Course Contents

Building Blocks of Biomolecules-Structure and dynamics Structure and functions of macromolecules Carbohydrates Proteins Lipids

Biomolecule A biomolecule is any organic molecule that is produced by a living organism, including large polymeric molecules such as proteins, polysaccharides, and nucleic acids as well as small molecules such as primary metabolites, secondary metabolites, and natural products.

Building Blocks of Biomolecules

BUILDING BLOCKS

Macromolecules form when smaller molecules (building blocks or subunits) come together
Monomers are joined by covalent bonds to form polymers

Building blocks of proteins

Amino acids20 common amino acids Central carbon with attached hydrogen, amino group, carboxylic acid group, and a R group

PROTEINS
Functions Structural Enzymatic Catalyze chemical reactions

Structure
Proteins are polymers of amino acids There are 20 common amino
Each has a central carbon attached to 4 groups
Hydrogen Amine Carboxylic acid An R group

Amino acids differ by their R groups

There are 20 different R groups.

2 amino acids are connected by dehydration synthesis

The covalent bond is called a peptide bond

Levels of organization of Protein

Primary structure
Sequence of amino acids.
The 20 different amino acids can be joined in any sequence This sequence is determined by the DNA sequence of the gene that encodes for that particular protein

Secondary structure
Due to interactions of the amino acids near each other
Hydrogen bonds between amino hydrogens and carboxyl oxygens

Results in an a -helix configuration or a b - sheet configuration

Tertiary structure The 3-dimensional folding of the polypeptide chain Due to interaction of R-groups of amino acids some distance away from each other
These interactions could be hydrogen bonding, ionic bonding, or covalent bonding.

Quaternary structure
Interaction between proteins

Building blocks of lipids

Fatty acids Long hydrophobic hydrocarbons Glycerol A triose

LIPIDS
FunctionLong term storage of energy
Also insulates and cushions major organs

Component of membranes

Types
Fats (lard and butter) are solids at room temperature Oils (vegetable oils) are liquids at room temperature

 Structure Lipids are composed of glycerol and three fatty acids

Two to three fatty acids are bonded to the glycerol by dehydration synthesis Fatty acids can be removed from the glycerol by hydrolysis

Fatty acids Hydrocarbon chains with a carboxyl group

Most have 16 - 18 carbons

Saturated fatty acids

No double bonds between the carbon atoms
The carbons are saturated with hydrogens

These will result in lipids that are less fluid

Unsaturated fatty acids

One or more (polyunsaturated) double bonds between the carbon atoms

These will result in lipids that are more fluid

Fatty acids are non-polar therefore hydrophobic

and

Phospholipids
Lipids with two fatty acids and phosphate group attached to glycerol Amphipathic
Has a hydrophilic head and hydrophobic tail

Lipid bilayer Two layers of phospholipids

Heads face out into the water Tails face towards each

Building blocks of nucleic acids(DNA & RNA)

Nucleotides Nitrogenous base
A, T, C, U, and G

Pentose sugar
Ribose in RNA Deoxyribose in DNA

Phosphate

NUCLEIC ACIDS
Function Store genetic information Transfer genetic information during reproduction Controls protein synthesis Types
DNA compromises the chromosomes RNA is used in protein synthesis

Monomers

Nucleic acids are polymers of nucleotides

Nucleotides are bonded by dehydration synthesis

Nucleotide consists of three parts

 Sugar
A pentose
Ribose in RNA Deoxyribose in DNA

Phosphate group Base

A, T, C, and G in DNA A, U, C, and G in RNA The order of these bases controls the amino acid sequence in proteins

Structure Backbone
Alternating sugars and phosphate

Bases
Stick out from the sugars

DNA is often double stranded, while RNA can be single stranded, double stranded, or both

Structure and Functions of Carbohydrates

Carbohydrates
One of the most abundant compounds of living cells Originally thought to have the formula (CH2O)n. Carbohydrate- polyhydroxy aldehyde or ketone or a larger molecule which can be hydrolyzed to a polyhydroxy aldehyde or ketone.

Occurance of carbohdrates
- First product of photoglucose - milk sugar: lactose - Stored in foods as starch, inulin and hemicelluloses components of - Supporting tissue of plants: cellulose - Degradation products: gums and mucilages - Miscellaneous : pectins, glucosides

in plants

- blood sugar : Dsynthesis - stored as glycogen - essential nucleic acids: ribose

in animals

Classification of Carbohydrates
Monosaccharide- one sugar residue. known is glucose, C6H12O6 Most well

Oligosaccharide- a few (2-9) sugar residues . Most well known is cane sugar or sucrose, C12H22O11. Polysaccharide- many sugar residues. Most common are glycogen, starch and cellulose, from animals, plants and plants.

CARBOHYDRATES
MONOSACCHARIDES (simple sugars)

Quick energy

Structural support

DISACCHARIDES

POLYSACCHARIDES

fructose

glucose

galactose

sucrose

maltose

lactose

starch

glycogen

cellulose

chitin

fruits

plants

milk

sugar beets sugar cane

grains

milk

stored glucose n plants

stored glucose n animals

forms cell walls in plants

insects

Table sugar

Carbohydrates
Monosaccharides (biological sugars ose)
Most frequently found in nature: - hexoses (six-carbon sugars) -> glucose and fructose - pentoses (five-carbon sugars) -> ribose

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Properties
Differences in structures of sugars are responsible for variations in properties Physical
Crystalline form; solubility; rotatory power

Chemical
Reactions (oxidations, reductions, condensations)

Physiological
Nutritive value (human, bacterial); sweetness; absorption

Functions of Carbohydrates
1. Energy source for plants and animals 2. Source of carbon in metabolic processes 3. Storage form of energy 4. Structural elements of cells and tissues

Functions of carbohydrates in foods

1. 2.
3. 4.

5.

Oxidized to furnish energy (respiration) Function as essential components of nucleic acids. DNA (deoxyribonucleicacid) Function as components of vitamins (ribose, riboflavin are parts of complex B-6 vitamin) Undergo fermentation by yeasts and other microorganisms to yield alcohol and various organic acids such as citric-, acetic-, propionic. Impart sweetness to the foods. When dissolved in water form syrups.

Functions of carbohydrates in foods

6. 7. At high concentrations the syrups can be used as preserving media On heating the sugars caramelize producing desirable taste and flavor compounds. In dissolved and colloidal form they bring about desirable textural effects. Pectins form gels. Pectins and gums are added to food as thickeners and stabilizers. Reducing sugars react with amino acids to produce dark colors. (browning reactions)

8.

9.

Proteins Proteins are organic compounds made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues.

The building blocks of proteins

Like carbohydrate and lipid molecules proteins contain the elements : Oxygen(O), Carbon(C),and Hydrogen(H)

In addition they always contain the element Nitrogen(N).

Characteristics of Proteins
Contain carbon, hydrogen, oxygen, nitrogen, and sulfur Serve as structural components of animals Serve as control molecules (enzymes) Serve as transport and messenger molecules Basic building block is the amino acid

Levels of Structure
A polypeptide is one linear chain of amino acids. Each gene produces one polypeptide. A protein may contain one or more polypeptides. Proteins also sometimes contain small helper molecules (co-factors) such as heme.

The primary structure (1o) is just the sequence of amino acids in the polypeptide. The secondary structure (2o) is local folding patterns, mostly alpha helix and beta sheet. The tertiary structure (3o) is the overall folding pattern of the entire polypeptide. The quaternary structure (4o) is the joining of individual polypeptides (subunits) into an active protein. Proteins that are just a single monomeric polypeptide have no quaternary structure.

Amino Acid

Amine group acts like a base, tends to be positive. Carboxyl group acts like an acid, tends to be negative. R group is variable, from 1 atom to 20. Two amino acids join together to form a dipeptide. Adjacent carboxyl and amino groups bond together.

 20 Different Amino Acids are required by body (Found in plants & animals)
Essential : synthesized (9) Can not be

Non-Essential : (14) Can be manufactured by the body

essential (9) methionine threonine tryptophan isoleucine leucine lysine valine phenylalanine histidine

Amino acids

nonessential (14) alanine, arginine aspartic acid, cysteine, cystine glutamic acid glycine hydroxyproline proline, serine tyrosine asparagine glutamine hydroxylysine

Another View of Amino Acid Properties

One Letter Amino Acid Codes

Peptide Chain
The amino acids are linked together by peptide bonds, which are the same as amide bonds. The peptide backbone is made up of the C and N involved in the peptide bond, plus the C that links them. The beginning of every protein is the N-terminus and the end is the Cterminus.
This means that there is a free amino group at the N terminus and a free acid

Formation of a Dipeptide Bond

Dehydration synthesis

Tertiary protein structure

This is when a polypeptide is folded into a precise shape. The polypeptide is held in bends and tucks in a permanent shape by a range of bonds including: Disulphide bridges [sulphur-sulphur bonds] Hydrogen bonds Ionic bonds.

Tertiary protein structure

Quaternary protein structure

Some proteins consist of different polypeptides bonded together to form extremely intricate shapes. A haemoglobin molecule is formed for separate polypeptide chains. It also has a haem group, which contains iron. The inorganic group is known as the prosthetic group. In haemoglobin it aids oxygen transport.

Quaternary protein structure

Functions of Proteins Structural component of body tissues

Average cell is 16% protein Varies from 10% (Brain) to 20% (RBC, muscle, heart, glands, & liver) Skeletal muscle protein = 65% of bodys total protein content.
Can be increased with resistance training

 Regulate acid base quality of body fluids.

Buffers the large quantities of acidic metabolic byproducts.

Assist with fluid balance

Globulins & albumins in blood plasma maintain osmotic gradient to prevent blood plasma loss from capillaries.

How useful are proteins?

Cell membrane proteins: Transport substances across the membrane for processes such as facilitated diffusion and active transport. Enzymes: Catalyse biochemical reactions, e.g. pepsin breaks down protein in to polypeptides.

