option c - human biochemistry c.1 diet. c.1.1 requirements of a healthy human diet: water: necessary...

Option C - Human biochemistry

C.1 Diet

C.1.1 Requirements of a Healthy

Human Diet:

• Water: necessary for life, biochemical activities within the body

Food groups:

• 1) milk group-milk, cheese, yoghurt -->supplies calcium, protein, vit A&D

• 2) meat group-meat, fish, poultry, eggs, legumes, nuts --> iron, vit B,energy

• 3)vegetable and fruit group -->vit A&C

• 4)bread and cereal group -->energy, vit, minerals, protein

Carbohydrates

• source of calories (energy), glucose important in energy-producing cycles within cells. RDA

Proteins-

• enzymes to catalyze the body's chemical reactions, hormones, muscle, connective tissue

Fats (& oils)-

• concentrated source of energy RDA

Vitamins-

Minerals:

• Calcium- blood, cells, body fluids, bones (its absorption is enhanced by vit D) Magnesium- maintains the electric potential across nerve-and-muscle-cell membranes

• Phosphorus- bones & teeth• Iodine- essential for functioning of thyroid gland• Iron- hemoglobin, enzymes• Zinc- part of important enzymes in the body

Importance of a Balanced Diet:

• -deficiency in caloric assumption results in deficiency diseases, starvation, or death

• -overnutrition results in obesity, high blood pressure, diabetes, heart attacks

• -excess in saturated fat consumption leads to rise in blood cholesterol levels- strokes

• -deficiency in protein and minerals- anemia, edema, loss of pigment and hair, retarded growth

C.1.2 Calories and Enthalpy of Combustion:

• -calories are the energy content of food• -energy is stored in chem bonds that link atoms

and molecules. Energy is captured by the body during biochemical reactions involving the combustion of nutrients. This energy is used to drive life processes of cells.

• Proteins and Carbohydrates- 4kcal/g• Fat- 9kcal/g• Alcohol- 7kcal/g

C.2 Proteins

NH2 C

R1

CO

H

NH C

R2

COOH

H

NH2 C

R

COOH

H

amino acid

20 different types

Amino acid Polypeptide Protein

NH2 C

R1

COOH

H

NH2 C

R2

COOH

H

C.2.1 2-Amino Acids:

• -there are 20 different 2-amino acids

• -they contain an amine group (NH2) on the central carbon atom (a), a carboxyl group and different R-groups.

• -all amino acids are optically active (not needed, but good to know)

Amino Acid

StructureStructure

All amino acids have this general structure. All amino acids have an amino group, a carboxyl

group and a side chain.

C CN

H

H H O

O HR

The amino group is the nitrogen atom and the attached hydrogen atoms.

A carboxyl groupcontains these parts: a carbon atom, an oxygen atom and a hydroxyl group (O-H).R stands for a side chain that can contain

different combinations of carbon, hydrogen, oxygen, and nitrogen or sulfur.

C.2.2 POLYPEPTIDES: 

• -two amino acids join to form a dipeptide---the bond is called PEPTIDE BOND

• -condensation reaction: a hydroxyl group is lost from one of the amino acids' carboxyl group, while the other amino acid loses a H from its amine group. (again, a diagram would be good, but...)

• -amino acids join to form proteins

Dehydration Synthesis• Let’s see how amino acids combine to make

proteins.• Amino acids combine in the presence of an

enzyme during dehydration synthesis.

C CN

H

H H O

O HR

C CN

H

H H O

O HR

H2O

Dehydration Synthesis

• The compound produced from the dehydration synthesis of two amino acids is a dipeptide.

• Water is also produced during the reaction.

• The bond between the carbon atom and the nitrogen atom is a peptide bond.

• A polypeptide is a long chain of amino acids containing many peptide bonds.

• Proteins can contain two or more polypeptide chains.

