Chapter 11 dna biology & technology

Introduction to Biology
Chapter 11

Professor Zaki Sherif, MD., PhD
Strayer University

Essentials of
Biology
Sylvia S. Mader

Chapter 11
Lecture Outline

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

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.
• There was a controversy over whether DNA
or protein was the genetic message.
• Experiment using viruses showed only DNA
directed the formation of new viruses.

Figure 11.1 The genes are composed of DNA.

•Alfred Hershey and Martha Chase determined that DNA
is the genetic material.
•Their experiment involved a virus which 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.

Figure 11.1 The genes are composed of DNA


DNA

capsid

E. coli
cytoplasm

(tissue left): © Sercomi/Photo Researchers, Inc.

• Structure of DNA
 Race to determine the structure
 Chargaff’s Rules
• Knew DNA contains 4 types of nucleotides
• Examined DNA from many species
1.The amount of A, T, G, and C in DNA varies from
species to species.
2.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.

Figure 11.2 Nucleotide composition of DNA and RNA


C
P CH2
O
sugar

OH

a.

Figure 11.2 continued

Nitrogen-containing bases

NH2 O
Phosphate C C
N H N
O N C N C
C H C H
HO P O– H C C C C
N N H2N N N
–
O
H H
Adenine (A) Guanine (G)
b.

Sugars
H H NH2 O O
HO C H HO C H C H C CH3 C H
O OH O OH N C H N C H N C
C H H C C H H C C C H C C C C
O N O N H O N H
H C C H H C C H
H H H
OH H OH OH
Cytosine (C) Thymine (T) Uracil (U)
deoxyribose ribose (DNA only) (RNA only)
(DNA only) (RNA only)

c. d.

Figure 11.3 X-ray
diffraction pattern
• Franklin’s X-ray diffraction
of DNA data
 Rosalind Franklin was studying
the structure of DNA.
 Her data showed DNA to be a
helix with some portions
repeating over and over.

Figure 11.4 Watson and Crick
• The Watson and Crick model of DNA

Model
 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.
 Won the Nobel Prize

© A. Barrington Brown/Photo Researchers, Inc.

James Watson (left) and Francis Crick (right)

• 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
halves of helix together.

Figure 11.5 DNA structure

C P
sugar-phosphate
G
C backbone
P
G
T

A P
P

A
a. Space-filling model
T
P complementary
base pairing
P
hydrogen
bond
OH G
P
2′ 3′
5′ T C
1′ A 1′ S 4′
4′ S P
3′ 2′ 5′
3′ end 5′ end
P
C
P
OH
b. Nucleotide pair 5′ end

G
P
hydrogen bonds

sugar

OH 3′ end

c. Structure of DNA

© Photodisk Red/Getty RF

• Replication of DNA
 Process of copying DNA before cell division
 2 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.

• 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.


Figure 11.6
3′

5′
Semiconservative
replication
G

G
C

parental DNA helix
G
G
C
G
C

movement C
of G C
C region of replication: New
replication G nucleotides are pairing with
for K A
those of parental strands.
A

G
T

T G
G
T A C region of
completed
G replication
C G
G

G
G

direction
C

of DNA
C

sythesis 3′
G
5′

C G new old
strand strand
C G
daughter molecule
5′
3′
old new
strand strand

daughter molecule

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

Figure 11.7 Eukaryotic replication

replication bubble
fork

daughter
daughter strand
DNA molecules

parental strand

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• RNA structure and function
 Ribonucleic acid (RNA)
 Contains sugar ribose
 Uses uracil, not thymine
• Uses A, C, and G like DNA
 Single-stranded
 3 majors types
• Messenger RNA (mRNA)
• Transfer RNA (tRNA)
• Ribosomal RNA (rRNA)

Figure 11.8 Structure of RNA

G

P
S Base is uracil
U
instead of thymine.
P

S
A

G P

U S C

A P

one S
C nucleotide ribose

• The 3 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
attached to ER.

11.2 Gene Expression
• Early 1900’s, 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.
• Central dogma of molecular biology
 Information flows from DNA to RNA to protein.

