DNA Structure and Replication

Day 1
 DNA Structure
• DNA: Deoxyribonucleic acid
• Chromosomes are made of DNA pieces
coiled around proteins called histones.
• Eukaryotic cells have many strands of
DNA in the nucleus. Each strand
becomes one chromosome (many
chromosomes)
• Most prokaryotic cells (bacteria) have
one circular DNA molecule (1 chromosome)
 Prokaryotic Chromosome
Section 12-2
Structure

Chromosome

E. coli, a bacterium
Bases on the
chromosome
(circular DNA)
 Eukaryotic Chromosome
Structure
Section 12-2
DNA
double
helix
Chromosome Nucleosome

Coils
Supercoils

Histones
 DNA is ….
• DNA is an organic macromolecule (Nucleic Acid)
• DNA is a polymer
• 2 types of nucleic acids: DNA and RNA
• The monomers (basic building blocks) of nucleic
acids are NUCLEOTIDES

• DNA is made of
– 2 strands connected
– Shape of a twisted ladder
– DOUBLE HELIX
 Nucleotides
Nucleotides are made up of:
•Deoxyribose: a sugar
•Phosphate
•Nitrogen Base:
– Adenine = A
– Guanine = G
– Cytosine = C
– Thymine = T
 Section 12-1
DNA Nucleotides
Adenine Guanine Cytosine Thymine

Phosphate
Deoxyribose
group

- The sugar and phosphate molecules are held

together by covalent bonds (strong bonds).
- Sugar and phosphate make the sides or rails of the
double helix (ladder)
Nucleotides and Pairing: A-T C-G
 Structure of DNA
Section 12-1

Nucleotide
Hydrogen
bonds

Sugar-phos
phate
backbone
 DNA complementary strands
• For simplicity, the 2 DNA strands are
represented by the sequence of nitrogen bases
AT C G AA C G T TA
TA G C T T G C AAT
• Write the complementary DNA strand:
AT C G G G T TAA C G TAT C C

• The sequence of bases in one strand is

the code to make a particular protein
 The People Behind
1. 1949: Erwin Chargaff
discovers the rules of
base pairing
- Studied the amount of each DNA
base in different organisms
- Using this information he
discovered the rules of base
pairing

A-T
C-G
2. 1952: Rosalind Franklin and Maurice
Wilkins determined that the DNA
molecule was a coiled spiral.
- Franklin used x-ray photographs of DNA to describe
the shape and size of DNA (X-ray diffraction)
3. 1953: James
Watson (USA)
and Francis
Crick (UK)
determine the
exact structure
of DNA – a
double helix
• Received the
Nobel Prize in
1962
 DNA Replication
(=chromosome copy)
• This is the duplication of chromosomes that
we will study during cell division
• Occurs in the nucleus of eukaryotes and in the
cytoplasm of prokaryotes
• Occurs during interphase in eukaryotes
• There are approximately 3 billion pairs of
nucleotides in human body cells (3 billion in
haploid)
• It takes about six hours to copy all your DNA
 DNA Replication is SEMI-CONSERVATIVE:
Duplicated DNA is 50% original, 50% new
Original strand = Template

Complementary
New Strand

Original strand = Template

 Models of DNA Replication
• Alternative models
– conservative and dispersive were disproven through
experimentation
conservative semiconservative dispersive

2
 Steps of Replication
1. Enzymes unwind and unzip the DNA double
helix
(The enzyme helicase breaks up the
H-bonds between the nitrogen bases
separating the 2 strands)
2. The enzyme DNA polymerase brings
complimentary nucleotides and attaches them
to the matching nucleotides in the open
strands
- The 2 original strands of DNA are called templates
- The newly formed strands are called complementary
 DNA Replication
Section 12-2

