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Macro Molecules

The document discusses the structure and function of DNA as the genetic material, highlighting key historical experiments that established DNA's role in heredity. It covers the discovery of DNA's double-helix structure by Watson and Crick, supported by X-ray crystallography images from Rosalind Franklin. Additionally, it explains the mechanisms of DNA replication and the significance of base pairing in genetic information transfer.

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0% found this document useful (0 votes)
3 views74 pages

Macro Molecules

The document discusses the structure and function of DNA as the genetic material, highlighting key historical experiments that established DNA's role in heredity. It covers the discovery of DNA's double-helix structure by Watson and Crick, supported by X-ray crystallography images from Rosalind Franklin. Additionally, it explains the mechanisms of DNA replication and the significance of base pairing in genetic information transfer.

Uploaded by

raniaalyssa606
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
You are on page 1/ 74

BIOLOGY TENTH EDITION

Global Edition

Campbell • Reece • Urry • Cain • Wasserman • Minorsky • Jackson

16
Nucleic Acids and
Inheritance

Lecture Presentation by
Nicole Tunbridge and
Kathleen Fitzpatrick

© 2015 Pearson Education Ltd

Life’s Operating Instructions

a) In 1953, James Watson and Francis Crick introduced


an elegant double-helical model for the structure of
deoxyribonucleic acid, or DNA

b) Hereditary information is encoded in DNA and


reproduced in all cells of the body

c) This DNA program directs the development of


biochemical, anatomical, physiological, and
(to some extent) behavioral traits

© 2015 Pearson Education Ltd

2
Figure 16.1

© 2015 Pearson Education Ltd

Figure 16.1a

© 2015 Pearson Education Ltd

4
a) DNA is copied during DNA replication, and cells can
repair their DNA

© 2015 Pearson Education Ltd

Concept 16.1: DNA is the genetic material

a) Early in the 20th century, the identification of the


molecules of inheritance loomed as a major challenge
to biologists

© 2015 Pearson Education Ltd

6
The Search for the Genetic Material: Scientific Inquiry

a) When T. H. Morgan’s group showed that genes are


located on chromosomes, the two components of
chromosomes—DNA and protein—became
candidates for the genetic material

b) The role of DNA in heredity was first discovered


by studying bacteria and the viruses that
infect them

© 2015 Pearson Education Ltd

Evidence That DNA Can Transform Bacteria

a) The discovery of the genetic role of DNA began with


research by Frederick Griffith in 1928
b) Griffith worked with two strains of a bacterium, one
pathogenic and one harmless

© 2015 Pearson Education Ltd

8
a) When he mixed heat-killed remains of the pathogenic
strain with living cells of the harmless strain, some
living cells became pathogenic

b) He called this phenomenon transformation, now


defined as a change in genotype and phenotype due
to assimilation of foreign DNA

© 2015 Pearson Education Ltd

Figure 16.2

Experiment
Living S cells Living R cells Heat-killed S cells Mixture of heat-
(pathogenic (nonpathogenic (nonpathogenic killed S cells and
control) control) control) living R cells

Results

Mouse dies Mouse healthy Mouse healthy Mouse dies

Living S cells

© 2015 Pearson Education Ltd

10
a) In 1944, Oswald Avery, Maclyn McCarty, and Colin
MacLeod announced that the transforming substance
was DNA

b) Many biologists remained skeptical, mainly because


little was known about DNA

© 2015 Pearson Education Ltd

11

Evidence That Viral DNA Can Program Cells

a) More evidence for DNA as the genetic material came


from studies of viruses that infect bacteria
b) Such viruses, called bacteriophages (or phages),
are widely used in molecular genetics research

c) A virus is DNA (sometimes RNA) enclosed by a


protective coat, often simply protein

© 2015 Pearson Education Ltd

12
Figure 16.3

Phage
head

DNA

Tail
sheath

Tail fiber
Genetic
material

100 nm
Bacterial
cell

© 2015 Pearson Education Ltd

13

Animation: Phage T2 Reproductive Cycle

© 2015 Pearson Education Ltd

14
a) In 1952, Alfred Hershey and Martha Chase showed
that DNA is the genetic material of a phage known as
T2

b) They designed an experiment showing that only one


of the two components of T2 (DNA or protein) enters
an E. coli cell during infection
c) They concluded that the injected DNA of the phage
provides the genetic information

© 2015 Pearson Education Ltd

15

Figure 16.4

Experiment
Batch 1: Radioactive sulfur (35S) in phage protein
1 Labeled phages 2 Agitation frees outside 3 Centrifuged cells
infect cells. phage parts from cells. form a pellet.

