Essentials of

Biology
Sylvia S. Mader
Michael Windelspecht

Chapter 11
DNA Biology
Lecture Outline

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11-1
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 11.1 DNA and RNA Structure
and Function
Mendel knew nothing about DNA.
It took years for investigators to conclude
Mendel’s factors (genes) were on chromosomes.
Controversy over whether DNA or protein was
the genetic message
• Experiment using viruses showed only DNA directed
the formation of new viruses

11-2
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 DNA Is the Genetic Material
Alfred Hershey and Martha Chase determined that DNA
is the genetic material.

Their experiment involved a virus that infects bacteria,

such as E. coli.

They wanted to know which part of the virus entered the

bacterium
• Capsid made of protein
• DNA inside the capsid
Radioactive tracers showed that DNA, not protein, enters
the bacterium and guides the formation of new viruses.

Therefore, DNA must be the genetic material. 11-3

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 Figure 11.1 DNA as the Genetic
Material

© Lee Simon/Science Source

11-4
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 Structure of DNA
Structure of DNA
• Race to determine the structure
• Chargaff’s rules
• Knew DNA contains four types of nucleotides
• Examined DNA from many species
• The amount of A, T, G, and C in DNA varies from species to
species.
• In each species, the amount of A = T and the amount of G
= C.
• All nucleotides contain phosphate, a 5-carbon
sugar, and a nitrogen-containing base. 11-5
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Figure 11.2a Nucleotide Composition
of DNA and RNA

11-6
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 Figure 11.2 b,c,d Nucleotide
Composition of DNA and RNA

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 Franklin’s X-Ray Diffraction Data
Franklin’s X-ray diffraction data
• Rosalind Franklin was studying the structure
of DNA.
• Her data showed DNA to be a helix with some
portions repeating over and over.

(both): © Science Source 11-8

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 The Watson and Crick Model

The Watson and Crick

model
• 1951—James Watson
and Francis Crick set
out to bring together all
the data on DNA and
build a model
• The model suggested
how replication works.
• Their model holds true
today with few changes. © A. Barrington Brown/Science Source

• Won the Nobel Prize 11-9

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 DNA Structure

DNA structure
• DNA structure is a double helix, like a twisted ladder
• Deoxyribose sugar and phosphate molecules are
bonded, forming the sides, with the bases making up
the rungs of the ladder.
• Complementary base pairing of A&T and G&C
• Hydrogen bonding between the bases holds the
halves of the helix together.

11-10
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 Figure 11.5 DNA Structure

a. Structure of DNA

b. Nucleotide pair
11-11
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 Replication of DNA
Replication of DNA
• Process of copying DNA before cell division
• Two strands separate
• Each strand serves as a template for a new strand
• Semiconservative—each new DNA molecule is made
of one parent strand and one new strand
• Replication requires
• Unwinding—helicase
• Complementary base pairing
• Joining—DNA polymerase and DNA ligase
• New DNA molecule exactly identical to original
molecule 11-12
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 Semiconservative Replication

Semiconservative replication
• Parent strand unwinds and separates by actions of
helicase
• New strands form through complementary base
pairing by actions of DNA polymerase.
• DNA ligase seals any breaks in the sugar-phosphate
backbone.
• New DNA molecule will be half old and half new
• New DNA molecule will be exactly identical to original
molecule
11-13
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 Figure 11.6 Semiconservative
Replication

a. The mechanism of DNA replication b. The products of replication

11-14
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 DNA Replication in Eukaryotes

DNA replication in eukaryotes

In eukaryotes, DNA replication begins at
numerous origins of replication.
• Forms “replication bubbles”
• Bubbles spread in both directions until they
meet.

11-15
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 Figure 11.7 Eukaryotic Replication

11-16
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 RNA Structure and Function

RNA structure and function

• Ribonucleic acid (RNA)
• Contains sugar ribose
• Uses uracil, not thymine
• Uses A, C, and G like DNA
• Single-stranded
• Three major types
• Messenger RNA (mRNA)
• Transfer RNA (tRNA)
• Ribosomal RNA (rRNA) 11-17
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 Figure 11.8 Structure of RNA

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 Table 11.1 Comparison of DNA and
RNA
Table 11.1 Comparison of DNA and RNA
SIMILARITIES OF DNA AND RNA
Both are nucleic acids.
Both are composed of nucleotides.
Both have a sugar-phosphate backbone.
Both have four different types of bases.

