BC 1008 - Structure and

Function of Biomolecules

Devaka Weerakoon (18 L) and Dilrukshi de Silva (12 L)

Department of Zoology
(3 Cr 30L + 30P)

Objectives and Learning Outcomes

To Introduce the four basic biomolecules, their structure and function
What an amino acids is and their properties
Structure of a protein

Few examples of fibrous and globular proteins

What an enzyme is and their functioning Structure of Nucleic acids Information storage and expression What a carbohydrate is and diferent types of carbohydrates

and functions
What a lipid is and different types of lipids and their functions

Substances Found in Living Organisms

Water

Macromolecules: Giant Polymers

There are four major types of biological macromolecules: Proteins

Carbohydrates
Lipids

Nucleic acids

Macromolecules: Giant Polymers

These macromolecules are made the same way in all living things, and are present in all organisms in roughly the same proportions An advantage of this biochemical unity is that organisms can use these molecules interchangebly Macromolecules are giant polymers Polymers are formed by covalent linkages of smaller units called monomers Molecules with molecular weights greater than 1,000 daltons (atomic mass units) are usually classified as macromolecules

Macromolecules: Giant Polymers

The functions of macromolecules are related to the shape and the chemical properties of their monomers Some of the roles of macromolecules include:
Energy storage
Structural support

Transport
Protection and defense Regulation of metabolic activities Means for movement, growth, and development Information storage

Condensation and Hydrolysis Reactions

Macromolecules are made from smaller monomers

by means of a condensation or dehydration

reaction in which an OH from one monomer is linked to an H from another monomer Energy must be added to make or break a polymer The reverse reaction, in which polymers are broken back into monomers, is a called a hydrolysis reaction

Condensation and Hydrolysis of Polymers

Condensation and Hydrolysis of Polymers

Condensation and Hydrolysis Reactions How are organic molecules synthesized?

Molecules can be metabolized (broken down)

Structure and Function of Biomolecules

1. Introduction to proteins; Protein structure; fibrous proteins; myoglobin and haemoglobin; immunoglobulins;

Introduction to enzymes; enzyme kinetics and inhibition;

modes of enzyme catalysis; serine proteases 2.Introduction to nucleic acids; Structure of DNA and RNA; information storage and retrieval; the genetic code 3.Introduction to lipids; steroids and eicosanoids;

phospholipids and membranes; transport across membranes

4.Introduction to carbohydrates; linear and cyclic

structures; stereochemistry and Fischer projections;

Haworth projections; glycosidic bonds; disaccharides; polysaccharides and complex carbohydrates

Proteins: Polymers of Amino Acids

Proteins are polymers of amino acids. They are molecules with diverse structures and functions

Each different type of protein has a characteristic amino acid composition and order Proteins range in size from a few amino acids to thousands of them
Folding is crucial to the function of a protein and is influenced largely by the sequence of amino acids

Protein Functions
1. Structural e.g. Collagen, elastin 2. Mobility e.g. Actin/myosin, tubulin, flagella 3. Receptors e.g. Insulin receptor 4. Ligands e.g. Insulin

5. Defense e.g. Antibodies

6. Housekeeping e.g. Enzymes of glycolysis

7. Signalling e.g. Signalling molecules

8. Enzymes e.g. Proteases 9. Storage e.g. Ovalbumin, casein 10.Transport e.g. Haemoglobin

The Monomeric Unit is the Amino Acids

An amino acid has four groups attached to a central carbon atom: Central carbon atom - a carbon A hydrogen atom An amino group (NH2) A carboxylic group (COOH) Differences in amino acids come from the side chains, or the R group

Twenty amino acids used by the living organisms for synthesis of proteins

Proteins: Polymers of Amino Acids

Amino acids can be classified based on the characteristics of their R groups A. Nonpolar hydrophobic side chains B. Polar but uncharged side chains C. Charged hydrophilic side chains D. Special amino acids

Non Polar Hydrophobic R groups

Charged R groups

Polar but Uncharged R groups

Unusual Amino Acids

Cysteine has a terminal sulphydral group (SH) Glycine has a H atom as the side chain Proline - the R group forms a covalent bond with the amino group, forming a ring (imino acid)