Radioactive 4 Radioactivity
protein (phage protein)
found in liquid

Centrifuge

Pellet
32
Batch 2: Radioactive phosphorus ( P) in phage DNA
Radioactive
DNA

Centrifuge

Pellet 4 Radioactivity (phage


© 2015 Pearson Education Ltd
DNA) found in pellet

16
Figure 16.4a

Experiment
Batch 1: Radioactive sulfur (35S) in phage protein
1 Labeled phages 2 Agitation frees 3 Centrifuged cells
infect cells. outside phage form a pellet.
parts from cells.
Radioactive
protein

Centrifuge

Pellet 4 Radioactivity
(phage protein)
found in liquid

© 2015 Pearson Education Ltd

17

Figure 16.4b

Experiment
Batch 2: Radioactive phosphorus (32P) in phage DNA
1 Labeled phages 2 Agitation frees 3 Centrifuged cells
infect cells. outside phage form a pellet.
parts from cells.
Radioactive
DNA

Centrifuge
Pellet 4 Radioactivity
(phage DNA)
found in
pellet

© 2015 Pearson Education Ltd

18
Animation: Hershey-Chase Experiment

© 2015 Pearson Education Ltd

19

Additional Evidence That DNA Is the Genetic Material

a) It was known that DNA is a polymer of nucleotides,


each consisting of a nitrogenous base, a sugar, and a
phosphate group

b) In 1950, Erwin Chargaff reported that DNA


composition varies from one species to the next

c) This evidence of diversity made DNA a more credible


candidate for the genetic material

© 2015 Pearson Education Ltd

20
Figure 16.5
Sugar– 5ʹ end Nitrogenous
phosphate bases
backbone
Thymine (T)

Adenine (A)

Cytosine (C)

Phosphate
Guanine (G)
3ʹ end
Sugar
DNA (deoxyribose)
Nitrogenous
nucleotide base
© 2015 Pearson Education Ltd

21

Animation: DNA and RNA Structure

© 2015 Pearson Education Ltd

22
a) Two findings became known as Chargaff’s rules
a)The base composition of DNA varies between species
b)In any species the number of A and T bases are equal
and the number of G and C bases are equal

b) The basis for these rules was not understood until the
discovery of the double helix

© 2015 Pearson Education Ltd

23

Building a Structural Model of DNA: Scientific Inquiry

a) After DNA was accepted as the genetic material, the


challenge was to determine how its structure
accounts for its role in heredity

b) Maurice Wilkins and Rosalind Franklin were using a


technique called X-ray crystallography to study
molecular structure
c) Franklin produced a picture of the DNA molecule
using this technique

© 2015 Pearson Education Ltd

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Figure 16.6

(a) Rosalind Franklin (b) Franklin’s X-ray diffraction


photograph of DNA

© 2015 Pearson Education Ltd

25

Figure 16.6a

(a) Rosalind Franklin

© 2015 Pearson Education Ltd

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Figure 16.6b

(b) Franklin’s X-ray diffraction


photograph of DNA

© 2015 Pearson Education Ltd

27

a) Franklin’s X-ray crystallographic images of DNA


enabled Watson to deduce that DNA was helical
b) The X-ray images also enabled Watson to deduce the
width of the helix and the spacing of the nitrogenous
bases

c) The pattern in the photo suggested that the DNA


molecule was made up of two strands, forming a
double helix

© 2015 Pearson Education Ltd

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Figure 16.7

5ʹ end
C G
C G Hydrogen bond 3ʹ end
G C
G C T A

3.4 nm
T A
G C G C
C G
A T

1 nm C G
T A
C G
G C
C G A T

A T 3ʹ end
A T
0.34 nm
T A 5ʹ end
(a) Key features of (b) Partial chemical structure (c) Space-filling
DNA structure model

© 2015 Pearson Education Ltd

29

Figure 16.7a

C G
C G
G C
G C

3.4 nm
T A
G C
C G
A T

1 nm
T A
C G
G C
C G

A T
A T
0.34 nm
T A

© 2015 Pearson Education Ltd


(a) Key features of DNA structure

30
Figure 16.7b
5ʹ end
Hydrogen bond
3ʹ end
T A

G C

C G

A T

3ʹ end

5ʹ end
(b) Partial chemical structure
© 2015 Pearson Education Ltd

31

Figure 16.7c

© 2015 Pearson Education Ltd


(c) Space-filling model

32
Animation: DNA Double Helix

© 2015 Pearson Education Ltd

33

Video: Stick Model of DNA (Deoxyribonucleic Acid)

© 2015 Pearson Education Ltd

34
Video: Surface Model of DNA (Deoxyribonucleic Acid)

© 2015 Pearson Education Ltd

35

a) Watson and Crick built models of a double helix to


conform to the X-rays and chemistry of DNA
b) Franklin had concluded that there were two outer
sugar-phosphate backbones, with the nitrogenous
bases paired in the molecule’s interior

c) Watson built a model in which the backbones were


antiparallel (their subunits run in opposite directions)

© 2015 Pearson Education Ltd

36
a) At first, Watson and Crick thought the bases paired
like with like (A with A, and so on), but such pairings
did not result in a uniform width

b) Instead, pairing a purine with a pyrimidine resulted in


a uniform width consistent with the X-ray data

© 2015 Pearson Education Ltd

37

Figure 16.UN02

Purine + purine: too wide

Pyrimidine + pyrimidine: too narrow

Purine + pyrimidine: width


consistent with X-ray data

© 2015 Pearson Education Ltd

38
a) Watson and Crick reasoned that the pairing was more
specific, dictated by the base structures
b) They determined that adenine (A) paired only with
thymine (T), and guanine (G) paired only with
cytosine (C)
c) The Watson-Crick model explains Chargaff’s rules: in
any organism the amount of A = T, and the amount of
G=C

