Biology

Sylvia S. Mader
Michael Windelspecht

Chapter 12
Molecular Biology of the Gene
Lecture Outline

12-1
Copyright ©2019 McGraw-Hill Education. All rights reserved. No reproduction or distribution without the prior written consent of McGraw-Hill Education.
 Outline
• 12.1 The Genetic Material
• 12.2 Replication of DNA
• 12.3 The Genetic Code of Life
• 12.4 First Step: Transcription
• 12.5 Second Step: Translocation

۲
 12.1The Genetic Material
• Frederick Griffith investigated virulence of
Streptococcus pneumoniae
 Concluded that virulence could be passed
from a dead strain to a nonvirulent living strain
 Transformation
• Further research by Avery et al.
 Discovered that DNA is the transforming
substance
 DNA from dead cells was being incorporated
into the genome of living cells
۳
 The Genetic Material
• Griffith’s Transformation Experiment
 Mice were injected with two strains of
pneumococcus: an encapsulated (S) strain
and a non-encapsulated )R) strain.
• The S strain is virulent (the mice died); it has a
mucous capsule.
• The R strain is not virulent )the mice lived); it has
no capsule.

٤
 Griffith’s Transformation
Experiment
.Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display

capsule

Injected live
Injected live R strain has Injected heat- Injected heat-killed
S strain has no capsule killed S strain S strain plus live
capsule and and mice does not cause R strain causes
causes mice do not die. mice to die. .mice to die Live S strain is
to die. withdrawn from
. dead mice

a. b. c. .d

٥
 The Genetic Material (3)
Avery, MacLeod, and McCarty’s Experiment
•Scientists argued that DNA lacked variability to be able to
store genetic information.
Avery and colleagues used enzymes that break down
DNA (DNase), or RNA (RNase), or protein (protease) in
separate experiments to digest the substance which
allowed Streptococcus to produce a capsule and become
virulent.
The only enzyme that had an effect was the DNase,
which prevented the “transformation” from occurring.
•These experiments show that DNA was the
transforming substance. 12-6
Copyright ©2019 McGraw-Hill Education. All rights reserved. No reproduction or distribution without the prior written consent of McGraw-Hill Education.
 The Genetic Material
• DNA contains:
 Two Nucleotides with purine bases
• Adenine (A)
• Guanine (G)
 Two Nucleotides with pyrimidine bases
• Thymine (T)
• Cytosine (C)

۷
 The Genetic Material
• Chargaff’s Rules:
 The amounts of A, T, G, and C in DNA:
• Are constant among members of the same species
• Vary from species to species
 In each species, there are equal amounts of:
• A and T
• G and C
 All this suggests that DNA uses
complementary base pairing to store genetic
information
 Each human chromosome contains, on
average, about 140 million base pairs
 The number of possible nucleotide sequences
is 4140,000,000
۸
Nucleotide Composition of DNA Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
O
NH2
C CH3
adenine C thymine HN C
C N
(A) N (T)
CH nitrogen-containing C O CH
HC C base
N N
N
O O
P HO O 5 CH O P HO O 5 CH O
2 2

O O C H sugar = deoxyribose1H C
C4 H 1H C 4
H CH C H CC H NH2
3 2 O 3 2
H OH H OH C
guanine C cytosine N CH
C N
( (G HN ( (C
CH C CH
O
H2N C C N N
O N
O

phosphate P OHO O 5 CH2 O O CH5 O P HO

2

4C H C1H CO4 H1H C

C H 2C C H
C 2
H H OH H
a. Purine nucleotides 3 b. Pyrimidine nucleotides 3 H OH

DNA Composition in Various Species (%)

Species A T G C

Homo sapiens (human( 31.0 31.5 19.1 18.4

Drosophila melanogaster )fruit fly( 27.3 27.6 22.5 22.5
Zea mays (corn( 25.6 25.3 24.5 24.6
Neurospora crassa (fungus( 23.0 23.3 27.1 26.6
Escherichia coli (bacterium( 24.6 24.3 25.5 25.6
۹
Bacillus subtilis (bacterium( 28.4 29.0 21.0 21.6
c. Chargaff’s data
 The Genetic Material
• X-Ray diffraction:
 Rosalind Franklin studied the structure of DNA using
X-rays.
 She found that if a concentrated, viscous solution of
DNA is made, it can be separated into fibers.
 Under the right conditions, the fibers can produce an
X-ray diffraction pattern
• She produced X-ray diffraction photographs.
• This provided evidence that DNA had the following features:
– DNA is a helix.
– Some portion of the helix is repeated.

