IB Chemistry Option B Biochemistry

Introduction to Biochemistry The chemistry of living organisms is called biochemistry. Metabolism – the sum of all reactions happening in your body/cells. Respiration – energy that is made in cells through a complex series of oxidation reactions Bomb Calorimeter – special type of calorimeter used to measure heat of combustion of certain reactions – can also measure energy in food.

BOMB CALORIMETER Watch YouTube video

Calorimetry Energy content of food can be determined by calorimetry. The food is burned in a calorimeter, and the increase in temperature of surrounding water is measured: q = mcΔT q = heat (in joules) m = mass of water (in grams) C = specific heat of water (4.184 J g-1 ºC-1) ΔT = temperature change of water (in ºC)

Calorimetry Example: 1.13 g of rice raises the temperature of 525 g of water by 3.31ºC. Determine the energy content in kJ/g. Q = mcΔT = (525 g) (4.18 J g-1 ºC-1) (3.31ºC) = 7260 J = 7.26 kJ Energy content is 7.26 kJ / 1.13 g rice = 6.42 kJ per gram of rice

Calorimetry 1. A 0.78g sample of cheese is combusted in a bomb calorimeter. The temperature of 105.10g raised from 15.4 ºC to 30.6 ºC. Calculate the energy value of the cheese in kJ/g. Pay attention on the IB exam for units that the question is asking for. If the question asks for J/mol you must multiply your answer by the molar mass (g/mol) 8.56 kJ/g

Proteins Proteins are major groups of biological molecules Two Types Structural – fingernails, hair, tendons, muscles Act as tools – act as catalysts, enzymes, carrier molecules to transport oxygen, hormones

Examples

Proteins Proteins are polymers made up monomers – amino acids. They are made up of 2-amino acids. (this means that the amine group is on carbon number 2, while the carboxylic acid group is on carbon number 1)

Proteins Structure of 2-Amino Acids Carbon 2: contains amine group Carbon 1: carboxylic group Name comes from the fact that the amine Group is on C #2 Functional group – where one amino acid differs from the others

There are about 20 amino acids found in proteins. Each amino acid is assigned a three-letter abbreviation. Amino acids are listed in the IB data booklet Our bodies can synthesize about 10 amino acids. Essential amino acids are the other 10 amino acids, which have to be ingested (part of our diet). The -carbon (carbon 2) in all amino acids (except glycine is chiral) (has 4 different groups attached to it).

Examples of Amino Acids Ala Gly Arg

Amino Acids Amino acids: have very high melting points (above 200C) high solubility in water A zwitterion has both positive and negative charge in one molecule. The carboxyl group can behave like an acid and donate the H+ (forming COO-); the amine can behave like a base and accept an H+ (forming NH3+); if both occur at the same time, a zwitterion is formed Therefore it is amphoteric

Zwitterions

Amino Acids pH determines the net charge of the amino acid Positive charge = low pH Negative charge = high pH Isoelectric point – the intermediate point at which an amino acid is electrically neutral

Buffer Capability Amino acids are able to maintain a relatively constant pH despite the addition of small amounts of acid or base. This is very important b/c many proteins can be destroyed even in the slightest fluctuation of pH. Example – Blood has a pH of 7.4. Even a fluctuation of 0.5 can be fatal.

Polypeptides and Proteins Amino acids react together in a condensation reaction (water is eliminated) The new bond formed between amino acids is called a peptide bond and they form dipeptides Peptide Bond H2O Dipeptides will continue to react forming polypeptides

Examples 2. If cysteine has an isoelectric point of 5.1, what will the structure be when the pH is... 5.1 4.0 6.0 3. Draw a tripeptide with the following sequence: Cys-Val-Asn

Protein Structure Primary structure is the number and sequence of the amino acids in the polypeptide chain (protein). Example: NH2-leu-his-ala-…-ala-val-ser-COOH A change in one amino acid can alter the biochemical behavior of the protein.

Protein Structure Secondary structure is the regular arrangement of segments of protein. The polypeptide chain folds as a result of the hydrogen bonding between peptide groups. One common secondary structure is the -helix. Contains hydrogen-bonding parallel to helix The polypeptide chain folds as a result of the hydrogen bonding between peptide groups four amino acids apart. It is flexible and elastic b/c H bonds can break and reform as it is stretched Ex. keratin … = H bond

Another secondary structure is the β-pleated sheet. Contains H-bonding perpendicular to the sheet The helix or pleated sheet is held together by hydrogen bonds between N-H bonds and carbonyl groups. H bond β-pleated is flexible but INELASTIC. Found in spider webs.

Protein Structure Tertiary Structure is the overall shape of the protein. It refers to the twisting, folding, and coiling of the the polypeptide chain as a result of interactions between the R groups (side chains). The 3-d compact structure that results is know as the protein’s conformation. Conformation is important in globular proteins. (enzymes and hormones) They are water soluble b/c the polar R groups are on the outer surface where they can interact with water.

Forces Affecting Tertiary Structure: Ionic Bonding – between side chains that have a charge Hydrogen Bonding – between polar side chains Hydrophobic interactions – between non-polar side chains Covalent Bonds (disulfide bridges) – between sulfur in the amino acid cysteine – very strong (held together by INTRAmolecular forces) Proteins can be denatured – or lose their tertiary structure due to changes in pH or temperature. hydrophobic

Protein Structure Quaternary Structure – not very common This is the structure if a protein is made up of more than one polypeptide chain. Ex. Collagen – found in skin and tendons and Hemoglobin – carries oxygen in blood Held together by INTERmolecular forces (H-bonds, dipole-dipole, vdW) collagen hemoglobin

Analysis of Proteins – 2 ways 1. Chromatography solvents final position Amino acids will spread according to their different solubilities.

Analysis of Proteins – 2 ways Chromatography Paper is removed and sprayed with ninhydrin (a reagent that makes the amino acid turn purple since they are colorless) Each amino acid has a specific Rf value.

Analysis of Proteins 2. Gel Electrophoresis – Separate amino acids based on isoelectric point (ip) ip = isoelectric point = the pH at which positive and negative charges are balanced (no net charge on amino acid or polypeptide) Mixture of amino acids placed on gel (or paper) Gel (or paper) is saturated with a buffer of known pH. Electric Current is applied and amino acids move towards oppositely charged electrodes. UV light helps identify the position of the amino acids.

If pH = ip, amino acid does not move Electrophoresis If pH = ip, amino acid does not move If pH > ip, amino acid moves toward “+” Amino acid loses H+ in basic solution and becomes negative, moving toward anode. If pH < ip, amino acid moves toward “-” Amino acid gains H+ in acidic solution and becomes positive, moving toward cathode. The further the pH is from ip, the faster the amino acid will move. ****Note – Anode is + and Cathode is – Just like electrolytic cell!****

Electrophoresis

What if the buffer used has a pH of 7.0? Example – A mixture of 5 amino acids (shown below with pi values) is to be separated by electrophoresis. A buffer with a pH of 6.0 is used. What will happen when the current is turned on? Cys Gln Gly His Lys 5.1 5.7 6.0 7.6 9.7 What if the buffer used has a pH of 7.0? + -

Examples 4. Explain why in gel electrophoresis the amino acid isoleucine migrates towards the anode at high pH and the cathode at low pH. 5. You are attempting to separate a mixture of glutamic acid and histidine by gel electrophoresis. Give a suggested pH value for the buffer solution and say which way each acid will migrate.

Gel Electrophoresis Go to: http://learn.genetics.utah.edu/content/labs/ and click on gel electrophoresis. This will give you a general idea of how it works. On #6 on your sheet, draw the DNA sample sizes once you have completed the simulation.

Major Functions of Proteins Structure – fibrous proteins Muscle, cartilage, skin, bones, hair, nails Collagen (skin), keratin (hair) Enzymes – Catalyze specific chemical reactions in the body. Energy Source Protection –antibodies (immunoproteins) Control – hormones – ex. Insulin Transport - hemoglobin