New strand DNA

polymerase

DNA polymerase

New strand Original

= complementary strand
strand
If you’re interested, here are some more details:
 Why is DNA important to a cell?
• It is a code that provides a set of instructions
that tells your cells how to make proteins.
• The Genetic Code is the sequence of DNA
nucleotides
• We are all different because we have a different
sequence of DNA
Why are Proteins important?
• Your body is made up of proteins.
• Proteins are made of amino acids joined
together.
 Why are Proteins important?
• Make your body: Bones, muscles, tendons,
ligaments, hair, skin, nails, etc. are made of proteins
• Enzymes: Proteins that drive chemical reactions in
your body. (DNA replication, formation of spindle
fibers, cellular respiration, digestion of food)

• Hormones: Chemical messengers that travel

through your bloodstream and help your body work.
• Estrogen, Testosterone, Insulin

• Antibodies: Proteins that function as part of your

immune system to keep you healthy.
 RNA and Protein Synthesis
(Transcription & Translation)
Day 2
 RNA and Protein Synthesis
Remember:
• The DNA molecule (in the nucleus) contains all
the instructions to make proteins
• The instructions are the sequence of
nucleotides in DNA – the sequence of letters
in a segment of DNA
• A gene is a sequence of nucleotides (letters)
in the DNA molecule
• BUT… This sequence has to be translated into
amino acids
 RNA is ….
• RNA: Ribonucleic Acid
• RNA is a macromolecule
(Nucleic Acid)
• The monomers (basic building
blocks) of nucleic acids are
NUCLEOTIDES
• RNA:
– ONE single strand
– Found inside and outside the
nucleus
 RNA - Ribonucleic acid
• RNA is single stranded
• Made of nucleotides:
– 5-C Sugar (Ribose)
– Phosphate group
– Nitrogen Bases:
Adenine - Uracil
Cytosine – Guanine
• There are 3 types of
RNA:
mRNA, tRNA; rRNA
 The 3 Types of RNA
1. Messenger RNA
(mRNA)
• Carries information from DNA
in the nucleus -- to the
ribosomes in the cytoplasm.
• mRNA is a copy of a section of
the DNA.
• mRNA contains genetic
information.
• CODON: sequence of 3
nucleotides in mRNA. It codes
for one amino acid.
2. Transfer RNA (tRNA)
• Transports amino acids
from the cytoplasm to the
ribosomes during protein
synthesis
• ANTICODON: sequence of 3
nucleotides on the tRNA.
• The tRNA anticodon
matches the mRNA codon.
3. Ribosomal RNA (rRNA)
• Ribosomes are made of ribosomal RNA
(rRNA)
• mRNA brings the message from the DNA in the
nucleus to the ribosome (rRNA). The tRNA
brings the corresponding amino acids.
• The ribosomes allow mRNA and tRNA to work
together to join amino acids making proteins.

This is a ribosome: rRNA

 DNA vs. RNA
Deoxyribonucleic Acid Ribonucleic Acid

1. Double stranded 1. Single stranded

2. Sugar is deoxyribose 2. Sugar is ribose
3. N-bases are 3. N-bases are
A, T, C, G A, U, C, G
4. Cannot leave the 4. Can leave the
nucleus nucleus
5. One type 5. Three types:
mRNA, tRNA, rRNA
 Protein Synthesis:
Making Proteins
• Cells make proteins by joining together different
AMINO ACIDS
• The DNA code determines the ORDER of these
amino acids. But DNA cannot leave the nucleus.
• RNA is used to help assemble amino acids into
proteins.
• The 3 types of RNA help in making proteins
mRNA, tRNA, rRNA

• Protein Synthesis = Transcription + Translation

1. Transcription: from DNA to mRNA
• Transcription is the
process of making
messenger RNA
(mRNA) from a DNA
template (original)

• DNA must be copied into

mRNA because DNA
cannot leave the
nucleus
Transcription (cont.): Making mRNA
1. The DNA unzips and
RNA bases attach to the
exposed bases of the
DNA strand, making a
strand of mRNA
2. mRNA separates from
the DNA template
3. mRNA leaves the
nucleus and goes to
the ribosomes (in the
cytoplasm)
• mRNA is made in
the nucleus using
DNA as the
template (blueprint
or original)

