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Option B: Biochemistry

IB Chemistry SL and HL
by

Natasha P

on 30 April 2013

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Transcript of Option B: Biochemistry

B2: Proteins B1: Energy B4: Lipids B5: Micronutrients and Macronutrients B6: Hormones Option B:
Biochemistry Somya Sha
Shona Joseph
Divya Sha
Devin Luka
Steven Matthew
George Matthew
Natasha Pereira B3: Carbohydrates The End What are
Lipids? Structure of triglycerides- fats and oils Structure of phospholipids A lipid composed of four fused rings
Cholesterol is an important steroid which is used in the body in the synthesis of many other steroids including sex hormones A range of biological molecules which are characterized by being hydrophobic or insoluble in water
Contain carbon, hydrogen, and oxygen
Most common lipids are fats and oils, steroids, and phospholipids Contain stored energy that can be released when they are broken down in the reactions of respiration in cells
This energy is stored in adipose tissue found in different parts of our body
Sex hormones and estrogen are made from lipids in the form of steroids
Cholesterol is another lipid that is important in plasma membrane structure
Atherosclerosis is a condition where blood flow is restricted due to low soluble excess lipids
Obesity is caused from a diet too rich in lipids which can cause diabetes and cancer
Essential fatty acids such as fish oil cannot be produced by the body Functions and negative effects of lipids These are esters formed by condensation reactions between glycerol and three fatty acids
The length of the hydrocarbon chain in the fatty acids cause different properties within fats and oilsThe number and position of carbons causes also cause different propertiesOils are unsaturated fatty acids that form triglycerides with weak intermolecular forcesLinoleic acid and linolenic acid are essential fatty acids that the body needsUnsaturated fatty acids can undergo addition reactionsThe iodine number is the number of grams of iodine which reacts with 100 grams of fatFats and oils are broken down in the gutThis involves hydrolysis reactions under the control of lipase enzymes Have only two fatty acids rather than three
The third fatty acid is replaces with a phosphate groupLecithin is a common phospholipidsPhospholipids usually have a polar head and two non-polar tails which results in a phospholipid bilayer Structure of Steroids Standard Level Nutrients are the components of food that provide growth, energy and replacement of body tissue.
Oxidizing macro-nutrients, fats, carbohydrates, and proteins produces carbon dioxide, water, and energy The chemical reactions in living organisms that convert the food we eat into energy and produces various materials that our body needs How do we obtain energy in the human body? What is metabolism? Foods Energy Storage Capacity Fats are used to store energy and make about 37 kJ/g of energy available, more energy than carbohydrates
Proteins make about 17 kJ/g
Carbohydrates are the main source of our energy - The amount of energy stored in food, its calorific value, can be found experimentally by completely burning different foods and using the energy released to raise the temperature of a specific mass of water while using an insulated food calorimeter What are
essential amino acids? What are proteins? What are Amino Acids? What is the isoelectric point? What are enantiomers? Secondary Structure What is an alpha helix? What is a complete protein? What are incomplete proteins? Amino Acids and pH Four ways in which parts of the amino acid chains interact to stabilize their tertiary shapes: Tertiary Structure What is the
beta-pleated sheet? - Proteins are polymeric substances made up of long molecules formed by sequences of smaller
nitrogen containing units called amino acids.
- They are natural polymers, made up of C, H, O, N, and S.
- Their primary use is to provide amino acids - Amino acids are molecules that contain both a carboxyl group (–COOH) and an amino group (–NH2).

- Amino acids are the building blocks of new proteins in the body.

- Amino acids are used to produce new proteins for growth and repair of body tissues also to make hormones, enzymes, and antibodies. - The proteins that are important to human life are made of 20 -amino acids.
- Out of these 20 amino acids, there are ten amino acids which our bodies cannot synthesize and cannot
store as they do fat
- These amino acids must be obtained through food consumption.
- These are called essential amino acids. - A protein that contains all ten of the amino acids we cannot make on our own and in a ratio similar to that which we need, is called a complete protein

- Examples of this are: milk, cheese, eggs and soybeans - Incomplete proteins include most plant proteins; wheat protein does not have lysine; rice protein does not contain lysine or threonine - Amino Acids have the ability to behave both as an acid and as a base in aqueous solution.

- A majority of the amino acids contain one basic and one acidic group both of which can ionize in an aqueous solution.

- At lower pH, the H+ added reacts with OH– present in the equilibrium and the forward reaction is favored to replace some of the OH– used up. Thus in an acidic solution, the NH2 group is protonated.