© 2015 Pearson Education Ltd

39

Figure 16.8

Sugar
Sugar
Adenine (A) Thymine (T)

Sugar
Sugar

Guanine (G) Cytosine (C)


© 2015 Pearson Education Ltd

40
Concept 16.2: Many proteins work together in DNA
replication and repair

a) The relationship between structure and function is


manifest in the double helix
b) Watson and Crick noted that the specific base pairing
suggested a possible copying mechanism for genetic
material

© 2015 Pearson Education Ltd

41

The Basic Principle: Base Pairing to a Template Strand

a) Since the two strands of DNA are complementary,


each strand acts as a template for building a new
strand in replication

b) In DNA replication, the parent molecule unwinds, and


two new daughter strands are built based on base-
pairing rules

© 2015 Pearson Education Ltd

42
Figure 16.9-1

A T

C G

T A

A T

G C

(a) Parental
molecule

© 2015 Pearson Education Ltd

43

Figure 16.9-2

A T A T

C G C G

T A T A

A T A T

G C G C

(a) Parental (b) Separation of parental


molecule strands into templates

© 2015 Pearson Education Ltd

44
Figure 16.9-3

A T A T A T A T

C G C G C G C G

T A T A T A T A

A T A T A T A T

G C G C G C G C

(a) Parental (b) Separation of parental (c) Formation of new strands


molecule strands into templates complementary to template
strands

© 2015 Pearson Education Ltd

45

a) Watson and Crick’s semiconservative model of


replication predicts that when a double helix
replicates, each daughter molecule will have one old
strand (derived or “conserved” from the parent
molecule) and one newly made strand
b) Competing models were the conservative model (the
two parent strands rejoin) and the dispersive model
(each strand is a mix of old and new)

© 2015 Pearson Education Ltd

46
Figure 16.10
First Second
Parent cell replication replication

(a) Conservative
model

(b) Semiconserva-
tive model

(c) Dispersive
model

© 2015 Pearson Education Ltd

47

a) Experiments by Matthew Meselson and Franklin Stahl


supported the semiconservative model
b) They labeled the nucleotides of the old strands with a
heavy isotope of nitrogen, while any new nucleotides
were labeled with a lighter isotope

© 2015 Pearson Education Ltd

48
a) The first replication produced a band of hybrid DNA,
eliminating the conservative model
b) A second replication produced both light and hybrid
DNA, eliminating the dispersive model and supporting
the semiconservative model

© 2015 Pearson Education Ltd

49

Figure 16.11
Experiment
1 Bacteria cultured 2 Bacteria transferred
in medium with 15N to medium with 14N
(heavy isotope) (lighter isotope)

Results
3 DNA sample 4 DNA sample Less dense
centrifuged centrifuged
after first after second
replication replication More dense

Conclusion
Predictions: First replication Second replication

Conservative
model

Semiconservative
model

Dispersive
model
© 2015 Pearson Education Ltd

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Figure 16.11a

Experiment
1 Bacteria cultured 2 Bacteria transferred
in medium with 15N to medium with 14N
(heavy isotope) (lighter isotope)

Results
3 DNA sample 4 DNA sample Less dense
centrifuged centrifuged
after first after second
replication replication More dense

© 2015 Pearson Education Ltd

51

Figure 16.11b

Conclusion
Predictions: First replication Second replication

Conservative
model

Semiconservative
model

Dispersive
model

© 2015 Pearson Education Ltd

52
DNA Replication: A Closer Look

a) The copying of DNA is remarkable in its speed and


accuracy
b) More than a dozen enzymes and other proteins
participate in DNA replication

© 2015 Pearson Education Ltd

53

Getting Started

a) Replication begins at particular sites called origins of


replication, where the two DNA strands are
separated, opening up a replication “bubble”

b) A eukaryotic chromosome may have hundreds or


even thousands of origins of replication

c) Replication proceeds in both directions from each


origin, until the entire molecule is copied

© 2015 Pearson Education Ltd

54
Figure 16.12

(a) Origin of replication in an E. coli cell (b) Origins of replication in a eukaryotic cell
Origin of Parental (template) Origin of
replication strand replication Eukaryotic chromosome
Daughter
(new) strand Parental (template)
Double-stranded strand
Replication DNA molecule Daughter (new)
Bacterial
fork strand
chromosome
Double-
Replication
stranded
DNA molecule bubble Replication
Bubble
fork

Two daughter
DNA molecules

Two daughter DNA molecules

0.25 µm
0.5 µm

© 2015 Pearson Education Ltd

55

Figure 16.12a
(a) Origin of replication in an E. coli cell
Origin of Parental (template) strand
replication Daughter
(new) strand
Bacterial Replication
chromosome fork
Double-stranded
DNA molecule
Replication
bubble

