Chapter 10 The Structure and Function of DNA Laura Coronado Bio 10 Chapter 10.

Chapter 10Chapter 10

The Structure and Function of DNA

Laura Coronado Bio 10 Chapter 10

Biology and Society: Tracking a Killer– The influenza virus is one of the

deadliest pathogens in the world.

– Each year in the United States, over 20,000 people die from influenza infection.

– In the flu of 1918–1919, about 40 million people died worldwide.

– Vaccines against the flu are the best way to protect public health.

– Because flu viruses mutate quickly, new vaccines must be created every year.


DNA: STRUCTURE AND REPLICATION

– DNA:• Was known to be a chemical in cells by the end of the

nineteenth century• Has the capacity to store genetic information• Can be copied and passed from generation to

generation

– DNA and RNA are nucleic acids.• They consist of chemical units called nucleotides.• The nucleotides are joined by a sugar-phosphate

backbone.


Sugar-phosphatebackbone

Phosphate group

Nitrogenous base

DNA nucleotide

Nucleotide Thymine (T)

Sugar

Polynucleotide

DNAdouble helix

Sugar(deoxyribose)

Phosphategroup

Nitrogenous base(can be A, G, C, or T)

Figure 10.1Laura Coronado Bio 10 Chapter 10

Discovery of the Double Helix

• James Watson and Francis Crick determined that DNA is a double helix.

• Rosalind Franklin collected the X-ray crystallography data.

• Watson and Crick used X-ray crystallography data to reveal the basic shape of DNA.


X-ray image of DNA

Rosalind Franklin

Figure 10.3bLaura Coronado Bio 10 Chapter 10

DNA Structure– DNA is like a rope ladder twisted into a spiral.

• The ropes at the sides represent the sugar-phosphate backbones.

• Each wooden rung represents a pair of bases connected by hydrogen bonds.

– The four nucleotides found in DNA differ in their nitrogenous bases. These bases are:• Thymine (T), Cytosine (C), Adenine (A) & Guanine (G)

– RNA has uracil (U) in place of thymine.– DNA bases pair in a complementary fashion:

• Adenine (A) pairs with thymine (T) • Cytosine (C) pairs with guanine (G)


TwistFigure 10.4


(c) Computermodel

(b) Atomic model(a) Ribbon model

Hydrogen bond


DNA Replication

– When a cell reproduces, a complete copy of the DNA must pass from one generation to the next.

– Watson and Crick’s model for DNA suggested that DNA replicates by a template mechanism.

– DNA replication in eukaryotes:• Begins at specific sites on a double helix• Proceeds in both directions


Parental (old)DNA molecule

Daughter (new) strand

DaughterDNA molecules (double helices)


DNA Polymerases

–Are enzymes–Make the covalent bonds between the

nucleotides of a new DNA strand–Are involved in repairing damaged DNA• DNA can be damaged by ultraviolet light.


Origin ofreplication



Parental strands

Parental strand

Daughter strand

Two daughter DNA molecules

Bubble


THE FLOW OF GENETIC INFORMATION FROM DNA TO RNA TO PROTEIN

– DNA functions as the inherited directions for a cell or organism.– An organism’s genotype is its genetic makeup, the sequence of

nucleotide bases in DNA.– The phenotype is the organism’s physical traits, which arise

from the actions of a wide variety of proteins.– DNA specifies the synthesis of proteins in two stages:• Transcription, the transfer of genetic information from DNA

into an RNA molecule• Translation, the transfer of information from RNA into a

protein– Transcription and translation are how genes control: The

structures & the activities of cellsLaura Coronado Bio 10 Chapter 10

TRANSLATION

Protein

RNA

TRANSCRIPTION

DNA

Cytoplasm

Nucleus

Figure 10.8-3Laura Coronado Bio 10 Chapter 10

Overview - The Big Picture– The function of a gene is to dictate the production

of a polypeptide.• In DNA, it is the linear sequence of nucleotide bases.• A typical gene consists of thousands of nucleotides.• A single DNA molecule may contain thousands of genes.

– When DNA is transcribed, the result is an RNA molecule.

– RNA is then translated into a sequence of amino acids in a polypeptide.