 Hormones: are passed through the blood and trigger reactions in other parts of the body e.g. insulin regulates blood sugar. Immuno-proteins: e.g. antibodies are made by lymphocytes and act against antigenic sites on microbes. Structural proteins: give strength to organs, e.g. collagen makes tendons tough.

 Transport proteins: e.g. haemoglobin transports oxygen in the blood. Contractile proteins: e.g. actin and myosin help muscles shorten during contraction Storage proteins: e.g. aleurone in seeds helps germination, and casein in milk helps supply valuable protein to babies.
Buffer proteins: e.g. blood proteins, due to their high charge, help maintain the pH of plasma.

Lipids
Lipids are biomolecules that contain fatty acids or a steroid nucleus. soluble in organic solvents, but not in water. named for the Greek word lipos, which means fat. extracted from cells using organic solvents.

Characteristics of Lipids
Composed of Carbon, Hydrogen, and Oxygen Greater than 2:1 ratio of H:O Includes fats, oils, phospholipids, and cholesterol Building blocks are fatty acids and glycerol. Energy storage molecules Phospholipids part of cell membrane

Major Categories of Lipids

Fats and Oils Biosynthesis of fatty acids Phospholipids Waxes Terpenes Steroids Prostaglandins

Fats
Esters of fatty (long chain carboxylic) acids Common are triacyl glycerols, which can be hydrolyzed (saponified) into soaps:
O CH2OC O CH2O2C CHOC CHOO 2C
CH2O2 CH2OC C CH2OH CHOH CH2OH
+

aq. NaOH

Soap (mixture of salts of fatty acids): C13H27CO2 Na

+

C15H31CO2 Na

C17H35CO2 Na

Micelles: mode of action of soap

Na O O

Soap (above) can be represented as:

H2O
H2O
P P P P P P P P P P P

H2O
P P P

H2O
P P P P P P P

P
Soap (and detergents) form spherical clusters (right) called micelles; micelles surround and dissolve non-polar substances (oily stains) and render them soluble.

H2O
H2O

Oil
P P P

Oils (polyunsaturated fats)

O O CH2OC

CO CH O CH2OC

Presence of cis double bonds in oils makes it difficult for the molecules to pack regularly in a solid structure; oils have lower melting points than fats, and are liquids at RT.

Biosynthesis of Fatty Acids

Polyunsaturated Fatty Acids

Polyunsaturated fatty acids (PUFAs) include those having two and three double bonds.

A common omega-3 fatty acid found in fish oil is linolenic acid:

Omega-3 fatty acids are considered beneficial for brain function.

Composition of Fats and Oils

lauric C12 Animal Fats Lard Beef Fat Butter Fat Human Fat Whale Blubber Vegetable Oils Coconut oil Corn oil Olive oil Peanut oil Soybean oil 2 1 48 myristic C14 1 10 3 8 18 1 1 palmitic stearic C16 C18 25 27 29 25 12 11 10 7 7 10 8 14 10 8 3 2 3 3 5 2 oleic linoleic C18(1) C18(2) 50 50 27 46 35 7 45 82 58 29 10 3 5 10 10 1 35 6 24 51

Lipid Bilayer of Cell Membranes

Outside the cell (aqueous)
P P P P P P P

Cell membrane

Inside the cell (aqueous)

Steroids
Involved in regulatory processes and in sexual characteristics and functions Common steroids include cholesterol, estradiol, testosterone, estrone and progesterone

Major Functions of Lipids

Fats and oils used as energy storage in many organisms. Phospholipids and Sterols major structural elements of biological membranes. Others can serve as enzyme cofactors and messenger molecules.

Enzymes Enzymes are a group of biological catalysts responsible for supporting almost all of the chemical reactions that maintain animal homeostasis. The macromolecular component of almost all enzymes are composed of Protein except for ribozymes

Enzyme Nomenclature& Classifications

Traditionally, enzymes were simply assigned names by the investigator who discovered the enzyme. Currently enzymes are grouped into six functional classes by the International Union of Biochemistry & Molecular Biology (I.U.B.M.B)

Nomenclature of enzymes Recommended name 1.adding ase to the substrate of the reaction e.g .glucosidase, urease.

2.Description of action of the enzyme + ase e.g. lactate dehydrogenase.

Old names not related to function :e.g . pepsin, trypsin.

Systematic Name In this system of nomenclature, enzymes are divided into classes and subclasses The suffix-ase is attached to complete description of the chemical reaction
E.g.,D-glyceraldehyde3-phosphate:NAD oxidoreductase

Sources of enzymes Animal tissues Plants Microorganisms Culture media Subcellular fractions (e.g. mitochondria, membranes) etc.

Comparison of chemical and enzyme catalysis

Enzymes are biomolecules that catalyze (i.e., increase the rates of) chemical reactions. But Enzymes are different from chemical catalysts Enzymes work at specific temperature range (called optimum temperature , 25-45 o C). Enzymes are usually very specific as to which reactions they catalyze and the substrates that are involved in these reactions.

Enzymes are proteins, while chemical catalysts may be organic or metal. Enzymes have short life span comparatively chemical catalysts.