Two cysteines can form a Cystine

Amino Acids Display Stereoisomerism

An isomer is a compound that has the same molecular formula but exist in different forms

Amino Acids Display Steroeisomerism

Compounds that carry asymmetric carbon atoms or chiral centers show optical isomerism i.e. they can cause plane polarized light to rotate in left or right direction Amino acids show stereoisomerism as all of them except

Glycine carry chiral centers

Amino acids that exist in nature are the L forms

Special Amino Acids

Hydroxyproline Ornithine Citrulline Thyroxine

Amino Acids can act as Week Acids/ Bases

CH3COOH CH3COO- + H+

The relationship between the chemical species and dissociation constant is expressed by the Henderson-Hasselbalch equation pH = pKa + log[A-]/[HA]

Amino Acids can act as Buffers

Amino acids contain a basic amino group and an acidic carboxyl group

Formation of Peptide Linkages

Proteins are synthesized by a condensation reactions between the amino group of one amino acid and the carboxyl group of another This forms a peptide linkage Peptide bond has partial double bond character

Causes linkage to be planar no rotation around peptide bond

Amino acid linkage results in a Peptide

Dipeptide peptide consisting of two amino acids Tripeptide - peptide consisting of three amino acids Oligopeptide - peptide consisting of several amino acids

Polypeptide - peptide consisting of many amino acids

Some examples of naturally occurring peptides
glutathione tripeptide (glu-cys-gly) - scavenger of free radicals leucine enkephalen - naturally occurring analgesic

Oxytocin Hormone comprising of nine amino acids

L-aspartyl L-phenylalanine - aspartame

The Four Levels of Protein Structure: Primary Structure

There are four levels of protein structure: primary, secondary, tertiary, and quaternary

The precise sequence of amino acids is called its primary structure

The peptide backbone consists of repeating units of atoms: NCCNCC

The Four Levels of Protein Structure: Secondary Structure A proteins secondary structure consists of regular, repeated patterns in different regions in a polypeptide chain This shape is influenced primarily by hydrogen bonds arising from the amino acid sequence (the primary structure) The two common secondary structures are the alpha helix and the beta pleated sheet

The Four Levels of Protein Structure: Secondary Structure

The alpha helix is a right-handed coil The peptide backbone takes on a helical shape due to hydrogen bonds. The R groups point away from the peptide backbone and stabilize the structure by forming H bonds Fibrous structural proteins have a-helical secondary structures, such as the keratins found in hair, feathers, and hooves

The Four Levels of Protein Structure: Secondary Structure b pleated sheets form from peptide regions that lie parallel to each other Sometimes the parallel regions are in the same peptide, sometimes they are from different peptide strands This sheet like structure is stabilized by H bonds between N-H groups on one chain with the C=O group on the other

Spider silk is made of b pleated sheets from separate peptides

Secondary Structure of Proteins

Other elements of secondary structure include beta turns and omega loops

The Four Levels of Protein Structure: Tertiary Structure

Tertiary structure is the three-dimensional shape of the completed polypeptide

The Four Levels of Protein Structure: Tertiary Structure

The primary determinant of the tertiary structure is the interaction between R groups

Factors determining tertiary structure:

The nature and location of secondary structures

Hydrophobic side-chain aggregation and van der Waals forces, which help stabilize them
The ionic interactions between the positive and negative charges and hydrogen bonding between polar residues Disulfide bridges, which form between cysteine residues

The Four Levels of Protein Structure: Quatenary Structure

Quaternary structure results from the ways in which multiple polypeptide subunits bind together and interact

This level of structure adds to the threedimensional shape of the finished protein
Hemoglobin is an example of such a protein; it has four subunits

The Four Levels of Protein Structure: Summary

Bonds Contributing to the Structure of a Protein

Primary Structure
Peptide bond (Covalent)

Irregular contortions Secondary, Tertiary and from bondings Quaternary Structures between side Noncovalent Linkages chains. Hydrogen 4-20
van der Waals

Hydrophobic Hydrophobic clusters at the Ionic core of Covalent Linkages proteins Disulphide Bridges

Proteins: Chaperon Proteins

Chaperonins are specialized proteins that help keep other proteins from interacting inappropriately with one another When a protein fails to fold correctly, serious complications can occur Incorrectly folded proteins are digested by proteosomes and the amino acids are recycled

Proteins: Polymers of Amino Acids

Shape or conformation is crucial to the functioning of proteins

The final conformation will be governed by the type of amino acids that make up the protein which will influence the folding pattern
Changes in amino acids can take place due to changes in DNA a process called mutation that can drastically change protein structure and therefore the function

Protein Denaturation
Changes in temperature, pH, urea, salt concentrations, and oxidation or reduction conditions can change the shape of proteins. This loss of a proteins normal three-dimensional structure is called denaturation.