C CN

H

H H O

R

C CN

H H O

O HRH2O Peptide Bond

C.2.4 PROTEIN STRUCTURE:-PRIMARY:

• amino acids arranged in linear order

• 20 different amino acids: many combinations

PROTEIN STRUCTURE: -SECONDARY:

• -alpha helix:coil of polypeptides, with hydrogen bonds between the amide hydrogen atom in one peptide and the carbonyl oxygen atom of another peptide, at a distance of three amino acids. Coil chains are held together by DISULFIDE BONDS between adjacent chains.

• -beta-pleated sheet: a folded sheet, stabilized by hydrogen bonds between the chains. There are NO disulfide bonds in this structure.

Alpha Helix

Secondary Structure- Sheet

Oxygen Nitrogen

R Group

Hydrogen

Carbon Carbonyl C

H Bond

PROTEIN STRUCTURE: TERTIARY-

• folded structure of chains of amino acids. 4 types of interactions

• 1) Ionic bonds between R+ and R-• 2) H-bonds between partial - and partial + R-

groups• 3) Disulfide bonds• 4) Hydrophobic interactions- non polar R-groups

tend to stay close together because repelled polar substances surrounding proteins.

PROTEIN STRUCTURE:QUATERNARY• : more than one polypeptide chain join to

form a protein--several folded chains joined by disulfide bonds (eg. hemoglobin)

Quaternary Structure

The classic example- hemoglobin 2-2

B/T- Figure 3.7 END OF PART 1

Disulfide Bonding

V/V/P- Figure 16.6

Protein Separations

Paper Chromatography

Electrophoresis

An Experiment…

• The solvent rises up the paper when the two touch.

• The spot on the filter paper contains four different amino acids.

• Watch what happens when the paper touches the solvent in the beaker…

Amino Acid Experiment

• Which amino acid is the most soluble in this solvent (1-4)?

– Number 1 is the most soluble. It remains dissolved in the solvent longer than the other amino acids and travels farther up the paper.

• Which amino acid adheres most tightly to the paper (1-4)?

– Number 4 sticks tightly to the paper and does not move as far as the other amino acids.

1

2

3

4

Gel Electrophoresis

• Movement of charged molecules in an electric field.

• Polyacrylamide gel provides a porous matrix– (PAGE – Polyacrylamide Gel Electrophoresis)

• Sample is stained to make it visible in the gel.• Sample placed in wells on the gel.• Electric field across gel separates molecules.

– Negatively charged molecules travel towards the positive terminal and vice-versa.

• Cheap, fast and easy!

1-D Gel electrophoresis

• Separation in only 1 dimension: size.

• Smaller molecules travel further through the gel – large ones get stuck earlier creating a separation.

1-D cont.

• DNA/RNA are stained with Ethidium Bromide which fluoresces under UV light.

• Protein stained with Coomassie Blue which is blue in visible light.

• Southern blots (DNA), Northern blots (RNA), Western blots (Protein).

• Proteins are treated with the denaturing detergent SDS (sodium dodecyl sulfate) which coats the protein with negative charges, hence SDS-PAGE.

 C.2.5 FUNCTIONS: 

• -structure, eg collagen (fibrous proteins)

• -biological catalysts (eg. enzymes)

• -transport eg. hemoglobin

• -energy source

Functional Classes of ProteinsFunctional Classes of Proteins

• Receptors- sense stimuli, e.g. in neurons

• Channels- control cell contents

• Transport- e.g. hemoglobin in blood

• Storage- e.g. ferritin in liver

• Enzyme- catalyze biochemical reactions

• Cell function- multi-protein machines

• Structural- collagen in skin

• Immune response- antibodies

Structural Classes of ProteinsStructural Classes of Proteins

2. Fibrous Proteins (fibrils, structural proteins)

One dominating secondary structure

Typically narrow, rod-like shape

Poor water solubility

Function in structural roles (e.g. cytoskeleton,

bone, skin)

