Intro chapter 10 part2a

Chapter 10

Molecular Biology of the GenePart 2

Molecular GeneticsProtein Synthesis

Now that we understand (hopefully) how the DNA replicates, we can finally begin to

discuss how the genes work.We already know that the gene controls

the making of a protein. This process is called protein synthesis.


Before discussing the process itself, it is important to understand that the genes are

in the nucleus and the protein building apparatus (ribosomes) are in the

cytoplasm.


DNA cannot leave the nucleus. It is too large a molecule to pass through the pores

in the nuclear membrane.Getting the information from the gene to

the ribosome is done by a “middleman.” This is RNA.


There are 3 types of RNA. Each has a specific role in the process of protein

construction.The 3 types are:

Ribosomal RNA (rRNA)Transfer RNA (tRNA)

Messenger RNA (mRNA)

Molecular GeneticsProtein SynthesisRibosomal RNA (rRNA)

Ribosomal RNA combines with protein to form the ribosomes.

Each ribosome is composed of 2 subunits.These subunits fit together like two beans

face to face, so there is a little opening between them.

Ribosome with tRNA and mRNA and the growing polypeptide.


Ribosomal RNAThere are 2 active sites (transfer RNA

binding sites) on the ribosome that allow the amino acids to line up and attach to each

other.These 2 sites are called the A site (where the

amino acid comes in) and the P site (where the amino acid is added to the polypeptide

chain).Ribosomal RNA is the factory or the assembly line for manufacturing protein.


Transfer RNA (tRNA)Transfer RNA is a highly motile form of RNA. It moves throughout the cytoplasm picking up amino acids and taking them to

the ribosome.tRNA is the truck that carries the raw

materials (amino acids) to the factory.


Transfer RNA (tRNA)tRNA has an unusual shape.

It is somewhat similar in shape to an upside down 3 leaf clover, although it is

twisted around itself making it hard to see this clover shape.


Transfer RNA (tRNA)There are two sites of importance in the tRNA.

At the top of the molecule is a site where the amino acid attaches. Each tRNA can carry

only a single specific amino acid. There are 22 different amino acids and more than 60 different

tRNAs, so there is some overlap.


Transfer RNA (tRNA)At the bottom of the molecule are 3 nitrogen bases

called the anticodon. These 3 bases have 2 jobs. 1. They determine which specific amino acid can

be carried by that tRNA. 2. They line up with the mRNA codons (3

complementary bases on the mRNA) so the amino acid is brought to the right place in the protein.


Transfer RNA (tRNA)

Molecular GeneticsProtein SynthesisMessenger RNA (mRNA)

Messenger RNA carries the genetic information to the ribosome. It is the blueprint for the process of

building the protein.mRNA is a simple straight chain of nucleotides.

It is composed of a cap, exons, introns and a tail.


Not all of the mRNA is needed to code for the protein.

The cap allows the mRNA to feed into the ribosome.

Introns are extraneous bits of material that must be edited out before the mRNA can be used.


The tail stabilizes the mRNA as the last bits of it feed into the ribosome so it doesn’t fall out too

soon.The exons carry the code that is needed to make

the protein. There are parts of the exons that are unused. These parts just add to the cap and tail.

Molecular Genetics

cap intron exon 2 intron exon3 intron exon4 tailexon1

This represents a newly made mRNA molecule. It has not yet been edited.


The nucleotides in the body or the translational portion of the mRNA are functionally (not

structurally) divided into groups of 3.These groups are called codons.

Each codon calls for a specific amino acid at a specific spot in the amino acid chain.


So, now we have all the players for the process of protein synthesis.

rRNA is the factory, with all the enzymes and binding sites needed for protein assembly.

tRNA is the truck, carrying the amino acids to the docking sites in the factory.

mRNA is the blueprint, telling the tRNAs which amino acid to bring in at each point.

Lets begin the process.


There are 2 parts to protein synthesis.1. transcription = the building of the

mRNA2. translation = the building of the amino

acid chain (polypeptide or protein).