• Transcription
 DNA serves as template to make mRNA.
• Translation
 mRNA directs sequence of amino acids in a
protein.
 rRNA and tRNA assist

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or
display. Figure 11.9 Flow of genetic
Nucleus
CT information
CT
C
A A G
G T G G
DNA A
G A
double helix C
C T

DNA 3′ 5′
C C T C T T
A G G
Transcription
G G A G A A
U C C
mRNA 5′ 3′

Cytoplasm
codon
mRNA
U C C
G G A G A A
Translation
A G G
C C U C U U
tRNA
anticodon
Polypeptide Gly Arg Thr

• 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

Figure 11.10 Messenger RNA codons


Second base
U C A G
UUU UCU UAU UGU U
phenylalanine (Phe) tyrosine (Tyr) cysteine (Cys)
UUC UCC UAC UGC C
U serine (Ser)
UUA UCA UAA stop UGA stop A
leucine (Leu) UCG
UUG UAG stop UGG tryptophan (Trp) G
U
CUU CCU CAU histidine (His) CGU
CUC CCC CAC CGC C
C leucine (Leu) proline (Pro) arginine (Arg)

Third base
CUA CCA CAA CGA A
CCG CAG glutamine (Gln)
CUG CGG
First base

G

AUU ACU AAU AGU U
asparagine (Asn) serine (Ser)
AUC isoleucine (Ile) ACC AAC AGC C
A AUA threonine (Thr)
ACA AAA AGA A
ACG AAG lysine (Lys) arginine (Arg)
AUG methionine (Met) (start) AGG G

GUU GCU GAU GGU U
aspartic acid (Asp)
GUC GCC GAC GGC C
G GUA valine (Val) alanine (Ala) glycine (Gly)
GCA GAA GGA A
GUG GCG GAG glutamic acid (Glu) GGG G

• 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.

Figure 11.11 Transcription
G to form mRNA
C G
G C

Transcription is taking place—
template the nucleotides of mRNA are
DNA joined by the enzyme RNA
strand polymerase in an order
G
C

G C complementary to a strand
of DNA.
3′

RNA
G G C polymerase

C C G

T U A
G G C
T

G

This mRNA transcript is
G ready to be processed.
G

C
G C

mRNA
5′

to processing

• Newly made pre-mRNA must be processed.
 Capping and addition of poly-A tail provide 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.

Figure 11.12 mRNA processing

DNA to be transcribed

DNA e i e i e

transcription
poly-A
cap tail
primary e i e i e
mRNA
5′ (cut out) (cut out) 3′

enzyme i i enzyme

mature
mRNA

e = exons
i = introns

Figure 11.13 tRNA
• Translation structure and function
 tRNA brings in amino acids Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or
display.

• Anticodon – group of 3 bases amino acid
complementary to a specific
codon of mRNA complementary
base pairing
 After translation is
complete, a protein
contains the sequence of
amino acids originally
specified in the DNA.

U
G G

anticodon
a. tRNA–amino acid

• Ribosomes are composed of protein and rRNA.
 Site of translation – protein synthesis
 Binds mRNA and 2 tRNA molecules
• P site for a tRNA attached to a peptide
• A site for newly arrived tRNA with an amino acid


tRNA binding sites

P site A site

large subunit

mRNA
binding small subunit
site
b. Ribosome peptide U
U
U

anticodon U G G
A C C A A A
mRNA
5′ 3′
ribosome

c. tRNA–amino acid at ribosome

Figure 11.14 Polyribosome structure and function

3′
mRNA
codon

5′

a.

• Polyribosome – several ribosomes attach to 400,000
b. and
translate the same piece of mRNA. b: Courtesy Alexander Rich

• 3 phases of translation
1. Initiation
2. Elongation
3. Termination
• Initiation
• mRNA binds to small subunit of ribosome.
• Large subunit then joins

Figure 11.15 Initiation

amino acid
methionine
initiator tRNA

mRNA
small
ribosomal
subunit start codon

P site A site
large ribosomal
subunit

mRNA
5′ 3′

• 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

Figure 11.16 Elongation cycle
display.
• Elongation
1. tRNA in P site
bears growing
polypeptide.

codon

P site A site
5′ 3′

1 anticodon


• Elongation
peptide
2. This tRNA
passes peptide
2
to tRNA in A site.

codon

P site A site
5′ 3′

1 anticodon


•
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction
or display.
Elongation
peptide 3. Empty tRNA
leaves P site.
2

new
peptide
bond
codon 3

P site A site
5′ 3′

1 anticodon

display.
• Elongation
peptide
4. Translocation –
2 ribosome moves
forward one
codon.
 tRNA-peptide
now in P site and
new A site open for
peptide new tRNA
bond
codon 3

P site A site
5′ 3′

1 anticodon

4

Figure 11.17 Summary of gene expression in eukaryotes

Transcription 1. DNA in nucleus
serves as a template. 3. mRNA moves into
2. Pre-mRNA is cytoplasm and becomes amino
processed associated with acids
DNA before leaving ribosomes.
the nucleus. large and small
introns tRNA
ribosomal subunits 4. tRNAs with
peptide
primary anticodons
mRNA carry amino
mature 6. Polypeptide acids to mRNA.
anticodon
mRNA mRNA synthesis takes
place one amino 5. Anticodon–codon
acid at a time. complementary base
pairing occurs.
Translation

ribosome codon

8. At termination, the
ribosome detaches from
7. When a ribosome the ER; ribosomal subunits
attaches to rough ER, and the mRNA dissociate.
the polypeptide enters
its lumen, where the
polypeptide folds and
is modified further.


