine

DNA Replication
Telomerase Replicates the Ends of Eukaryotic Chromosomes
LAGGING STRAND Problem…..
Telomere Length Varies by Cell Type and with Age

DNA Repair
DNA Damage Occurs Continually in Cells
XERODERMA PIGMENTOSUM
- Patients cannot fix damage by UV

radiation
- They have a defective gene for repair

protein
- They have severe skin lesions – skin

cancer – due to accumulation of
mutations
 Although high fidelity and proofreading abilities of DNA polymerase prevens errors, rare mistake do happen
 Backup System = MISMATCH REPAIR PATHWAY – corrects 99% of these rare mistakes
 Improves overall accuracy to 1 mistake in 109 nucleotides synthesized
DNA Repair
Failure to Repair DNA Damage Can Have Severe
Consequences for a Cell or Organism
GLU to VAL amino acid change (6th

amino acid position)
Patient with 2 copies of mutant b-

globin gene will be sickle-cell anemia
Advantage – more resistant to

MALARIA than unaffected individuals
 parasite that causes malaria grows
poorly in RBCs that contain sickle-cell
form of hemoglobin..


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* Chapter 5

DNA and Chromosomes

Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton &

THE STRUCTURE OF DNA

Essential Cell Biology, Fifth Edition

Essential Cell Biology, Fifth Edition

 A GENE = segment of dsDNA containing instructions for

 Coding region can be found on either DNA strand (see orange

 RNA have diverse functions as well – structural, catalytic, gene

 In humans – total number of genes = 24,000

 GENES are interspersed amidst NON-CODING DNA

 Genome size to complexity of organism

Essential Cell Biology, Fifth Edition

 Each chromosome = multiple ORIGINS OF REPLICATION

Interphase chromosomes are undergoing:

NUCLEOLUS  example of chromosomal organization

DNA binding Proteins:

Both protein classes + DNA = CHROMATIN

 NUCLEOSOME = chromatin packing by histones

 8 HISTONE MOLECULES (abundant in positively

Essential Cell Biology, Fifth Edition

 ATP-dependent CHROMATIN REMODELING COMPLEXES -  HISTONE MODIFYING ENZYMES

DNA Replication and Repair

Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton &

 Each strand (S or S’) serves as TEMPLATE for replication

 DNA Replication is SEMI-CONSERVATIVE = each daughter dsDNA

 Replication will be performed (copying of billion of nucleotide pairs) with

Essential Cell Biology, Fifth Edition

Essential Cell Biology, Fifth Edition

- it breaks H-bonds between bases

- in bacteria/yeast, it spans ~100 bp

- Bacteria have 1 replication origin

- Human ~10,000 origins (220/ chromosome

This process attracts other proteins involved in

Essential Cell Biology, Fifth Edition

 Y-shaped junctions = REPLICATION FORKS

Recall – Phosphodiester bonds (3’ - OH to 5’-phosphate); energy from incoming deoxyribonucleotide

- DNA Polymerase moves ONLY 5’-to- 3’

 DNA Polymerase carefully monitors  When it does make a mistake

Essential Cell Biology, Fifth Edition

Essential Cell Biology, Fifth Edition

 RNA PRIMERS MUST BE

1. Synthesized by RNA Polymerase =

 Need 1 RNA primer on LEADING

 DNA TOPOISOMERASE – relieves TENSION from the excess TWISTIN

Essential Cell Biology, Fifth Edition

Telomere Length Varies by Cell Type and with Age

- Patients cannot fix damage by UV

- They have a defective gene for repair

- They have severe skin lesions – skin

GLU to VAL amino acid change (6th

Patient with 2 copies of mutant b-

Advantage – more resistant to

Essential Cell Biology, Fifth Edition

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