chapter 5 : expression of biological information

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CHAPTER 5 : EXPRESSION OF BIOLOGICAL INFORMATION

SUBTOPIC 5.1 : DNA and genetic information

LEARNING OUTCOMES:

a) State the concept of Central Dogma.

MAIN IDEAS /

KEY POINT EXPLANATION NOTES

Concept of

Central Dogma

Definition of Central Dogma :

The process by which the instructions in DNA are converted into a

functional product.

It was first proposed in 1956 by Francis Crick (the discoverer of the

structure of DNA)

• In molecular biology, the central dogma explains the flow of

genetic information, from DNA to RNA to make a protein.

• The central dogma states that the pattern of information that

occurs most frequently in our cells is :

o From existing DNA to make new DNA through DNA

replication

o From DNA to make new RNA via transcription

o From RNA to make new proteins through translation

• The central dogma suggests that DNA contains information needed

to make all of our proteins. RNA is a messenger that carries this

information to ribosomes. At ribosomes, the information is

translated from a code into proteins.

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• The process by which the DNA instructions are converted into

proteins is called gene expression.

• Gene expression has two key stages - transcription and translation.

• In transcription, information in DNA is converted into small,

portable RNA messages.

• During translation, these RNA messages travel from the cell

nucleus to ribosomes where they are ‘read’ to make specific

protein.

SUBTOPIC 5.2 : DNA replication

LEARNING OUTCOMES:

a) Describe semi-conservative replication of DNA.

b) State the enzymes and proteins involved in DNA replication.

c) Describe the mechanism of DNA replication and the enzymes involved.

MAIN IDEAS /


Semi-

conservative

replication of

DNA

DNA replication is the biological process of producing two identical

DNA molecules from one original DNA molecule.

• Semi-conservative replication model has been demonstrated by

Meselson and Stahl.

• DNA is a double helix molecule

made up of two complementary strands.

• During replication, the two original

DNA strands are separated. Each

strand of the original DNA molecule

then act as a template for the

synthesizing of new complementary

DNA strand. As a result, the new

DNA molecule consist of one original

strand and one new strand. This process

is referred to as semi-conservative

replication of DNA.

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https://en.wikipedia.org/wiki/DNA


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Enzymes and

proteins involved

in DNA

replication

Enzymes /

Protein

Function

Helicase

Catalyzed the unwind and separate the

double helix of original DNA strands at

replication forks

Single-strand

binding proteins

Hold the separated original DNA strands

apart and prevent them from re-forming

helix while they act as template

Topoisomerase

Catalyzed in relieving overwinding strain

ahead of replication fork (by breaking,

swiveling and rejoining the strands)

Primase

Catalyzed the synthesis of RNA primer at 5’

end of leading strand and at 5’ end of each

Okazaki fragment of lagging strand

DNA polymerase

III

Catalyzed the synthesizing of new DNA

strand by adding DNA nucleotides to the 3’

end of RNA primer or pre-existing DNA

strand (by specific base pairing rule)

DNA polymerase I

Catalyzed the removal of RNA nucleotides

of primer and replacing them with DNA

nucleotides

DNA ligase

Catalyzed the joining of Okazaki fragments

of lagging strand DNA // Catalyzed the joining

of 3’ end of DNA that replaces primer to the

rest of leading strand DNA.


MAIN IDEAS /


Mechanism of

DNA replication

DNA Replication : Getting Started

• During S phase of interphase, the replication of DNA begins at

particular sites called origins of replication

• A eukaryotic chromosome may have hundreds or even a few

thousand origins of replication

• Proteins that initiate DNA replication recognize this sequence and

attach to the DNA, separating the two strands and opening up a

replication bubble

• Replication of DNA proceeds in both directions until the entire DNA

molecule is copied.

• Multiple replication bubbles

form and eventually fuse,

thus speeding up the copying

of the very long DNA

molecules.

• At each end of a replication

bubble is a replication fork,

a Y-shaped region where the

parental strands are being

unwound.


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• Helicases are enzymes that untwist the double helix at the replication

forks and separating the two parental (original) strands, making them

available as template strands.

• After the parental strands separate, single-strand binding proteins

bind to the unpaired DNA strands, keeping them from re-forming

helix.

• The unwinding of the double helix causes tighter twisting and strain

ahead of the replication fork. Topoisomerase is an enzyme that helps

relieve the strain by breaking, swiveling and rejoining DNA strands.