– A protein may consist of two or more different polypeptides.


– The RNA message is translated into a polypeptide by using a codon is a triplet of bases, which codes for one amino acid.

– The genetic code is:• The set of rules relating nucleotide sequence to amino

acid sequence • Shared by all organisms

– There are 64 codons:• 61 code for amino acids • 3 are stop codons, indicating the end of a polypeptide


TRANSLATION

Amino acid

RNA

TRANSCRIPTION

DNA strand

Polypeptide

Codon

Gene 1

Gene 3

Gene 2DNA molecule


Second base of RNA codonFi

rst b

ase

of R

NA

codo

n

Phenylalanine(Phe)

Leucine(Leu)

Cysteine(Cys)

Leucine(Leu)

Isoleucine(Ile)

Valine(Val)

Met or start

Serine(Ser)

Proline(Pro)

Threonine(Thr)

Tyrosine(Tyr)

Histidine(His)

Glutamine(Gln)

Asparagine(Asn)

Alanine(Ala)

Stop Stop

Stop

Glutamicacid (Glu)

Asparticacid (Asp)

Lysine(Lys)

Arginine(Arg)

Tryptophan (Trp)

Arginine(Arg)

Serine(Ser)

Glycine(Gly)

Third

bas

e of

RN

A co

don


Transcription: From DNA to RNA

– Transcription:• Makes RNA from a DNA template• Uses a process that resembles DNA replication• Substitutes uracil (U) for thymine (T)

– RNA nucleotides are linked by RNA polymerase.– The “start transcribing” signal is a nucleotide

sequence called a promoter.– The first phase of transcription is initiation, in which:• RNA polymerase attaches to the promoter • RNA synthesis begins


RNA Elongation– During the second phase of transcription, called

elongation:• The RNA grows longer • The RNA strand peels away from the DNA template

– During the third phase of transcription, called termination:• RNA polymerase reaches a sequence of DNA bases

called a terminator• Polymerase detaches from the RNA• The DNA strands rejoin


Newlymade RNA

RNA nucleotides

RNA polymerase

Templatestrand of DNA

Direction oftranscription

(a) A close-up view of transcription (b) Transcription of a gene

RNApolymerase

Completed RNA

Growing RNA

Termination

Elongation

Initiation Terminator DNA

Area shown inpart (a) at left

RNA

PromoterDNA

RNA polymerase

DNA of gene


The Processing of Eukaryotic RNA

–After transcription:• Eukaryotic cells process RNA• Prokaryotic cells do not

–RNA processing includes:• Adding a cap and tail• Removing introns• Splicing exons together to form messenger RNA

(mRNA)


TranscriptionAddition of cap and tail

Coding sequence

mRNA

DNA

Cytoplasm

Nucleus

Exons spliced together

Introns removed Tail

CapRNAtranscriptwith capand tail

Exon Exon ExonIntronIntron


Translation: The Players

– Translation is the conversion from the nucleic acid language to the protein language.

– Translation requires:• Messenger RNA (mRNA)• ATP• Enzymes• Ribosomes• Transfer RNA (tRNA)


Transfer RNA (tRNA)

– Transfer RNA (tRNA):• Acts as a molecular interpreter• Carries amino acids• Matches amino acids with codons in mRNA

using anticodons


tRNA polynucleotide(ribbon model)

RNA polynucleotidechain

Anticodon

Hydrogen bond

Amino acid attachment site

tRNA (simplifiedrepresentation)


Ribosomes

–Ribosomes are organelles that:• Coordinate the functions of mRNA and tRNA• Are made of two protein subunits• Contain ribosomal RNA (rRNA)• A fully assembled ribosome holds tRNA and

mRNA for use in translation.


Next amino acidto be added to polypeptide

Growingpolypeptide

tRNA

mRNA

tRNA binding sites

Codons

Ribosome

(b) The “players” of translation(a) A simplified diagramof a ribosome

Largesubunit

Smallsubunit

P site

mRNA binding site

A site


Translation: The Process

– Translation is divided into three phases:• Initiation• Elongation• Termination


Initiation– Initiation brings together:• mRNA• The first amino acid, Met, with its attached tRNA• Two subunits of the ribosome

– The mRNA molecule has a cap and tail that help it bind to the ribosome.

