BIOLOGY NOTES

TOPIC 2B
ENZYMES
 A catalyst is a substance that changes the rate of reaction without changing the substance
produced. Catalyst is unaffected at the end of the reaction and can be used again. Enzymes make life
possible by speeding up a reaction without changing the conditions of a cytoplasm.
 Enzymes are globular protein which are produced during protein synthesis as MRNA transcribed
from the DNA molecule is translated. They have a very specific shape as a result of primary,
secondary, tertiary, quaternary. This means each enzyme catalyses a specific reaction. Temperature
and PH effect the efficiency of enzyme because they affect the intermolecular bond within the
protein are responsible for shape.
 Chemical reactions are going in the body all the time they are known as anabolic reaction means
building up and catabolic reactions means breaking down the combination of these two processes
metabolism. Most of these reactions occur as a sequence known as metabolic chain or pathway.

NAMING ENZYMES
The enzyme that catalyses the reactions inside the cells are known as intracellular enzymes. examples:
DNA polymerase and DNA ligase. Cell secrets other enzymes that work outside the cell membrane
known as extracellular enzymes. Example the digestive enzyme called lysozyme, the enzyme in your
tears.

Most enzyme both intra and extra cellular have several names;
 A short name which is often the name of the molecule that the enzyme works on (the substrate)
with “–ase” on the end of the substrate with an indication of what it does e.g. (creatine kinase).
 A longer systematic name describing the type of reaction being catalyzed. E.g. (ATP: creatine
phosphotransferase).
 A classification number e.g. (EC: 2.7.3.2)

HOW ENZYMES WORK

Activation energy is needed to start a reaction. Raising the temperature increases the rate of chemical
reaction by giving more molecules sufficient energy to react. However, cells can’t survive high
temperatures. The energy demand to produce the heat would be enormous. Enzymes solves the
problem by lowering activation energy.

To lower the activation energy enzymes, form a complex with the substrate. A simple model of enzyme
in a catabolic reaction is: substrate + enzyme ⇌ enzyme- substrate complex ⇌ enzyme + products.
Once the products of the new reaction are made they are released and the enzyme is free to form a new
complex with more substrate.
THE LOCK AND KEY MECHANISM
 Within the globular protein structure of each enzyme is
an area known as acti ve site it has a very specifi c
shape. Only one substrate or a type of substrate will fi t
in the shape of acti ve site and this gives each enzyme
its specifi city. The enzyme and substrate slot together
to make a complex in the same way as a key fi ts into
the lock. This lowers the acti vati on energy. the bonds in the substrate makes it easier for
them to break. The reacti ng substances are bought closer making it easier for bonds to form
between them. Once the reacti on is completed the products are not in the right shape to stay
in the acti ve site and the complex breaks up. This frees the enzyme for further catalyti c
acti vity.

 Induced fi t hypothesis a modifi ed version of lock and key mechanism where the acti ve site
has a more fl exible shape; aft er the substrate enters the acti ve site, the shape of that site
changes around it to form the acti ve complex, aft er the products have left the complex the
enzyme returns to its inacti ve relaxed form.

Structure and properties of enzyme

Enzymes are globular protein. They contain an active site which is functioning of an enzyme. The active
site is small depression on the surface of the molecule that has a specific shape. Because of the way of
whole large protein molecule is folded. Anything affecting the shape of protein affects its ability to do its
job. This indicates a 3D structure and it’s important for the way it works. Change in shape affects the
shape of active site and so enzyme no longer functions. Enzyme changes only the rate of reaction. The
do not change or contribute the end products and they do not affect the equilibrium of the reaction
they act only as catalysts.

EVIDENCE BETWEEN THE STRUCTURE AND FUNCTION OF ENZYME

 Enzymes speed up reactions so much that only very small amount of them are needed to catalyze
the reaction of many substrate molecules into the products. This is described by the molecular
activity or the turnover number which measures the substrate molecules transformed per minute by
a single enzyme. if every enzyme molecule is involved in a reaction it will
Vmax = maximum rate of reaction
not go any faster unless there is an increase in enzyme concentration.
 Temperature affects the rate of enzyme catalyzed reaction because the
number of successful collisions leading to a reaction increases at
Rate of reaction
higher temperatures. Coefficient = Vmax approached as all sites
becomes occupied.

At lower substrate concentration

some enzyme molecules have
their active sites free.
 Denaturation: the loss of the 3D shape of a protein
Substrate caused by
concentration

Changes in temperature or PH.

 Initial rate of reaction: the measure taken to compare the rates of enzyme- controlled reactions
under different conditions.
 Molecular activity: the number of substrate molecules transformed per minute by a single enzyme
molecule.
THE STRUCTURE OF DNA AND RNA
MONONUCLEOTIDES

 They provide the energy currency of cells in form of

(ATP).

 They provide building blocks for the mechanism of

inheritance in the form of DNA and RNA.

Each nucleoti de has three parts:

 A 5-carbon pentose sugar

 A nitrogen containing base
 A phosphate group

 The most common type of nucleoti des either have purine base which has two nitrogen
containing rings or pyrimidine base which has one. The most common purine is
adenine (A) and guanine (G) and most common pyrimidine are cytosine (C), thymine
(T) and uracil (U).

 A phosphate group (PO₄³⁻) is a third component of a nucleoti de. Inorganic phosphate

ions are present in cytoplasm of every cell. Phosphate group means nucleoti des are
acidic molecules and carry negati ve charge. The sugar the phosphate and the base are
all joined thru a condensati on reacti on to form a mononucleoti de .

POLYNUCLEOTIDES
 Nucleic acids also known polynucleoti des are the informati on molecules of the cell.
They carry all the informati on needed to make to new cells. They are polymers
consisti ng of many mononucleoti des monomer units. The chromosome in the
nucleolus of eukaryoti c cells stores geneti c info but in prokaryoti c the DNA is found
fl oati ng freely in the cytoplasm of the cell. The info is stored as a code in the
molecules of DNA. Parts of the code are used as a template to make a complementary
strand of messenger RNA or MRNA and direct the producti on of the protein that
builds the cell and controls its acti on.

BUILDING THE POLNUCLEOTIDES

 Nucleic acid are chains of nucleoti des linked together by condensati on
reacti on that produce the phosphodiester bonds between the sugar on
one nucleoti de and the phosphate group pf the next nucleoti de. It can
be millions of units long. Both RNA and DNA have this sugar phosphate
backbone. The sugar of one nucleoti de bonds to the phosphate group
of next nucleoti de and so polynucleoti des always have a hydroxyl
group at one end and a phosphate group on the other. Long chains of
nucleoti des containing the bases C, G, A and T join to form DNA. Chains
of nucleoti des containing C, G, A, and U make RNA.
 RNA molecules form single polynucleoti de strands. These can either fold into complex
shapes held in place by hydrogen bonds, or remain as long thread
Differences between DNA and
like molecules. DNA molecules consists of two polynucleoti de
RNA.
strands twisted around each other. The sugar and phosphate from
the backbone of the molecule and pointi ng inward from the sugar-  RNA is single stranded
 They have different
phosphate backbones, are the bases which makes pairs in a pentose sugars
specifi c way. Purine base always pairs with pyrimidine base. In  In RNA the base U
DNA adenine pairs with thymine and cytosine pairs with guanine. replaces T found in DNA

This results in double helix.

 the two strands of DNA double helix are held together by

hydrogen bonds between the complementary base pairs. These
bonds form between the amino acid and the carboxyl group of
the purine and pyrimidine bases on the opposite strands. There
are three hydrogen bonds between C and G but only two
between A and T. there are 10 base pairs for each complete
twist of the helix.

HOW DNA WORKS

Conservati ve replicati on: a model of DNA replicati on that suggests
that the original double helix stays intact and in some way instructs
the informati on of new, identi cal double helix made up enti rely of new material.

Semi conservati ve replicati on: the accepted model of DNA

replicati on in which the DNA unzips and new nucleoti de align
along each strand. Each new double helix contains one strand
of the original DNA and one strand made up of new material .

 Nitrogen is a key component of DNA and can exist as a

heavier 15N or a lighter 14N

 DNA molecules were prepared using the heavier 15N and Meselson and stahl experiment
then induced to replicate in the presence of the lighter
14N

 DNA samples were then separated via centrifugati on to

determine the compositi on of DNA in the replicated
molecules

The results supported the semi-conservati ve model of DNA

 Aft er one division, DNA molecules were found to contain a

mix of 15N and 14N, disproving the conservati ve model.

 Aft er two divisions, some molecules of DNA were found to consist solely of 14N,
disproving the dispersive model.
 DNA helicase unzips the two strands of the DNA. DNA polymerase lines up the
nucleoti des along the DNA template strands. And DNA ligase catalyzes the formati on
of the phosphodiester bond between the new nucleoti de.

 The chains of nucleoti de fi t together perfectly as long as cytosine and guanine,

adenine and thymine are always matched together.

 When the DNA replicates the two strands of DNA molecule unzip along the line of
hydrogen bonds and unravel. This is bought by the enzyme DNA helicase. These
strands act as template for the new DNA strands.

 The exposed bases att ract free DNA nucleoti des and new hydrogen bonds are formed
between the matching base pairs. DNA polymerase lines up and catalyzes the linking
up of the nucleoti de along the template strand. DNA ligase catalyzes the formati on of
phosphodiester bond between the two strands of DNA.

 The result is two new strands of DNA identi cal with the original piece. The new
molecules automati cally coil up into the double helix as weak hydrogen bonds form
within the structure.

THE GENETIC CODE

 Translation: the process by which proteins are produced, via RNA using the genetic code found in
the DNA, it takes place on the ribosomes.
 Triplet code: the code of 3 bases that is the basis of genetic info in the DNA.

 A sequence of three bases on the DNA or RNA is called a codon. The codon of the DNA
is diffi cult to work out because molecules are large so most work is done by a codon
on smaller molecule messengerRNA or (MRNA). This MRNA is complementary strand
to the DNA so it’s like the reverse image of the base sequence of the DNA. 98% of the
human DNA is non coding.

 In the 2% of the human DNA that codes for proteins, some codons code for a
parti cular amino acid. While others code for the beginning or the ending of parti cular
amino acid sequence. So for example the codon to start the polypepti de chain is TAC.
This is also the codon for methionine which is the fi rst amino acid in a polypepti de
chain. Geneti c code is no only triplet code. It’s also non-overlapping or degenerate
code.
Cells decode mRNAs by reading their
NON-OVERLAPPING CODE AND DEGENERTATE CODE nucleotides in groups of three, called
codons. Here are some features of
codons:
No overlapping Most codons specify an amino acid
Three "stop" codons mark the end of a
 The genetic code is no overlapping, i.e. The adjacent codons do not protein
One "start" codon, AUG, marks the
overlap. A no overlapping code means that the same letter is not used beginning of a protein and also encodes
for two different codons. In other words, no single base can take part the amino acid methionine
in the formation of more than one codon.
Degeneracy
 The code is degenerate which means that the same amino acid is coded by more than one base
triplet. For example, the three amino acids arginine, alanine and leucine each have six synonymous
codons.

DNA AND PROTEIN SYNTHESIS

In eukaryotes, the DNA codes for the
individual protein is in the nucleus of the cell. They proteins are synthesized at the
ribosomes, which are in the cytoplasm. DNA from the nucleus has never been detected in
the cytoplasm. So the message cannot be carried directly RNAs carry the info from the
nuclear DNA to the ribosomes.

DIFFERENT TYPES OF RNA

The sequence of base along a strand of RNA release to the sequence of bases on the small
part of the DNA in the nucleus. Three diff erent type of RNA carries out three main
functi on;

 It carries the instructi ons for a polypepti de from the DNA in the nucleus to the
ribosomes where proteins are made.

 It picks up a specifi c amino acid from the protoplasm and carries them to the surface
of the ribosome.

 It makes up a bulk of ribosomes themselves.

MESSGENER RNA

 Messenger RNA (mRNA) is formed in the nucleus.

A piece of mRNA usually has instructi ons for one
polypepti de. This is diff erent from double helix of
DNA which carries info about the vast array of
proteins. The sense strand of the DNA strand carries the code for protein to be
formed. But the messenger RNA form the anti sense strand of the DNA also called
template strand it allows the code of the mRNA to refl ect the sense code of the DNA.
The mRNA which is formed codes for a polypepti de.

 Part of the DNA unravels and unzips exposing the bases which acts as a template.
Beginning at a start codon which is also the code for methionine. RNA nucleoti des
along the exposed sequence of DNA bases in the normal complementary fashion. Then
RNA polymerase joins the chain of RNA nucleoti de together. The process ends when
the chain reaches the stop codon and the mRNA chain separates from the DNA
template allowing the DNA chains of double helix to rejoin.

 Hydrogen bonds maintain the helical structures of RNA molecule. In the same way the
DNA the bases of the mRNA from a triplet code and each triplet of bases in codon. The
relati vely small mRNA molecules pass easily thru the pores of the nuclear membrane
carrying the instructi ons from the genes in the nucleus to the cytoplasm they can
move to the surface of ribosomes. Where protein synthesis takes place.
TRANSFER RNA
Transfer RNA or (tRNA) is found in the cytoplasm. It has a complex shape that enables it to carry out its
function