• mRNA leaves the

nucleus and travels
to the ribosome to
make proteins
 2. Translation: from mRNA to Protein
1. mRNA travels from the nucleus to the
ribosome
2. tRNA picks up free amino acids from the
cytoplasm and brings them to the ribosome
3. The tRNA anticodon attaches to the mRNA
codon and releases the amino acid
5. Another tRNA brings another amino acid and a
chain of amino acids begins to form
6. Eventually a STOP codon appears in the
mRNA marking the end of the protein.
Protein
Synthesis:
----------------
Transcription
+
Translation
The Genetic Code: mRNA codons
• A sequence of
3 nucleotides
in mRNA codes
for one amino
acid
• AUG=Methionine
(This is the start
codon)
• UCA = Serine
• GCG = Alanine
• AAA = Lysine
• UGA = Stop
 Protein Synthesis

Transcription Translation
DNA mRNA Protein
Nucleus Ribosome
(cytoplasm)

t-RNA
Brings amino acids
to the ribosome
Mutations
Day 4
 Mutations
• Mutation: A change in the DNA sequence
– Mutations alter (change) genes
• Mutations can be:
- harmful (deleterious) to the organism
EX: Cancer, sickle cell anemia
- neutral - have no effect
EX: hair color
- beneficial
EX: skin color
A gene is a sequence of DNA that codes for a protein
(and determines a trait /characteristic).
 Gene
Sequence

Start signal Gene Stop signal

 Types of Mutations
1. GENE MUTATIONS: Mutations that
produce changes in a single gene
a. Point mutations
b. Frameshift mutations

2. CHROMOSOMAL MUTATIONS:
changes in the number or structure of
chromosomes
 1. Gene Mutations: Changes in the
DNA sequence of a particular gene.

A. Point Mutation
Change in one or a
few bases.
One base is changed
to another:
substitution
Substitutions
usually affect a
single amino
acid
Sickle Cell Anemia
• Problem: a point mutation in
the gene that codes for
hemoglobin, the protein that
carries the oxygen.
• Normal hemoglobin makes
normal red blood cells.
• Mutated hemoglobin changes
the shape of the cells. Sickled
red blood cells get stuck in
narrow blood vessels,
damaging organs. It can be
fatal.
1 amino acid out of 237 is
different!!
B. Frameshift
Mutation
These mutations occur
when a base is
inserted or deleted
from the DNA
sequence.
Insertions and
deletions affect the
reading frame of a
protein by shifting
the codons.
 Cystic Fibrosis: 3 DNA bases
deleted (inherited disease)
Chromosome
#7

CFTR
gene
The cells in the
3 DNA bases are The transport lungs can’t
missing. The amino protein in the cell transport chloride
acid phenylalanine is membrane does ions. As a result, the
missing from a not work lungs become
protein in the cell clogged with a thick
membrane. mucus.
 Eukaryotic Chromosome
Structure
Section 12-2
DNA
double
helix
Chromosome Nucleosome

Coils
Supercoils

Histones
 2. Chromosomal Mutations:
Changes in the number and structure of
chromosomes (involves many genes)
A. Deletion: a piece of chromosome is lost

B. Duplication: a piece of chromosome is

duplicated
C. Inversion: a piece of chromosome is
reversed or flipped around

D. Translocation: A piece of chromosome

breaks off and attaches to another
 Are mutations good or bad?
• Mutations that cause drastic changes in the
structure of a protein can be deleterious (cystic
fibrosis, sickle cell anemia) ☹
• If the change affects only one base, the
mutation may be neutral because the amino
acid sequence may not change
• Some mutations are the source of genetic
variability (variation) in species, and these
changes can be beneficial. ☺
 Are all mutations passed to the
offspring?
• Only mutations that occur in the
reproductive cells (gametes) can be
passed to the offspring.

• Mutations that occur in the body cells

(somatic) affect the living individual but
are not passed to the offspring.
 Mutagens or mutagenic agents
• Mutagens: a natural or human-made agent
which can change the structure or
sequence of DNA.
- Chemicals: Asbestos, Mustard gas.
(Poisoned gas used in World Wars I and II,
cause mutations in cells)
- Radiation: X-rays, UV radiation (Ultraviolet
light). UV radiation damages the DNA in the
skin cells and the cells cannot control cell
division. It causes skin cancer.
The Cell Cycle and Mitosis
(Cell Division)
Day 5
 Unit 5:
Cell Cycle
Mitosis

Mitosis
The Cell Cycle: Cell Division /Mitosis
Why do cells divide?