Molecular GeneticsPart 1: Transcription

Transcription is similar to DNA replication. There are a few differences:

A) Only a small part of the DNA opens (not all).B) Only one strand (the template or 35 strand) of

the open portion of DNA is copied.

Molecular GeneticsTranscription

C) RNA polymerase and RNA nucleotides are used rather than DNA polymerase and DNA

nucleotides.(RNA nucleotides have a different sugar (ribose) than DNA nucleotides and RNA does not use the base, thymine…but

uses uracil instead).

D) Once the mRNA is made, it leaves the DNA and the DNA closes back up.


The processRNA polymerase attaches to the DNA molecule triggering the DNA to open at a specific site where

the gene of interest is located.

RNA polymerase

Transcription

AG

T C

G C

AA

T

C T

GA

TG

C T

A T

G C C

A C

TC

AG

GC

TT

A

GA

CT

AC

GA

TA

CGG

TG

Transcription

AG

T C

G C

AA

T

C T

GA

TG

C T

A T

G C C

A C

TC

AG

GC

TT

GA

CT

AC

GA

TA

CGG

TG


Once the DNA has opened, RNA nucleotides begin to line up with their complementary bases on the

Template strand of the DNA. Remember, RNA has uracil instead of thymine.

When joining DNA nucleotides to RNA nucleotides the following bases make complementary pairs.

DNA to RNAAdenine – Uracil

Thymine – AdenineCytosine – GuanineGuanine – Cytosine

Transcription

AG

T C

G C

AA

T

C T

GA

TG

C T

A T

G C C

A C

TC

AG

GC

TT

GA

CT

AC

GA

TA

CGG

TG

U

G

A

C


The polymerase runs down the template strand, connecting the sugar-phosphate backbone of the

newly forming messenger RNA strand.

