Chapter 12: DNA & RNA

What do you already know about DNA?

12.1 Contributors to the Genetic Code

1. Griffith and Transformation– Worked with bacteria causing pneumonia– Two Strains

1. S – strain (smooth) – DEADLY

2. R – strain (rough) - HARMLESS

12.1. Contributors to the Genetic Code

1. Griffith Experiment

1. The Experiment

• Mouse + R = Life

• Mouse + S = Death

• Mouse + heat-killed S = Life

• Mouse + heat-killed S and R = Death

Transformation: changing one strain of bacteria into another using genes. Pointed to some type of “transforming” factor.

12.1. Contributors to the Genetic Code1. Griffith

• Conclusion: “something” transformed the living R-strain (harmless) into the S-strain (deadly) = Transformation

2. Oswald Avery – repeated Griffith’s work

• Destroyed all the organic compounds in heat killed bacteria except DNA: Result = transformation occurred.

• Destroyed all the organic compounds and DNA: Result = transformation did not occur.

• Conclusion: DNA was the transforming factor that caused the change in the R-strain

12.1 Contributors to the Genetic Code

3. Alfred Hershey & Martha Chase• Question: Are genes made of DNA or Proteins• What they know: viruses use other organisms to

reproduce

Phage attachesto bacterial cell.

Phage injects DNA. Phage DNA directs hostcell to make more phageDNA and protein parts.New phages assemble.

Cell lyses and releases new phages.

12.1. Contributors to the Genetic Code3. Alfred Hershey and Martha Chase

• Experiment• They tagged the virus DNA with blue radioactive

phosphorous

• They tagged the protein coat with radioactive sulfur

Conclusion: Virus only injects DNA

(DNA is the genetic material)

Bacteriophage Images

12.1 Three important functions of DNA

1. Store genetic information – stores genes

2. Copy information – copy genes prior to cell division

3. Transmit the information – pass genetic information along to next generation

12.2 Structure of DNA• DNA = Deoxyribonucleic Acid• A nucleotide is composed of:

1. Sugar (deoxyribose)2. Phosphate group3. Nitrogenous Base

• A nucleotide is the monomer of a DNA strand (polynucleotide):

DNA polynucleotide

A

C

T

G

T

Sugar-phosphate backbone

Phosphate group

Nitrogenous base

SugarA

C

T

G

T

Phosphategroup

O

O–

OO P CH2

H3C C

C

C

CN

C

N

H

H

O

O

C

O

O

H

C H H

H

C

H

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

Thymine (T)

Sugar(deoxyribose)

DNA nucleotide

DNA nucleotide

12.2 Structure of DNA

Nitrogenous Bases1. Purines – Adenine & Guanine (two rings in

structure)2. Pyrimidines – Cytosine & Thymine (one ring)

CC

C

CC

C

O

N

C

H

H

ONH

H3C

H H

H

H

N

N

N

H

OC

H HN

H C

N

N N

N

C

CC

C

H

H

N

N

H

C

CN

C HN

CN

H C

O

H

H

Thymine (T) Cytosine (C) Adenine (A) Guanine (G)

Purines – two ring structurePyrimidines – one ring structure

12.2 Structure of DNA

DNA is a double-stranded helixJames Watson and Francis Crick

• Worked out the three-dimensional structure of DNA, based on work (photos taken using x-ray crystallography) by Rosalind Franklin

12.2 Structure of DNA

The structure of DNA• Consists of two polynucleotide strands wrapped

around each other in a double helix (twisted ladder)

Twist

12.2 Structure of DNA

Hydrogen bonds (weak) between bases• Hold the strands together

Each base pairs with a complementary partner• A with T, and G with C

G C

T A

A T

G

G

C

C

A T

GC

T A

T A

A T

A T

G C

A T

O

O

OH–O

P

OO

–OPO

OO

P– O

– O OP

OO

O

OH

H2C

H2C

H2C

H2C

O

O

O

O

O

O

O

O

PO–

O–

O–

O–

OH

HO

O

O

O

P

P

P

O

O

O

O

O

O

O

O

T A

G C

C G

A T

CH2

CH2

CH2

CH2

Hydrogen bond

Basepair

Ribbon model Partial chemical structure Computer model

Chromosome structure

• Chromatin = DNA that is tightly packed around proteins called histones

- during cell division, chromatin form packed chromosomesChromosome

Supercoils

Coils

Nucleosome

Histones

DNA

double

helix

12-3 DNA Replication

When does DNA replicate?– DNA must copy before cell division (mitosis)

How does it replicate?