Two daughter
DNA molecules
0.5 µm

© 2015 Pearson Education Ltd

56
Figure 16.12aa

0.5 µm
© 2015 Pearson Education Ltd

57

Figure 16.12b
(b) Origins of replication in a eukaryotic cell
Origin of replication Eukaryotic chromosome

Double-stranded Parental (template) strand


DNA molecule Daughter (new)
strand

Bubble Replication
fork

Two daughter DNA molecules


0.25 µm

© 2015 Pearson Education Ltd

58
Figure 16.12ba

0.25 µm
© 2015 Pearson Education Ltd

59

Animation: Origins of Replication

© 2015 Pearson Education Ltd

60
a) At the end of each replication bubble is a replication
fork, a Y-shaped region where
new DNA strands are elongating

b) Helicases are enzymes that untwist the double helix


at the replication forks

c) Single-strand binding proteins bind to and stabilize


single-stranded DNA

d) Topoisomerase corrects “overwinding” ahead of


replication forks by breaking, swiveling, and rejoining
DNA strands
© 2015 Pearson Education Ltd

61

Figure 16.13

Primase

Topoisomerase

RNA

3ʹ primer

Replication
3ʹ fork


Helicase
Single-strand binding
proteins

© 2015 Pearson Education Ltd

62
a) DNA polymerases cannot initiate synthesis of a
polynucleotide; they can only add nucleotides to an
existing 3′ end

b) The initial nucleotide strand is a short RNA primer

© 2015 Pearson Education Ltd

63

a) An enzyme called primase can start an RNA chain


from scratch and adds RNA nucleotides one at a time
using the parental DNA as a template

b) The primer is short (5–10 nucleotides long), and the


3′ end serves as the starting point for the new DNA
strand

© 2015 Pearson Education Ltd

64
Synthesizing a New DNA Strand

a) Enzymes called DNA polymerases catalyze the


elongation of new DNA at a replication fork
b) Most DNA polymerases require a primer and a DNA
template strand

c) The rate of elongation is about 500 nucleotides per


second in bacteria and 50 per second in human cells

© 2015 Pearson Education Ltd

65

a) Each nucleotide that is added to a growing DNA


strand is a nucleoside triphosphate
b) dATP supplies adenine to DNA and is similar to the
ATP of energy metabolism

c) The difference is in their sugars: dATP has


deoxyribose while ATP has ribose

d) As each monomer of dATP joins the DNA strand, it


loses two phosphate groups as a molecule of
pyrophosphate

© 2015 Pearson Education Ltd

66
Figure 16.14
New strand Template strand
5ʹ 3ʹ 5ʹ 3ʹ

Sugar A T A T
Phosphate Base
C G C G

G C DNA G C
poly-
OH merase
3ʹ A T A
T OH
P P Pi
P C 3ʹ C
P Pyro-
OH phosphate
Nucleotide
5ʹ 5ʹ
2 Pi
© 2015 Pearson Education Ltd

67

Antiparallel Elongation

a) The antiparallel structure of the double helix affects


replication
b) DNA polymerases add nucleotides only to the free 3′
end of a growing strand; therefore, a new DNA strand
can elongate only in the 5′ to 3′ direction

© 2015 Pearson Education Ltd

68
Figure 16.15
Overview
Origin of replication
Leading strand Lagging strand

Primer

Leading strand
Lagging strand
Overall
directions
1 DNA pol III starts to of replication Origin of replication
synthesize leading 3ʹ
strand.

RNA primer
5ʹ 3ʹ
3ʹ Sliding clamp
DNA pol III
Parental DNA 5ʹ


3ʹ 2 Continuous
3ʹ elongation in the
5ʹ to 3ʹ direction

© 2015 Pearson Education Ltd

69

Figure 16.15a

Overview
Origin of replication
Leading strand Lagging strand

Primer

Leading strand
Lagging strand
Overall directions
of replication

© 2015 Pearson Education Ltd

70
Figure 16.15b

1 DNA pol III starts to Origin of replication


synthesize leading

strand.

RNA primer
5ʹ 3ʹ
3ʹ Sliding clamp
DNA pol III
Parental DNA 5ʹ


2 Continuous
3ʹ 3ʹ
elongation in the
5ʹ to 3ʹ direction

© 2015 Pearson Education Ltd

71

Animation: Leading Strand

© 2015 Pearson Education Ltd

72
a) Along one template strand of DNA, the DNA
polymerase synthesizes a leading strand
continuously, moving toward the replication fork

© 2015 Pearson Education Ltd

73

a) To elongate the other new strand, called the lagging


strand, DNA polymerase must work in the direction
away from the replication fork

b) The lagging strand is synthesized as a series of


segments called Okazaki fragments, which are
joined together by DNA ligase

© 2015 Pearson Education Ltd

74
Figure 16.16
Overview
Lagging Origin of replication
Leading strand Lagging
strand strand
2
1
Leading
strand RNA primer
Overall directions for fragment 2
of replication 5ʹ Okazaki 4 DNA pol III
1 Primase makes 3ʹ fragment 2 makes Okazaki