۱۰
 X-Ray Diffraction of DNA
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Rosalind Franklin

diffraction pattern
diffracted
X-rays
a.
X-ray beam

Crystalline
DNA

.c
.b
© Photo Researchers, Inc.; c: © Science Source/Photo Researchers, Inc.

۱۱
 The Genetic Material
• The Watson and Crick Model
 Double helix model is similar to a twisted ladder
• Sugar-phosphate backbones make up the sides

• Hydrogen-bonded bases make up the rungs

 Complementary base pairing ensures that a purine is

always bonded to a pyrimidine (A with T, G with C)

 Received a Nobel Prize in 1962

۱۲
Watson and Crick Model of DNACopyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
3.4nm
0.34nm

2 nm

b.

d.

C
a. sugar-phosphate
G
T backbone
′5end 3′ end
P
A P
G C
S S A
T
P
P P
T A S G
S P C
′3end ′5end P
complementary C
c.
base pairing

G
P

hydrogen
sugar bonds ۱۳
a: © Photodisk Red/Getty RF; d: © A. Barrington Brown/Photo Researchers
 12.2Replication of DNA
• DNA replication is the process of copying
a DNA molecule.
• Semiconservative replication -each
strand of the original double helix )parental
molecule) serves as a template )mold or
model) for a new strand in a daughter
molecule.

۱٤
Semiconservative Replication
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
5′ 3′
G
C G
C G
A T
A

region of parental T A
DNA double helix
C G
DNA
A T polymerase
A enzyme
G
C G
C G
A

region of
replication:
new nucleotides
are pairing
with those of
parental strands

region of
completed
replication
3′
new old
strand strand

′5 daughter DNA double helix

old new ۱٥
strand strand
daughter DNA double helix
 Replication of DNA
• Replication requires the following steps:
 Unwinding, or separation of the two strands of the
parental DNA molecule

 Complementary base pairing between a new

nucleotide and a nucleotide on the template strand

 Joining of nucleotides to form the new strand

• Each daughter DNA molecule contains one old strand and one
new strand

۱٦
 Replication of DNA
• Prokaryotic Replication
 Bacteria have a single circular loop of DNA
 Replication moves around the circular DNA molecule
in both directions
 Produces two identical circles
 The process begins at the origin of replication
 Replication takes about 40minutes, but the cell
divides every 20minutes
• A new round of replication can begin before the previous
round is completed

۱۷
 Replication of DNA
• Eukaryotic Replication
 DNA replication begins at numerous points
along each linear chromosome
 DNA unwinds and unzips into two strands
 Each old strand of DNA serves as a template
for a new strand
 Complementary base-pairing forms a new
strand paired with each old strand
• Requires enzyme DNA polymerase

۱۸
 Replication of DNA
• Eukaryotic Replication
 Replication bubbles spread bidirectionally until
they meet
 The complementary nucleotides are joined to form
new strands. Each daughter DNA molecule
contains an old strand and a new strand.
 Replication is semiconservative:
• One original strand is conserved in each daughter
molecule, i.e., each daughter double helix has one
parental strand and one new strand.