- At higher pH, the base added reacts with H3O+ present in the equilibrium and the forward reaction is favored to replace some of the H3O+ used up. Thus in an alkaline solution, the carboxylic acid group donates a proton and is converted to the carboxylate ion. - A specific pH exists for each amino acid when the above two ionizations are identical and the amino acid exists only as zwitterions or dipolar ions

- This is called the isoelectric point, pI, of the amino acid , where the pH at which the positive and negative charges are balanced

- So because of this the molecule has no net charge and it shows no net migration in an electric field. - Within the 2–amino acids, when R H, the 2–carbon atom is chiral, and the molecule is asymmetric and gives rise to two possible stereoisomers.

- These mirror images are called enantiomers

- So, because of that all amino acids, except glycine where R = H, can exist as a pair of enantiomers Primary Structure - The primary structure is simply the sequence of amino acid residues that form the protein.
- This is indicated by using three–letter codes for the amino acids.
- Each type of protein in a biological organism has its own unique primary sequence of amino acids. It is this sequence that gives the protein its ability to carry out its characteristic functions. - The secondary structure is the manner in which a polypeptide chain folds itself, due to intramolecular hydrogen bonding, in particular patterns that repeat themselves.

- This affects the arrangement in space of the polypeptide chain.

- Two features commonly found in a protein’s secondary structure are referred to as an –helix and a - pleated sheet. - In the alpha helix structure, the peptide chain resembles a right handed spiral staircase or coiled spring; this shape is called a helix.

- This can make the protein elastic or sponge–like in fibrous proteins such as hair and wool.

- The alpha helix maintains its shape through regular intramolecular hydrogen bonds. - In the beta-pleated sheet arrangement one, or more, different polypeptide chains are bound together by hydrogen bonds (intramolecular if just one chain, or intermolecular if more than one) to create an orderly alignment of protein chains

- In this alignment the direction of H–bonding is perpendicular to the sheet structure giving rise to a repeating, pleated pattern - This is the folding or curling due to the interaction between the sequence of amino acids that maintains the three dimensional shape of the protein.

- The amino acid secondary structure in the helical, pleated or random coil form arranges itself to form the unique twisted or folded three dimensional shape of the protein. Covalent bonding, for example disulfide bridges can form between different parts of the protein when the – SH functional groups of two cysteine groups link when oxidized under enzyme control

Hydrogen bonding between -NH2 and –COOH groups on the side chain.

Salt bridges (electrostatic attraction) between –N+H3 and –COO– groups.

The R group side chain affects the 3–D structure of the resulting proteins depending on whether it is nonpolar containing mostly C–H bonds and therefore hydrophobic or polar containing N–H and O–H bonds and therefore hydrophilic. Hydrophobic interactions occur when non–polar, hydrophobic side groups tend to clump together on the inside, forcing the protein chain into a tertiary shape with the polar parts of the molecule on the outside. Hydrophobic interactions involve the exclusion of water from the non-polar interior of the protein. Quaternary Structure Proteins that comprise more than one polypeptide chain
These are held together by noncovalent bonds
Consist of hydrophobic interaction, hydrogen bonding, and ionic bonds
When a quaternary structure consists of multiple polypeptide chains, each is called a subunit
Proteins can be denatured, which may cause them to lose their function because the protein’s shape may be essential for its function
Proteins can be denatured through heat, high ionizing radiation, strong acids, bases and concentrated salt solutions, and organic solvents and detergents Collagen is a triple helix of three polypeptide chains, with inter-chain hydorogen bonds between them












Haemoglobin is made up of four polypeptide chains Analysis of
Proteins Electrophores Chromatography A protein can be analyzed by first hydrolyzing the peptide bonds
Hydrolysis reaction, usually using acid, chemically separate the amino acids from each other by breaking the peptide bonds