DIFFERENCES BETWEEN DNA AND RNA

DNA RNA

Found in nucleus Found in nucleus and

cytoplasm
Genetic material Helper to DNA

Sugar is deoxyribose. Sugar is ribose.

Bases are A,T,C,G. Bases are A,U,C,G.

Double-stranded Single-stranded

DNA is transcribed (to give a mRNA is translated

variety of RNA molecules). (to make proteins).
11-19
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 Types of RNA
The three types of RNA
• Messenger RNA (mRNA)
• Produced in the nucleus from DNA template
• Carries genetic message to ribosomes
• Transfer RNA (tRNA)
• Produced in the nucleus from DNA template
• Transfers amino acids to ribosomes
• Each type carries only one type of amino acid
• Ribosomal RNA (rRNA)
• Produced in the nucleolus of the nucleus from DNA template
• Joins with proteins to form ribosomes
• Ribosomes may be free or in polyribosomes (clusters) or
11-20
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 11.2 Gene Expression

Early 1900s, Sir Archibald Garrod

suggests a relationship between
inheritance and metabolic diseases
• First to suggest a link between genes and
proteins

DNA provides a blueprint to synthesize

proteins.
• Information flows from DNA to RNA to protein
11-21
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 Transcription and Translation

Transcription
• DNA serves as template to make mRNA

Translation
• mRNA directs sequence of amino acids in a
protein
• rRNA and tRNA assist

11-22
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 Figure 11.9 Flow of Genetic
Information
1. DNA: sequence of bases is genetic information.

2. Transcription:
genetic information
is passed from DNA
to mRNA.

3. Translation: amino acids in a polypeptide are

sequenced as specified by the template DNA strand.

11-23
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 The Genetic Code

The genetic code

• Translates from nucleic acids to amino acids
• Triplet—3 nucleotide sequence in DNA
• Codon—3 nucleotide sequence in mRNA
• A codon encodes a single amino acid.
• Start and stop codons

11-24
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 Figure 11.10 Messenger RNA
Codons
Second base U Second base C Second base A Second base G

First base U UUU phenylalanine (Phe) UCU serine (Ser) UAU tyrosine (Tyr) UGU cysteine (Cys) Third base U
First base U UUC phenylalanine (Phe) UCC serine (Ser) UAC tyrosine (Tyr) UGC cysteine (Cys) Third base C
First base U UUA leucine (Leu) UCA serine (Ser) UAA stop UGA stop Third base A
First base U UUG leucine (Leu) UCG serine (Ser) UAG stop UGG tryptophan (Trp) Third base G
First base C CUU leucine (Leu) CCU proline (Pro) CAU histidine (His) CGU arginine (Arg) Third base U
First base C CUC leucine (Leu) CCC proline (Pro) CAC histidine (His) CGC arginine (Arg) Third base C
First base C CUA leucine (Leu) CCA proline (Pro) CAA glutamine (Gln) CGA arginine (Arg) Third base A
First base C CUG leucine (Leu) CCG proline (Pro) CAG glutamine (Gln) CGG arginine (Arg) Third base G
First base A AUU isoleucine (Ile) ACU threonine (Thr) AAU asparagine (Asn) AGU serine (Ser) Third base U

First base A AUC isoleucine (Ile) ACC threonine (Thr) AAC asparagine (Asn) AGC serine (Ser) Third base C

First base A AUA isoleucine (Ile) ACA threonine (Thr) AAA lysine (Lys) AGA arginine (Arg) Third base A

First base A AUG methionine (Met) (start) ACG threonine (Thr) AAG lysine (Lys) AGG arginine (Arg) Third base G

First base G GUU valine (Val) GCU alanine (Ala) GAU aspartic acid (Asp) GGU glycine (Gly) Third base U

First base G GUC valine (Val) GCC alanine (Ala) GAC aspartic acid (Asp) GGC glycine (Gly) Third base C

First base G GUA valine (Val) GCA alanine (Ala) GAA glutamic acid (Glu) GGA glycine (Gly) Third base A

First base G GUG valine (Val) GCG alanine (Ala) GAG glutamic acid (Glu) GGG glycine (Gly) Third base G

11-25
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 Transcription

Transcription
• During transcription, complementary RNA is
made from a DNA template.
• Portion of DNA unwinds and unzips at the
point of attachment of RNA polymerase
• Bases join in the order dictated by the
sequence of bases in the template DNA
strand.