Collagen: A Fibrous ProteinCollagen: A Fibrous Protein

V/V/P- Figures 6.17/18

Triple Helix

Gly-Pro-Pro Repeat

StabilizingInter-strand

H-bonds

Structural Classes of ProteinsStructural Classes of Proteins

3. Membrane Proteins (receptors, channels)

Inserted into (through) membranes

Multi-domain- membrane spanning,

cytoplasmic, and extra-cellular domains

Poor water solubility

Function in cell communication (e.g. cell

signaling, transport)

C.3 Carbohydrates

• Contain the elements Carbon Hydrogen & Oxygen

• There are 3 types:

Monosaccharides Disaccharides Polysaccharides

C.3.1 MONOSACCHARIDES:

• -all sugars that contain a single carbohydrate unit, with an empirical formula: CH2O

• -contain a carbolyl group (C=O), and at least two hydroxyl groups (-OH)

• -eg. -glucose, fructose, galactose

Monosacharides

• If n=3, triose (glyceraldehyde)

• If n=5, pentose (fructose, ribose)

• If n=6, hexose (glucose, galactose)

• Used for Energy and Building Blocks

C.3.2 GLUCOSE:

• -C6H12O6

• -a main source of energy• -contains six carbons with an aldehyde group (H-

C=O) on the first and hydroxyl groups on each of the remaining carbons

• -in water, the 2nd C and the 6th C form a bond, forming a cyclic structure

• -a-glucose: hydroxyl group on the sixth carbon is DOWN

• -b-glucose: it is UP

Isomerism

• They can exist as isomers:

& glucose OH

OH

Disaccharides

• Formed from two monosaccharides

• Joined by a glycosidic bond

• A condensation reaction:

– glucose + glucose maltose– glucose + galactose lactose– glucose + fructose sucrose

C 3.3 Condensation reaction

O

C C

C C

C

CO

C C

C C

C

C

OH OH

Condensation reaction

O

C C

C C

C

CO

C C

C C

C

C

OH OH

Condensation reaction

O

C C

C C

C

CO

C C

C C

C

C

O

H2O

Condensation reaction

O

C C

C C

C

CO

C C

C C

C

C

O

A disaccharide1,4 glycosidic bond

41

Polysaccharides

• Polymers formed from many monosaccharides

• Three important examples:– Starch– Glycogen– Cellulose

Starch

• Amylose

-glucose

1,4 glycosidic bonds

Spiral structure

• Amylopectin

-glucose

1,4 and some 1,6 glycosidic bonds

Branched structure

Glycogen

• Insoluble compact store of glucose in animals

-glucose units

• 1,4 and 1,6 glycosidic bonds

• Branched structure

Cellulose

• Structural polysaccharide in plants-glucose

• 1,4 glycosidic bonds

• H-bonds link adjacent chainsO

O

O

O

O

C.3.4 FUNCTIONS OF POLYSACCHARIDES:

• a number of monosaccharides joined together eg. Starch, a polymer of glucose, with formula (C6H10O5)n eg. Glycogen, same molecular formula--gives glucose when hydrolised, stored in liver and muscles as a reserve of carbohydrates. (this is not needed)

• -basic energy sources for living organisms• -GLYCOGEN- an energy reserve, (stored in

liver), can break down into glucose when it is needed

• -Precursors for other biologically important molecules---i.e. monosaccharides are used to make other molecules like glycerol and fatty acids and some amino acids.

• -Cellulose-structural material in plants (not in syllabus)

C.4 Fats

C.4.1 COMPOSITION OF FATS/OILS:

• -fatty acids: long chain of carbon and hydrogen atoms with a carbonyl group at the end (C=O)

• -TRIGLYCERIDES: molecules formed by the joining of three fatty acids to a molecule of glycerol by dehydration synthesis.