Transcription

AG

T C

G C

AA

T

C T

GA

TG

C T

A T

G C C

A C

TC

AG

GC

TT

GA

CT

AC

GA

TA

CGG

TG

U

G

A

C

G

Transcription

AG

T C

G C

AA

T

C T

GA

TG

C T

A T

G C C

A C

TC

AG

GC

TT

GA

CT

AC

GA

TA

CGG

TG

U

G

A

C

GC

Transcription

AG

T C

G C

AA

T

C T

GA

TG

C T

A T

G C C

A C

TC

AG

GC

TT

GA

CT

AC

GA

TA

CGG

TG

U

G

A

C

GC

A

Transcription

AG

T C

G C

AA

T

C T

GA

TG

C T

A T

G C C

A C

TC

AG

GC

TT

GA

CT

AC

GA

TA

CGG

TG

U

G

A

C

GC

A U

Transcription

AG

T C

G C

AA

T

C T

GA

TG

C T

A T

G C C

A C

TC

AG

GC

TT

GA

CT

AC

GA

TA

CGG

TG

U

G

A

C

GC

A U

A

Transcription

AG

T C

G C

AA

T

C T

GA

TG

C T

A T

G C C

A C

TC

AG

GC

TT

GA

CT

AC

GA

TA

CGG

TG

U

G

A

C

GC

A U

AG

Transcription

AG

T C

G C

AA

T

C T

GA

TG

C T

A T

G C C

A C

TC

AG

GC

TT

GA

CT

AC

GA

TA

CGG

TG

U

G

A

C

GC

A U

AG

C

Transcription

AG

T C

G C

AA

T

C T

GA

TG

C T

A T

G C C

A C

TC

AG

GC

TT

GA

CT

AC

GA

TA

CGG

TG

U

G

A

C

GC

A U

AG

CA

Transcription

AG

T C

G C

AA

T

C T

GA

TG

C T

A T

G C C

A C

TC

AG

GC

TT

GA

CT

AC

GA

TA

CGG

TG

U

G

A

C

GC

A U

AG

CA U

Transcription

AG

T C

G C

AA

T

C T

GA

TG

C T

A T

G C C

A C

TC

AG

GC

TT

GA

CT

AC

GA

TA

CGG

TG

U

G

A

C

GC

A U

AG

CA U

C

Transcription

AG

T C

G C

AA

T

C T

GA

TG

C T

A T

G C C

A C

TC

AG

GC

TT

GA

CT

AC

GA

TA

CGG

TG

U

G

A

C

GC

A U

AG

CA U

CA

Transcription

AG

T C

G C

AA

T

C T

GA

TG

C T

A T

G C C

A C

TC

AG

GC

TT

GA

CT

AC

GA

TA

CGG

TG

U

G

A

C

GC

A U

AG

CA U

CAG

Transcription

AG

T C

G C

AA

T

C T

GA

TG

C T

A T

G C C

A C

TC

AG

GC

TT

GA

CT

AC

GA

TA

CGG

TG

U

G

A

C

GC

A U

AG

CA U

CAG U

Transcription

AG

T C

G C

AA

T

C T

GA

TG

C T

A T

G C C

A C

TC

AG

GC

TT

GA

CT

AC

GA

TA

CGG

TG

U

G

A

C

GC

A U

AG

CA U

CAG U

C

Transcription

AG

T C

G C

AA

T

C T

GA

TG

C T

A T

G C C

A C

TC

AG

GC

TT

GA

CT

AC

GA

TA

CGG

TG

U

G

A

C

GC

A U

AG

CA U

CAG U

CG

Transcription

AG

T C

G C

AA

T

C T

GA

TG

C T

A T

G C C

A C

TC

AG

GC

TT

GA

CT

AC

GA

TA

CGG

TG

U

G

A

C

GC

A U

AG

CA U

CAG U

CGA

Transcription

AG

T C

G C

AA

T

C T

GA

TG

C T

A T

G C C

A C

TC

AG

GC

TT

GA

CT

AC

GA

TA

CGG

TG

U

G

A

C

GC

A U

AG

CA U

CAG U

CGA

C


Once the messenger RNA is completed, the polymerase leaves the DNA.

The newly formed mRNA leaves the DNAThe DNA simply closes back up as it was before.

Transcription

AG

T C

G C

AA

T

C T

GA

TG

C T

A T

G C C

A C

TC

AG

GC

TT

GA

CT

AC

GA

TA

CGG

TG

U

G

A

C

GC

A U

AG

CA U

CAG U

CGA

C

Transcription

AG

T C

G C

AA

C T

GA

TG

C T

A T

G C C

A C

TC

AG

GC

TT

GA

CT

AC

GA

TA

CGG

TG

GC

A U

AG

CA U

CAG U

CGA

C


Before the new mRNA leaves the nucleus, it has to be edited, removing the introns and rejoining the exons so that the mRNA leaves the nucleus as a

“mature” mRNA molecule.

Molecular Genetics

cap intron exon 2 intron exon3 intron exon4 tailexon1

A mature mRNA molecule ready to leave the nucleus and move to the ribosome to produce protein.

Newly made “immature” mRNA

Editing involves cutting out and discarding introns, then rejoining the exons.

Molecular GeneticsPart 2:Translation

Before we can understand the process of translation, we need a better understanding of the

codons on the mRNA.Each codon is composed of three bases and

codes for a single, specific amino acid.Because the codons are lined up in an exact order,

they call for the amino acids to be lined up in an exact order as well.

Molecular GeneticsTranslation

The next slide is a codon chart which tells us what amino acid each codon codes for.

If we know the sequence of bases on the template DNA strand, we can determine the complementary

sequence of bases on the mRNA codons.If we know the codon sequence, we can determine

the amino acid sequence for the protein.

Cod

on T

rans

latio

n C

hart


As you look at the chart, along the left side are letters that represent the 1st base of the codon.

Across the top are additional letters that represent the 2nd base of the codon.

Down the right hand side of the chart are the letters that represent the 3rd base of each codon.

So, if you have the codon CGA, find C on the left, then U on top and then A on the right. Where these three

letters come together, you will find the amino acid that is called for by this codon.

Cod

on T

rans

latio

n C

hart


There are 4 special codons.AUG is the start codon.

AUG calls for the amino acid, methionine, but the first AUG on the mRNA is also the start codon. It tells the ribosome

when to start reading the mRNA and bringing in amino acids.