Transcription

amino
acids
DNA
large and small
introns tRNA
ribosomal subunits peptide
primary
mRNA
mature anticodon
mRNA mRNA

Translation

ribosome codon


serves as a template.
amino
acids
DNA
large and small
introns tRNA
primary
mRNA
mature anticodon
mRNA mRNA

Translation

ribosome codon


serves as a template.
2. Pre-mRNA is amino
processed acids
DNA before leaving
introns ribosomal subunits tRNA
peptide
primary
mRNA
mature anticodon
mRNA mRNA

Translation

ribosome codon


cytoplasm and becomes amino
2. Pre-mRNA is
associated with acids
processed
DNA ribosomes.
before leaving
introns tRNA
primary
mRNA
mature anticodon
mRNA mRNA

Translation

ribosome codon


2. Pre-mRNA is
processed
DNA ribosomes.
before leaving
introns ribosomal subunits tRNA 4. tRNAs with
peptide
primary anticodons
mRNA carry amino
mature acids to mRNA.
anticodon
mRNA mRNA

Translation

ribosome codon


peptide 4. tRNAs with
primary anticodons
mRNA carry amino
mature acids to mRNA.
anticodon
mRNA mRNA
5. Anticodon–codon
complementary base
pairing occurs.
Translation

ribosome codon


2. Pre-mRNA is
processed
DNA ribosomes.
before leaving
introns tRNA
ribosomal subunits 4. tRNAs with
peptide
primary anticodons
mRNA carry amino
mature 6. Polypeptide anticodon acids to mRNA.
pairing occurs.
Translation

ribosome codon


peptide 4. tRNAs with
primary anticodons
mRNA carry amino
mature 6. Polypeptide anticodon acids to mRNA.
pairing occurs.
Translation

ribosome codon

7. When a ribosome
attaches to rough ER,
the polypeptide enters
its lumen, where the
polypeptide folds and
is modified further.

• Gene mutation
 Change in the sequence of bases in a gene
 Causes
• Replication error
 Rare due to proofreading
• Transposons
 “Jumping genes” – pieces of DNA that move within and
between chromosomes
• Mutagens
 Environmental influences – radiation
 Chemical mutagens
 Repair enzymes


Figure 11.18 Transposons

a.

Normal gene Mutated gene

transposon
codes for cannot code
purple for purple
pigment pigment

purple kernel white kernel
b. c.
a: Courtesy of Cold Spring Harbor Laboratory

• Types and effects of mutations
 Many mutations go undetected – no
observable effect.
 Point mutations
• Change in single DNA nucleotide
• Results can be minor or severe
• Sickle cell disease
 Frameshift mutations
• Extra or missing nucleotides
• Usually much more severe
• All downstream codons affected
• THE CAT ATE THE RAT – C removed
• THE ATA TET HER AT

11.3 DNA Technology
• Genetic engineering – inserting cloned
genes into an organism
 Transgenic organism
 Cloning genes – making identical copies
• Because the genetic code is nearly
universal, it’s possible to transfer cloned
genes between virtually any organism.

• Recombinant DNA
technology
 Recombinant DNA

(rDNA) contains DNA
from 2 or more different DNA
duplex
A G A A T T C G C
T C T T A A G C G
organisms.
restriction
 A vector is used to carry enzyme
the foreign DNA.
• May be a plasmid from A A T T C G C
bacteria “sticky ends” G C G
A G
 Restriction enzymes are T C T T A A

molecular scissors
• Cut DNA at specific sites
• “Sticky ends”
 DNA ligase used to join
pieces of DNA together

• Human insulin made by bacterial cells
 Human gene removed
 Inserted into plasmid
 Plasmid inserted into bacteria
 Bacteria produce insulin as if it was one of
their own gene products.

Figure 11.19 Recombinant DNA technology

Insulin plasmid DNA
gene

human cell bacterial host cell

cut with
restriction
enzyme

insulin gene plasmid DNA

add DNA ligase

recombinant DNA

bacterial host cell

cell multiplies;
produces insulin

insulin

cloned genes for insertion
into another host cell insulin
© SIU/Visuals Unlimited


recombinant DNA

bacterial host cell

cell multiplies;
produces insulin

insulin

cloned genes for insertion
into another host cell insulin

• Transgenic organisms
 Biotechnology – use of natural biological systems to create a
product
 Organisms can be genetically engineered for use in
biotechnology.
 Transgenic bacteria
• Grown in bioreactors
• Gene product collected from growth medium
 Transgenic plants and animals
• Cotton, corn and potato make their own insecticide.
• Soybeans herbicide resistant
• Larger fishes, cows and pigs from inserted growth hormone gene
• “Pharming” – use of transgenic farm animal to produce
pharmaceuticals in milk.
• Transgenic animals may be cloned – nucleus from adult cell
introduced into enucleated egg cell produces identical genotype
of adult donor.

Figure 11.20 Use of
transgenic
organisms

a.

b.

c.
a. Transgenic bacteria in
bioreactors
b. Salmon grow larger
with growth hormone
gene.
c. Unblemished peas
d.
have a pest inhibitor
gene.
d. Transgenic bacteria
used for oil cleanup
e. Transgenic corn can
resist herbicides to
e. increase crop yield.
a: © Nita Winter; b: Courtesy Robert H. Devlin, Fisheries and Oceans Canada; c: © Richard Shade; d: © Jerry Mason/Photo Researchers, Inc.; e: © AGStockUSA,
Inc./Alamy

• Polymerase chain reaction (PCR)
 Amplifies specific DNA sequences
 DNA polymerase – makes DNA
• From Thermus aquaticus – tolerates high
temperatures
 Primers – specific DNA segment to be
amplified
• Doesn’t amplify all DNA – only target
 Cycles over and over again doubling
amount of DNA at each cycle

Figure 11.21 Polymerase chain reaction

DNA from one homologue
DNA polymerase, First cycle 5′ 3′
primers, 3′ 5′
nucleotides

5′ 3′
Heating separates strands
3′ 5′

Cooling allows primers 5′ 3′
to base pair at target site 3′ 5′
and for DNA polymerase 5′ 3′
to make new DNA 3′ 5′

end of first cycle
5′ 3′
3′ 5′
to second cycle
5′ 3′
3′ 5′

• DNA fingerprinting
 Makes use of repeating noncoding DNA
segments
 People differ in how many repeats.
 Can use PCR to increase amount of
DNA sample
 Electrophoresis separates samples by
size.
• Longer DNA strands are larger and migrate
less on the gel.

Figure 11.22 DNA fingerprinting

Collect
DNA
crime scene suspect suspect
evidence A B

12 repeats

12 repeats

12 repeats

16 repeats
16 repeats
12 repeats

Perform
PCR on
repeats

Use gel electrophoresis to identify criminals

11.4 Genomic and Proteomics
• Genomics – study of genomes
 Human and other organisms
 Coding and noncoding segments
• Human Genome Project
 13-year effort
 Found many small regions of DNA vary among
individuals
 Some individuals even have extra copies of genes.
 Differences may have no effect or may increase or
decrease susceptibility to disease.

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Figure 11.23 Variations in DNA
Met Pro polypeptide sequence
5' 3' mRNA
A U G C C C

T A C G G G
3' 5' template DNA strand
Gene A Gene B Gene C

A T G C C C G T C T C A
T A C G G G C A G A G T

Intergenic DNA Intergenic DNA
a. Normal chromosomal DNA

Met Thr polypeptide

5' 3' mRNA
A U G A C C

T A C T G G
3' 5' template DNA strand

A T G A C C G T C T C A
T A C T G G C A G A G T

b. Variation in the order of the bases within a gene due to a mutation


A T G C C C G T C G C A
T A C G G G C A G C G T

c. Variation in the order of the bases within an intergenic sequence due to a mutation

Gene A Gene B Gene B Gene C

A T G C C C G T C T C A
T A C G G G C A G A G T

Intergenic DNA Intergenic DNA Intergenic DNA
d. Variation in the gene copy number

• Genome comparisons
 Clues to evolutionary origins
 Genes of humans and chimps 98% alike
• Humans and mice 85% alike
• Humans also share genes with bacteria
 Comparing human and chimp chromosome 22
• Among the genes that differed were several that
may have played a role in human evolution.
 Speech, hearing and smell
• Comparing genomes may be a way of finding genes
associated with human diseases.

Figure 11.24 Studying genomic differences between
chimpanzees and humans

a.

b.

c. a(both), b(left): © Getty RF; b(right): © The McGraw-Hill Companies/Bob Coyle, photographer; c(both): ©
Getty RF

Figure 11.25 Bioinformatics

• Proteomics – explores structure and function of
cellular proteins and how they interact to
produce traits
 Important in drug development
• Bioinformatics – application of computer
technologies to study genome and proteome
 Using computer to analyze large amount of data to
find significant patterns

Chapter 11 dna biology & technology

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