– Initiation occurs in two steps:• First, an mRNA molecule binds to a small ribosomal

subunit, then an initiator tRNA binds to the start codon.• Second, a large ribosomal subunit binds, creating a

functional ribosome.


Start of geneticmessage

Tail

End

Cap


InitiatortRNA

mRNA

Startcodon

Met

P site

Small ribosomalsubunit

A site

Large ribosomalsubunit


Elongation– Elongation occurs in three steps.• Step 1, codon recognition:– the anticodon of an incoming tRNA pairs with the mRNA

codon at the A site of the ribosome.• Step 2, peptide bond formation:– The polypeptide leaves the tRNA in the P site and

attaches to the amino acid on the tRNA in the A site– The ribosome catalyzes the bond formation between the

two amino acids• Step 3, translocation:– The P site tRNA leaves the ribosome – The tRNA carrying the polypeptide moves from the A to

the P siteLaura Coronado Bio 10 Chapter 10

Termination

– Elongation continues until:• The ribosome reaches a stop codon• The completed polypeptide is freed• The ribosome splits into its subunits


Newpeptidebond

Stopcodon

mRNAmovement

mRNA

P site

Translocation

Peptide bond formation

Polypeptide

ELONGATION

Codon recognition

Asite

Codons

Anticodon

Amino acid


Review: DNA RNA Protein

– In a cell, genetic information flows from DNA to RNA in the nucleus and RNA to protein in the cytoplasm.


Transcription RNA polymerase

mRNA DNA

Intron

Nucleus

mRNAIntron

TailCap

RNA processing

tRNA

Amino acid

Amino acidattachment

EnzymeATP Initiation

of translation

Ribosomalsubunits

Elongation

AnticodonCodon

Termination

Polypeptide

Stopcodon


– As it is made, a polypeptide:• Coils and folds• Assumes a three-dimensional shape, its tertiary structure

– Several polypeptides may come together, forming a protein with quaternary structure.


Mutations

– A mutation is any change in the nucleotide sequence of DNA.

– Mutations can change the amino acids in a protein.– Mutations can involve:• Large regions of a chromosome • Just a single nucleotide pair, as occurs in sickle cell anemia

– Mutations within a gene can occur as a result of:• Base substitution, the replacement of one base by another• Nucleotide deletion, the loss of a nucleotide • Nucleotide insertion, the addition of a nucleotide



– Insertions and deletions can:• Change the reading frame of the genetic

message • Lead to disastrous effects• Have beneficial effects

Normal hemoglobin DNA

mRNA

Normal hemoglobin

Mutant hemoglobin DNA

mRNA

Sickle-cell hemoglobin


Mutagens

–Mutations may result from:• Errors in DNA replication • Physical or chemical agents called mutagens

–Although mutations are often harmful, they are the source of genetic diversity, which is necessary for evolution by natural selection.


mRNA and protein from a normal gene

Deleted

(a) Base substitution

Inserted(b) Nucleotide deletion

(c) Nucleotide insertionFigure 10.22


VIRUSES AND OTHER NONCELLULAR INFECTIOUS AGENTS

– Viruses exhibit some, but not all, characteristics of living organisms. Viruses:• Possess genetic material

in the form of nucleic acids • Are not cellular and

cannot reproduce on their own.

– Bacteriophages, or phages, are viruses that attack bacteria.


DNA

Protein coat

Bacterial cell

Head

Tail

Tailfiber

DNAofvirus

Bacteriophage(200 nm tall)

Colorized TEM


Bacteriophages Reproduction

–Phages have two reproductive cycles.(1) In the lytic cycle:– Many copies of the phage are made within the

bacterial cell, and then – The bacterium lyses (breaks open)

(2) In the lysogenic cycle:– The phage DNA inserts into the bacterial chromosome

and – The bacterium reproduces normally, copying the

phage at each cell division


Phage

Phage DNA

Phage injects DNA

Phageattachesto cell.

Bacterialchromosome (DNA)

Phage DNAcircularizes.

Phages assemble

OR

New phage DNA andproteins are synthesized.

LYTIC CYCLE

Cell lyses,releasingphages.