Protein Modification
In some proteins further modification is needed for functioning

Glycosylation adding carbohydrate moieties which takes place in the golgi complex Adding lipid moieties especially in membrane proteins

Membrane Proteins
Lipid anchored proteins (a) Glycolipid covalent attachment by glycophosphatidyl inositol (GPI anchored proteins) (b) Covalent attachment of the protein to fatty acid like myristic acid or palmitic acid or the prenyl group (15-C franesyl hydrocarbons with repeating vinyl groups)

Protein Modification
In some proteins further modification is needed for functioning

Glycosylation adding carbohydrate moieties which takes place in the golgi complex Adding lipid moieties especially in membrane proteins
Covalent modification e.g. acetylation and methylation of Lys, methylation of Arg and His, phosphorylation of Ser, Thr or Tyr

Sometimes they need prosthetic groups

Sometimes cleavage is necessary for final action

Domains
The term domain is used to describe an area of a protein which is functionally or physically distinct Steroid Hormone Receptors
Inhibitory protein complex Transcription activating domain Hormone binding domain

DNA binding domain

Another example would be transmembrane proteins that have cytosolic, transmembrane and extracellular domains

Globular and Fibrous Proteins

Globular proteins proteins Fibrous

spherical shape fibers Insulin

Hemoglobin

long, thin Hair

Wool

Enzymes
Antibodies

Skin
Nails
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Fibrous proteins
Proteins which are folded to a more or less rod like shape

They consist of long fibers or large sheets tend to be mechanically strong are insoluble in water and dilute salt solutions play important structural roles in nature
Involved in structure: tendons ligaments blood clots, hair, hooves feathers etc., (e.g. Collagen, elastin, keratin and fibrin)

Fibrous Proteins
Keratin:

Long, fiber-like shapes

Typically structural

Ex: a-keratins
hair, wool, skin, and nails 3 a-helices held together by disulfide bonds Ex: b-keratins Feathers, scales large amounts of beta-pleated sheet structure

Fibrous Proteins
Collagen Connective tissue, skin, tendons, and cartilage

Consists of three polypeptide chains wrapped around each other in a ropelike twist to form a triple helix called tropocollagen; MW approx. 300,000 30% of amino acids in each chain are Pro and Hyp (hydroxyproline); hydroxylysine also occurs that contain OH groups for hydrogen bonding

Collagen Triple Helix

Every third position is Gly and repeating sequences are X-Pro-Gly or X-Hyp-Gly

The three strands are held together by hydrogen bonding involving hydroxyproline and hydroxylysine
With age, collagen helices become cross linked by covalent bonds formed between Lys and His residues Deficiency of Hyp results in fragile collagen

Globular Proteins
Proteins which are folded to a more or less spherical shape

They Tend to be soluble in water and salt solutions Most of their polar side chains are on the outside and interact with the aqueous environment by hydrogen bonding and iondipole interactions Most of their nonpolar side chains are buried inside Nearly all have substantial sections of a-helix and b-sheet

Myoglobin and Hemoglobn

Myoglobin is a protein (globin) containing a single heme unit, which stores oxygen in cells (especially muscles)

Hemoglobin is a multimeric protein with four sub units

May occur intracellulary or extracellularly Extracellular hemoglobin has a very high molecular weight

Both Proteins Contain a Prosthetic Group

Porphyrins: Metal complexes derived from porphyrin Many respiratory pigments are designed around the porphyrin molecule After the two H atoms bound to N are lost, porphyrin is a tetradentate ligand Two important porphyrins are heme (Fe2+) and chlorophyll (Mg2+)