RNA primer. 2 fragment 2.
Origin of
5ʹ replication 3ʹ
3ʹ 1
5ʹ 3ʹ 5ʹ
Template 5ʹ
strand 5ʹ
2 DNA pol III 3ʹ 5 DNA pol I
3ʹ RNA primer makes Okazaki replaces RNA
for fragment 1 fragment 1. with DNA.
2
1 3ʹ
5ʹ 5ʹ
1 3ʹ 5ʹ 3ʹ

6 DNA ligase
5ʹ forms bonds
3 DNA pol III 3ʹ
between DNA
3ʹ detaches. fragments.
2
Okazaki
fragment 1 1 3ʹ
5ʹ 5ʹ
1 3ʹ
5ʹ Overall direction of replication
© 2015 Pearson Education Ltd

75

Figure 16.16a

Overview
Lagging Origin of replication
Leading strand Lagging
strand strand

2
1
Leading
strand
Overall directions
of replication

© 2015 Pearson Education Ltd

76
Figure 16.16b-1

1 Primase makes

RNA primer.
Origin of
replication
5ʹ 3ʹ
Template 5ʹ 3ʹ

strand

© 2015 Pearson Education Ltd

77

Figure 16.16b-2

1 Primase makes

RNA primer.
Origin of
replication
5ʹ 3ʹ
Template 5ʹ 3ʹ

strand
2 DNA pol III
3ʹ RNA primer makes Okazaki
for fragment 1 fragment 1.


1 3ʹ 5ʹ 3ʹ

© 2015 Pearson Education Ltd

78
Figure 16.16b-3

1 Primase makes

RNA primer.
Origin of
replication
5ʹ 3ʹ
Template 5ʹ 3ʹ

strand
2 DNA pol III
3ʹ RNA primer makes Okazaki
for fragment 1 fragment 1.


1 3ʹ 5ʹ 3ʹ

3 DNA pol III


3ʹ detaches.
Okazaki
fragment 1

1 3ʹ

© 2015 Pearson Education Ltd

79

Figure 16.16c-1
RNA primer
for fragment 2
5ʹ Okazaki 4 DNA pol III
3ʹ fragment 2 makes Okazaki
2 fragment 2.

1 3ʹ

© 2015 Pearson Education Ltd

80
Figure 16.16c-2
RNA primer
for fragment 2
5ʹ Okazaki 4 DNA pol III
3ʹ fragment 2 makes Okazaki
2 fragment 2.

1 3ʹ


3ʹ 5 DNA pol I
replaces RNA
with DNA.
2
1 3ʹ

© 2015 Pearson Education Ltd

81

Figure 16.16c-3
RNA primer
for fragment 2
5ʹ Okazaki 4 DNA pol III
3ʹ fragment 2 makes Okazaki
2 fragment 2.

1 3ʹ


3ʹ 5 DNA pol I
replaces RNA
with DNA.
2
1 3ʹ

6 DNA ligase
5ʹ forms bonds
3ʹ between DNA
fragments.
2
1 3ʹ

Overall direction of replication
© 2015 Pearson Education Ltd

82
Figure 16.17

Overview
Leading Origin of
strand replication
Lagging
Leading strand strand
template 3ʹ
Leading
Single-strand Lagging strand
strand 5ʹ
binding proteins
Leading strand Overall directions
Helicase of replication
5ʹ DNA pol III
3ʹ Primer
3ʹ 5ʹ
3ʹ Primase
Parental 5 DNA pol III
5ʹ Lagging
DNA 3ʹ DNA pol I
4 strand DNA ligase

3 2

1

Lagging strand 5ʹ
template

© 2015 Pearson Education Ltd

83

Figure 16.17a

Overview
Leading Origin of
strand replication
Lagging
strand

Leading
Lagging strand
strand
Overall directions
of replication

© 2015 Pearson Education Ltd

84
Figure 16.17b

Leading strand
template
Single-strand
binding proteins
Leading
Helicase
strand
5ʹ DNA pol III
3ʹ Primer
3ʹ 5ʹ Primase

Parental 5
DNA

© 2015 Pearson Education Ltd

85

Figure 16.17c

DNA pol III Lagging


5ʹ DNA pol I
4 3ʹ strand DNA ligase

3 2 1

Lagging strand 5ʹ
template

© 2015 Pearson Education Ltd

86
Table 16.1

© 2015 Pearson Education Ltd

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Table 16.1a

© 2015 Pearson Education Ltd

88
Table 16.1b

© 2015 Pearson Education Ltd

89

The DNA Replication Complex

a) The proteins that participate in DNA replication form a


large complex, a “DNA replication machine”
b) The DNA replication machine may be stationary
during the replication process

c) Recent studies support a model in which DNA


polymerase molecules “reel in” parental DNA and
“extrude” newly made daughter DNA molecules

