Home ADVANCED LEVEL TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

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TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5
TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

Proteins are polymers of amino acids joined together by peptide bond.

OTHER BONDS FOUND IN PROTEINS.

Ionic bonds: is an electrostatic attraction between positive and negative charge.

Hydrogen bond: this occurs between hydrogen atom and more electronegative atoms.

Disulphide bond: the bond between two crystalline molecules.

Van-de-Waal forces: these are weak non-attraction forces (hydrophobic interactions) created between –CH3 groups which are non-polar.

CLASSIFICATION OF PROTEINS.

CRITERIA

Level of organization.

According to function.

According to composition.

To whether they contain essential amino acids.

According to structure.

ACCORDING TO LEVEL OR ORGANISATION.

Primary structure.

Secondary structure.

Tertiary structure.

Quaternary structure.

Primary structure.

This is a linear sequence of amino acids joined together by peptide bonds. Also disulphide bond may be found.

 

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5
Secondary structure

This is due to coiling or twisting of the polypeptide.

Diagram

α helical

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

This is due to attraction of various amino acids.

This is a component of hair, claws, nails, as well as skin.

β pleated sheets (zig zag structures)

Collagen is a compound of tissues like bones and cartilage. Collagen is an example of β pleated sheets.

Tertiary structure.

Tertiary structure is due to coiling and twisting of the polypeptide helix forming a globular or spherical shape.

Bonds present in the coiled structure are ionic bond, hydrogen bonds, hydrophobic interactions, disulphide bridges.

Examples of tertiary structures. (They are very soluble).

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

Immune globin( antibodies)

homornes

enzymes

Quaternary structure.

Quaternary structure is due to coiling and twisting of various polypeptide chains usually the structure is associated with non-protein parts called prosthetic groups e.g. hemoglobin.

Hemoglobin has four polypeptide chains, two α-chains and two β chains each surrounding an iron atom.

 

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

The hemoglobin consists of protein parts. The protein part consist of 4 polypeptide chains, of the four polypeptide chains, 2α chains and 2 β chains and is called globin.

The non protein parts is called HAEM consist of poiphyding surrounding an iron atom.

THE FOUR LEVELS OF PROTEIN STRUCTURE

 

 

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BASED ON WHETHER THEY CONTAIN ESSENTIAL OR NON ESSENTIAL AMINO ACIDS.

Essential amino acids Vs non essential amino acids

Essential amino acids are those which cannot be synthesized by human cells but are obtained from food.

All of the 20 α amino acids are needed to make different proteins in the body of a human.

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

Twelve of these amino acids can be synthesized by the cells from other substances that are present in the body; these are called non-essential amino acids.

The other eight cannot be synthesized by the body and must be included in the persons diet are called essential amino acids.

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BASED ON COMPOSITION.

1. Simple proteins

Simple proteins are made up of amino acids only.

E.g. – Histones (nucleoprotein)

Globulin( immunoglobulin)

Schleroproteins ( e.g. Keratin)

Albumins

Pastamins

1. Conjugated proteins.

Made up of amino acids; are globular proteins associated with non protein materials.

E.g. haemoglobin glycoprotein (components of cell membrane), mucin (component of saliva), lipoproteins (components of cell membrane).

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ACCORDING TO FUNCTION.

NOTE:these are also functions proteins.

 

TYPE
EXAMPLE
OCCURRENCE/ FUNCTION.
1.
Structural
  • Collagen
  • Keratin
-Elastin
  • Components of the connective tissue, bone, tendon,cartilage, skin,hair,feather, nails and horns.
  • Elastic connective
tissues(ligaments „wraps up‟ nucleic acid for virus.
-viral coat protein
Trypsin
Catalyze hydrolysis of
Ribulose proteins biphosphate carboxylase.
Catalyses carboxylation
(oxidation)CO2 of ribulase
2. biphosphate in photosynthesis.
Enzymes
Catalyze synthesis of amino
acids, glutamine from glutamic acid and ammonia.
Glutamine synthesase.
3.
Hormones
-Insulin
– glucagon
Adrenaline corticotrophic hormone (ACTH).
  • Helps to regulate glucose metabolism.
  • Stimulates growth and activity of the adrenal cortex.
4.
Respiratory pigment.
  • Haemoglobin
  • Myoglobin
  • Transports oxygen in vertebrate‟s blood.
  • Stores O2 in muscles.
5.
Transport
– Serum albumin
Transports fatty acids and lipids in the blood.
6.
Protective
  • Antibodies – Fibrinogen
  • Thrombin
  • Form complexes with foreign proteins
  • Form fibrin in blood clotting
  • Involved in blood clotting mechanism.
7.
Contractile
  • Myosin
  • Actin
  • Moving filaments in myofibrils of muscles
  • Stationary filaments in m myofibrils in muscles.
8.
Storage
  • Ovalbumin
  • Casein
  • Egg white protein
  • Milk proteins
9.
Toxins
  • Snake venom
  • Diphtheria toxin
  • Enzymes
  • Toxin made by diphtheria bacteria.