After hydrolysis, separation of the resulting amino acid mixture into its components can then be achieved in two ways Paper chromatography is suitable for separating hydrophilic substances such as proteins
Amino acids take on color when they are treated with a locating reagent
At the origin, a sample of the amino acid mixture is spotted
The paper is then suspended in the chromatographic tank containing a small amount of solvent that will not exceed the sample spot
The solvent will then rise up the paper and over the sample spot due to capillary action
Amino acids in the spot will spread out according to their different solubilities
The solvent front is a position that should be marked where the solvent almost reaches the top of the paper
Amino acids that are most soluble in the solvent will travel the farthest in the direction of the solvent flow The paper is removed from the tank and is sprayed with ninhydrin, causing the amino acids to stain purple
The position of each amino acid can be expressed as a retention factor or Rf
Rf = distance moved by the amino acid/ distance moved by the solvent
Comparison of Rf values allows for identification of the components of a mixture A technique for the analysis and separation of a mixture based on the movement of charged particles in an electric field
Amino acids can be separated when placed in a buffered solution because they carry different charges depending on the pH
In gel electrophoresis, the medium is a gel that is usually made of polyacrylamide
The amino acid mixture is placed in wells in the center of the gel and an electric field is applied
Different amino acids will move at different rates toward the oppositely charged electrodes
Each amino acid has a different isoelectric point
Amino acids with a positive charge move to the cathode while amino acids with a negative charge move to the anode
After separation, the can be detected by a stain or made to fluoresce under UV light and identified from their position using data tables. Functions of Proteins Provide Structure and Strength
They act as biological catalysts, lowering the activation energy and speeding up the reaction
Hormones: Example - Insulin
Antibodies are used to provide immunity to diseases
Transport: Example- Haemoglobin in the blood transports oxygen from the lungs to the body’s cells
Can be used to provide energy in starvation conditions Composed of three elements:
- carbon
- hydrogen
- oxygen
Hydrogen and Oxygen are always in the same ratio as water 2:1
Can be expressed in the general formula Cx (H2O)y
Two main types of carbohydrates: simple sugars or monosaccharides and condensation of polymers or polysaccharides
The main energy source of our body and are vital to the synthesis of the cells
Most Carbohydrates are changed to glucose after digestion 1. Functions of Carbohydrates 2. Structure of Carbohydrates Examples 4. Digestion of Polysaccharides The monosaccharides are soluble in water and are used as the main substrate for respiration
Polysaccharides are insoluble, are used as the storage form of carbohydrates mostly in the form of glycogen
Human beings do not really use carbohydrates for structural materials but plants do in the form of cellulose Disaccharides Monosaccharides are the simplest form of carbohydrates
These sugar molecules all have two or more alcohol groups (-OH) and a carbonyl grup
Solubility in water is due to their large number of polar hydroxyl groups
All monosaccharides can be represented by the empirical formula: CH2O
Glucose and Fructose are isomers of one another Polysaccharides Monosaccharides Formed by linking two monosaccharides in a condensation reaction
The resulting bond between the monosaccharides in known as a glycosidic link.
Soluble molecules
Combing different monosaccharides produces different disaccharides Long chains of monosaccharide units held together by glycosidic bonds
Insoluble molecules Main storage carbohydrate in plants
Mixture of two separate polysaccharides: amylase and amylopectin Glycogen Starch •Main storage of carbohydrates in animals Cellulose Used as a structural material in cell walls
Forms cables known as microfibrils, which gives it its rigid structure Because they are insoluble, they must be broken down in their monosaccharide subunits in the reactions of digestion, which involves hydrolysis reactions
Human body produces enzymes to digest starch and glycogen but not for cellulose, so these substances will not be digested and will contribute to the majority of faeces
Cellulose and other substances that cannot be digested by the body are known as dietary fibre
These dietary fibre are good for our health. It prevents conditions such as constipation and diverticulosis, irritable bowel syndrome, obesity, crohn’s disease, and haemorrhoids II. Vitamins are organic micronutrients I. Nutrients are classified according to amounts recommended for daily intake III.Malnutrition is the result of deficiencies of imbalance in the diet a) Micronutrients b) Macronutrients i) These nutrients are needed in extremely small amounts.
ii) These substance allow the body to produce enzymes, hormones and other substances essential for health.
iii) They include the vitamins and trace minerals i) These nutrients are needed in extremely large amounts

ii) They provide energy in the body and build and maintain its structure.

iii) They include carbohydrates, proteins, lipids, and also large scale minerals. a) Vitamins are organic compounds, needed in small amounts for normal growth and metabolism, which are no synthesized in the body.

b) Vitamins vary in whether they are principally soluble in water or in fat. Differences in their structures determine solubility.

c) Water-Soluble Vitamins
i) They are transported directly in the blood and excess are filtered out by the kidneys.
ii) They have polar bonds and the ability to form hydrogen bonds with water.

d) Fat Soluble Vitamins
i) They are slower to be absorbed and excesses tend to be stored in fat tissues.
ii) They are non-polar molecules with long hydrocarbon chains or rings. b) Micronutrient deficiencies

i) Iodine is needed in the diet for the synthesis of the hormone thyroxin, which regulates the metabolic rate.
- A lack of iodine in the diet causes swelling of the thyroid gland, known as goiter.