11-26
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 Figure 11.11 Transcription to Form
mRNA

Transcription is taking place-

the nucleotides of mRNA are
joined by the enzyme RNA
polymerase in an order
complementary to a strand
of DNA.

This mRNA transcript is

ready to be processed.

11-27
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 Processing Pre-mRNA

Newly made pre-mRNA must be processed.

• Capping and addition of poly-A tail provides stability
• Introns (non-coding) removed
• Leaves only exons (coding)
• Alternative splicing can produce different versions of
mRNA leading to different proteins.
• Now mature mRNA leaves nucleus and associates with
ribosome on cytoplasm.

11-28
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 Figure 11.12 mRNA Processing

e = exons

i = introns
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 Figure 11.13 tRNA Structure and
Function

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 Translation, 1

Translation
• tRNA brings in amino acids
• Anticodon—group of three bases
complementary to a specific codon of mRNA
• After translation is complete, a protein
contains the sequence of amino acids
originally specified in the DNA.

11-31
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 Translation, 2
Ribosomes are composed of protein and rRNA.
• Site of translation—protein synthesis
• Binds mRNA and two tRNA molecules
• P site for a tRNA attached to a peptide
• A site for newly arrived tRNA with an amino acid

Three phases of translation

• Initiation
• Elongation
• Termination
11-32
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 Translation, 3

Three stages of translation in detail

• Initiation
• mRNA binds to small subunit of ribosome
• Large subunit then joins
• Elongation
• Peptide lengthens one amino acid at a time
• Termination
• 1 of 3 stop codons reached
• Release factor causes ribosomal subunits and mRNA to
dissociate
• Complete polypeptide released
11-33
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 Figure 11.14 Initiation

A small ribosomal subunit

binds to mRNA; an initiator
tRNA pairs with the mRNA
start codon AUG.
The large ribosomal subunit
completes the ribosome.
Initiator tRNA occupies the P
site. The A site is ready for
the next tRNA.

11-34
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 Figure 11.15 Elongation

1. A tRNA-amino acid
approaches the ribosome
and binds at the A site.
2. Two tRNAs can be at a
ribosome at one time;
the anticodons are
paired to the codons.
3. Peptide bond formation
attaches the peptide
chain to the newly
arrived amino acid.
4. The ribosome moves forward; the
“empty” tRNA exits from the E
site; the next amino acid-tRNA
complex is approaching the
ribosome.

11-35
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 Figure 11.16 Termination

The ribosome comes to a stop

codon on the mRNA. A release
factor binds to the site.

The release factor hydrolyzes the bond

between the last tRNA at the P site and
the polypeptide, releasing them. The
ribosomal subunits dissociate.

11-36
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 Figure 11.17 Summary of Gene
Expression in Eukaryotes

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 11.3 Gene Regulation

Levels of gene expression Figure 11.18 Gene

control expression in
specialized cells
• Body contains many cells
that differ in structure and
function
• Only certain genes are active
in cells that perform
specialized functions
• Housekeeping genes govern
functions common to all cells
• Activity of selected genes
accounts for specialization 11-38
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 Gene Expression in Prokaryotes, 1
Gene expression in prokaryotes
• Escherichia coli lives in our intestine and can
quickly adjust its enzymes according to what
we eat.
• If we drink milk, E. coli immediately begins to
make three enzymes needed to metabolize
lactose.
• Operon—cluster of bacterial genes along with
DNA control sequence
• François Jacob and Jacques Monod—Nobel Prize
1961 for lac operon 11-39
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 Gene Expression in Prokaryotes, 2

Lactose not available most of the time

• E.coli does not normally transcribe the genes
of the lac operon.
• When lactose is not present, repressor binds to
the operator and RNA polymerase cannot
attach to the promoter.
• Inhibits transcription

11-40
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 Figure 11.19a The lac Operon

a. Lactose is absent-operon is turned off.

Enzymes needed to metabolize lactose are not produced.

11-41
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 Figure 11.19b The lac Operon

b. Lactose is present-operon is turned on.

Enzymes needed to metabolize lactose are
produced.