© 2015 Pearson Education Ltd

90
Figure 16.18

Leading strand template

DNA pol III


Parental DNA Leading strand

5ʹ 3ʹ 3ʹ


3ʹ 5ʹ

Connecting protein
Helicase
DNA pol III

Lagging 3ʹ 5ʹ
strand Lagging strand
5ʹ 3ʹ
template

© 2015 Pearson Education Ltd

91

BioFlix: DNA Replication

© 2015 Pearson Education Ltd

92
Proofreading and Repairing DNA

a) DNA polymerases proofread newly made DNA,


replacing any incorrect nucleotides
b) In mismatch repair of DNA, repair enzymes correct
errors in base pairing

c) DNA can be damaged by exposure to harmful


chemical or physical agents such as cigarette smoke
and X-rays; it can also undergo spontaneous
changes
d) In nucleotide excision repair, a nuclease cuts out
and replaces damaged stretches of DNA
© 2015 Pearson Education Ltd

93

Figure 16.19-1
5ʹ 3ʹ

3ʹ 5ʹ

Nuclease

5ʹ 3ʹ

3ʹ 5ʹ

© 2015 Pearson Education Ltd

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Figure 16.19-2
5ʹ 3ʹ

3ʹ 5ʹ

Nuclease

5ʹ 3ʹ

3ʹ 5ʹ
DNA
polymerase

5ʹ 3ʹ

3ʹ 5ʹ

© 2015 Pearson Education Ltd

95

Figure 16.19-3
5ʹ 3ʹ

3ʹ 5ʹ

Nuclease

5ʹ 3ʹ

3ʹ 5ʹ
DNA
polymerase

5ʹ 3ʹ

3ʹ 5ʹ
DNA
ligase

5ʹ 3ʹ

3ʹ 5ʹ
© 2015 Pearson Education Ltd

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Evolutionary Significance of Altered DNA Nucleotides

a) Error rate after proofreading repair is low but


not zero
b) Sequence changes may become permanent and can
be passed on to the next generation

c) These changes (mutations) are the source of the


genetic variation upon which natural selection
operates

© 2015 Pearson Education Ltd

97

Replicating the Ends of DNA Molecules

a) Limitations of DNA polymerase create problems for


the linear DNA of eukaryotic chromosomes
b) The usual replication machinery provides no way to
complete the 5′ ends, so repeated rounds of
replication produce shorter DNA molecules with
uneven ends
c) This is not a problem for prokaryotes, most of which
have circular chromosomes

© 2015 Pearson Education Ltd

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Figure 16.20

Ends of parental Leading strand
DNA strands Lagging strand

Next-to-last
Last fragment fragment
Lagging strand RNA primer


Parental strand Removal of primers and
replacement with DNA
where a 3ʹ end is available


Second round
of replication

New leading strand 3ʹ
New lagging strand 5ʹ

Further rounds
of replication
Shorter and shorter daughter molecules
© 2015 Pearson Education Ltd

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Figure 16.20a


Ends of parental Leading strand
DNA strands Lagging strand

Next-to-last
Last fragment fragment

Lagging strand RNA primer



Parental strand Removal of primers and
replacement with DNA
where a 3ʹ end is available


© 2015 Pearson Education Ltd

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Figure 16.20b



Second round
of replication

New leading strand 3ʹ
New lagging strand 5ʹ

Further rounds
of replication

Shorter and shorter daughter molecules

© 2015 Pearson Education Ltd

101

Important Biological
Macromolecules
Biology for Majors

102
Proteins

Proteins are one of the most abundant organic molecules in living systems and
have the most diverse range of functions of all macromolecules.

Each cell in a living system may contain thousands of proteins, each with a
unique function and structure.

All proteins are polymers of amino acids arranged in a linear sequence.

103

Amino Acids

Amino acids are the monomers


that make up proteins.
Each amino acid has the same
fundamental structure, which
consists of a central carbon
atom, also known as the alpha
(α) carbon, bonded to an amino
group (NH2), a carboxyl group
(COOH), a hydrogen atom, and
an R group.

104
Peptide Bonds

• The sequence and the number of amino


acids ultimately determine the protein’s
shape, size, and function. The amino
acids are attached by a covalent bond,
known as a peptide bond, which is
formed by a dehydration reaction. The
carboxyl group of one amino acid and
the amino group of the incoming amino
acid combine, releasing a molecule of
water.

105

Protein Structure

The shape of a protein is critical to its function.

To understand how the protein gets its final shape or conformation, we need to
understand the four levels of protein structure: primary, secondary, tertiary, and
quaternary

106
Primary Structure

The unique sequence of amino acids in a polypeptide


chain is its primary structure.

107

Genes and Primary Structure

• The unique sequence for every


protein is ultimately determined
by the gene encoding the
protein. A change in nucleotide
sequence of the gene’s coding
region may lead to a different
amino acid being added to the
growing polypeptide chain,
causing a change in protein
structure and function.

108
Secondary Structure

The local folding of the


polypeptide in some regions
gives rise to the secondary
structure of the protein.

109

Tertiary Structure

The tertiary structure of proteins


is determined by a variety of
chemical interactions including
hydrophobic interactions, ionic
bonding, hydrogen bonding
and disulfide linkages.

110
Quaternary Structure

Some proteins are formed from several polypeptides, also known as subunits,
and the interaction of these subunits forms the quaternary structure.