۱۹
Prokaryotic versus Eukaryotic Replication
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
origin

replication is
complete

replication is
occurring in
two directions

a. Replication in prokaryotes

replication fork replication bubble

parental strand

new DNA
duplexes
۲۰
daughter strand
b. Replication in eukaryotes
Aspects of DNA Replication Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

OH P Is attached here
base is attached here
′5
CH2
O OH
′4C C
H H ′1 1
H H
C C ′2
3′
OH H
Deoxyribose m o lec ule

2 DNA polymerase
5′ end attaches a new
nucleotide to the
P 3 ′ carbon of the
previous nucleotide.

P
P

G C ′3end
P

P
P C G

′5
P ′3
P T A

C P template
P G
strand

3 ′end P DNA polymerase

′5end 4leading
template strand new strand
new strand
Direction of replication ′3 3 helicase at replication fork
RNA primer
template 6Okazaki fragment
lagging strand
5
strand 3′

′5
′5 parental DNA helix
۲۱
7DNA ligase DNA polymerase
′3
Replication fork introduces complications
 Replication of DNA
• Accuracy of Replication
 DNA polymerase is very accurate, yet makes
a mistake about once per 100,000base pairs.
• Capable of identifying and correcting errors

۲۲
 12.3The Genetic Code of Life
Genes Specify Enzymes

Genes Specify a Polypeptide

۲۳
 The Genetic Code of Life
• The mechanism of gene expression
 DNA in genes specify information, but
information is not structure and function
 Genetic information is expressed into
structure and function through protein
synthesis
• The expression of genetic information into
structure and function:
 DNA in a gene determines the sequence of
nucleotides in an RNA molecule
 RNA controls the primary structure of a
protein ۲٤
The Central Dogma of Molecular Biology
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
nontemplate strand
5 3

A G C G A C C C C

DNA T C G C T G G G G

3 5
template strand
transcription
in nucleus

5 3

A G C G A C C C C
mRN A

translation codon 1 codon 2 codon 3

at ribosome

O O O

polypeptide N C C N C N C C

R1 R2 R3
۲٥
Serine Aspartate Proline
 The Genetic Code of Life
• RNA is a polymer of RNA nucleotides
 RNA nucleotides contain the sugar ribose instead of
deoxyribose
 RNA nucleotides are of four types: uracil )U),
adenine )A), cytosine )C), and guanine(G(
 Uracil )U) replaces thymine )T) of DNA
• Types of RNA
• Messenger )mRNA) - Takes a message from DNA in the
nucleus to ribosomes in the cytoplasm
• Ribosomal )rRNA) - Makes up ribosomes, which read the
message in mRNA
• Transfer )tRNA) - Transfers the appropriate amino acid to
the ribosomes for protein synthesis

۲٦
 Structure of RNA
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

5′ end

P
G

U S

A P
base is
uracil instead
C of thymine
S

ribose one nucleotide

3′ end
۲۷
RNA Structure Compared to
DNA structure

۲۸
 The Genetic Code of Life
• The unit of the genetic code consists of codons,
each of which is a unique arrangement of symbols
• Each of the 20 amino acids found in proteins is
uniquely specified by one or more codons
 The symbols used by the genetic code are the mRNA bases
• Function as “letters” of the genetic alphabet
• Genetic alphabet has only four “letters” (U, A, C, G)
 Codons in the genetic code are all three bases )symbols)
long
• Function as “words” of genetic information
• Permutations:
– There are 64 possible arrangements of four symbols taken
three at a time
– Often referred to as triplets
• Genetic language only has “ 64words”