11-42
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 The lac Operon

When lactose is present, it binds to the

repressor.
• Repressor is inactivated and cannot attach to
operator
• RNA polymerase can bind and transcription
occurs.
• System can also work for genes normally
turned on
• Binding of tryptophan (gene for synthesis
normally on) causes operator to be turned off 11-43
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 Gene Expression in Eukaryotes

Gene expression in eukaryotes

• Each gene has its own promoter.
• Employ a variety of mechanisms
• Affect whether gene is expressed, speed of
expression, and length of expression
• Some mechanisms occur in nucleus and
others in cytoplasm
• Nucleus—chromatin condensation, mRNA
transcription, and mRNA processing
• Cytoplasm—delay of transcription, duration of
mRNA or protein 11-44
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 Figure 11.20 Control of Gene
Expression in Eukaryotic Cells, 1

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 Figure 11.20 Control of Gene
Expression in Eukaryotic Cells, 2

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 Chromatin Condensation

Chromatin condensation
• Way to keep genes turned off
• More tightly compacted = less gene expression
• Heterochromatin—dark staining regions of
tightly compacted, inactive chromatin
• Barr body—second X chromosome in
mammalian females
• Which X is inactivated? —female tortoiseshell cat

11-47
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 Figure 11.21 X-Inactivation in
Mammalian Females

Females have two X chromosomes. One X chromosome is inactivated in Coats of calico cats
each cell. Which one is by chance. have patches of orange
and black.

© Photodisc/Getty RF

11-48
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 Euchromatin

Euchromatin
• Unpacked heterochromatin
• Contains active genes
• Nucleosome—portion of DNA wrapped around
histones
• Transcription activator pushes aside histones
so that transcription can begin.

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 Figure 11.22 Histone Displacement,
1

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 Figure 11.22 Histone Displacement,
2

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 DNA Transcription in Eukaryotes
Same principles as prokaryotic transcription but with
more regulatory proteins per gene

Allows for greater control but also a greater chance for

malfunction

Transcription factors—DNA-binding proteins that help

RNA polymerase bind to a promoter
• Several needed in each case, need all of them
• Form complex that helps pull apart helix and helps position RNA
polymerase
• Same ones used in different combinations
• If one is defective, it can have serious effect—Huntington disease
• Speed up transcription
• Bind to enhancer region of DNA 11-52
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 Figure 11.23 Transcription Factors
and Transcription Activators

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 Transcription Factors

Possible for a single

transcription factor to
have dramatic effect on
gene expression
• MyoD alone can activate
the genes necessary for
fibroblasts to become
muscle cells.
• Ey can bring about the
formation of a complete
© Prof. Walter Gehring

eye in flies. 11-54

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 mRNA Processing

mRNA processing
• After transcription, introns must be removed
and exons spliced together.
• Alternative mRNA processing allows cells to
produce multiple proteins from the same gene
by changing the way exons are joined.
• Fruit fly DScam gene can produce over
38,000 different combinations

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 Figure 11.25 Processing of mRNA
Transcripts

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 mRNA Translation

mRNA translation
• Cytoplasm contains proteins that determine whether
translation takes place.
• Environmental conditions can delay translation.
• Red blood cells do not produce hemoglobin unless heme is
available.
• The longer mRNA remains in the cytoplasm before it is
broken down, the more gene product is produced.
• It can be affected by length of poly A tail or presence of
hormones.

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 Protein Activity

Protein activity
• Some proteins are not
active immediately
after synthesis.
• Insulin must be
processed before it is
an active form.
• Allows protein’s
activity to be delayed
until needed
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 Signaling Between Cells in
Eukaryotes
Signaling between cells in eukaryotes
• In multicellular organisms, cells are constantly sending
out chemical signals that influence the behavior of other
cells.
• During development, signals determine what a cell becomes.
• Later, they help coordinate growth and daily functions.
• Cell-signaling pathway
• Begins when chemical signal binds to receptor on target cell
plasma membrane
• Initiates signal transduction pathway
• End product affects cell (not original signal itself)
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 Figure 11.27 Cell-Signaling

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Appendix for long description
 Figure 11.2 b,c,d Nucleotide
Composition of DNA and RNA Long
description
The phosphate give DNA an overall negative charge; DNA bases include adenine, guanine, cytosine,
thymine, and in RNA uracil replaces thymine.

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