• The enzymes that synthesize DNA cannot initiate the synthesis of a

polynucleotide; they can only add DNA nucleotides to the end of an

already existing strand.

• The initial nucleotide chain that is produced during DNA synthesis

is actually a short chain of RNA called a primer and is synthesized

by the enzyme primase.

• The new DNA strand start from the 3’ end of the RNA primer.

• Enzymes called DNA polymerase III (abbreviated DNA pol III)

catalyze the synthesis of new DNA by adding DNA nucleotides to

the 3’ end of pre-existing RNA primer.

Helicase disrupts

the hydrogen

bonding between

DNA base pairs.


MAIN IDEAS /


• DNA polymerases can add nucleotides only to the 3’ end of a primer

or growing DNA strand. Thus, a new DNA strand can elongate in

the 5’ to 3’ direction.

• Along one template strand, DNA pol III synthesize a complementary

strand continuously by elongating the new DNA in 5’ to 3’ direction

thus, producing the leading strand. Only one primer is required for

DNA pol III to synthesize the entire leading strand.

• To elongate the other new strand of DNA in 5’ to 3’ direction, DNA

pol III must work along the other template strand in the direction

away from the replication fork. The DNA strand elongating in this

direction is called the lagging strand.

• The lagging strand is synthesized discontinuously, consisting of a

series of Okazaki fragments. Each Okazaki fragment on the lagging

strand must be primed separately.

• Another DNA polymerase, DNA polymerase I (abbreviated DNA

pol I) replaces the RNA nucleotides of the primer with DNA

nucleotides.

• Enzyme DNA ligase catalyze the joining of all Okazaki fragments

into a continuous strand.

DNA ligase catalyze

the formation of

phosphodiester

bond.


MAIN IDEAS /



CHAPTER 5 : EXPRESSION OF BIOLOGICAL INFORMATION

SUBTOPIC 5.3 : Protein synthesis (transcription and translation)

LEARNING OUTCOMES:

a) Give an overview of the relationship between DNA and protein synthesis.

b) Explain transcription which involves RNA polymerase to form mRNA.

c) Show the relationship between codon on mRNA with sequence of amino acid using genetic code table.

d) Explain translation of mRNA forming polypeptide chain.

MAIN IDEAS

/ KEY POINT EXPLANATION NOTES

Relationship

between DNA

and protein

synthesis.

Genes provide the instructions for making specific proteins. The bridge between DNA and protein

synthesis is the single strand RNA. Getting from DNA to protein requires two stages : transcription

and translation. Transcription is the synthesis of RNA using information in the DNA. The

resulting RNA molecule is messenger RNA (mRNA) because it carries a genetic message from

the DNA to the protein-synthesizing machinery of the cell. (Note that, transcription is the general

term for the synthesis of any kind of RNA on a DNA template). Translation is the synthesis of a

polypeptide using the information in the mRNA. The cell must translate the nucleotide

sequence of an mRNA molecule into the amino acid sequence of a polypeptide. The sites of

translation are ribosomes. In eukaryotic cells, transcription occurs in the nucleus, but the

mRNA must be transported to the cytoplasm for translation.

Definition of protein synthesis :

A process by which amino acids are linearly arranged into proteins through the involvement of

ribosomal RNA, transfer RNA, messenger RNA and various enzymes.


MAIN IDEAS


Transcription

which

involves RNA

polymerase to

form mRNA.

• An enzyme called RNA polymerase unwinds the two strands of DNA

apart and joins together RNA nucleotides complementary to the DNA

template strand, thus elongating the RNA polynucleotide.

• Like the DNA polymerases, RNA polymerases can assemble a

polynucleotide only in its 5’ to 3’ direction, adding the RNA

nucleotides at 3’ end.

• Unlike DNA polymerases, however, RNA polymerases are able to

initiate the synthesis of RNA polynucleotide (they do not need any

pre-existing primer).

• Bacteria have one type of RNA polymerase that synthesizes mRNA

and other types of RNA such as ribosomal RNA (rRNA).

• Eukaryotes have at least three types of RNA polymerase in their

nuclei, the one used for pre-mRNA synthesis is called RNA

polymerase II.

• The three stages of transcription are initiation, elongation and

termination.

Initiation of Transcription

• Specific sequences of nucleotides along the DNA mark where

transcription of a gene begins and ends. The DNA sequence where

RNA polymerase attaches and initiates transcription is known as the

promoter.