Weak interactions between the subunits help to stabilize the overall structure.

111

The Four Levels


of Protein
Structure

112
Denaturation

If the protein is subject to changes in temperature, pH, or exposure to


chemicals, the protein structure may change, losing its shape without losing its
primary sequence in what is known as denaturation.

Denaturation may be reversible or irreversible.

Denaturation leads to loss of function.

113

Protein Folding

Protein folding is critical to its function.

Proteins often receive assistance in the folding process from protein


helpers known as chaperones (or chaperonins) that associate with
the target protein during the folding process. They act by preventing
aggregation of polypeptides that make up the complete protein
structure, and they disassociate from the protein once the target
protein is folded.

114
Protein Types and Functions
Type Examples Functions

Help in digestion of food by


Amylase, lipase, pepsin,
Digestive Enzymes catabolizing nutrients into
trypsin
monomeric units
Carry substances in the
Transport Hemoglobin, albumin blood or lymph throughout
the body
Construct different
Structural Actin, tubulin, keratin structures, like the
cytoskeleton

Coordinate the activity of


Hormones Insulin, thyroxine
different body systems

Protect the body from


Defense Immunoglobulins
foreign pathogens

Contractile Actin, myosin Effect muscle contraction

Provide nourishment in
Legume storage proteins,
Storage early development of the
egg white (albumin)
embryo and the seedling

115

Lipids

Lipids are a class of macromolecules that are nonpolar and hydrophobic in


nature.

Major types include fats and oils, waxes, phospholipids, and steroids.

116
Fats

Fats are a stored form of energy


and are also known as
triacylglycerols or triglycerides.
Fats are made up of fatty acids
and either glycerol or
sphingosine.
Fatty acids may be unsaturated
or saturated, depending on the
presence or absence of double
bonds in the hydrocarbon
chain.

117

Types of
Fatty Acids

118
Omega Fatty Acids

Alpha-linolenic acid is an example


of an omega-3 fatty acid. It has
three cis double bonds and, as a
result, a curved shape.
For clarity, the carbons are not
shown. Each singly bonded carbon
has two hydrogens associated with
it, also not shown.

119

Waxes

Wax covers the feathers of some


aquatic birds and the leaf surfaces of
some plants.
Because of the hydrophobic nature of
waxes, they prevent water from
sticking on the surface as in the leaves
at right.
Waxes are made up of long fatty acid
chains esterified to long-chain
alcohols.

120
Phospholipids

Phospholipids have a
glycerol or sphingosine
backbone to which two
fatty acid chains and a
phosphate-containing
group are attached.

121

Phospholipids in Membranes

Phospholipids make up the matrix of membranes

122
Steroids

Steroids are another class of lipids. Their basic structure has four fused carbon rings.
Cholesterol is a type of steroid and is an important constituent of the plasma
membrane, where it helps to maintain the fluid nature of the membrane. It is also
the precursor of steroid hormones such as testosterone.

123

Carbohydrates

Carbohydrates are a group of macromolecules that are a vital energy source


for the cell and provide structural support to plant cells, fungi, and all of the
arthropods that include lobsters, crabs, shrimp, insects, and spiders.

Carbohydrates are classified as monosaccharides, disaccharides, and


polysaccharides depending on the number of monomers in the molecule.

124
Monosaccharides

Monosaccharides are simple


sugars.

Glucose, galactose, and fructose


are common monosaccharides

125

Monosaccharide
Rings

Monosaccharides can be linear


chains or as ring-shaped
molecules.

126
Disaccharides

Monosaccharides are
linked by glycosidic bonds
that are formed as a result
of dehydration reactions,
forming disaccharides and
polysaccharides with the
elimination of a water
molecule for each bond
formed.
Common disaccharides
include lactose, maltose,
and sucrose.

127

Polysaccharides

Starch and glycogen, examples of polysaccharides, are the storage forms of


glucose in plants and animals, respectively.

Polysaccharides may also be structural components, such as the long chains


of glucose that form cellulose.

128
Cellulose

129

Polysaccharides (continued)

The long polysaccharide chains may be branched


like amylopectin (right) a constituent of starch.
Storage of glucose, in the form of polymers like
starch or glycogen, makes it slightly less accessible
for metabolism; however, this prevents it from
leaking out of the cell or creating a high osmotic
pressure that could cause excessive water uptake
by the cell.

130
Nucleic Acids

Nucleic acids are the most important macromolecules for the continuity of life.
They carry the genetic blueprint of a cell and carry instructions for the
functioning of the cell. The two main types of nucleic acids are
1.deoxyribonucleic acid (DNA)
2.ribonucleic acid (RNA)

131

Nucleotides

DNA and RNA are made up of monomers known as nucleotides.

The nucleotides combine with each other to form a polynucleotide, DNA or


RNA.

Each nucleotide is made up of three components: a nitrogenous base, a


pentose (five-carbon) sugar, and a phosphate group. Each nitrogenous base
in a nucleotide is attached to a sugar molecule, which is attached to one or
more phosphate groups.