Prosthetic Group
Four N atoms from the porphyrin ring are attached to the Fe2+ center Fifth coordination site is occupied by a base (Histidine), of the globin protein Sixth coordination site can be occupied by O2 (oxyhemoglobin) H2O in (deoxyhemoglobin) CO in (carboxyhemoglobin)

Role of the globin

Prevent oxidation of Iron Reduce affinity to CO

Factors that Effect Oxygen Binding

Binding of oxygen to Hb displays co-operativity Number of factors can influence binding of oxygen
CO2 pH Temperature Organic Phosphates (DPG/BPG)

Genetic Basis of Hemoglobin

Encoded by a multigene family a-globin family: a, z b-globin family: b, d, e, g Mutations of the Hb genes can result in diseases such as Sickle cell anaemia Thalassemia Composition of human hemoglobin chains at different life stages: Embryo : z2e2, a2e2 Fetus : a2g2 Adult : a2b2 (97%), a2d2 (2-3%), a2g2 (1%)

Sickle-Cell Anemia
Results from a single mutation in the beta chain

Glu Val
(-) charge is changed to a nonpolar (hydrophobic) group This site of mutation is at the surface of the protein in the deoxy form of hemoglobin.

This results in the beta chains sticking together in the deoxy form

Immunoglobulins
The antibody molecule comprise of the immunoglobulin domain Immunoglobulin domain comprise of a 100 110 aa held together by intra-chain disulfide bonds that forms a compact loop within the chain (globular domain) 2 Heavy chains 2 Light chains

The four chains are held together by disulphide linkages

The quaternary structure is Y shaped with three arms

Functions of Antibodies

Enzymes: Biological Catalysts

Almost all reactions in cells are catalyzed by enzymes

Generally most enzymes are proteins

However RNA can also catalyse reactions (Ribozymes) Enzymes accelerate reactions by lowering the free energy of activation Enzymes do this by binding the transition state of the reaction better than the substrate Transition state is halfway between substrate structure and product structure

Enzymes lower G (Activation energy) but do not affect G (standard state free energy) for a reaction

Lect. 11-

How Enzymes Aid in the Catalytic Process

Bind substrates Lower the energy of the transition state Directly promote the catalytic event Either through acidic or basic side chains that promote addition or removal of protons Or through holding ions in correct position to participate in the catalysis Release the products

Cofactors
In addition to the protein part, many enzymes also have a nonprotein part called a prosthetic group or a cofactor The protein part in such an enzyme is called an apoenzyme, and the combination of apoenzyme plus cofactor is called a holoenzyme. Only holoenzymes have biological activity; neither cofactor nor apoenzyme can catalyze reactions by themselves Cofactors form an intricate part of the active site and play a direct chemical role in the chemistry of the reaction
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Cofactors
A cofactor can be either an inorganic ion or an organic molecule, called a coenzyme

Many coenzymes are derived from vitamins, organic molecules that are dietary requirements for metabolism and/or growth
Nicotinamide adenine dinucleotide (NADH) Flavin adenine dinucleotide (FADH)
NH 2 N N N N R R S HO OH O R O

NADH
O P O O OH O P OHO R S

O R R OH

NH 2

O NH 2 N N N N R R HO O R S HO OH O OH OH O P O HO P O O R Me OH S N N O

Heme group
Metal atoms e.g. Zn++

FADH

Me

N NH

Classification of Enzymes
Class Reactions catalyzed

Oxidoreductoases oxidation-reduction Transferases transfer group of atoms

Hydrolases Lyases
Isomerases Ligases

hydrolysis
add/remove atoms to /from a double bond rearrange atoms combine molecules using ATP
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Enzyme Action: Lock and Key Model

An enzyme binds a substrate in a region called the active site Only certain substrates can fit the active site Amino acid R groups in the active site help substrate bind Enzyme-substrate complex forms Substrate reacts to form product Product is released
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Enzyme Action: Induced Fit Model

Enzyme structure flexible, not rigid Enzyme and active site adjust shape to bind substrate Substrate molecule induced to take up a configuration approximating the transition state Shape changes also improve catalysis during reaction Increases range of substrate specificity
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Lock and Key Model vs. Induced Fit Model

ES complex

E +
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Factors Affecting Enzyme Action: Temperature Little activity at low temperature

Rate increases with temperature

Most active at optimum temperatures (usually 37C in humans) Activity lost with denaturation at high temperatures