• The promoter sequence in DNA is said to be upstream.

• The parts of DNA downstream from the promoter that is transcribed

into RNA is called a transcription unit.

• The promoter of a gene includes within it the transcription start point

– the nucleotide where RNA polymerase actually begins synthesis of

the mRNA.

• In bacteria, the RNA polymerase itself specifically recognizes and

binds to the promoter.

The direction of

transcription is

referred as

downstream and the

other direction as

upstream.


MAIN IDEAS


• In eukaryotes, transcription factors (a collection of proteins) mediate

the binding the binding of RNA polymerase and the initiation of

transcription.

• Eukaryotic promoter commonly includes a TATA box (upstream from

the transcriptional start point).

• Several transcription factors (one recognizing the TATA box), bind to

the DNA. Additional transcription factors bind to the DNA along with

RNA polymerase II, forming the transcription initiation complex.

• RNA polymerase II then unwinds the DNA double helix and RNA

synthesis begins at the start point on the template strand.

Elongation of the RNA strand

• As RNA polymerase moves along the DNA, it unwinds the double

helix, exposing the DNA nucleotides for pairing with RNA

nucleotides.

• The enzyme adds RNA nucleotides to the 3’ end of the growing RNA

strand.

• The new RNA strand peels away from its DNA template and the DNA

double helix re-forms.


MAIN IDEAS


Termination of Transcription

• Bacteria and eukaryotes differ in the way they terminate

transcription.

• In bacteria, transcription proceeds through a terminator sequence

in the DNA. The transcribed terminator functions as the

terminator signal, causing the RNA polymerase to detach from the

DNA and release the RNA transcript (which requires no further

modification before translation).

• In eukaryotes, RNA polymerase II transcribes a sequence on the

DNA called the polyadenylation signal sequence, which specifies

a polyadenylation signal in the pre-mRNA.

• Once the polyadenylation signal sequence appears, it is immediately

bound by certain proteins in the nucleus. Then, these proteins cut the

RNA transcript free from the RNA polymerase II, releasing the pre-

mRNA.

• The pre-mRNA then undergoes RNA processing (RNA splicing)


MAIN IDEAS


Eukaryotic cells modify RNA after transcription

• Enzymes in the eukaryotic nucleus modify pre-mRNA before it is

carried to the cytoplasm

• This is because the pre-mRNA have long noncoding regions that are

not translated. Most of these noncoding sequences are interspersed

between coding segments of the pre-mRNA.

• The noncoding regions are called introns and the coding regions

are exons. (The terms intron and exon are used for both RNA

sequences and DNA sequences)

• During RNA splicing, certain sections of the pre-mRNA are cut out

and the remaining parts sliced together. These modifications

produce an mRNA molecule ready for translation.

• In RNA splicing, the introns are cut out from the pre-mRNA

molecule and the exons joined together, forming an mRNA

• The removal of introns is accomplished by spliceosome (large

complex made of proteins and small RNAs). Spliceosome binds to

intron. The intron is then released (and rapidly degraded) and the

spliceosome joins together the exons

Relationship

between

codon on

mRNA with

sequence of

amino acid

using genetic

code table

• The mRNA nucleotide triplets are called codons

• Codons are written in the 5’ to 3’ direction.

• There are 64 codons in genetic code table.

• 61 codons code for amino acids.

• The three codons that do not code for amino acids are the stop

(termination) codons, marking the end of translation.

The three stop codons : UAA, UAG, UGA

• Codon AUG codes for amino acid methionine (Met) and also function

as start (initiation) codon, marking the beginning of translation.


MAIN IDEAS


• Genetic code is nearly universal, shared by organisms from the

simplest bacteria to the most complex plants and animals.

• There is redundancy in the genetic code, but no ambiguity.

Example : Codons GAA and GAG both specify glutamic acid; Glu

(redundancy), GAA and GAG do not specify any other amino acid

(no ambiguity)

• The codons is non-overlapping

Translation of

mRNA

forming

polypeptide

chain.

• During translation, the sequence of codons along an mRNA molecule

is translated (decoded) into a sequence of amino acids making up a

polypeptide chain. This process occurs in cytoplasm.

• The function of a tRNA (transfer RNA) is to transfer an amino acid

from cytoplasm to a growing polypeptide in ribosome.

• The ribosome (a structure made of proteins and RNAs) adds each

amino acid brought to it by a tRNA to the growing end of a

polypeptide chain.