ii) Vitamin A is needed in the diet fir healthy skin, good eyesight and protection against some damaging effects of toxin as is it an antioxidant.
- A deficiency in vitamin A causes xerophthalmia, a condition characterized by dry eyes and also night blindness.

iii) Iron deficiency is currently considered to be the most prevalent micronutrient deficiency in the world. Iron is a major part of hemoglobin, which is the pigment in red blood cells responsible for transporting oxygen around the body
- A deficiency in iron leads to a serious condition known as anemia. a) When people do not obtain a regular, balanced supply of the diverse nutrients needed in the diet, they suffer from malnutrition. c) Macronutrient deficiencies

i) Marasmus is a condition resulting from protein deficiency found mainly in infants in developing countries.
- It is characterized by failure to gain weight, followed by weight loss and emaciation.

ii) Kwashiorkor affects young children whose diets are high in starch and low in protein Functions:

- The endocrine system is a major method of communication within the body, which is based on chemical messengers known as hormones.
- Some hormones are proteins, amino acids, or even fatty acids.
- All hormones are produced in a gland known as the endocrine glands
- Hormones circulate the body in search of cells with receptors within in them known as target cells. Oral contraceptives:
- The oral contraceptive pill is the most effective from of contraception which prevents ovulation

- The pill contains a mixture of female hormones progesterone and estrogen which suppress hormones that normally trigger ovulation

- In effect, it simulates the hormonal conditions of pregnancy Uses and abuses of steroids:
- Female steroid hormones are used in medications prescribed to women at menopause to alleviate some of the unpleasant symptoms
- These hormones replace the ones secreted in the body prior to menopause
- Androgens are male steroid hormones which include testosterone
- Testosterone is known as a anabolic steroid because it promotes tissue growth it the treatment of disorders in the testes and breast cancer
- Anabolic steroids have been used by athletes because it promotes growth of muscles; however, these steroids cause major medical conditions due to systematic hormone imbalances Steroid-based hormones all have a common structure:

- The different side chains and functional groups they possess give them their different properties.

For example:

i) The female sex hormone differs only slightly from the male sex hormone testosterone by having a ketone group rather than an alcohol group.
ii) Estradiol contains 2 alcohol groups and has an aromatic ring. Higher Level The tertiary and quaternary structures of the enzyme determine if it will work or not. The enzymes are specific and will only work with specific chemicals because these structures allow for only certain shapes to enter the active site. Enzymes will work better at higher temperatures, but when the temperatures get too high, they will denature. When the pH is too high or too low the H+ ions and the OH- ions will prevent the enzyme from working by blocking the active site. Thus, enzymes operate at optimal temperatures and pH.


Enzymes are highly efficient. For example, the enzyme nitogenase is capable of synthesizing ammonia. The Haber process requires 200 to 1000 atm of pressure and operates at 500O C. Enzymes increase the rate of reaction by factors as much as 108 to 1020 The reaction rate based on the concentration of enzymes is first order. The reaction rate based on the substrate concentration is more hyperbolic.


where k1 is the rate of reaction for the first forward reaction, k2 is the rate of reaction for the first reverse reaction, and k3 is the rate of reaction for the second forward reaction. ( the rate of the second reverse reaction is so small it is negligible) Inhibitors are chemicals that attach to an enzyme and stop them from working. If an inhibitor bonds to the enzyme chemically, its effects are irreversible. If it bonds though weak interactions then they are reversible. As stated before, all enzymes have certain conditions that they function the best in. When the environmental conditions around the enzyme change deviate too much, the enzyme will not function fast enough or even denature. Biotechnology is the application of harnessing microorganisms or biological processes to produce desired substances. Fermentation, for example, alcoholic fermentation of yeast is used to produce alcoholic beverages and bread.

Genetic engineering has allowed us to use the DNA from ourselves and other organism to create enzymes and proteins we need outside of the body. Insulin can be created by injecting human DNA vectors into bacteria which will produce insulin. Labs in Japan have created lipolase by taking a section for DNA from certain funguses to produce the enzyme in higher yields. It can also be used to produce interferons, natural anti-virals. Enzymes Enzymes are basically biological catalysis. Like catalysts, they speed up reaction by providing an alternate reaction pathway that lowers the activation energy. Enzymes do not change the position of the equilibrium or the equilibrium constant. Rate = V max [ S]/Km+[ S] where V max is the maximum rate of reaction. [S] is the substrate concentration, and Km = [k1+k2]/k3. It can be proven that Km = Vmax/2. Competitive inhibitors: chemicals that bond to the active site and block the substrate form reaching the active site.