» GROWTH
» DEVELOPMENT
» REPAIR
The Cell Cycle: Cell Division /Mitosis
Why do cells divide?
• GROWTH
– Larger organisms have more cells
– Limits to cell size 🡪 diffusibility

Will diffusion
occur faster
though a large
cell or a small
cell?
Agar Cube Lab
The Cell Cycle : Cell Division / Mitosis
Why do cells divide?

• DEVELOPMENT
– Multi-cell organisms
begin as single cell,
then # of cells
increases.
– As # of cell increases
🡪 specialization
The Cell Cycle : Cell Division / Mitosis
Why do cells divide?
• REPAIR
– Make new cells to heal a wound
– Replace old or damaged cells
 During the Cell Cycle
• a cell grows while doing its job
• prepares for division, and
• divides to form 2 daughter cells.

• Cell must prepare!

– Genetic information must be copied first so both
daughter cells gets a complete copy.
MITOSIS
– Cytoplasm must be evenly divided.
CYTOKINESIS
 The Cell Cycle has 2 main stages:
1. Interphase
• cell growth
• DNA replication
• prep for mitosis
• 78% of cell’s life

2. Cell Division
• Mitosis
• Cytokinesis
• 22% of cell’s life
1. Interphase- Longest phase of cell cycle
Phases of Interphase:
• G1 = Growth 1 phase
“Everyday” “Normal” period of cell’s life:
– Cell grows.
– Cell carries out its function.

• S = Synthesis phase
– DNA in form of chromatin is copied (duplicated)
– Cell prepares for division - duplicates all organelles

• G2 = Growth 2 phase
– Cell makes molecules needed for division;
continues to grow
2. CELL DIVISION:
i. Mitosis (PMAT) ii. Cytokinesis

Mitosis and
Cytokinesis
overlap!
 First a DNA primer….
DNA in its most DNA wraps Histones (protein)
condensed form around to condense into
chromatin.

DNA in its unraveled

condensed form
DNA molecule wrapped
around histones

DNA molecule
Duplicated chromosomes are
attached to each other at the
centromere, and are called
sister chromatids
How many chromosomes in the left picture?
in the right picture?

From: https://learnedify.blogspot.com/2019/03/the-cell-is-basic-structural-and.html
 1. Prophase
• DNA condenses • LABEL: centrioles,
(coils together) and nuclear membrane,
the chromosomes chromosomes, sister
become visible chromatids, cell
membrane, centromere
• Nuclear membrane
disappears
• Centrioles
separate
Prophase
 2. Metaphase
• LABEL: centrioles,
• Chromosomes centromere,
line up in the chromosomes,
middle of the cell spindle fibers
(equator)
• Chromosomes
connect to the
spindle fibers
 Metaphase

Chromosomes are aligned

along the equator of a
dividing cell

Notice the spindle fibers

produced by the centrioles
 3. Anaphase
• Centromeres divide • LABEL: centrioles,
centromere,
• Sister chromatids chromosomes,
separate and move spindle fibers
to opposite poles
(apart)
 Anaphase

Spindle fibers pull apart

sister chromatids
 4. Telophase
• Chromosomes reach the opposite ends of the
cell
• Nuclear membrane forms again
• Cell begins to split in half

Pinch = Cleavage Furrow

Telophase

Cytokinesis
begins

You can see

the cell
membrane
developing
between the
two cells
 Cytokinesis
• Cytoplasm splits in half forming 2 daughter
cells
• In animal cells the cell membrane pinches
inward → forms cleavage furrow.
• In plant cells, a cell plate forms between
the 2 daughter cells.
Cytokinesis in animal cell
→ note cleavage furrow
Cytokinesis
in a plant cell
 Cancer
(Uncontrolled Cell Division)
Day 6
Cells Don’t Continuously Grow Larger

