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Lecture 2: Part II

Life (Its Building Blocks & Processes)* Lipids, Fats & Steroids

* Amino Acids & Proteins

Department of Chemical and

Environmental Engineering

H83BCE Biochemical Engineering

•Lipids, Fats & Steroids

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Lipid Properties• Non polar biological compounds, hence insoluble in water.

• Present in non-aqueous biological phases � plasma and organelle membranes

• Serve as polymeric biological fuel storage � When energy is needed, fat splitting enzymes are used. � Microbes use similar mechanisms for energy release as mammals.

• Also act as an important mediator in biological activity.

• Saturated fatty acids are relatively simple lipids:� The value of n is typically between 12 to 20

• Unsaturated fatty acid forms when a (– C – C – ) bond is replaced by (– C = C – )

� CH3 – (CH2)16 – COOH (stearic acid, saturated)� CH3 – (CH2)7 – HC = CH – (CH2)7 – COOH (oleic acid, unsaturated)

• The long chain is insoluble in water but the carbonyl group is very hydrophilic.

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• Fats and oils are esters formed by condensation of fatty acids with glycerols

• Phosphoglycerides are molecules where phosphoric acid replaces a fatty acid esterified to one end on the glycerols.� Phosphoglycerides also consists of hydrophilic and hydrophobic portions.

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Phospholipids • A flat, double-molecular layer structure may be formed

across a small hole in a sheet submerged in lipid (or phospholipid) solution.� Phospholipids are fat derivatives in which one fatty acid has been

replaced by a phosphate group and one of several nitrogen-containing molecules.

� Example: Phosphatidyl ethanolamine (also known as cephalin)

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Lipids and Their Interaction with Water

• Representation of lipids involved in the formation of biological membranes. • The head groups are hydrophilic

and prefer contact with water.

• Hydrophobic tails face each other.

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The Basis of Membrane Formation in Water

• As lipids are insoluble in water, they initially form a monolayer on the surface of water.

• As more lipids are added, micelles form, allowing • hydrophobic tails to interact with one

another and not water.

• As more lipids are added, bilayeredvesicles eventually form, • containing two layers of lipids and an

internal compartment of water.

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Biological Membranes

• The hydrophobicallyconnected bilayers form the basic structure of biological membranes.

• Biological plasma membranes typically contain appreciable concentrations of phospholipids and other lipids.

• The membrane walls show apparent molecular bilayer of thickness (70 Å).

http://kvhs.nbed.nb.ca/gallant/biology/cell_membrane.jpg

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Lipid Membranes• Lipid membranes have high passive electrical resistance and capacitance.

� Hence, they are impermeable to highly charged species.� The membrane, thus, allows the cell to contain a reservoir of charged nutrients and metabolic

intermediates.

• The membrane determines which material enters, is confined and leaves the catalytic reaction network housed in the cell.

• The membranes act as a barrier. � The bi-layer is semi-permeable. � Toxic materials tend to be hydrophilic,

• Repelled by the hydrophobic internal layer.

� Hormones are hydrophobic, • Pass straight through.

• The selection of ion permeabilities can be modified by the addition of various substances � Antibiotics and other cation-complexing molecules can increase passive ion transport

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Vitamins• Substance required in trace amounts for normal cell function.

• Essential vitamins

� The cell cannot survive if they are absent in the external media.� Vitamins A, C, D, E, K, and the B vitamins (thiamine, riboflavin, niacin, pantothenic acid,

biotin, vitamin B6, vitamin B12, and folate) � They all can be obtained from food, and vitamin D and vitamin K can be synthesised by

the body

• Vitamins A, D, E, and K are lipids (water insoluble)

• Vitamin C (ascorbic acid) is not (water soluble)

• Many microorganisms can synthesise a number of vitamins � Example: yeast provides ergosterol, which is converted by sunlight to vitamin D2

(calciferol).

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• Extremely potent controller of biological reaction rates.

• A subgroup of hormones are Steroids: � A class of lipids with the general structure

• The familiar steroid cholesterol occurs exclusively in membrane of animal tissues.

• Currently, microbes are used to carry transformations of steroids to yield more valuable products.

� E.g.: progesterone to cortisone

Hormones

•Amino Acids & Proteins

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Amino Acids• The monomeric building block of polypeptides and proteins are

the α-amino acids.

• Amino acids are optically active � possess at least one asymmetrical carbon. � Solutions of pure isomer rotates plane polarised light either to the right

(dextro- or d-) or left (levo- or l-).

• The acid (-COOH) and the base (-NH2) groups of the amino acids can ionise in aqueous solution.

C COOHH2N

H

R

C COOHH2N

H

R

CHOOC N2H

H

R

L - form D - form

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• Amino acids are positively charged (cation) at low pH and negatively charged (anion) at high pH.

• At intermediate pH value, amino acid acts as a dipolar (zwitterion) with no net charge.

• The R group differentiate the amino acids, R can be polar(hydrophilic) or non-polar (hydrophobic)

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• Simple proteins are formed by condensation reaction between amino groupfrom one amino acid and the carboxyl group of another, forming a peptidebond.

• Every amino acid links with the next via peptide bond.

• Polypeptides are short condensation of amino acids.

• As the length of the chain increases, the physicochemical characteristics will be dominated by the R group of the residue with comparison to the amino and carboxyl groups.

• Many hormones are polypeptides � E.g. insulin and growth hormone.

R1

OHNH

H

C

H

C

O

OH + NH

H

C

H R2

C

O-H2O

NH

H

C

H R1

C

O

N

H

C

H

R2

C

O

OH

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Folding a chain of amino acids

(a) a geometric representation of amino acid chain. Each

symbol represent a side chain (a chemical group that

extends from the individual amino acids that make up

the main chain

(b) favourable interactions between the individual amino

acid side chains dictate how the chain will fold into

specific shape

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• Larger chains are called proteins� 50-100 amino acid residues

• Simple proteins: � only amino acids are present

• Conjugated proteins: � have other organic or inorganic components � E.g. Haemoglobin, the oxygen-carrying molecule in the blood, has four

heme groups (organometallic complex containing iron).

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Proteins• Most abundant molecules within the cell,

• Typically 30 – 70% of the cell’s dry weight.• Molecular weights: 6000 – 1 million.

• Consists of (weight %): • C (50%), H (7%), O (23%), N (16%) and S(3%).

• Two configurations, fibrous and globular.

• A critical role of proteins is catalysis - enzymes.

• Enzymes determine the rate of chemical reactions occurring in the cell.

• Found dispersed in the cytoplasm or attached to membranes or larger assemblies.

• Other membrane-associated proteins, permeases

• Aid the transport of specific nutrients to the cell.

• Many single-celled organisms posses small, hairlike extensions, flagella, whose motion serves to propel the cell.

• The flagella are driven by contractile proteins.

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Protein Structure• Described in three levels (A

fourth level is considered if more than a single chain is present):

1. Primary • amino acid sequence joint by

peptide bond.

2. Secondary • manner of extension of chain

due to hydrogen bonds.

3. Tertiary • folding and bending of chain

due to hydrogen, salt and covalent disulfide bonds, as well as hydrophobic-hydrophilic interaction.

4. Quaternary • how different chains fit together

due to same forces.

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Proteins: Primary Structure• A sequence of amino acid residues.

• Every protein has not only a definite amino acid content but also a unique sequence.

� The sequence of amino acid residues in many proteins is now known and no repeating patterns of residues have been found.

• The various side chains of amino acid residues interact with each other, and with the immediate environment to determine the geometrical configuration of the protein.

� This structure is dictated by the amino acid sequence.

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Secondary Structure

• Two general structures: � Helices � Sheets

• Appears in hair, wool and other fibrous proteins.

• Due to: hydrogen bonding between atoms in closely neighbouring residues four units down the chain.

• If the H-bond occur between the –C=O group of one residue and the –NH group of its neighbour, the protein chain is then coiled (α-helix).

• Collagen contains three α-helices. � The most abundant protein in higher animals. � Rigid and stretch-resistant

• E.g. skin, ligaments, eye cornea and other parts of the body.

• The plate sheeted structure is stabilised by hydrogen bonds which exist between neighbouring parallel chains.

• Parallel sheets are flexible� However, they are very resistant to stretching.

Helix Protein

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Tertiary Structure• Contains sub-domains of helical and sheet regions.

• Weak interactions between R groups widely separated along the chain determine the folding to form the globular structure.

� Ionic effects, hydrogen bonds, hydrophobic interactions

� These interactions can be easily disrupted by changes in protein environment

• E.g.: Temperature, pH, physical forces.

• Many globular proteins have their hydrophobic residues concentrated in the molecule’s interior and relatively hydrophilic groups on the outside

� Oil-drop model

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• Also important are covalent bonds formed by eliminating two hydrogen atoms,

� Disulfide bond formed (cysteinyl residue)

• These bonds cross-link within a polypeptide chain and sometimes separate chains.

• These covalent bonds are more thermal resistant.

• Most of the forces holding the geometrical structure of proteins are weak and allow the protein to flex.

• The 3-D structure determines the activity and to work properly � E.g.: Lock and key model for enzyme specificity

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Disulfide bond

-2H

C = O

C = O

– NH – C – S – S – C – NH –– NH – C – S – H

C = O H – S – C – NH –

C = O

Enzyme: active site on surface

Substrate

Enzyme-substrate

complex

Free enzyme

+

End product

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Enzymes

• Only definite substrates are converted by a particular enzyme.

• Enzyme has a specific site which is a geometrical compliment of the substrate.� Only substrates with the proper complimentary shape can bind to the enzyme.

• Denaturation:� Structural change of protein when exposed to conditions sufficiently different from its

biological environment.� cannot perform its normal function.� Relatively small changes in temperature (or pH) may cause denaturation without

severing the covalent bond. � When the denatured protein is slowly cooled (or pH retained) to its natural value, a

reverse process (renaturation), with restoration of function, often occur.

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Quaternary Structure

• Proteins may exist in more than one chain (haemoglobin). � These chains fit together in the molecule to form

the quaternary structure.

• The forces stabilising quaternarystructure are the same as those in tertiary structure.