MAIN IDEAS


• A tRNA molecule consists of

a single RNA strand.

• The 5’ and 3’ ends of the tRNA

both located near one end of the

structure.

• The protruding 3’ end act as the

attachment site for an amino acid.

• Anticodon is the particular

nucleotide triplet on tRNA that

base-pairs to a specific mRNA codon.

• Anticodons are written 3’ to 5’

to align properly with codons

written 5’ to 3’


MAIN IDEAS


• The correct matching up of tRNA and amino acid is carried out by

enzymes named aminoacyl-tRNA synthetases through a process

known as activation of amino acids

• The synthetase catalyzes the covalent attachment of the amino acid

to its tRNA with the help of ATP.

• The resulting aminoacyl tRNA will deliver its amino acid to a

growing polypeptide chain on a ribosome

• Ribosomes facilitate the specific pairing of tRNA anticodons with

mRNA codons during protein synthesis.

• A ribosome consists of a large subunit and a small subunit, each made

up of proteins and ribosomal RNA (rRNA)

• In both bacteria and eukaryotes, a large and a small subunit join

together only when attached to an mRNA molecule.

• Each ribosome has one binding site for mRNA and three binding sites

for tRNA : P site, A site and E site

• The P site (peptidyl-tRNA binding site)

holds the tRNA carrying the growing

polypeptide chain

• The A site (aminoacyl-tRNA binding site)

holds the tRNA carrying the next amino

to be added to the chain

• Discharged tRNAs leave the ribosome

from the E site (exit site)


MAIN IDEAS


• Ribosome holds the tRNA and mRNA

in close proximity and positions the

new amino acid so that it can be

added to the carboxyl end of the

growing polypeptide.

• It then catalyzes the formation of

peptide bond.

• When the polypeptide is complete,

it is released through the exit tunnel

in the ribosome’s large subunit.

• Translation can be divided into three

stages : initiation, elongation

and termination.

Initiation of Translation

• In bacteria and eukaryotes, the

start codon (AUG) signals the

start of translation

• In the first step of translation,

a small ribosomal subunit binds

to both the mRNA and a specific

initiator tRNA, which carries the

amino acid methionine.

• The initiator tRNA hydrogen-bonds

to the AUG start codon.

• This followed by the attachment

of a large ribosomal subunit,

forming the translation initiation

complex.

• At the end of the initiation process,

the initiator tRNA sits in the P site

of the ribosome, and the vacant

A site is ready for the next

aminoacyl tRNA.

• Polypeptide is always synthesized

in one direction, from the initial

methionine at the amino end

(N-terminus) toward the final

amino acid at the carboxyl end

(C-terminus)


MAIN IDEAS


Elongation of the Polypeptide Chain

• Amino acids are added one by one to the previous amino acids at the

carboxyl end (C-terminus) of the growing chain.

• Each addition involves three steps : codon recognition, peptide bond

formation and translocation.

• The mRNA move through the ribosome in one direction only,

starting from the 5’ end. This is equivalent to the ribosome moving

5’ → 3’ on the mRNA.

• The ribosome and the mRNA move relative to each other

unidirectionally, codon by codon

• During codon recognition :

Anticodon of an incoming

aminoacyl tRNA base pairs

with the complementary

mRNA codon in A site.

• During peptide bond formation :

An rRNA molecule of the large

ribosomal subunit catalyzes the

formation of a peptide bond

between the two amino acids

(between amino end / amino group

of the new amino acid in the A site

and the carboxyl end / carboxyl

group of the growing polypeptide

in P site)


MAIN IDEAS


• During translocation :

The mRNA together with its bound

tRNAs moves through ribosome

one codon at a time.

The ribosome translocate the tRNA

in the A site to the P site.

The empty tRNA in the P site

is moved to the E site, where it is

released and return to cytoplasm.

The next codon in A site is going

to be translated.

Termination of Translation

• Elongation continues until a stop codon

(UAG/UGA/UAA) in mRNA reaches

the A site.

• The stop codon do not code for amino

acids but instead act as signals to stop

translation.

• A release factor binds to the stop codon

in the A site.

• The release factor causes the hydrolysis

of the bond between the tRNA in the

P site and the last amino acid of the

polypeptide.

• Thus, releasing the polypeptide through

the exit tunnel of the large ribosomal subunit.

• The two ribosomal subunits and the other

components of the assembly dissociate.

chapter 5 : expression of biological information

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