Small cells with a high SA : V

ratio are most efficient

To remain small, cells have a

cycle through which they grow
and divide in a controlled
manner
- The Cell Cycle
The Cell Cycle
 Importance of a normally functioning cell cycle:

- Timing of cell division

- So that cells divide only when they
are supposed to divide
- Rate of cell division
- So that cells do not divide too
quickly or too slowly

- If these are not properly

regulated, the health of the
organism may be negatively
impacted
Cells progress through the cell cycle at different rates

- Timing and rate of cell division varies

by organism and cell type
How is progress through the cell cycle controlled?

Proteins
- Cyclins
- “The key”
- Binds to CDK

Enzymes

- Cyclin-Dependent Kinases (CDKs)

- “The ignition”
- Starts various activities of the
cell cycle
Checkpoints

- “Stop signs” that are

meant to halt the
cell cycle if anything
goes wrong

- If cyclin does not

bind with CDK, the
cell will not move on
to the next phase
What are the checkpoints checking?

G1 Checkpoint - Rest or divide?

- No DNA damage
- Sufficient resources
S Checkpoint - DNA ok?
- No errors during DNA replication
G2 Checkpoint - Fully equipped?
- DNA without damage
- Complete chromosome set
- Enough cells parts
M Checkpoint - Are any sister
chromatids unattached?
- All sister chromatids attached to
spindle fibers
Checkpoints
- Checkpoints will stop
the cell cycle if
something goes wrong
- This protects organisms
from replication of
damaged cells

- If the cell detects errors

that can be repaired, the
cell will do so
- If the cell detects errors
that cannot be repaired,
apoptosis may be
triggered
Apoptosis

Programmed cell death

- Removes damaged cells, such as precancerous and
virus-infected cells
- Also part of normal development
Apoptosis - development, life cycles, and protection

- Removes webbing between

fingers during
development
- Allows leaves to fall as
seasons change
- Removes cells damaged
beyond repair (e.g.
sunburn peeling)
- Helps protect against
development of cancerous
growth
Cancer

- Uncontrolled growth and

division of cells
- Caused by failure in
regulation of the cell
cycle
- When unchecked, cancer
cells can crowd out normal
cells and kill an organism
- Normal apoptosis
procedures fail
Cancerous Cells and the Cell Cycle

- Cancerous cells spend

more of their time
dividing (in mitosis)
and
- less time carrying out
normal cell functions
(in interphase)
Cancer terminology

- Tumor - abnormal
lump or growth of cells
- Malignant - cancerous
; can spread to other
tissues and organs

- Metastasis - spread of cancer cells from their primary location

(the organ in which the cancer began) to another region of the
body

- Benign - non-cancerous ; won’t spread

- Biopsy - procedure of taking a sample of cells, which are

then analyzed under a microscope
What causes cancer?

- Genetic mutations
(changes or damage in
DNA)

- Presence of cancerous mutations can be increased by:

- Inheritance
- Environmental factors
- Carcinogens
- E.g. tobacco, asbestos, crispy/brown foods
(acrylamide), formaldehyde, UV rays (sunlight),
alcohol, processed meat, engine exhaust, pollution
Lowering risk of cancer

The Food and Drug Administration

(FDA) is a federal agency that works
to protect people from exposures
to environmental factors that
increase risk of cancer, among
other things.

- Regulates the makeup of the

products we consume
How is cancer treated?
Asexual Reproduction
Day 7
Asexual Reproduction

- Generation of a new individual

that is essentially genetically
identical to the parent
- It typically involves a cell or
cells that were generated
by mitosis
- Any variation of cells is likely
due to mutations or
environmental effects
Asexual Reproduction - Methods

Binary Fission
- BACTERIA - cells are split in two (like
mitosis)

Spores
- FUNGUS, MOLD, FERNS - have tiny, asexual
reproductive cells

Budding
- HYDRA - unequal size cell division becomes
a new organism
- SPONGEBOB

Vegetative Propagation
- PLANTS - can often grow from a small piece
of another plant (leaf/stem/etc.)