Human Biochemistry  

These notes were written for the old IB syllabus (2009). The new IB syllabus for first examinations 2016 can be accessed by clicking the link below.

IB syllabus for first examinations 2016

Option C - Human biochemistry (HL)


The aim of this option is to give students an understanding of the chemistry of important molecules found in the human body and the need for a balanced and healthy diet. Although the role these molecules play in the body should be appreciated, the emphasis is placed on their chemistry, and students who have not followed a course in biology will not be at a disadvantage. Students will not be required to memorise complex structures but will be expected to recognize functional groups and types of bonding within molecules. Structures of some important biological molecules are given in the data booklet.

C.1 Diet

C.1.1: Describe what the human body requires for a healthy diet. Students should recognise the importance of a balanced diet, including minimum requirements and the need for essential minerals.

Food groups

Water: necessary for life, biochemical activities within the body

Food groups:

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

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

vegetable and fruit group -->vit A&C

bread and cereal group -->energy, vit, minerals, protein - Carbohydrates-source of calories (energy), glucose important in energy-producing cycles within cells.

Recommended daily allowance (RDA)

RDA-- -Proteins- enzymes to catalyse the body's chemical reactions, hormones, muscle, connective tissue

RDA- 56g -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  

more

 


C.1.2: Calculate the calorific value of a food from enthalpy of combustion data.

Energy from food

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 *for calculations, simply use deltaH = mc deltaT *divide the change in heat by the number of grams of food burned, and this will give the caloric value of the sample.  

 


C.1.3 Discuss the benefits and concerns of using genetically modified (GM) foods. Crops and animals can be modified to provide more food, be more resistant to disease and be more tolerant to heavy metals. Concerns include the release of genetically modified organisms into the environment where they could spread and compete with the naturally occurring varieties.

 

 

 

 

 


C.2 Proteins

C.2.1 State the basic structure of 2-amino acids. There are approximately 20 common 2-amino acids (a -amino acids) found in organism. 2 amino acids have the following formula. H2NCHRCOOH

Amino Acids:

There are 20 different 2-amino acids The structures are given in the data book. 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)  


C.2.2: Describe the condensation reaction of amino acids to form polypeptides.

Polypeptides:

Two amino acids join to form a dipeptide---the bond is called PEPTIDE BOND (in chemistry it is called an amide link) by a 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.

Amino acids join to form proteins which may be any length

 


C.2.3: Explain how proteins can be analysed by chromatography and electrophoresis. To use either of these techniques the peptide bonds in the proteins must first by hydrolysed to release individual amino acids. Include the use of Rf values in paper chromatography. Give isoelectric points, students should be able to determine a suitable pH to achieve good separation in electrophoresis.

 

CHROMATOGRAPHY:

 

ELECTROPHORESIS:

R-groups of amino acids have different isoelectric points, (i.e.where the charge on the amino acid is zero). Similarly sized molecules can be separated by using the charge on the individual amino acids.

Proteins are placed in a magnetic field- positive R-groups will be attracted to the negative pole of the magnet, while negative R-groups will tend to move towards the positive pole.

The position where the individual amino acids stop is indicative of their charge. This reveals the isoelectric point, and consequently the R-group of the amino acid.

pH can be used to separate proteins. They re placed in a pH gradient. Amino acids travel to where their net charge is zero. Given the position in which they stop, the amino acid can be identified.  

 


C.2.4: Describe and explain the primary, secondary, tertiary and quaternary structure of proteins.

PROTEIN STRUCTURE:

PRIMARY: amino acids arranged in linear order

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.

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.

QUATERNARY: more than one polypeptide chain join to form a protein--several folded chains joined by disulfide bonds (eg. hemoglobin)  

 


C.2.5: List the major functions of proteins in the body. These are structure, biological catalysts (enzymes) and energy sources.

Protein function

structure, eg collagen (fibrous proteins)

biological catalysts (eg. enzymes)

transport eg. hemoglobin

energy source  

 


C.3 Carbohydrates

C.3.1: Describe the structural features of monosaccharides. Monsaccharides contain a carbonyl group (C=O) and at least two -OH groups, and have the empirical formula CH2O.

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

 


C.3.2: Describe the straight-chain formula of glucose and the structural difference between a -glucose and b -glucose.

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

 


C.3.3: Describe the condensation of monosaccharides to form disaccharides and polysaccharides. Limit examples to disaccharides - lactose and sucrose; polysaccharides - starch

 

CONDENSATION/DEHYDRATION SYNTHESIS:

organic molecules join together by releasing water- a H is removed from one group, and an -OH group from another. A glycosidic bond is formed.

DISACCHARIDES-formed by two monosaccharides. eg. Lactose= glucose + galactose eg. Sucrose= glucose + fructose  

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 hydrolysed, stored in liver and muscles as a reserve of carbohydrates. (this is not needed)  

 


C.3.4: List the major functions of polysaccharides in the body. These are energy sources, energy reserves (eg. glycogen) and precursors for other biologically important molecules.

FUNCTIONS OF POLYSACCHARIDES:

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: Describe the composition of fats and oils.

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 (Propane 1,2,3-triol i.e.H2COH-HCOH-H2COH)- the latter loses the -H atoms (from the hydroxyl group) and the fatty acids lose -OH groups. 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, which links to an amine group of another molecule

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

 

 


C.4.2: Describe the difference in structure between saturated and unsaturated fats, and explain the difference in their melting points.

SATURATED/UNSATURATED 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 triglycerides) to have a lower boiling point-the double bond tends to keep the fat flat-linear----usually oils at room temp  

 


C.4.3: Calculate the number of C=C double bonds in an unsaturated fat using addition reactions. The number of C=C bonds can be determined from the number of moles of I2 which add to one mole of fat.

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.  

Calculating the iodine index


C.4.4: Describe the hydrolysis of fats to form soaps and the action of soaps.

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.  

 


C.4.5: List the major functions of fats in the body. These are energy sources, insulation and cell membranes.

FUNCTIONS: -Energy source (self-explanatory) -Insulation (ditto) -Cell membrane-made up of phospholipids  

 


C.5 Vitamins

C.5.1: Define the term vitamin.

Role in Metabolism:

Metabolism- all of an organism's biochemical reactions -In order for reactions to take place in the body, ctalysts 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: Deduce whether a vitamin is water or fat soluble from its structure.

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

 


C.5.3: Describe the structures and major functions of retinol (vitamin A), calciferol (vitamin D) and ascorbic acid (vitamin C). Vitamin A - required for the production of rhodopsin (light-sensitive material in the rods of the retina). Deficiency can cause night blindness and xerophthalmia. Vitamin D - required for the uptake of calcium from food. Deficiency can cause weak bones (rickets). Vitamin C - essential in the production of collagen : the protein of connective tissue. Deficiency can cause scrobutus (scurvy).

Vitamin Functions: (structures listed in data-booklet)

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 D (calciferol)--important in the production of a hormone involved in the metabolism of calcium. It is modified by the body (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 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)  

 


C.5.4: Describe the effects of food processing on the vitamin content of food. Most vitamins are unstable at higher temperatures so will be affected by prolonged cooking.

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

C.6.1: Outline the production and roles of hormones in the body. Hormones are chemical messengers produced in glands controlled by the pituitary gland, which in turn is controlled by the hypothalamus. Limit examples of production and roles to adrenalin, thyroxine, insulin and sex hormones.

 

Production/Roles:

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.

ADRENALIN: synthesized from amino acid Thyrosine :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.

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.

SEX HORMONES:

*Female :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 Progesterone (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: Testosterone-hormone secreted by the testes and the adrenal glands (above the kidneys). During puberty, the pituitary gland stimulates the release of a protein 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: Compare the structures of cholesterol and the sex hormones. Stress the common steroid backbone but the difference in functional groups (see the data booklet).

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.

CHOLESTEROL- most common steroid. An essential component of cell tissue and brain and nervous tissue. It has a chain of alkanes on one ring, and a -OH group on the last ring -Some steroids act as hormones, which send chemical messages to different parts of the body, these hormones are synthesized from cholesterol in the ovaries, testes, and other glands that produce them.