• -solid at room temperature-"fats"-and liquid at room temp- "oils"

• -PHOSPHOLIPIDS- similar to the above, but one or to of the fatty acids are replaced by a phosphate group,

• -ALL Fats are hydrophobic--contain a high proportion of C-H bonds, the carbonyl end of the molecule is hydrophilic

C.4.2 SATURATED/UNSATURATE

D FATS:• -SATURATED- fats with single bonds (no

double bonds, not even one), C atoms can hold no more H atoms than they already have

• -UNSATURATED- fats with at least one double bond

• -the double bond causes fats (eg triglyceerides) to have a lower boiling point-the double bond tends to keep the fat flat-linear----usually oils at room temp

CH3 CH2 CH2 CH2 CH2 CH2 CH2 C OH

O1245678 3

CH3 CH2 CH2 CH2 CH2 CH2 CH2 C OH

O1245678 3

3 - Octenoic Acid

3, 6 - Octadienoic Acid

Unsaturated Fatty Acids

CH3 CH2 CH2 CH2 CH2 CH2 CH2 C OH

O1245678 3

Octanoic Acid

Saturated Fatty Acids

C.4.3 FAT ADDITION REACTION:

• -The extent of unsaturation of a fat---tested by I2. By calculating the number of moles that react with a fat, the number of double bonds will be discovered. This is because the double bonds between C atoms are broken, and I bonds itself to the C. One I will bond to each former double-bond location--every molecule of I2 used indicates one double bond.Electrophillic addition R-C=C-R + I2 ---> R-I-C-C-I-R

• -When the reaction occurs, the iodine will become clear.

Number of iodine (g) absorbed by 100 g of oil.

Molecular weight and iodine number can calculate the number of double bonds. 1 g of fat adsorbed 1.5 g of iodine value 150.

Iodine Number

CH CH CH CH

Cl I

ICl

Iodine chloride

+ ICl KI KCl

I2

I2

Na2S2O3 Na2S4O6 NaI

+

+ 2 2+

+

Excess unreacted ICl

Iodine Value Determination

C.4.4. SOAP:

• -Soap is made by the hydrolysis of fats. NaOH is added as a source of alkali.

• -3 Na+ are required to saponify one fat molecule (generally a triglyceride). These will replace the glycerol, yielding three fatty acids with an Na+ tail.

Saponification - hydrolysis of ester under alkaline condition.

O

C R

O

O

C R

C R

O

H2C O

HC O

H2C O

NaOH

H

H

H

H2C O

HC O

H2C O

R C O Na++ 3 + 3

Saponification

C.4.5 FUNTIONS:

• -Energy source (self-explanatory)

• -Insulation (ditto)

• -Cell membrane-made up of phospholipids

Function of Lipids

• Formation of protective structures

• Metabolic reserve

• Structural component of cell organelles

• Hormones and signal compounds

• Vitamins

 C.5 Vitamins

C.5.1 Role in Metabolism:

• -Metabolism- all of an organism's biochemical reactions

• -In order for reactions to take place in the body, catalysts are needed-these are called enzymes (see section on enzymes for more info)

• -Enzymes do not work alone, and sometimes require the help of coenzymes in order to carry out their catalytic functions-->vitamins function as coenzymes (mainly water soluble vitamins)

C.5.2 Water/Fat Soluble:

• -WATER- coenzymes needed in metabolism. eg. Vitamin B and C. when in excess, they pass out the body in urine

• -FAT-other functions in body (not clear) eg. Vitamin A and D. These can be stored in fat tissue These vitamins can accumulate to toxic levels

Functions: (structures listed in data-booklet) 

Vitamin A (Retinol

• Vitamin A (Retinol)--at night, light shining on the eye strikes a receptor, rodopsin which sends an impulse to the brain. vit A is essential in the formation of rodopsin.

• Deficiency--night-blindness, xerophthalmia (tear glands cease to function)

Vitamin C

• Vitamin C (ascorbic acid)--essential in the formation of connective tissue-collagen. Works as a reducing agent to form one of the amino acids in the protein collagen

• Deficiency- scorbutus ("scurvy"-connective tissue breaks down, hemorrhage)

Vitamin D (calciferol) HO

CH2

HH

H3C

H3C CH3

CH3

CH3

• important in the production of a hormone involved in the metabolism of calcium.