There are also 3 stop codons: UAA, UAG and UGA.Stop codons do not code for any amino acid. They tell the

ribosome to stop adding amino acids…the chain is complete.

Molecular GeneticsTranslationThe process

The mature mRNA leaves the nucleus and moves to the ribosomes. The cap threads into the ribosome and

mRNA passes through until a codon bearing the 3 bases AUG enters the A site.

AUG is the start codon. It triggers the ribosome to start building the protein.

AUG also codes for the amino acid, Methionine.Methionine is always the first amino acid in any protein

or polypeptide.

Translation

ACU CCG AUG UUU CGC UGG AAC CAG UAC UAG CCA UAC AAA P A

The mRNA moves to the ribosome. It threads its way along, codon by codon…

Translation


until the A site lines up with the first AUG on the mRNA.

Translation


With the first AUG codon at the A site, a tRNA comes into the ribosome with the anticodon that complements

the codon (in this case, UAC). The tRNA carries the first amino acid, Methionine and the process of translation

begins.

UAC

met

Translation


Once the tRNA has hooked onto the codon, the mRNA shifts so that the codon with the tRNA moves to the P

site.

UAC

met

Translation


A new tRNA will now move to the codon at site A. In this example, its anticodon will have to be AAA and it will

carry the amino acid, phenylalanine.

UAC

met

Translation


Now the amino acids are in close proximity and an enzyme in the ribosome links the two amino acids

together.

UAC

met

AAA

phe

Translation


The tRNA at site P releases its hold on both its amino acid and the codon and leaves the ribosome.

UAC

met

AAA

phe

Translation


Again the mRNA shifts on the ribosome and a new tRNA will come into site A.

UAC

met

AAA

phe

Translation


The amino acids at site P will attach to the new amino acid at site A and the tRNA at site P will detach and

leave the ribosome.

met

AAA

phe

GCG

arg

Translation


The mRNA shifts again and another tRNA comes to the ribosome.

met

AAA

phe

GCG

arg

Translation


met phe

GUG

arg

ACC

trp


leave the ribosome.

Translation


met phe

GUG

arg

ACC

trp


Translation


met phe arg

ACC

trp

UUG

asn

The amino acids at site P will attach to the new amino acid at site A and the tRNA at site P will detach and leave the ribosome.

Translation



met phe arg

ACC

trp

UUG

asn

Translation


met phe arg trp

UUG

asn


leave the ribosome.

GUC

gln

Translation


met phe arg trp

UUG

asn


GUC

gln

Translation


met phe arg trp asn

GUC

gln

AUG

tyr


leave the ribosome.

Translation


met phe arg trp asn

GUC

gln

AUG

tyr

The mRNA shifts again.

Translation


met phe arg trp asn gln

AUG

tyr

We have now reached a STOP codon. It codes for no amino acid, so there is no amino acid for the chain to attach to. Thus, when the tRNA at P is released, the

polypeptide is also released.

Translation


AUG

met phe arg trp asn gln tyr

Translation


met phe arg trp asn gln tyr

The mRNA will finish its journey through the ribosome and may then be used again to make another copy or it

may be broken down by the cell.

Translation


metphe

argtrp

asngln

tyr



Translation


phearg

trpasn

glntyr

The mRNA will finish its journey through the ribosome and may then be used again to make another copy or it may be broken down by the cell.

Translation


argtrp

asngln

tyr



Translation


asngln

tyr



Translation

ACU CCG AUG UUU CGC UGG AAC CAG UAC UAG CCA UAC AAA



Complementary Base Pairing

Given the DNA template strand, you can determine the complementary strand, the mRNA, the anticodons on the tRNA and with a chart, the amino acid sequence.

Template DNA strand

TGA GGC TAC AAA GCG ACC TTG GTC ATG ATC GGT ATG TTT

Complementary DNA strand

ACT CCG ATG TTT CGC TGG AAC CAG TAC TAG CCA TAC AAA


Given the DNA template strand, you can determine the complementary strand….

