The Blueprint of Life, From DNA to Protein Chapter 7

The Blueprint of Life,From DNA to Protein

Chapter 7

The Blueprint of Life

Characteristics of each cell dictated by information contained on DNA DNA holds master blueprint

All cell structures and processes directed by DNA

Overview

Complete set of genetic information referred to as genome Genome of all cells is composed of DNA

Some viruses have RNA genome Functional unit of genome is the gene Gene codes for gene product

Gene product is most commonly protein Study of transfer of genes is genetics Study of sequence of DNA is genomic

Overview

Living cells must accomplish two general tasks to multiply DNA replication DNA expression (gene expression)

Expression involves two process Transcription

Copies information in DNA to RNA Translation

Interpret RNA to synthesize protein

Flow of information from DNA to RNA to protein Central dogma of molecular biology

Overview

Characteristics of DNA Made up of deoxy-

ribonucleotides Nucleotides include:

Phosphate group 5 carbon sugar

Deoxyribose Nucleotides bond covalently

between the 5’PO4 of one nucleotide and the 3’OH of another

Joining of nucleotides creates an alternating sugar-phosphate backbone

Overview

Characteristics of DNA Each sugar (deoxyribose) molecule is

connected to a nitrogenous base Nitrogenous bases

Adenine (A) - purine Thymine (T) - pyrimidine Guanine (G) - purine Cytosine (C) – pyrimidine

Overview

Characteristics of DNA Chemical structure and joining of

nucleotide subunits causes strands to differ at the ends

One strand has a phosphate attached at the number 5 carbon of the sugar.

Termed the five prime (5’) end The other strand has a hydroxyl

group attached to the number 3 carbon of the sugar.

Termed the three prime (3’) end

Overview Characteristics of DNA

DNA occurs as double-stranded molecule

Strands are complementary to each other

Due to the specific base pairing of bases

A:T C:G

Strands are held together with hydrogen bonds

Specific hydrogen bonding between bases

A is bound to T by two hydrogen bonds

G is bound to C by three hydrogen bond

Overview

Characteristics of DNA DNA molecule is antiparallel

Strands are oriented in opposite directions

Strands differ at the ends One strand oriented in

the 5’ to 3’ direction. The other strand is

oriented in the 3’ to 5’ direction.

Overview

Characteristics of RNA RNA is made up of nucleotides

Ribonucleotides RNA contains nitrogenous bases

Adenine Guanine Cytosine Uracil

Uracil replaces thymine in RNA

RNA usually exists as single stranded molecule

Overview

Characteristics of RNA Portion of DNA acts of template for RNA

synthesis RNA molecule called transcript

Numerous transcripts can be produced from one chromosome

Either strand of DNA can act as template Three different functional groups of RNA

Messenger RNA (mRNA) Ribosomal RNA (rRNA) Transfer RNA (tRNA)

Overview

Regulating the expression of genes Nucleotide sequence codes for regulation

mechanism for gene expression Mechanisms determine duration of synthesis

of gene products Products are only made when required

Key mechanism is regulation of mRNA synthesis from DNA

Regulation of transcription

DNA Replication

DNA is replicated to create second copy of molecule Molecule is identical to

original Replication is

bidirectional Replication begins at

specific starting point Proceeds in opposite

directions Allows replication to

proceed more quickly Bi-directional repli

cation

DNA Replication

DNA replication The two strands are unwound and separated Free, unbound nucleotides match up to the

newly separated nitrogenous bases of the parent strand

The parent strand is also called the template strand

DNA Replication

DNA replication Base pairing is specific in DNA replication

Where adenine is present only thymine binds in the new strand and vice versa

Where guanine is present only cytosine binds in the new strand and vice versa

Bases that are improperly inserted are removed and replaced with the correct base

Newly added bases are added by the enzyme DNA polymerase

DNA Replication

Specifics of DNA replication As the strands of DNA

unwind, it creates an area of replication called the replication fork

As nucleotides are added, the replication fork moves down the parental strand

DNA Replication

Specifics of DNA replication DNA polymerase adds new nucleotides as

they become available. DNA polymerase can only add nucleotides to the

free hydroxyl at the 3’ end DNA polymerase replicates in 5’ to 3’ direction Enzymes READS DNA template in 3’ to 5’ direction