LYSOGENIC CYCLE

Phage DNA is inserted intothe bacterial chromosome.

Many cell divisions

Prophage

Occasionally aprophagemay leave the bacterialchromosome.

Lysogenic bacteriumreproduces normally,replicating the prophageat each cell division.


Plant Viruses

–Viruses that infect plants can:• Stunt growth• Diminish plant yields• Spread throughout the entire plant

–Viral plant diseases:• Have no cure • Are prevented by producing plants that resist

viral infection, controversial


Tobacco mosaic virus

RNA

Protein


Animal Viruses

– Viruses that infect animals are:• Common causes of

disease • May have RNA or DNA

genomes

– Some animal viruses steal a bit of host cell membrane as a protective envelope.


Membranousenvelope

RNA

Protein coat

Protein spike

Viral Reproductive Cycle

– The reproductive cycle of an enveloped RNA virus can be broken into seven steps. 1. Entry2. Uncoating3. RNA Synthesis4. Protein Synthesis5. RNA Synthesis (other strand)6. Assembly7. Exit


Protein coat

mRNA

Protein spike

Plasma membraneof host cell

Envelope

Template

New viralgenomeNew viral proteins

Exit

VirusViral RNA (genome)

Viral RNA(genome)

Entry

Uncoating

Assembly

RNA synthesisby viral enzyme

RNA synthesis(other strand)

Protein synthesis


Protein spike

Envelope

Mumps virus

Colo

rized

TEM

Figure 10.29cLaura Coronado Bio 10 Chapter 10

The Process of Science: Do Flu Vaccines Protect the Elderly?

– Observation: Vaccination rates among the elderly rose from 15% in 1980 to 65% in 1996.

– Question: Do flu vaccines decrease the mortality rate among those elderly people who receive them?

– Hypothesis: Elderly people who were immunized would have fewer hospital stays and deaths during the winter after vaccination.


The Process of Science: Do Flu Vaccines Protect the Elderly?

– Experiment: Tens of thousands of people over the age of 65 were followed during the ten flu seasons of the 1990s.

– Results: People who were vaccinated had a:• 27% less chance of being hospitalized during the next flu

season and • 48% less chance of dying


HIV, the AIDS Virus

– HIV is a retrovirus, an RNA virus that reproduces by means of a DNA molecule.

– Retroviruses use the enzyme reverse transcriptase to synthesize DNA on an RNA template.

– HIV steals a bit of host cell membrane as a protective envelope.

– The behavior of HIV nucleic acid in an infected cell can be broken into six steps.

– AIDS (acquired immune deficiency syndrome) is:• Caused by HIV infection and• Treated with drugs that interfere with the reproduction of the

virus


Envelope

Reversetranscriptase

Surface protein

Proteincoat

RNA(two identicalstrands)


Reversetranscriptase

HIV (red dots) infecting a white blood cell

DNAstrand Chromosomal

DNA

Cytoplasm

Nucleus

Provirus

RNA

Viral RNA

DoublestrandedDNA

ViralRNAand proteins

SEM


Part of a T nucleotide

Thymine(T)

AZT


Viroids and Prions

– Two classes of pathogens are smaller than viruses:• Viroids are small circular RNA molecules that do not encode

proteins • Prions are misfolded proteins that somehow convert normal

proteins to the misfolded prion version

– Prions are responsible for neurodegenerative diseases including:• Mad cow disease• Scrapie in sheep and goats• Chronic wasting disease in deer and elk• Creutzfeldt-Jakob disease in humans


Figure 10.35

Evolution Connection: Emerging Viruses

• Emerging viruses are viruses that have:– Appeared suddenly or – Have only recently

come to the attention of science


Evolution Connection: Emerging Viruses

– Avian flu:• Infects birds• Infected 18 people in 1997• Since has spread to Europe and Africa infecting 300 people

and killing 200 of them• If avian flu mutates to a form that can easily spread between

people, the potential for a major human outbreak is significant.

– New viruses can arise by:• Mutation of existing viruses • Spread to new host species


Figure 10.UN7Laura Coronado Bio 10 Chapter 10

Chapter 10 The Structure and Function of DNA Laura Coronado Bio 10 Chapter 10.

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