۲۹
Messenger RNA Codons
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Second Base
First Third
Base U C A G Base
UUU UCU UAU UGU
U
phenylalanine serine tyrosine cysteine
UUC UCC UAC UGU
C
phenylalanine serine tyrosine cysteine
U
UUA UCA UAA UGA
A
leucine serine stop stop
UUG UCG UAG UGG
G
leucine serine stop tryptophan
CUU CCU CAU CGU U
leucine proline histidine arginine
CUC CCC CAC CGC C
leucine proline histidine arginine
C
CUA CCA CAA CGA
A
leucine proline glutamine arginine
CUG CCG CAG CGG G
leucine proline glutamine arginine
AUU ACU AAU AGU U
isoleucine threonine asparagine serine
AUC ACC AAC AGC C
isoleucine threonine asparagine serine
A
AUA ACA AAA AGA
A
isoleucine threonine lysine arginine
AUG (start( ACG AAG AGG G
methionine threonine lysine arginine
GUU GCU GAU GGU U
valine alanine aspartate glycine
GUC GCC GAC GGC C
valine alanine aspartate glycine
G
GUA GCA GAA GGA A
valine alanine glutamate glycine
۳۰
GUG GCG GAG GGG
G
valine alanine glutamate glycine
 The Genetic Code of Life
• Properties of the genetic code:
 Universal
• With few exceptions, all organisms use the code the same
way
• Encode the same 20 amino acids with the same 64triplets
 Degenerate (redundant(
• There are 64 codons available for 20amino acids
• Most amino acids encoded by two or more codons
 Unambiguous )codons are exclusive(
• None of the codons code for two or more amino acids
• Each codon specifies only one of the 20amino acids
 Contains start and stop signals
• Punctuation codons
• Like the capital letter we use to signify the beginning of a
sentence, and the period to signify the end
۳۱
 12.4First Step: Transcription
• Transcription
 A segment of DNA serves as a template for
the production of an RNA molecule
 The gene unzips and exposes unpaired bases
 Serves as template for mRNA formation
 Loose RNA nucleotides bind to exposed DNA
bases using the C=G and A=U rule
 When entire gene is transcribed into mRNA,
the result is a pre-mRNA transcript of the
gene
 The base sequence in the pre-mRNA is
complementary to the base sequence in DNA
۳۲
 First Step: Transcription
• A single chromosome consists of one very long molecule encoding
hundreds or thousands of genes
• The genetic information in a gene describes the amino acid
sequence of a protein
 The information is in the base sequence of one side )the “sense” strand)
of the DNA molecule
 The gene is the functional equivalent of a “sentence”
• The segment of DNA corresponding to a gene is unzipped to expose
the bases of the sense strand
 The genetic information in the gene is transcribed )rewritten) into an
mRNA molecule
 The exposed bases in the DNA determine the sequence in which the
RNA bases will be connected together
 RNA polymerase connects the loose RNA nucleotides together
• The completed transcript contains the information from the gene, but
in a mirror image, or complementary form

۳۳
 Transcription
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
′3 ′5

terminator

gene strand template

strand

′3 C
direction of
polymerase
movement
T
RNA
polymerase

DNA
template
strand

mRNA
transcript

promoter

′5

۳٤
′5 ′3 to RNA processing
12.5 Second Step: Translation
• Translation
 The sequence of codons in the mRNA at a ribosome directs the sequence of
amino acids into a polypeptide
 A nucleic acid sequence is translated into a protein sequence
• tRNA molecules have two binding sites:
 One associates with the mRNA transcript
 The other associates with a specific amino acid
 Each of the 20 amino acids in proteins associates with one or more of 64
types of tRNA
• Translation
 An mRNA transcript associates with the rRNA of a ribosome in the
cytoplasm or a ribosome associated with the rough endoplasmic reticulum
 The ribosome “reads” the information in the transcript
 Ribosome directs various types of tRNA to bring in their specific amino acid
“fares”
 The tRNA specified is determined by the code being translated in the mRNA
transcript

۳٥
 Second Step: Translation
• tRNA molecules come in 64different kinds
• All are very similar except that
 One end bears a specific triplet (of the 64
possible) called the anticodon
 The other end binds with a specific amino acid
type
 tRNA synthetases attach the correct amino acid
to the correct tRNA molecule
• All tRNA molecules with a specific anticodon
will always bind with the same amino acid
۳٦
 Structure of a tRNA Molecule Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

amino
acid
leucine

’3
’5

hydrogen
bonding

amino acid end

anticodon

G A A anticodon end

C A G U C C U U C C U C
mRNA
’5 ’3 ۳۷
codon
a. b.
 Second Step: Translation
Ribosomes:
Ribosomal RNA (rRNA(
Produced from a DNA template in the nucleolus of a nucleus
Combined with proteins into large and small ribosomal subunits

