Overview: The Flow of Genetic Information

• The information content of DNA is in the form of specific sequences of nucleotides

• The DNA inherited by an organism leads to specific traits by dictating the synthesis of proteins

• Proteins are the links between genotype and phenotype

• RNA is the manager• Gene expression, the process by which DNA

directs RNA and protein synthesis, includes two stages: transcription(RNA) and translation(protein)

Evidence from the Study of Metabolic Defects

• In 1902, British physician Archibald Garrod first suggested that genes dictate phenotypes through enzymes that catalyze specific chemical reactions

• He thought symptoms of an inherited disease reflect an inability to synthesize a certain enzyme

• Linking genes to enzymes required understanding that cells synthesize and degrade molecules in a series of steps, a metabolic pathway

Nutritional Mutants in Neurospora:

• George Beadle and Edward Tatum exposed bread mold to X-rays, creating mutants that were unable to survive on minimal media

• Using crosses, they and their coworkers identified three classes of arginine-deficient mutants, each lacking a different enzyme necessary for synthesizing arginine

• They developed a “one gene–one enzyme” hypothesis, which states that each gene dictates production of a specific enzyme

Lactose Operon of E. coli:

• In the 1950s, Jacob and Monod worked with bacterial mutants to dissect gene control circuits

• They and others developed evidence of a short-lived intermediate between a gene and the protein that it coded for

• This intermediate was required for protein synthesis

• Shown to be an RNA molecule-was named messenger RNA

Basic Principles of Transcription and Translation

• RNA is the bridge and the gatekeeper between genes and the proteins for which they code

• Transcription is the synthesis of RNA using coded information in DNA

• Transcription produces many classes of RNA• Translation is the synthesis of a polypeptide,

using information in one class: messenger RNA• Ribosomes are the sites of translation

• The “Central Dogma” is the old-fashioned concept that cells are governed by a cellular chain of command: DNA RNA protein

• Idea developed in 1960s• It is far more complicated than this in real life

Figure 17.3

DNA

mRNARibosome

Polypeptide

TRANSCRIPTION

TRANSLATION

TRANSCRIPTION

TRANSLATION

Polypeptide

Ribosome

DNA

mRNA

Pre-mRNARNA PROCESSING

(a) Bacterial cell (b) Eukaryotic cell

NuclearenvelopeOverview-steps in gene

Expression inProkaryotes andEukaryotesmRNA = messenger RNA

Figure 17.4

DNAtemplatestrand

TRANSCRIPTION

+mRNA

TRANSLATION

Protein

Amino acid

Codon

Trp Phe Gly

5

5

Ser

U U U U U3

3

53

G

G

G G C C

T

C

A

A

AAAAA

T T T T

T

G

G G G

C C C G G

DNAmolecule

Gene 1

Gene 2

Gene 3

C C

Codons in an mRNA molecule are read by translation machinery in the 5 to 3 direction

The Genetic Code is a triplet code

• How are the instructions for assembling amino acids into proteins encoded into DNA?

• There are 20 amino acids, but there are only four nucleotide bases in DNA

• Three nucleotides correspond to an amino acid?• codon

The Genetic Code is Universal

(a) Tobacco plant expressing a firefly gene gene

(b) Pig expressing a jellyfish

Second mRNA base

Fir

st m

RN

A b

ase

(5 e

nd

of

cod

on

)

Th

ird

mR

NA

bas

e (3

en

d o

f co

do

n)

UUU

UUC

UUA

CUU

CUC

CUA

CUG

Phe

Leu

Leu

Ile

UCU

UCC

UCA

UCG

Ser

CCU

CCC

CCA

CCG

UAU

UACTyr

Pro

Thr

UAA Stop

UAG Stop

UGA Stop

UGU

UGCCys

UGG Trp

GC

U

U

C

A

U

U

C

C

CA

U

A

A

A

G

G

His

Gln

Asn

Lys

Asp

CAU CGU

CAC

CAA

CAG

CGC

CGA

CGG

G

AUU

AUC

AUA

ACU

ACC

ACA

AAU

AAC

AAA

AGU

AGC

AGA

Arg

Ser

Arg

Gly

ACGAUG AAG AGG

GUU

GUC

GUA

GUG

GCU

GCC

GCA

GCG

GAU

GAC

GAA

GAG

Val Ala

GGU

GGC

GGA

GGGGlu

Gly

G

U

C

A

Met orstart

UUG

G

The code is redundant!(>1 codon/aa)

Second mRNA base

Fir

st m

RN

A b

ase

(5 e

nd

of

cod

on

)

Th

ird

mR

NA

bas

e (3

en

d o

f co

do

n)

UUU

UUC

UUA

CUU

CUC

CUA

CUG

Phe

Leu

Leu

Ile

UCU

UCC

UCA

UCG

Ser

CCU

CCC

CCA

CCG

UAU

UACTyr

Pro

Thr

UAA Stop

UAG Stop

UGA Stop

UGU

UGCCys

UGG Trp

GC

U

U

C

A

U

U

C

C

CA

U

A

A

A

G

G

His

Gln

Asn

Lys

Asp

CAU CGU

CAC

CAA

CAG

CGC

CGA

CGG

G

AUU

AUC

AUA

ACU

ACC

ACA

AAU

AAC

AAA

AGU

AGC

AGA

Arg

Ser

Arg

Gly

ACGAUG AAG AGG

GUU

GUC

GUA

GUG

GCU

GCC

GCA

GCG

GAU

GAC

GAA

GAG

Val Ala

GGU

GGC

GGA

GGGGlu

Gly

G

U

C

A

Met orstart

UUG

G

The code is punctuated (start and stop)

4 Important Characteristics of the Genetic Code

• Triplet: 5’ to 3’ in mRNA• Universal • Punctuated• Redundant

Molecular Components of Transcription

• RNA synthesis is catalyzed by RNA polymerase, which separates the DNA strands apart and links together the RNA nucleotides (condensation reaction)

• The RNA is complementary to the DNA template strand

• RNA synthesis follows the same base-pairing rules as DNA, except that uracil substitutes for thymine

Nontemplatestrand of DNA

RNA nucleotides

RNApolymerase

Templatestrand of DNA

3

35

5

5

3

Newly madeRNA

Direction of transcription

A

A A A

AA

A

T

TT

T

TTT G

GG

C

C C

CC

G

C CC A AA

U

U

U

end

Figure 17.7-4 Promoter

RNA polymeraseStart point

DNA

53

Transcription unit

35

Elongation

53

35

Nontemplate strand of DNA

Template strand of DNARNAtranscriptUnwound

DNA2

3535

3

RewoundDNA

RNAtranscript

5

Termination3

35

5Completed RNA transcript

Direction of transcription (“downstream”)

53

3

Initiation1

Eukaryotic complexities

• Nucleus has 3 types of RNA polymerase: (Rpol I, Rpol II, R pol III)

• All 3 need a lot of help to initiate RNA synthesis• Eukaryotic control signals are very complicated

Promoter Nontemplate strand

15′3′

5′3′

Start point

RNA polymerase II

Templatestrand

TATA box

Transcriptionfactors

DNA3′5′

3′5′

3′5′

2

3

Transcription factors

RNA transcript

Transcription initiation complex

3′5′5′3′

A eukaryoticpromoter

Severaltranscriptionfactors bindto DNA.

Transcriptioninitiationcomplexforms.

T A T AAAA

TA A T T T T

Transcription Terminology

• RNA polymerase• Template/non-template• +/- sense• Initiation, Elongation, Termination• Upstream/downstream• Promoter/terminator• Transcription unit• Rpol II (for messenger RNA)• Transcription factor• TATA box

Eukaryotes modify RNA after transcription

• A newly made RNA is called a primary transcript

• When a new RNA molecule is first made it is not RTU

• It has to be changed or modified prior to use• Enzymes in the eukaryotic nucleus modify

primary transcripts before they are sent to the cytoplasm (RNA processing aka RNA modification)

• Pre-RNA, mature RNA

RNA molecules are usually modified after transcription

• Enzymes catalyze changes to the RNA molecule before it is ready to be used.

• Changes or modifications can be at the ends or in the middle.

• Changes or modifications can involve a single nucleotide at a time or a group.

• Modifications help to control gene expression

Split Genes and RNA Splicing

• Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides that lie between coding regions

• These noncoding regions are called intervening sequences, or introns

• The other regions are called exons because they are eventually expressed, usually translated into amino acid sequences

• RNA splicing removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence

Splicing is the most dramatic modification:Many genes are organized into “expressed”

sections or exons separated by “unexpressed” sections or introns

5 Exon Intron Exon

5CapPre-mRNACodonnumbers

130 31104

mRNA 5Cap

5

Intron Exon

3 UTR

Introns cut out andexons spliced together

3

105 146

Poly-A tail

Codingsegment

Poly-A tail

UTR1146

The exons and introns are transcribed into RNA and then the exons are joined together at the RNA level:

Splicing

Diverse splicing mechanisms exist

• Spliceosomes consist of a variety of proteins and several small nuclear ribonucleoproteins (snRNPs) that recognize the splice sites

• The RNAs of the spliceosome also catalyze the splicing reaction

Spliceosome Small RNAs

Exon 2

Cut-outintron

Spliceosomecomponents

mRNA

Exon 1 Exon 2

Pre-mRNA

Exon 1

Intron

5′

5′

Ribozymes

• Ribozymes are catalytic RNA molecules that function as enzymes and some can splice RNA

• The discovery of ribozymes rendered obsolete the belief that all biological catalysts were proteins

• Three properties of RNA enable it to function as a catalyst

• It can form a three-dimensional structure because of its ability to base-pair with itself

• Some bases in RNA contain functional groups that may participate in catalysis

• RNA may hydrogen-bond with other nucleicacid molecules

RNA secondary structure-illustrations

tRNA

U1 snRNA and snRNP

The Functional and Evolutionary Importance of Introns

• Some introns contain sequences that may regulate gene expression

• Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing

• This is called alternative RNA splicing• Consequently, the number of different proteins

an organism can produce is much greater thanits number of genes

• More then one product from each gene• Adds flexibility

GeneDNA

Exon 1 Exon 2 Exon 3Intron Intron

Transcription

RNA processing

Translation

Domain 3

Domain 2

Domain 1

Polypeptide

Alternate splicing worksBecause genes and proteinsare made of modules

Exons = gene modulesDomains = protein modules

RNA has more roles and functions than any other component

• Ribsosomal RNA (rRNA) • Messenger RNA (mRNA)• Transfer RNA (tRNA)• Catalytic RNA (ribozymes)• Structural RNA• Regulatory RNA

• The RNA World Hypothesis– Did the first life forms evolve as RNA-based

systems?– Did DNA and protein evolve later?

Note Card Question (Review)

Promoter

RNA splicing/alternative splicing

Intron/exon

RNA secondary structure

Ribozyme

Protein domain

RNA World Hypothesis