PROGESTERONE- Carbonyl group (ring=O) attached to a methyl group on the first ring, carbonyl group (ring=O) on the last ring

TESTOSTERONE- -OH group on the first, ring=O on the last -Differences- cholesterol is primarily hydrophobic, with only one carbonyl group, the sex hormones have carbonyl groups and hydroxyl groups which make the molecule partly hydrophilic on both ends.

 


C.6.3: Describe the mode of action of oral contraceptives.

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: Outline the use and abuse of steroids.

Steroid Use and Abuse:        

 


C.7 Enzymes

C.7.1: Outline the basic characteristics of enzymes. Include:enzymes are proteins, activity depends on tertiary and quaternary structure the specificity of enzyme action.

Characteristics of enzymes:

Most of the proteins in the organism are enzymes. They act as catalysts for biochemical reactions in the body. An enzyme's activity depends on its tertiary and quaternary structure- different enzymes catalyse different reactions depending on their structure because substrates bind to the enzyme's active site during the reaction. this active site is only present in tertiary and quaternary structures. The properties and positions of the R-groups exposed at the active site determine which substrates will bind to the enzyme. Some enzymes do not bind to substrates unless their active sites don't contain additional ions or molecules.

CO-FACTOR: a substance held to the protein by other bonds eg ions Ca2+

CO-ENZYMES: non protein organic molecules eg vitamins

DNA

 


C.7.2: Determine Vmax and the value of the Michaelis constant (Km) by graphical means.

Substrate concentration:

A single enzyme can process only a limited amount of substrate in a given time, when substrate concentration increases, reaction rate increases. When all the enzymes are bound to substrates, the rate depends on the enzymes' rate of processing the substrates. The reaction rate eventually reaches a maximum limit.

 


C.7.3: Describe the significance of Vmax and Km.

The Michaelis constant

Vmax and Michelis Constant (Km): Rate is expressed as the number of reactions catalyzed by a given enzyme molecule per unit time. In a graph of substrate concentration vs rate of reaction, the graph rises in a curved fashion, with a decreasing slope. Vmax is recognized as being the point in which the graph continues in a horizontal line, parallel to the x-axis.

The Km is the substrate concentration at which the reaction rate is 1/2 Vmax. this is a measure of how readily the enzyme-substrate binding occurs. when Km is low, the reaction proceeds at a rapid rate even at low substrate concentrations Km is recognized on a graph by finding the 1/2 Vmax rate on the y-axis and drawing a perpendicular down to the x-axis. The perpendicular will reveal the concentration at Km.

Link - Very thorough explanation of Michaelis Menten and its significance  

 


C.7.4: Describe the concept of the active site in enzyme structure.

Active Site:

It is a cluster of chemical groupings formed as a part of the enzyme's folding pattern. The properties of the R-gouprs exposed at th active site determine which substrates will bind. When enzymes and substrates combine, they change shape: the active site is a flexible pert of the enzyme, which increases the surface area between the substrate and enzyme.

 


C.7.5: Explain competitive inhibition and non-competitive inhibition.

Inhibition:

COMPETITIVE: compounds that are similar to the substrate, which compete with the substrate by binding to the active site. This decreases the reaction rate because the enzyme cannot bind to the substrate.

NON-COMPETITIVE:
- The inhibitor binds to a site other that the active site
- Does not change the active site
- Increases the actuation energy
- Does not effect Enzyme-Substrate binding  

 


C.7.6: State and explain the effects of heavy metal ions, extremes of temperature and pH changes on enzyme activity.

Effects on Enzyme Activity:

HEAVY METAL IONS: Calcium ions are the most commonly found in animals, accounting for 1.5-2% of human body mass of which 99% comes from bones and teeth
- Half a gram phosphorous is required for attaching each gram of calcium to the bones
- Magnesium, potassium and sodium ions are also present in biological systems as ions in the fluids in and arouns the cells present in trace amounts in the human body

Iron was the first trace metal ion found to be essential in the human diet. The first row transition metals such as Co, Cr, Cu, Mn and Zn are present in trace amounts in the human body. These are essential to many enzymes such as Zn (charge 2+) in carboxypeptidase; Zn is found in almost 100 enzymes and is also present in insulin. Co (3+) is found in vitamin B12 and iron is present in the hemoglobin molecule of red blood cells. Magnesium is a secondary element of bones and teeth as well as regulating intracellular chemical activity, helping to form protein and transmitting electrical signals from cell to cell. Mn is essential for healthy bones and Cr plays a key role in glucose metabolism. On the other hand, iron deficiency produces anemia and causes fatigue as cells are deprived of oxygen and Cu deficiency gives rise to bone disease. The need for trace amounts of some metal ions such as tin and arsenic has been established in animals such as rats but not yet in humans.

TEMPERATURE: when temp rises, molecules move faster, colliding harder and more often, therefore they are more likely to react than at lower temp. When the temp increase is too high (above 60\260C), the enzymes will be denatured permanently, and will no longer function-their 3-D structure will be destroyed. At low temp reactions proceed slowly, and at very low temperatures (below 0\260C) the enzymes are denatured. They normally function at body temperature 37ºC

pH-enzymes are electrically charged because R-groups may ionize when they dissolve in water. The pH therefore determines the changes in the enzyme. Enzymes will function only at given pH's depending on their electrical charge. Most enzymes function best at neutral pH's.  

 


C.7.7: Describe the uses of enzymes in biotechnology. Possible examples include proteases in biological detergents, glucose isomerase converting glucose to fructose and streptokinase in breaking down blood clots.

 

 


C.8 Nucleic acids

C.8.1: Describe the structure of nucleotides and their condensation polymers (nucleic acids). A nucleotide contains a phosphate group, a pentose sugar group and an organic base. Students should be able to recognise, but need not recall, the structures of the five nucleotide bases : adenine, cytosine, guanine, thymine and uracil.

 

 


C.8.2: Describe the double helical structure of DNA. Students should be able to describe the hydrogen bonding between specific pairs of nucleotide bases.

 

 

 


C.8.3: Outline the role of DNA as the repository of genetic information, including the triplet code.

 

 


C.8.4: Describe the principles and uses of DNA profiling. Include forensic uses and paternity cases.

 


C.9 Metal Ions in Biological Systems

C.9.1: Explain that different metal ions fulfill different roles in the body due to their different chemical properties. Emphasise differences in charge density, redox properties and complex ion formation.

Roles in the Body/Chemical Properties: -Sodium and Potassium are vital the the functioning of nerves and muscles. -Calcium is necessary for muscular activity -Calcium and phosphorus are needed for bone formation

 


C.9.2: Describe the importance of the difference in Na+ and K+ concentrations across the cell membrane. Explain active transport using the Na+/K+ pump as an example.

 

Ion Concentration Across Cell Membrane:

Active transport-moves substances either with or against their electrochemical gradients, and requires energy. A source of energy may be Na+ of H+ concentration on the two sides of the membrane Sodium/Potassium Pumps- it uses energy from ATP to transfer sodium ions out of the cell and potassium ions inside. This pump is responsible for the electrical potential across plasma membranes. In the membrane, 3 sodium ions are moved for every two potassium ions that move in. The cell becomes more negative compared with the outside. when the tendency of K+ leaving the cell balances its tendency to enter it, the membrane potential is reached. K+ movement ceases. This type of pump controls the water content of the cell. It also drives the transport of sugars and amino acids. This process controls: the ability of nerves to conduct electricity, kidneys to form urine, muscles to contract, absorption of food in digestive tract.  

 


C.9.3: Outline the importance of copper ions in electron transport and iron ions in oxygen carriers. Use cytochromes and haemoglobin as examples.

Copper Ions in Electron Transport:

The electron transport system accepts hydrogen atoms and passes their electrons from one member of the chain to the next. Cytochromes-electron carrier molecule consisting of a protein and a porphyrin ring, containing a copper ion   Iron Ions in Oxygen Carriers: -haemoglobin-respiratory pigment that carries oxygen in the blood -contain a heme group with an iron atom a its center. The iron atom binds to the oxygen. When O binds to Fe, the hemoglobin is oxygenated and appears bright red. Without the iron center, oxygen wouldn't bind to hemoglobin, and oxygen couldn't be carried through the blood stream and to the cells in the body.

 


Resources

 


Useful links

The Michaelis Menten graph and its significance  

 

 


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