Noncompetitive inhibitors: chemicals that bond to the enzymes and cause it to change the shape of the active site preventing the proper substrate from fitting into the active site. When the pH drops too high or too low, the high concentration of ions around the enzyme permanently denature the enzymes sharply reducing the rate. The optimal ph for enzymes range; some work the best in basic solution, other in acidic, and many in neutral solutions. Temperature: at low temperatures, the enzyme rate will be very slow. It will increase with a higher temperature, but if the temperature is too high, the enzyme will start to denature. The optimal temperature for human enzymes is 37o C, about the same as our internal body temperature. DNA’s Role in Conferring Genetic Information DNA Profiling Nucleic Acids • Two main types of nucleic acid, DNA and RNA, which differ in some base pairs as well as the sugars that form their backbones

• The two types of sugars are ribose in RNA and Deoxyribose in DNA •The Nucleotides are split between the double ringed purines Adenine and Guanine and the single ringed pyrimidines cytosine, thyamine in DNA, and uracil in RNA

•The Nucleic Acid strand forms by catalyzed condensation reactions between the phosphate group one nucleotide and the hydroxyl group of the c3 carbon What are
nucleic acids? Polymer chain with repeating subunits: a phosphate group, a pentose sugar, and organic nitrogenous base. DNA
Structure DNA forms from nucleotides with the nitrogenous base adenine, thymine, cytosine, and guanine

Adenine forms hydrogen bonds with thymine and cytosine bonds with guanine

The structure is held stable by dipole-dipole hydrophobic intercations and van der Wall’s forces between base pairs

The polymer chains form a helical structure to minimize electrostatic repulsions between negatively charged phosphate groups on the backbone DNA uses the nucleotide sequence to store genetic information. The nucleotide series is converted into RNA that is responsible for forming proteins and acting as catalysts

The DNA in every organism is the same for all of the cells in that organism unless the DNA is altered or damaged by faulty copping or damage due to UV lights, X-Rays, or radiation

DNA contains information stored in codons, a series of three nucleotides, that are coded into proteins by a universal translation “language” Each individual has a different DNA fingerprint which can be used to help solve crimes with DNA evidence as well as in paternity cases

The process involves finding unique fragments of DNA and then organizing them to compare.

There are two methods of developing unique fragments from DNA
The first method involves using restriction enzymes to cut DNA ate points that have the same 4 to 8 base pairs. Because each person has slightly different DNA, this method produces DNA fragments unique to each person, but is not very sensitive.

The second method uses Variable number tandem repeats (VNTR) that consists of various repetitions of the same segment of code. The number differs among people and with a combination of server of these segments, making the DNa fragments both sensitive and unique to each individual.

Once these fragments are isolated, Gel electrophoresis is used. The DNA is placed at the top of an electrically conductive gel and a current is applied to move the fragments depending on their mass. Because the small pieces move faster than the larger ones, gel electrophoresis separates the strands by size, producing a fingerprint unique to each individual. What is respiration? Anaerobic Respiration Aerobic
Respiration Metal ions in biological systems • Cytochromes: part of the electron transport chat that generates ATP. Iron(II) and copper (I) undergo oxidation reactions to create iron(III) and copper(II) which produce electrons. The electrons react with H+ ions and allow them to bond with water and produce energy. The energy is used to bond a phosphate group to ADP and create ATP

• Hemoglobin: contains iron (II) molecules. The environment allows for oxygen and carbon dioxide to bond to the iron without oxidizing it. Respiration The conversion of the chemical energy in molecules like glucose and sometimes amino acids and fatty acids, into usable chemical energy

Two Types: Anaerobic without oxygen and aerobic with oxygen

Both start with glycolysis which splits glucose into the pyruvate molecules, each with three carbon atoms where NAD+ molecules and ATP are reduced •When there is not enough oxygen, aerobic respiration cannot occur and the pyruvate ion is reduced to lactic acid or ethanol

•The average oxidation number decreases from 0 to -2 in ethanol and increases to +4 in carbon dioxide •When Oxygen is present, aerobic respiration occurs and the pyruvate molecules are converted into carbon dioxide and water with the overall formula: 2CH3COCOO– + 2NADH + 4H+ + 6O2 6CO2 + 6H2O + 2NAD+ with an overall H° = – 2820 kJ mol-1 of glucose
•The average oxidation number of Carbon increases from 0 to 4
•This reaction, even in amino acids and fatty acids, produces large amounts of energy. • Transition metals ions are important in biological processes because they can form complex ions and exist in multiple oxidation states. The most common transition metals include iron, copper, and cobalt
• The metal acts as a Lewis acid and accepts protons from the nitrogen base, the electron pair donor.
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