NEUTRAL AMINO ACIDS.

This is because their side chains have no charge at the pH of body cell.

Thus are divided into;-

Natural hydrophobic amino acids. Natural hydrophilic amino acids.

Natural hydrophobic amino acids.

Seven natural amino acids have side chains(R) that are non polar or hydrophobic.

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

These hydrophobic are either alkyl or aromatic in nature.

Alanine (ala).

Valine (Val).

Leusine (leu).

Iso leusine. Proline

Phenyl donine (phe) Tryptophan (trp).

Neutral hydrophilic amino acids.

Eight amino acids are classified as hydrophilic.

In general these amino acids are more soluble than hydrophobic amino acids.

The acid chain of glycine (gly) is just hydrogen.

The other seven neutral hydrophilic amino acids have side chains that can form either strong or weak hydrogen bond with water.

These have hydroxyl group in either side chain serine (ser) theorine (Thr) or tyrosine (try).

Two contain an amino functional group, asparagines (asp) and glutamine (gln).

The remaining two contain a sulphur atom cysterine (cys) and methionine (met).

Others include: tyrosine, asparagines, cysterine, glutamine, and methionine.

ACIDIC AMINO ACIDS

Acidic amino acids have side chains that contain a second carbonyl group.

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

At the pH of cells in the body, these carboxylic groups exist primarily as negative charged carboxylate ions and this interact strongly with water molecules.

Aspartic acid (asp)

Glutamic acid (glu)

BASIC AMINO ACIDS.

Three of the amino acids contain a side chain that act as a proton acceptor or base.

They are thus classified as basic amino acids, these are lysine (lys), arginine (arg) and histamine.

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BASED ON STRUCTURE

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fibrous protein.

Have a secondary structure and little or no tertiary structure.

Insoluble in water.

Physically tough.

Form long polypeptide chain cross linked at intervals forming long fibres or sheets.

Functions of fibrous proteins.

Perform structural function in cell and organism e.g. collagen (tendon, bones, connective tissues) myosin in muscles, (silk) spider web, keratin (nail, hair, feathers).

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globular proteins.
Found mostly in tertiary structure.
Polypeptide chain highly folded to form spherical shape.
Easily soluble in water.

Functions of globular proteins.

Forms enzymes, antibodies and some hormone e.g. insulin.

C. intermediate protein.

Fibrous in nature but soluble in water e.g. fibrinogen.

Function of intermediate protein.

Fibrinogen forms insoluble fibrin when blood clots.

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

NUCLEIC ACIDS.

Like proteins, nucleic acids are largely polymers made up of small number of different building blocks called nucleotides.

Each nucleotide is in turn composed of 3 smaller parts.

A phosphate group.
Monosaccharide
A nitrogen containing base.

The term nucleotide is used to refer to nitrogenous base bound to a monosaccharides.

And the nucleotide is a nucleotide phosphate.

There are two major types of nucleic acids.

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TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5
deoxyribose nucleic acids (DNA).

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ribonucleic acid (RNA).

Diagrams

 

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

 

There are two main differences between the deoxyribonucleotide components of DNA and the ribonucleotide component of RNA.

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

 

criterion DNA RNA
1. Sugar component
– Has its sugar D-ribose lacking hydroxyl group in carbon #2 of ribose; hence the prefix De-oxy is used to denote the absence of oxygen at that position.
– Has its sugar D-ribose having oxygen at carbon number 2.
2. Organic bases.
– Have four possible organic bases, 3 of which are adenine, guamine and cytosine and the fourth is thymine which is lacking in RNA.
– Have four possible organic bases, 3 of which are adenine, guamine and cytosine and the fourth is uracil which is lacking in
DNA.