132
Molecular
Structure of
Nucleotides

133

DNA Double Helix


DNA is the genetic material found
in all living organisms that is passed
on from parents to offspring. DNA is
an antiparallel double helix. The
phosphate backbone (the curvy
lines) is on the outside, and the
bases are on the inside. Each base
interacts with a base from the
opposing strand.

134
Base Complimentary Rule

Only certain types of base pairing are allowed. This is known as the base
complementary rule.

A can pair with T, and G can pair with C.

In this way, the DNA strands are complementary to each other. During DNA
replication, each strand is copied, resulting in a daughter DNA double helix
containing one parental DNA strand and a newly synthesized strand.

135

RNA

Ribonucleic acid, or RNA, is mainly involved in the process of protein synthesis


under the direction of DNA.
RNA is usually single-stranded and is made of ribonucleotides that are linked by
phosphodiester bonds.
A ribonucleotide in the RNA chain contains ribose (the pentose sugar), one of
the four nitrogenous bases (A, U, G, and C), and the phosphate group.
There are four major types of RNA: messenger RNA (mRNA), ribosomal RNA
(rRNA), transfer RNA (tRNA), and microRNA (miRNA).

136
mRNA

Messenger RNA or mRNA, carries the message from DNA, which controls all of
the cellular activities in a cell.
If a cell requires a certain protein to be synthesized, the gene for this product is
turned “on” and the messenger RNA is synthesized in the nucleus.
The RNA base sequence is complementary to the coding sequence of the
DNA from which it has been copied but with the base U instead of T.

137

rRNA
Ribosomal RNA (rRNA) is a major
constituent of ribosomes on which the
mRNA binds.

The rRNA ensures the proper alignment of


the mRNA and the ribosomes; the rRNA of
the ribosome also has an enzymatic
activity (peptidyl transferase) and
catalyzes the formation of the peptide
bonds between two aligned amino acids.

138
tRNA

Transfer RNA (tRNA) is one of the smallest of the four types of RNA, usually 70–90
nucleotides long.

It carries the correct amino acid to the site of protein synthesis. It is the base
pairing between the tRNA and mRNA that allows for the correct amino acid to
be inserted in the polypeptide chain.

139

mRNA and tRNA in the Ribosome

140
microRNA

microRNAs are the smallest RNA molecules and their role involves the
regulation of gene expression by interfering with the expression of certain
mRNA messages.

141

Features of DNA and RNA


Feature DNA RNA

Carries genetic Involved in protein


Function
information synthesis

Remains in the
Location Leaves the nucleus
nucleus
DNA is double-
stranded “ladder”:
Structure sugar-phosphate Usually single-stranded
backbone, with base
rungs.

Sugar Deoxyribose Ribose

Pyrimidines Cytosine, thymine Cytosine, uracil

Purines Adenine, guanine Adenine, guanine

142
The Central Dogma of Life

Information flow in an organism takes place from DNA to RNA to protein.

DNA dictates the structure of mRNA in a process known as transcription, and


RNA dictates the structure of protein in a process known as translation.

This is known as the Central Dogma of Life, which holds true for all organisms.

143

Comparing Macromolecules
Basic
Macromolecule Formula, key Monomer Examples Uses
features
CHON
Storage; Signals;
−NH2 +
Enzymes, some Structural; Contractile;
Proteins −COOH +R Amino acids
hormones Defensive; Enzyme;
group
Transport; Receptors

C:H:O
Greater than Energy storage;
Fatty acid and Butter, oil, cholesterol,
Lipids 2:1 H:O Protection; Chemical
glycerol beeswax
(carboxyl messengers; Repel water
group)
Glucose, Fructose,
C:H:O
Carbohydrates Monosaccharides Starch, Glycogen, Energy storage; Structure
1:2:1
Cellulose
CHONP
pentose,
Nucleic Acids nitrogenous Nucleotides DNA, RNA Genetic information
base,
phosphate

144
Dehydration Synthesis

Forming these macromolecules requires combined monomers together. Most


monomers combine with each other using covalent bonds to form larger
molecules known as polymers. In doing so, monomers release water molecules
as byproducts. This type of reaction is known as dehydration synthesis, which
means “to put together while losing water.”

145

Hydrolysis

Polymers are broken down into monomers in a process known as hydrolysis,


which means “to split water,” a reaction in which a water molecule is used
during the breakdown.
During these reactions, the polymer is broken into two components: one gains
a hydrogen atom (H+) and the other gains a hydroxyl molecule (OH–) from a
split water molecule.

146
Energy and Macromolecules

Dehydration and hydrolysis reactions are catalyzed, or “sped up,” by specific


enzymes.

Dehydration reactions involve the formation of new bonds, requiring energy,


while hydrolysis reactions break bonds and release energy.

Breakdown of these macromolecules provides energy for cellular activities.

147

Quick Review

• Describe the structure and function proteins


• What are the different types of lipids? How do the structure of each support
its role in biological systems?
• What roles do carbohydrates play in biological systems?
• What are nucleic acids? What role do they play in DNA and RNA?
• What are macromolecules? What are the differences between the four
classes of macromolecules?

148

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