Structure and Function of Bio Molecules

8/3/2019 Structure and Function of Bio Molecules

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Course Contents

•Building Blocks of Biomolecules-Structure anddynamics

•Structure and functions of macromolecules

•Carbohydrates•Proteins

•Lipids



Biomolecule

• A biomolecule is any organic molecule thatis produced by a living organism, includinglarge polymeric molecules such as

proteins, polysaccharides, and nucleicacids as well as small molecules such asprimary metabolites, secondary

metabolites, and natural products.



Building Blocks of Biomolecules

• BUILDING BLOCKS

• Macromolecules form when smallermolecules (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

• EnzymaticCatalyze 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 dehydrationsynthesis – 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 inany sequence

– This sequence is determined by the DNAsequence of the gene that encodes for thatparticular 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 configurationor a b - sheet configuration



Tertiary structure

• The 3-dimensional folding of thepolypeptide chain

• Due to interaction of R-groups of

amino acids some distance away fromeach other

• These interactions could be hydrogenbonding, 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 andthree fatty acids

• Two to three fatty acids are bonded to theglycerol by dehydration synthesis

• Fatty acids can be removed from the

glycerol by hydrolysis



Fatty acids

• Hydrocarbon chains with a carboxylgroup

• 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 bondsbetween the carbon atoms

– These will result in lipids that are more fluid

–Fatty acids are non-polar andtherefore hydrophobic



Phospholipids• Lipids with two fatty acids and a

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

B ildi bl k f l i



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 ofnucleotides

• 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 aminoacid sequence in proteins



Structure

• Backbone –Alternating sugars and phosphate

• Bases

–Stick out from the sugars

• DNA is often double stranded,

while RNA can be singlestranded, double stranded, or

both



Structure and Functions ofCarbohydrates



• One of the most abundant compounds ofliving cells

• Originally thought to have the formula

(CH2O)n.

• Carbohydrate- polyhydroxy aldehyde or

ketone or a larger molecule which can behydrolyzed to a polyhydroxy aldehyde orketone.

Carbohydrates



Occurance of carbohdrates

in plants in animals- First product of photo- - blood sugar : D-

glucose synthesis- milk sugar: lactose

- Stored in foods as starch, - stored as glycogeninulin and hemicelluloses - essentialcomponents of

- Supporting tissue of nucleic acids: riboseplants: cellulose

- Degradation products:gums and mucilages

- Miscellaneous : pectins,glucosides



• Monosaccharide- one sugar residue. Most wellknown is glucose, C6H12O6

• Oligosaccharide- a few (2-9) sugar residues .Most well known is cane sugar or sucrose,C12H22O11.

• Polysaccharide- many sugar residues. Mostcommon are glycogen, starch and cellulose, fromanimals, plants and plants.

Classification of Carbohydrates



CARBOHYDRATES

MONOSACCHARIDES(simple sugars)

DISACCHARIDES POLYSACCHARIDES

Structural

support

fructose glucose galactose sucrose maltose lactose starch glycogen cellulose chitin

plants milk sugar beetssugar cane

grains milk storedglucoseİn plants

forms cellwalls inplants

insectsstoredglucose

İn animals

Quick

energy

fruits

Table sugar



29

Carbohydrates

Monosaccharides (biological sugars –ose)

Most frequently found in nature: - hexoses (six-carbon sugars) -> glucose and fructose

- pentoses (five-carbon sugars) -> ribose



Properties

• Differences in structures of sugars areresponsible for variations in properties

• Physical

• Crystalline form; solubility; rotatory power

• Chemical• Reactions (oxidations, reductions, condensations)

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



1. Energy source for plants and animals

2. Source of carbon in metabolicprocesses

3. Storage form of energy

4. Structural elements of cells andtissues

Functions of Carbohydrates



Functions of carbohydrates infoods

1. Oxidized to furnish energy (respiration)2. Function as essential components of nucleic acids.

DNA (deoxyribonucleicacid)

3. Function as components of vitamins (ribose,riboflavin are parts of complex B-6 vitamin)

4. Undergo fermentation by yeasts and othermicroorganisms to yield alcohol and various organic

acids such as citric-, acetic-, propionic.5. Impart sweetness to the foods. When dissolved inwater form syrups.



Functions of carbohydrates infoods

6. At high concentrations the syrups can be usedas preserving media

7. On heating the sugars caramelize producing

desirable taste and flavor compounds.8. 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.9. Reducing sugars react with amino acids toproduce dark colors. (browning reactions)



Proteins

Proteins are organic compoundsmade 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 proteinscontain the elements : Oxygen(O),Carbon(C),and Hydrogen(H)

• In addition they always contain the elementNitrogen(N).



Characteristics of Proteins

•Contain carbon, hydrogen, oxygen,

nitrogen, and sulfur

•Serve as structural components ofanimals•Serve as control molecules (enzymes)

•Serve as transport and messengermolecules•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 betasheet.

• 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 anactive 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 arerequired by body (Found in

plants & animals)

–Essential : (9) Can not be

synthesized

–Non-Essential : (14) Can be

manufactured by the body



Amino acidsessential (9) nonessential (14)

methionine alanine, argininethreonine aspartic acid,tryptophan cysteine, cystineisoleucine glutamic acid

leucine glycinelysine hydroxyprolinevaline proline, serinephenylalanine tyrosine

histidine asparagineglutaminehydroxylysine

A h i f A i A id i



Another View of Amino Acid Properties

O L



One LetterAmino Acid

Codes

P tid Ch i



Peptide Chain

• The amino acids are linked

together by peptide bonds,which are the same asamide bonds.