 

JOINING THE NUCLEOTIDES TO FORM A POLYMER OF DNA OR RNA.

The bond that holds these polymers together are ester linkage formed between the phosphate on the number 5 carbon of ribose in one nucleotide and the hydroxyl on the number 3 carbon of ribose in the next nucleotide (deoxyribose in the case of DNA)

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

Two nucleic acids are said to have 3l5l– phosphate ester bridge/bond between their nucleotide components

Diagram of a long nucleic acid.

 

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

The DNA consists of two long polynucleotide strands and the base components of each nucleotide on one strong can form hydrogen bonds with only one specific nucleotide base on the other strand.

Guamine (G) can hydrogen bond only to cytosine in another DNA strands form a base pair.

Adenine (A) can hydrogen bond with thymine (T).

ATP (ADENINE TRIPHOSPHATE)

ATP is formed from the nucleotide adenosine monophosphate by the addition of two further phosphate molecules.

Its structure:

Diagram

 

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

ATP is an energy store, because the last branches are highly energetic on breaking.

The hydrolysis of ATP to ADP is catalyzed by the enzyme ATPase and the removal of the terminal phosphate yield 30.6kj mol-1 of free energy.

So does the second one to from ADP and AMP respectively.

AMP and ADP may be re-converted to ATP by the addition of phosphate molecule in a process called phosphorylation of which there two main forms.

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5
Photosynthetic phosphorylationoccurring during photosynthesis in chlorophyll containing cells.
Oxidative phosphorylation – occurring during cellular respiration in all aerobic cells.

USES OF ATP.

A metabolic active cell may require up to two million ATP molecules every second. ATP is the source of energy for;

1. Anabolic processes.

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

It provides the energy needed to build up macromolecules from components units.

Examples

Polysaccharide synthesis from monosaccharide.

Protein synthesize from amino acids. DNA replication.

2. Movement- it provides the energy for many forms of cellular movements, including;

-muscle contraction

Cilliary actioning
Spindle action in cell division.

Active transport – it provides the energy necessary to move materials against concentration gradient e.g. ion pumps.

Secretion – it is secreted to form the vesicle in the secretions of the cell product.

Activation of chemicals – it makes chemicals more enabling them in reacting (more readily) e.g. the phosphorylation of glucose at the start of glycolysis.

ENZYMES

Enzymes are simple or compound organic proteins which are organic catalysts catalyzing reactions in living tissues.

ENZYME: Greek word “en” means in and “zyme” means yeast cell.

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

They are bio catalysts found in living things.

Catalysts accelerate chemical reactions although a catalyst is a participant in a reaction and undergoes physical change during the reaction.

It reverts to its original state when the reaction is complete.

Enzymes are protein catalysts for chemical reactions in biological systems.

Most chemical reactions of living cells would occur very slowly, were it not for catalyzing enzymes as illustrated below.

Energy diagram under catalyst action showing progress of the reaction.

Fig. reduction of necessary activation energy by enzymes.

 

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

NB: as seen in the above graph, the activation energy (Ea) necessary to initiate the reaction is much less in the presence of the catalyst than in its absence.

It is this lowering of activation energy barrier by enzyme catalysts that makes possible most of the chemical reactions in life.

By contrast to non-protein catalyst (e.g. H+, OH , or metal ions) each enzyme catalyze a small number of reactions, frequently only one and thus enzymes are reaction –specific catalysts.

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

Most inorganic catalysts are relatively non specific for example platinum, often used to catalyze the formation of water from hydrogen gas and oxygen gas.

Will catalyze almost any reaction in which H2 is one of the reactants and the reaction of materials as well.

Properties of enzymes.

They generally work fast than inorganic catalysts and greatly lower the activation energy.

Enzymes are not consumed by the reaction they catalyze i.e. a given molecule of an enzyme can be used indefinitely if the conditions are kept suitable.

Enzymes can work in either direction i.e. catalyze reversible reactions.

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

This is due to the fact that metabolic reactions are reversible and the direction of the reaction depends on the relative amount of substrates and products present.

Enzymes are denatured by excess heat (temperature) by the virtue of their proteineous nature.

Enzymes are sensitive to pH.

Every enzyme has its own range of pH at which it functions effectively.

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

Enzymes are specific in the action they catalyze.

Normally a given enzyme will catalyze only one reaction or one type of reaction.