1. DNA is separated

2. Nucleotides are added according to base pairing rules, using DNA polymerase (enzyme).A T

C G

G C

A T

T A

A T

C G

G C

A T

T A

A T

C G

G C

A T

T A

A T

C G

G C

A

T

A T

C G

AC

T

A

Parental moleculeof DNA

Both parental strands serve as templates

Two identical daughtermolecules of DNA

12-3 DNA Replication

DNA replication is semi-conservative

1. The parent strand gives rise to two daughter strands.

2. Each daughter strand is composed of one half the parent (old strand) and one half new.

Parental strandOrigin of replication

Two daughter DNA molecules

Daughter strand

Bubble

12.3 DNA Replication

DNA replication is a complex process:• The helical DNA molecule must untwist• Each strand of the double helix is oriented in the

opposite direction (antiparallel)

P

P

P

P

P

P

P

P

HO

OH

A

C

G

T

T

C

G

A

2134

5

15 4

32

5 end 3 end

3 end 5 end

G C

A TG C

A TC G

AGA

CG

CGCG

TAG

C

TAT

AA

TT

A

CG

CG

CG

TA

G

C

T

A

TA

AT

TA

TCT

DNA ReplicationReplication = process of copying DNA

- occurs during S phase of Interphase

- process:

1. DNA is separated into two strands by an enzyme

2. Free nucleotides are added by DNA polymerase according to base pairing rule

DNA Replication

Nitrogenous bases

Growth

Growth

Replication fork

DNA polymerase

New strand

Original strand DNA

polymerase

Replication fork

Original strand

New strand

Chapter 13: Protein Synthesis

Central Dogma of Cell Biology• DNA codes for DNA = REPLICATION

• DNA codes for RNA = TRANSCRIPTION

• RNA codes for protein = TRANSLATION

– The DNA of the gene is transcribed into RNA• Which is translated into protein

• The flow of genetic information from DNA to RNA to Protein is called the CENTRAL DOGMA

DNA

Transcription

RNA

Protein

Translation

Chapter 13 Protein Synthesis - Overview

FLOW IS FROM DNA TO RNA TO PROTEIN

• Genes on DNA are expressed through proteins, which provide the molecular basis for inherited traits

• A particular gene, is a linear sequence of many nucleotides

– Specifies a polypeptide (long protein made of amino acids)

Chapter 13 Protein Synthesis (Overview)

13-1 Messenger (mRNA)

1. Monomer: nucleotide2. Parts of a mRNA Nucleotide

• Ribose Sugar• Phosphate• Nitrogenous Base

3. Three main differences between mRNA and DNA

• Ribose instead of deoxyribose• mRNA is generally single stranded• mRNA has uracil in place of thymine (U instead of

T)

13.1 RNA4. Three Types of RNA

• Messenger RNA (mRNA) – carries copies of genes (DNA) to the rest of the cell.

• Ribosomal RNA (rRNA) – make up the ribosomes.

• Transfer RNA (tRNA) – transfers the amino acids to the ribosomes as specified by the mRNA

from to to make up

also called which functions to also called also called which functions towhich functions to

can be

RNA

13.1 TRANSCRIPTION: The process of making mRNA from DNA

– Why do you need this process?• Location of DNA?

Nucleus

• Location of Ribosome? Cytoplasm

– mRNA takes code from DNA in the nucleus to the cytoplasm

T A C T T C A A A A T C

A T G A A G T T T T A G

A U G A A G U U U U A G

Transcription

Translation

RNA

DNA

Met Lys PhePolypeptide

Startcondon

Stopcondon

Strand to be transcribed

13.1 Transcription produces genetic messages in the form of mRNA

– During transcription, segments of DNA serve as templates to produce complementary RNA molecules.

RNADNA

RNApolymerase

Adenine (DNA and RNA)Cytosine (DNA and RNA)Guanine(DNA and RNA)Thymine (DNA only)Uracil (RNA only)

Transcription – Transcription requires an enzyme,

known as RNA polymerase, that is similar to DNA polymerase.

– RNA polymerase binds to DNA during transcription and separates the DNA strands.

RNADNA

RNApolymerase

Adenine (DNA and RNA)Cytosine (DNA and RNA)Guanine(DNA and RNA)Thymine (DNA only)Uracil (RNA only)

Promoters

– RNA polymerase binds only to promoters, regions of DNA that have specific base sequences.

– Promoters are signals in the DNA molecule that show RNA polymerase exactly where to begin making RNA.

– Similar signals in DNA cause transcription to stop when a new RNA molecule is completed.

13.1 In the nucleus, the DNA helix unzips• And RNA nucleotides line up along one strand of the

DNA, following the base pairing rules

– As the single-stranded messenger RNA (mRNA) is released away from the gene

• The DNA strands rejoin

RNApolymerase

RNA nucleotides

Direction of transcription

Template Strand of DNA

Newly made RNA

TC

A T C C A A TT

GG

CC

AATTGGAT

G

U

C A U C C AA

U

13.1 Eukaryotic mRNA is processed before leaving the nucleus

– Noncoding segments called introns are spliced out leaving only the coding exons

• A 5’ cap and a poly A tail are added to the ends of mRNA

• Cap and tail protect mRNA

Exon Intron Exon Intron Exon

DNA

Cap TranscriptionAddition of cap and tail

RNAtranscript with capand tail

Introns removedTail

Exons spliced together

mRNA

Coding sequence Nucleus

Cytoplasm

The Genetic Code– Proteins are made by joining amino acids

together into long chains, called polypeptides.

– As many as 20 different amino acids are commonly found in polypeptides.

The Genetic Code– The specific amino acids in a

polypeptide, and the order in which they are joined, determine the properties of different proteins.

– The sequence of amino acids influences the shape of the protein, which in turn determines its function.

The Genetic Code– RNA contains four different bases: adenine,

cytosine, guanine, and uracil.

– These bases form a “language,” or genetic code, Each three-letter “word” in mRNA is known as a codon.

– A codon consists of three consecutive bases that specify a single amino acid to be added to the polypeptide chain.

How to Read Codons – Because

there are four different bases in RNA, there are 64 possible three-base codons (4 × 4 × 4 = 64) in the genetic code.

How to Read Codons – Most amino acids

can be specified by more than one codon.

– For example, six different codons—UUA, UUG, CUU, CUC, CUA, and CUG—specify leucine. But only one codon—UGG—specifies the amino acid tryptophan.

Start and Stop Codons – The methionine

codon AUG serves as the initiation, or “start,” codon for protein synthesis.

– Following the start codon, mRNA is read, three bases at a time, until it reaches one of three different “stop” codons, which end translation.

DNA:CCGTCATGTTCGCGCTACAAATGAAATGAGGCAGTACAAGCGCGATGTACTTTACT

mRNA:

Polypeptide:

13-2 Protein Synthesis - Translation

• Translation is defined as going from mRNA to protein– tRNA which have amino acids attached are

going to the ribosome.• What are amino acids? monomers of proteins

• Does the order of amino acids matter? Yes, they must be in order for the protein to fold correctly.

– How does the correct tRNA (with amino acid attached) bind to the mRNA? The tRNA contains an anticodon which matches up with the mRNA sequence (codon).

– A ribosome attaches to the mRNA and translates its message into a specific polypeptide aided by transfer RNAs (tRNAs)

• tRNAs can be represented in several ways

Amino acid attachment site

Hydrogen bond

RNA polynucleotide chain

AnticodonAnticodon

Amino acid attachment site

Transfer RNA (tRNA) molecules serve as interpreters during translation

– Translation

• Takes place in the cytoplasm

– Each tRNA molecule • Is a folded molecule bearing a base triplet

called an anticodon on one end

– A specific amino acid • Is attached to the other end

Amino acidattachment site

Anticodon

13.2 Translation

Ribosomes build polypeptides (proteins)– A ribosome consists of two subunits

• Each made up of proteins and a kind of RNA called ribosomal RNA

tRNAmolecules

mRNA Small subunit

Growingpolypeptide

Largesubunit

13.2 Translation

– The subunits of a ribosome• Hold the tRNA and mRNA close together

during translation

Largesubunit

mRNA-binding site

Smallsubunit

tRNA-binding sites

Growing polypeptide

Next amino acid to be added to polypeptide

mRNA

tRNA

Codons

13.2 Translation

– An initiation codon marks the start of an mRNA message

– mRNA, a specific tRNA, and the ribosome subunits assemble during initiation

Met Met

Initiator tRNA

1 2mRNA Small ribosomal

subunit

Startcodon

Large ribosomalsubunit

A siteU A CAU C

A U G A U G

P site

Elongation adds amino acids to the polypeptide chain until a stop codon terminates translation

– Once initiation is complete amino acids are added one by one to the first amino acid

– The mRNA moves a codon at a time• A tRNA with a complementary anticodon pairs with

each codon, adding its amino acid to the peptide chain

– Each addition of an amino acid• Occurs in a three-step elongation process

Polypeptide

P site

mRNA Codons

mRNAmovement

Stopcodon

NewPeptidebond

Anticodon

Aminoacid

A site

Figure 10.14

1 Codon recognition

2 Peptide bondformation

3 Translocation

13.3 Mutations• Mutations – heritable changes in genetic information

(changes to the DNA sequence)• Two types - gene and chromosomal mutations• Mutations can be caused by chemical or physical agents

(mutagens)– Chemical – pesticides, tobacco smoke, environmental pollutants– Physical – X-rays and ultraviolet light

13.3 Mutations• Gene mutations

– Point Mutation: mutations that affect a single nucleotide– Frameshift mutation: shift the reading frame of the

genetic message.• Can change the entire protein so it doesn’t work• Gene Mutations Explained

13.3 Mutations

13.3 Chromosomal Mutations• Chromosomal mutation: mutation

that changes the number or structure of chromosomes.

13.3 Chromosomal Mutations

• Types of chromosomal mutations:

– Deletion: The loss of all or part of a chromosome

– Duplication: A segment is repeated

– Inversion: part of the chromosome is reverse from its usual direction.

– Translocation: one chromosome breaks off an attaches to another chromosome.