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Factors Affecting Enzyme Action

Optimum temperature

Reaction Rate

Low
Temperature

High

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Factors Affecting Enzyme Action: Substrate Concentration

Increasing substrate concentration increases the rate of reaction (enzyme concentration is constant) Maximum activity reached when all of enzyme combines with substrate
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Factors Affecting Enzyme Action: pH Maximum activity at optimum pH R groups of amino acids have proper charge Tertiary structure of enzyme is correct Narrow range of activity Most lose activity in low or high pH

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Factors Affecting Enzyme Action: pH Optimum pH

Reaction Rate

11

pH

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Regulation at Enzyme Function

This can be achieved through two mechanisms Regulation of synthesis Regulation of degradation Synthesis can be regulated at two levels Transcription regulation Translation regulation
Gene RNA Protein Enzyme Modification Functional Enzyme Active Enzyme

Inactive Enzyme

Allosteric Regulation

Stimulation & Inhibition by Control Proteins

Enzyme is regulated by binding of specific stimulatory or inhibitory protein Eg. Calcium-calmodulin Regulatory subunit of cAMP dependent protein kinase

Ca++ / Calmodulin

Target Ca++/CAM dependent protein Kinase

Activated Ca++/CAM dependent protein Kinase

Proteolytic Cleavage
Some enzymes are produced as inactive Zymogens or proenzymes The active site of these enzymes are masked by a part of the molecule Cleavage of the masking portion by spontaneous degradation or other proteolytic enzymes leads to exposure of the active site and therefore activation

Digestive enzymes: Procarboxypeptidase, Pepsinogen, Trypsinogen,

Reversible Covalent Modification

This result in conformational changes of the enzyme Covalent modification is targeted at a R group of one of the amino acids moieties of the protein Phosphorylation at serine, threonine or tyrosine residues eg. Glycogen phosphorylase

Adenylylation at tyrosine residues eg Glutamine synthase

Carboxymethylation at aspartic or glutamic acid residues

Compartmentalization within Organelles or Organs

Some enzymes and enzyme complexes have fixed locations within the cells or body Nucleus: DNA replication, synthesis of tRNA and mRNA and some nuclear proteins Ribosomes: Protein synthesis Chloroplast: Photosynthesis Liver: Fatty acid metabolism, Gluconeogenesis, Glucose metabolism, Glycogen synthesis Adipose tissue: Fat metabolism

Enzyme Kinetics
For a given amount of enzyme the relationship between reaction velocity and substrate concentration
E + S k1 k -1 ES k2 P

Michaelis Menton rate equation

V init =

V max [S] KM + [S]

Enzyme Kinetics
Lineweaver-Burk equation and plot allows us to determine Vmax and Km

Enzyme Inhibition
Cause a loss of catalytic activity There are FOUR types of enzyme inhibition: 1. Irreversible 2. Competitive 3. Non-Competitive 4. Uncompetitive

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Irreversible Inhibition
A compound interferes with the active site so as to disable it Commonly it is done by forming a stable covalent adduct with the enzyme

Diisopropyl Fluorophosphate (DIFP)

May also block substrate access to site Almost all are toxic substances

Competitive Inhibition
When an unreactive molecule bind to an enzymes active site and compete with the substrate to bind enzyme

Vmax remain unchanged

Km appear to increase

* Increased substrate can overcome inhibition

Non-Competitive Inhibition
An inhibitor that binds to the enzyme, but not at the active site. In this case the inhibitor is not competing for the

active site

- Binding distorts the enzyme and reduces its activity e.g. allosteric regulation of the enzyme

This form of inhibition causes:

Vmax to drop

Km remains unchanged

* increased substrate cannot overcome a non-competitive inhibitor

Uncompetitive inhibition
Substrate binding to enzyme is not inhibited Inhibitor binds to the ES complex occurs ESI complex is stabilized relative to ES complex so Km is reduced ESI complex is non-productive so Vmax is lowered

How enzymes aid in the catalytic process Bind substrates Lower the energy of the transition state Directly promote the catalytic event Either through acidic or basic side chains that promote addition or removal of protons Or through holding ions in correct position to participate in the catalysis Or by inducing stress that makes bonds labile Release the products