۳۸
 Ribosome Structure and Function
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

large subunit

5 3

mRNA
tRNA binding
sites

small subunit
a. Structure of a ribosome b. Binding sites of ribosome outgoing
tRNA

polypeptide
incoming
tRNA

mRNA

c. Function of ribosomes d. Polyribosome

Courtesy Alexander Rich ۳۹

 Second Step: Translation
• Initiation:
 Components necessary for initiation are:
• Small ribosomal subunit
• mRNA transcript
• Initiator tRNA, and
• Large ribosomal subunit
• Initiation factors (special proteins that bring the
above together(
 Initiator tRNA:
• Always has the UAC anticodon
• Always carries the amino acid methionine
• Capable of binding to the P site

٤۰
 Second Step: Translation
• Small ribosomal subunit attaches to
mRNA transcript

 Beginning of transcript always has the START

codon (AUG(

• Initiator tRNA )UAC) attaches to P site

• Large ribosomal subunit joins the small

subunit ٤۱
 Initiation
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

amino acid methionine

Met

initiator tRNA

5 mRNA E site P site A site

3 Met

small ribosomal subunit

large ribosomal subunit U AC

AU G

5 start codon 3

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.

٤۲
Initiation
 Second Step: Elongation
• “Elongation” refers to the growth in length
of the polypeptide
• RNA molecules bring their amino acid
fares to the ribosome
 Ribosome reads a codon in the mRNA
• Allows only one type of tRNA to bring its amino
acid
• Must have the anticodon complementary to the
mRNA codon being read
• The incoming tRNA joins the ribosome at its A site
 Methionine of the initiator tRNA is connected
to the amino acid of the 2nd tRNA by a peptide٤۳
bond
 Elongation
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Met Met
asp
Met Met Thr
Ser Ser
peptide tRNA
Ser bond Ser Ala
Ala
Ala CU G Ala
Trp Trp
peptide
Trp anticodon Trp Val bond Val
Val Val Asp
Asp Asp

CA U CAUCUG GU C U G
CAUCUG GU
GUAGA C AGA C AGA C GUAGACACC

3
5 3 5 5 3 5 3

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

Elongation

٤٤
 Second Step: Translation
• Termination:
 Previous tRNA moves to the P site
 Spent tRNA moves to the E site and exits
 Ribosome reads the STOP codon at the end of the
mRNA
• UAA, UAG, or UGA
• Does not code for an amino acid
 A protein called a release factor binds to the stop
codon and cleaves the polypeptide from the last tRNA
 The ribosome releases the mRNA and dissociates
into subunits
 The same mRNA may be read by another ribosome
٤٥
 Termination
Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Trp
release factor
Val

Trp

Val
U U
AAU G A

′5 stop codon ′3

The ribosome comes to a stop

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

′3

′5

The release factor hydrolyzes the bond

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

Termination ٤٦
Summary of Protein Synthesis in Eukaryotes
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

TRANSCRIPTION .1DNA in nucleus serves

TRANSLATION
as a template for mRNA.

DNA .3mRNA moves into

.2mRNA is processed before large and small cytoplasm and
leaving the nucleus. ribosomal subunits 5 becomes associated
mRNA with ribosomes.
introns
pre-mRNA
3
mRNA amino .4tRNAs with
acids
nuclear pore anticodons carry
amino acids
peptide to mRNA.

ribosome tRNA
UAC
5
AU G 3
anticodon

codon
.5During initiation, anticodon-codon
complementary base pairing begins
.8During termination, a
as the ribosomal subunits come
together at a start codon. ribosome reaches a stop
codon; mRNA and
CCCUGGUU U
5 GGGACCAAA G ribosomal subunits
3 disband.

.6During elongation, polypeptide

synthesis takes place one
amino acid at a time.
.7Ribosome attaches to rough
ER. Polypeptide enters lumen,
where it folds and is
modified.

٤۷