Enzymes react in only small amount.

A very small amount of catalyst will transfer in a very large amount of reactants.

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

They are colloidal in nature and thus provide large surface area for reaction to take place.

Enzyme activity can be accelerated or inhibited.

The accelerators are called activators

e.g. Cu, Zn, Co, Cl, Ca. while the inhibitors are for example DOT, Pb, and Hg etc.

NATURE AND MODES OF ENZYME ACTIVITY.

Hypothesis explains the nature and mode of enzyme activity.

The lock and key theory (hypothesis) by Fischer.

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

In the model the three dimensional configuration of the enzyme represented the lock (the active title) into which particular substrate (key) will fit.

The active site presumes to be rigid.

The induced fit model by Koshland.

Originally little more than an attractive hypothesis, this model now has received considerable experiment support.

An essential feature is the flexibility of the region of the active site.

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

In this mode, the substrate induce the conformation change in an enzyme just like the shape of a glove is affected hand wearing.

MOLECULAR STRUCTURE OF ENZYMES.

Enzymes are either composed of;

Protein alone-simple enzymes.
Protein and other non-protein molecule( i.e. conjugated enzymes)

The protein part of an enzyme is called Apanzyme.

Non- protein part is called co-enzyme.

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

The protein part of an enzyme is made up of enzyme protein zymoprotein.

The two component (the apoenzyme and coenzymes) make up the active enzymes called holloenzymes.

Holoenzymes= coenzyme + apoenzyme.

Prosthetic groups are usually metallic ions such as Co, Mg, Ni, Cu, Zn (mineral salt).

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

This is also a non-protein part, the well known co-enzyme are those which function as hydrogen carriers, inoxidation-reduction in energy metabolism.

For instance coenzyme NAD, NADP, Q, A. Coenzyme A is involved in transfer of an acetyl group.

These are substances which increase the activity of the halo enzymes.

Their absence may retard the catalytic activity of the enzymes or preventing it from acting.

Activators are usually inorganic ions e.g. Ca2+ for thrombo kinase, Cl for ptyalin, Mg2+ for phosphate.

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

Coenzymes and activators are needed by the enzymes for proper activities.

FACTORS AFFECTING ENZYMATIC ACTIVITY.

Over a limited range of temperature, the velocity of enzyme catalyzed reactions increase as the temperature rises.
The exact ratio by which the velocity change for a 100C temperature rise is the Q10 or temperature coefficient.

The velocity of many biological reactions roughly doubles with a 100C rise in temperature ( Q10 = 2) and is halved if the temperature is decreased by 100C.

Many physiological processes e.g. the rate of contraction of an exercised heart- consequently exhibit Q10 of about 2.

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

When the rate of enzyme catalyzed reaction is measured at several temperature the result shows in the figure below is typical.

There is an optimal temperature which the reaction is most rapid.

Above this reaction the rate decrease sharply due to heat denaturation of the enzyme and below this the energy content of enzymes is too low to make them participate in their reaction.

Fig. enzymes activity as a function of temperature.

 

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5
Although temperature sensitivity varies somewhat from one enzyme to another the curve shown here may be taken as applying to an average enzyme.

Its activity rises steadily with temperature (approximately) doubling for each 100C increase until thermal denaturation cause a sudden sharp decline, beginning between 400C and 450C.

The enzyme because completely ineffective/ inactive at temperature above 600C presumably because its three dimensional configuration has been severely disrupted.

Denaturation of a protein enzyme by heat is the loss of it biological activity.

This can be done also by heat, acid or high salt concentration.

2. pH.

Moderate pH changes affect the ionic state of the enzyme and frequently that of the substrate also.

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

When enzyme activity is measured as several pH values optimal activity is generally observed between pH values of 5 and 9.

However the few enzymes eg pepsin is active at pH values well outside this range.

The shape of pH activity curves is determined by the following factors.

1. Enzyme denaturation.

At extremely high or low pH values.

 

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

1. Since the only forms that will interact are SH+ and E.

Extreme pH values will lower the effective concentrations of E and SH+ thus lowering the reaction velocity as shown below.

Diagram

 

 

Only the crossed-hatched area of S and E in the appropriate ionic state and thermal concentration of E and S are correctly charged at X the result is a bell-

TOPIC 1: CYTOLOGY (III) ~ BIOLOGY FORM 5

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