• The peptide backbone is

made up of the C and Ninvolved in the peptidebond, plus the Cα that linksthem.

• The beginning of every

protein is the N-terminusand the end is the C-terminus. – This means that there is a

free amino group at the Nterminus and a free acid



Formation of a Dipeptide Bond

Dehydration synthesis



Tertiary protein structure

• This is when a polypeptide is folded intoa precise shape.

• The polypeptide is held in ‘bends’ and

‘tucks’ in a permanent shape by a rangeof bonds including:

• Disulphide bridges [sulphur-sulphurbonds]

• Hydrogen bonds• Ionic bonds.



Tertiary protein structure



Quaternary protein structure

• Some proteins consist of different polypeptidesbonded together to form extremely intricateshapes.

• A haemoglobin molecule is formed for separatepolypeptide 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.

Q i



Quaternary protein structure



Functions of Proteins

• Structural component of bodytissues

–Average cell is 16% protein –Varies from 10% (Brain) to 20%

(RBC, muscle, heart, glands, & liver)

–Skeletal muscle protein = 65% ofbody’s total protein content. • Can be increased with resistance

training



• Regulate acid – base quality ofbody fluids.

–Buffers the large quantities ofacidic metabolic byproducts.

• Assist with fluid balance –Globulins & albumins in blood

plasma maintain osmotic gradient

to prevent blood plasma loss fromcapillaries.



How useful are proteins?

• Cell membrane proteins: Transportsubstances across the membrane forprocesses 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 bloodand trigger reactions in other parts of the

body e.g. insulin regulates blood sugar.

• Immuno-proteins: e.g. antibodies aremade 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 transportsoxygen in the blood.

• Contractile proteins: e.g. actin and myosin helpmuscles shorten during contraction

• Storage proteins: e.g. aleurone in seeds helpsgermination, and casein in milk helps supply

valuable protein to babies.

• Buffer proteins: e.g. blood proteins, due to theirhigh 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, whichmeans “fat.”

• extracted from cells using organic solvents.



Characteristics of Lipids

•Composed of Carbon, Hydrogen, andOxygen•Greater than 2:1 ratio of H:O

•Includes fats, oils, phospholipids, andcholesterol•Building blocks are fatty acids andglycerol.

•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 behydrolyzed (saponified) into soaps:

CH2O2C

CHO2C

CH2O2C

NaOHaq.

CH2OH

CHOH

CH2OH

+ C13H27CO2 C15H31CO2 C17H35CO2Na Na Na+ +

Soap (mixture of salts of fatty acids):

O

CH2OC

CHOC

CH2OC

O

O



Micelles: mode of action of soap

P

P

P

P

P

P

P

P

P

P

P

P

P

P

P

P

P

P

P

P

P

P

P

P

Na O

O

P

Soap (above) can be represented as:

Soap (and detergents) form spherical clusters(right) called micelles; micelles surroundand dissolve non-polar substances (oilystains) and render them “soluble.”

Oil

H2O

H2O

H2O

H2OH2O

H2O



Oils (polyunsaturated fats)

CH2OCO

CH

O

CH2OC

CO

O

Presence of cis double bonds in oils makes it difficultfor 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 havingtwo and three double bonds.

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

Omega-3 fatty acids are considered beneficial for brain

function.



Composition of Fats and Oils

lauric myristic palmitic stearic oleic linoleic

C12 C14 C16 C18 C18(1) C18(2)

Animal Fats

Lard - 1 25 8 50 10

Beef Fat - - 27 14 50 3

Butter Fat 2 10 29 10 27 5

Human Fat 1 3 25 8 46 10

Whale Blubber - 8 12 3 35 10

Vegetable Oils

Coconut oil 48 18 11 2 7 1Corn oil - 1 10 3 45 35

Olive oil - 1 7 3 82 6

Peanut oil - - 7 5 58 24

Soybean oil - - 10 2 29 51



Lipid Bilayer of Cell Membranes

P P P P P P P

P P P P P P P

Cell membrane

Outside the cell (aqueous)

Inside the cell (aqueous)



Steroids

• Involved in regulatory processes and in sexualcharacteristics and functions

• Common steroids include cholesterol, estradiol,testosterone, estrone and progesterone

Major Functions of Lipids



Major Functions of Lipids

• Fats and oils – used as energy storage inmany organisms.

• Phospholipids and Sterols – majorstructural elements of biologicalmembranes.

• Others can serve as enzyme cofactorsand messenger molecules.



Enzymes

Enzymes are a group of biologicalcatalysts responsible for supporting almost all of the chemical reactions

that maintain animal homeostasis.

The macromolecular component of

almost all enzymes are composed ofProtein except for ribozymes



Enzyme Nomenclature&

Classifications • Traditionally, enzymes were simplyassigned names by the investigator who

discovered the enzyme.

• Currently enzymes are grouped into six

functional classes by the InternationalUnion of Biochemistry & Molecular Biology(I.U.B.M.B)

Nomenclature of enzymes



Recommended name1.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 classesand subclasses

• The suffix-ase is attached tocomplete description of thechemical reaction

• E.g.,D-glyceraldehyde3-phosphate:NADoxidoreductase



•



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.

•

Structure and Function of Bio Molecules

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