Because of the antiparallel nature of the strands of DNA, the two new strands will grow in opposite directions

One strand is the leading strand One strand is the lagging strand

DNA Replication

Specifics of DNA replication Leading strand

Is synthesized CONTINUOUSLY as the DNA polymerase moves towards the replication fork

Lagging strand Is synthesized DISCONTINUOUSLY in pieces as

DNA polymerase moves away from the replication fork

DNA Replication

Specifics of DNA replication DNA polymerase must bind to an RNA primer

to begin synthesis A second DNA polymerase removes any RNA

primers An RNA primer is required at each newly

synthesized section of the lagging strand DNA ligase joins the fragments of the lagging

strand

DNA Replication

Specifics of DNA replication Replication is completed when the replication

fork reaches the end of the parent strands The original parent strand and the newly

synthesized daughter strand rewind Each new strand of DNA consists of one parent

strand and one daughter strand DNA replication is referred to as semiconservative

DNA Replication

Gene Expression

Involves two separate but interrelated process Transcription

Process of synthesizing RNA from DNA template Translation

RNA is deciphered to synthesize protein

Gene Expression

Transcription Transcription is the synthesis of a strand of

mRNA from a DNA template mRNA carries the coded information from DNA to

the ribosome, which is the site of protein synthesis

mRNA also plays an important role in translation

Gene Expression

Transcription During transcription the

enzyme, RNA polymerase, synthesizes a complementary strand of mRNA from a portion of unwound DNA

Gene Expression

Specifics of Transcription RNA polymerase binds to a region of the DNA

called the promoter Only one strand of DNA acts as a template

This is called the sense strand The strand not transcribed is the nonsense strand

Genet Expression

Specifics of transcription Nucleotides in RNA are the same as those in

DNA with one exception Thymine is replaced with uracil

Binding in RNA is A:U or U:A C:G or G:C

Gene Expression

Specifics of transcription RNA polymerase continues down strand of

DNA until it reaches a site on DNA called the terminator

At the terminator RNA polymerase and the new strand of mRNA are released from strand of DNA

Transcription

Gene Expression

Translation Translation is the decoding of information held

in the mRNA to synthesize proteins Two more RNA molecules become involved in

translation Ribosomal RNA (rRNA) Transfer RNA (tRNA)

Gene Expression

rRNA forms part of the ribosomal machinery used in protein synthesis rRNA builds the ribosomes

tRNA recognizes specific sequences of mRNA and transports the required amino acids to form a polypeptide chain

Gene Expression

Translation The language of mRNA is in the form of

codons Codons are groups of three nucleotides situated

next to each other on DNA Codons are written in terms of their base

sequence in mRNA The sequence of codons determines the

sequence of amino acids in the protein

Gene Expression

Translation There are 64 codons that make up the

“alphabet” of proteins Of the 64 codons, 61 are sense codons

Each coding a specific amino acid The remaining 3 are nonsense codons

These code for termination of the message

Codons contained in mRNA are read into proteins through translation

The site of translation is the ribosome

Gene Expression

In response to each codon, tRNA brings the appropriate amino acid to the site of translation

Each codon has an anticodon The anticodon is

complementary sequence to the codon

Gene Expression

Translation Ribosomes

The 30s and the 50s ribosomal subunits join together around the mRNA

The ribosomes direct the binding of tRNA to the correct codon on the mRNA

tRNA binds to the P site and the A site of the 50s ribosomal subunit

The ribosomes bind to the mRNA to be translated

Gene Expression

Specifics of Translation The first tRNA binds to a start

codon in the P site of the ribosome

AUG is the start codon for EVERY protein

AUG codes for the amino acid methionine

When the second tRNA binds to the A site, the amino acid of the first tRNA forms a peptide bond with the amino acid of the second tRNA

P site A site

Gene Expression

Specifics of translation After the peptide bond is formed between the

two amino acids, the tRNA P site leaves the ribosome

The ribosome moves distance of one codon Amino acid in the A site moves to the P site A new tRNA fills the now empty A site

Gene Expression

Specifics of translation The ribosome continues down the strand of

mRNA Amino acids form peptide bonds along the way

Translation is terminated when the ribosomes come to a stop or nonsense codon

At this point the ribosomes separate The new polypeptide chain is released

The ribosome and the mRNA are free to begin translation again

Gene Expression

Specifics of translation As the ribosome moves down the strand of

mRNA, the start codon is exposed Once exposed, a new ribosome will attach and

begin another polypeptide chain

Translation

Regulation of Gene Expression

Microorganisms posses mechanism to synthesize maximum amount of cell material from limited energy Controls directed at metabolic pathways

Two general mechanism Allosteric inhibition of enzymes Controlling synthesis of enzymes

Directed at making only what is required

Principles of regulation Not all genes subjected to regulation Enzymes can be classified according to characteristics of

regulation Constitutive enzymes

Constantly synthesized Enzymes of glycolysis

Inducible enzymes Not regularly produced turned on in certain conditions

Β-galactosidase Repressible enzymes

Routinely synthesized Generally involved in biosynthesis


Mechanisms controlling transcription Often controlled by regulatory region near

promoter Protein binds to region and acts as “on/off” switch

Binding protein can act as repressor or activator Repressor blocks transcription Activator facilitates transcription

Set of genes controlled by protein is called an operon



Repressors Control mechanism that inhibits gene expression and

decreases the synthesis of enzymes Repression is usually in response to the overabundance

of an end product Repression decreases the rate synthesis of enzymes

leading to the formation of the particular end product Regulatory proteins called repressors mediate

repression Repressors block the ability of RNA polymerase to bind and

initiate protein synthesis


Activators Control mechanism that turns on the

transcription of a gene or set of genes Inducers are substances that act to induce

transcription Enzymes synthesized in the presence of inducers

are called inducible enzymes


Operon model of gene expression An operon is a set of genes that includes an

operator, promoter and structural genes An operon is divided into two regions, the control

region and the structural region The control region include the operator and the

promoter This region controls transcription The operator acts as the “on-off” switch

The structural region includes the structural genes This region contains the genes being transcribed

Operon structure

Promoter – Binding site for RNA polymerase

Operator – binding site for the repressor protein for the regulation of gene expression

Structural Genes – DNA sequence for specific proteins

Operator

Gene 1 Gene 3Gene 2

Promoter


Lac operon Example of induction of gene expression

Near the operon on the DNA is a regulatory gene called the “I” gene

This codes for the repressor protein When lactose is absent, the repressor protein

binds to the operator gene Binding of the repressor gene prevents RNA

polymerase from transcribing the structural genes No mRNA is made and no enzymes are

synthesized


Lac operon When lactose is present the repressor binds to

lactose instead of the operator With the repressor bound to lactose, RNA

polymerase is able to bind to the promoter and transcribes the structural genes

Lactose acts as an inducer by keeping the repressor from binding to the operator

It induces the transcription of the structural genes

Lac Operon

Operator

Gene 1 Gene 3Gene 2

Promoter

1.

2.

Lactose

3.

RNA polymerase

Repressor

Lac Operon

Gene Expression and Environmental Fluctuations Many organisms adapt to changing

environments by altering level of gene expression

Mechanisms include Signal transduction Natural selection

Signal transduction Process that transmits information from external

environment to inside cell Allows cell to respond to changes

Two-component regulatory systems Relies on sensor and response regulator proteins

Sensors recognize change in environment Response regulators activate or repress gene

expression Quorum sensing

Organisms sense density of population Enables activation of genes beneficial to the mass

Gene Expression and Environmental Fluctuations

Natural selection Mechanisms to enhance survivability

Antigenic variation Alteration in characteristics of certain surface

proteins Example: Neisseria gonorrhoeae hides from host

immunity by changing numerous surface proteins

Phase variation Routine switching on and off of certain genes

Altering expression allows portions of population to survive and multiply

Gene Expression and Environmental Fluctuations

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The Blueprint of Life, From DNA to Protein Chapter 7