Template DNA strand



ACT TGGCCG ATG TTT CGC AAC TACCAG TAC TAG CCA AAA

DNA to DNAADENINE - THYMINETHYMINE - ADENINEGUANINE - CYTOSINECYTOSINE - GUANINE


Template DNA strand




the mRNA codons…

ACU UGGCCG AUG UUU CGC AAC UACCAG UAC UAG CCA AAAmRNA

DNA to RNAADENINE - URACIL

THYMINE - ADENINEGUANINE - CYTOSINECYTOSINE - GUANINE



Template DNA strand




UAC GCG ACC UUG GUC AUGAAA

The tRNA anticodons…RNA to RNA

ADENINE - URACILURACIL - ADENINE

GUANINE - CYTOSINECYTOSINE - GUANINE



Template DNA strand TGA GGC TAC AAA GCG ACC TTG GTC ATG ATC GGT ATG TTT



met phe arg trp asn tyrgln

UAC GCG ACC UUG GUC AUGAAA

and, with the codon chart, the amino acid sequence.

MutationsWhen discussing Chromosomes and

Genetics, we have mentioned mutations that can occur on our DNA.

We will now look at how these mutations work.

Mutations1. Point Mutations

A point mutation alters a single nucleotide on the DNA molecule. There are 2 basic types of point

mutations:a) substitution mutationsb) frame shift mutations

Mutations1. Point Mutationsa) substitution mutations

In a substitution mutation, one nitrogen base in the original DNA sequence is

replaced with a different nitrogen base.There are 3 possible consequences of

this substitution.

Mutations1. Point Mutations

a) substitution mutations(i) A silent mutation occurs if the base change does not

cause a change in the amino acid at that point in the protein. (This occurs most often when the 3rd base of a

codon is altered).(ii) A missense mutation occurs if the base change causes

a single amino acid to change in the polypeptide sequence. (This can occur with a change in the 1st, 2nd and

sometimes the 3rd base of the codon).(iii) A nonsense mutation occurs if the substitution causes

the codon to change to a stop codon which causes the polypeptide or protein to cut off before it is complete.

ACU CCG AUG UUU CGC UGG AAU CAG UAC UAG CCA UAC AAA

Mutated Template DNA strand

TGA GGC TAC AAA GCG ACC TTA GTC ATG ATC GGT ATG TTT


Point mutations1.Substitution

a. silentOriginal Template DNA strand


Mutated mRNA


Original A.A. sequence

Mutated A.A. sequence

ACU CCG AUG UUU CGC UGG AAA CAG UAC UAG CCA UAC AAA


TGA GGC TAC AAA GCG ACC TTT GTC ATG ATC GGT ATG TTT



b. missenseOriginal Template DNA strand


Mutated mRNA

met phe arg trp lys tyrgln



ACU CCG AUG UUU CGC UAG AAG CAG UAC UAG CCA UAC AAA


TGA GGC TAC AAA GCG ATC TTG GTC ATG ATC GGT ATG TTT



c. nonsenseOriginal Template DNA strand


Mutated mRNA

met phe arg


Mutated A.A. sequencestop

Mutations1. Point Mutationsb) Frameshift mutations

If a single base is deleted or added to the DNA nucleotide sequence, it changes the mRNA codons in such a way that all

of the codons beyond that point are altered. This can have serious

consequences on the functionality of the resulting protein.

ACU CCG AUG UUU CGC UGG AAC UCA GUA CUA GCC AUA CAA A


TGA GGC TAC AAA GCG ACC TTG AGT CAT GAT CGG TAT GTT T


Point mutations2. Frame shift

a. additionOriginal Template DNA strand


Mutated mRNA

met phe arg trp asn glyser


leu ala ile gln


ACU CCG AUG UUU CGC UGG AAC A GU ACU AGC CAU ACA AA


TGA GGC TAC AAA GCG ACC TTG TC A TGA TCG GTA TGT TT


Point mutations2. Frame shift

b. deletionOriginal Template DNA strand


Mutated mRNA

met phe arg trp asn thrser


ser his thr


Intro chapter 10 part2a

Technology

Transcript of Intro chapter 10 part2a