• (2 -OH groups are added) and it functions as a hormone which causes the intestines to absorb calcium from food.

• Deficiency--rickets (weak bones, low blood calcium level)

Vitamin E O

R1

R2

HO

R3

CH3(CH2CH2CH2CH2)2CH2CH2CH2CH(CH3)2

CH3

C.5.4 Food Processing:

• -most vitamins are destroyed or altered during cooking, especially water soluble vitamins. (fat soluble vit are relatively stable)

• -vit B is destroyed during milling processes

C.6 Hormones

• -organic molecules secreted by one part of the organism but having an effect on another. They are controlled by the pituitary gland, which is controlled by the hypothalamus. Secreted by endocrine glands.

C.6.1 Production/Roles:

• -ADRENALIN synthesized from amino acid Tyrosine:when exercise is done, impulses are sent for adrenaline to be released into the blood stream. It causes blood to be sent into areas of more active circulation. Increase in volume of blood available. Increase in rate of heart beat, stimulated respiration. the breakdown of glycogen to glucose is stimulated-raises level of sugar in the blood stream.

C.6.1 Production/Roles:

• -THYROXINE:: iodated amino acid derivative, produced by the thyroid gland :stimulates growth and metabolism

• INSULIN: made up of 2 poypeptide chains held together by disulfide bonds. Made in the pancreas by the Islet of Langerhorn. : regulates cellular intake of glucose from the blood. It is secreted in response to a rise in blood sugar or amino acid concentration. It also inhibits the breakdown of glycogen in the liver.

Female Sex Hormones

• pituitary hormones (LH and FSH) are secreted at puberty, Estrogen: (produced by ovary) stimulates an increase in secretion of a hormone, which brings about the maturation of the follicle and the ovulation. stimulates the development of female features: breasts, subcuataneous fat, menstrual cycle Porgesterone (corpus luteum of ovary)- stimulate the endometrium (lining of the uterus) to thicken and to secrete a nourishing fluid-in preparaton for a fertilized egg.

Male Sex Hormones

• *Male: Testosterone-hormone secreted by the testes and the sdrenal glands (above the kidneys). During puberty, the pituitary gland stimulates the release of a potein ABP, which has high affinity for testosterone. :stimulates development of male features: deepening of voice, development of male musculature, growth of hair on the face and other parts of the body.

C.6.2 Steroids: (see structure in data booklet)

• -a type of lipid (hydrophobic)

• -Structure: consist of four contiguous carbon rings (the common backbone)

• -Different steroids have different functional groups attached to the backbone.

Sterols

Steroids• Based on a core structure

consisting of three 6-membered rings and one 5-membered ring, all fused together

• Cholesterol is the most common steroid in animals and precursor for all other steroids in animals

• Steroid hormones serve many functions– salt balance– metabolic function – sexual development

Cortisol Testosterone

Progesterone Estradiol

Cholic acid Deoxycholic acid

Steroid HormoneStructures

OH

CH3

CH3

cholesterol

OH

CH3

CH3

Cholesterol

•Key lipid found in cell membranes•Precursor to steroid hormones:

Sexual Developmentestradiol

testosterone

Metabolic Regulationglucocorticoids

Pregnancyprogesterone

DigestionBile Acids

C.6.3 Oral Contraceptive:

• C.6.3 Oral Contraceptive:• -the "pill" consists of estrogen and progesterone

hormones (synthetic). The excess of these hormones (at a given dosage) will prevent ovulation, thus avoiding pregnancy.

• -Negative feedback control--The increased levels of estrogen inhibit the levels of LH hormone released by the pituitary gland. The drop in LH and FSH levels stops the development of the endometrium lining-without it the egg cannot implant and therefore no pregnancy will occur.

C.6.4 Steroid Use and Abuse: