1. Option B Biochemistry Jeff Venables Northwestern High School

2. The chemistry of living organisms is called biochemistry. Biochemical molecules tend to be very large and difficult to synthesize. Living organisms are highly ordered. Therefore, living organisms have very low entropy. Most biologically important molecules are polymers, called biopolymers. Biopolymers fall into three classes: proteins, carbohydrates, and nucleic acids. Introduction to Biochemistry

3. 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 )  T = temperature change of water (in ºC) Calorimetry

4. Example: 1.13 g of rice raises the temperature of 525 g of water by 3.31ºC. Determine the energy content in kJ per 100 g of rice. Calorimetry Q = mC  T = (525 g) (4.184 J g -1 ºC -1 ) (3.31ºC) = 7260 kJ Energy content is 7260 kJ / 1.13 g rice = 6.42 kJ per gram of rice Multiply by 100 g to get 642 kJ per 100 g of rice.

5. Amino Acids Proteins are large molecules present in all cells. 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) There are two forms of an amino acid: one that is neutral (with -NH 2 and -COOH groups) and one that is zwitterionic (with -NH 3 + and -COO - groups). A zwitterion has both positive and negative charge in one molecule.Proteins

6. Structure of 2-Amino AcidsProteins Carbon 1: carboxyl group Carbon 2: contains amine group Functional group – where one amino acid differs from the others

8. There are about 20 amino acids found in most 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).

9. Polypeptides and Proteins Proteins are polyamides. When formed by amino acids, each amide group is called a peptide bond. Peptides are formed by condensation of the -COOH group of one amino acid and the NH group of another amino acid. Water is also produced in the reaction

10. The acid forming the peptide bond is named first. Example: if a dipeptide is formed from alanine and glycine so that the COOH group of glycine reacts with the NH group of alanine, then the dipeptide is called glycylalanine. Glycylalanine is abbreviated gly-ala. Polypeptides are formed with a large number of amino acids (usually result in proteins with molecular weights between 6000 and 50 million amu).

11. Protein Structure Primary structure is the sequence of the amino acids in the protein. Example: NH 2 -leu-his-ala-…-ala- val-ser-COOH A change in one amino acid can alter the biochemical behavior of the protein. Secondary structure is the regular arrangement of segments of protein. One common secondary structure is the  -helix. Contains hydrogen-bonding parallel to helix

12. Another 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.

13. Tertiary Structure is the overall shape of the protein. 1.Fibrous Proteins – provide strength for tissue (muscle, hair, cartilage) 2.Globular Proteins (sphere-shaped) Transport and store nutrients Catalyze reactions (enzymes) Fight invasion Participate in metabolism

14. Forces Affecting Tertiary Structure: Ionic Bonding Hydrogen Bonding Covalent Bonds (disulfide linkage) London Dispersion Forces Dipole-dipole Forces Denaturation – A change in the function of a protein as a result of a change in tertiary structure.

15. Quaternary Structure How multiple polypeptide chains are held together in large proteins containing more than one polypeptide molecule –Intermolecular forces (H-bonds, dipole- dipole, LDF)

16. Analysis of Proteins Paper Chromatography Hydrolysis of protein (6 M HCl, 110°C) Break peptide bonds, obtain amino acids Place sample spot on paper, set paper in solvent Spray ninhydrin to “develop” spots Amino acids separate based on polarity

17. Electrophoresis – Separate amino acids based on isoelectric point (pI) pI = isoelectric point = the pH at which positive and negative charges are balanced (no net charge on amino acid or polypeptide) –Depends on acid-base properties of “R” 1.Mixture of amino acids placed on gel (or paper) 2.Gel (or paper) is saturated with a buffer of known pH. 3.Electric Current is applied

18. If pH = pI, amino acid does not move If pH > pI, amino acid moves toward “+” –Amino acid loses H + in basic solution and becomes negative, moving toward anode. If pH < pI, amino acid moves toward “-” –Amino acid gains H + in acidic solution and becomes positive, moving toward cathode. The further the pH is from pI, the faster the amino acid will move.

19. 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? CysGlnGlyHisLys 5.15.76.07.69.7 What if the buffer used has a pH of 7.0? + -

20. Major Functions of Proteins 1.Structure – fibrous proteins Muscle, cartilage, skin, bones, hair, nails Collagen (skin), keratin (hair)Collagenkeratin 2.Enzymes – Catalyze specific chemical reactions in the body. 3.Movement and storage of energy and nutrients 4.Protection –antibodies 5.Control - hormones