BIOCHEM STUDY GUIDE BIOCHEM C785 Western University

BIOCHEM STUDY GUIDE BIOCHEM C785 1. Unit 2 Amino acids, peptide bonds, and protein structures 2. Amino Acids: The building blocks of proteins 3. Chemical elements, atoms and bonds—Optional Review a. Electrons-only subatomic particle involved in chemical reactions b. Energy- compacity to cause change (doing work) c. Covalent bonds- sharing a pair of valance electrons by two atoms ex: H—H d. Ionic bonds- chemical bond resulting from attraction of atoms of opposite charge (salt bridge) e. Hydrogen bonds- weak chemical bond formed when slightly + hydrogen atom and a polar covalent bond in one molecule is attracted to the slightly negative atom of a polar covalent bond in another molecule or in another region of the same molecule ex: H20 & NH3 (ammonia) 4. Amino Acid Structure and Chemical Properties a. Amino- tends to pick up a proton- giving it a positive charge ex: NH2 b. Carboxyl- group tends to have negative charge- because it tends to lose a proton ex: COOH c. Hydrophobic (nonpolar)- water hating i. makes hydrophobic interactions ii. Only has carbon and hydrogen ex: CH2, CH3 iii. Heat breaks hydrophobic interactions d. Hydrophilic (polar)- Water loving i. makes hydrogen bonds ii. In addition to C & H, R group has O, N, or S iii. Change in pH or adding salt can break hydrogen bonds, reducing agents break the disulfide bonds. e. Charged- positive (basic) or negative (acidic) i. Makes ionic bonds ii. Change in pH or adding of salt can break ionic bonds f. Disulfide bonds i. Strongest bond ii. A double bond btw two Sulphur atoms in cysteine side chains iii. What type of amino acids participate in disulfide bonds? Cysteine iv. Disrupted by reducing agents g. Zwitterions- a molecule or ion having separate positively and negatively charged groups. h. What is the basic structure of amino acid? i. Carboxyl group- tends to have a neg charge (COOH-) ii. Amino group- tends to pick up a proton- giving it a positive charge (NH2) iii. Carbon- alpha carbon, can form 4 covalent bonds iv. R- where amino acids differ from one another (side chair/variable) 5. Polypeptides and Functional Proteins a. Polypeptides- A single protein chain consisting of several amino acids bonded by peptide bonds b. Peptide bonds- amino acids are linked together by a specific type of bond called a peptide bond. 6. Levels of protein structure a. Dehydration- associated with water loss in the body b. Hydrolysis- chemical breakdown of a compound due to reaction with water c. Alpha helix- delicate coil held together by hydrogen bonds btw 4th amino acid ex: a-keratin, hair (chain twists) d. Beta sheet- 2 or more segments of polypeptide chains lying side/side ex: spider web, silk fibers parallel to one another e. Denaturation-Process of ruining the functional structure of a molecule. It will no longer be able to carry out its intended function. A process by which the native functional structure of a molecule has been disrupted f. What are the 4 level of protein structure? List distinguishing features of each i. Primary sequence of amino acids forming a protein or polypeptide chain, the most basic element of its structure (peptide bonds) ii. Secondary three-dimensional structure of sheets, helices, or other forms taken on by polypeptide chain, due to electrostatic attractions between neighboring resides (stabilized by hydrogen bonds) iii. Tertiary three-dimensional structure resulting from folding and covalent crosslinking of a protein (hydrogen bonds, ionic bonds-positive or negative charges, and disulfide bridges) iv. Quaternary overall protein structure consisting of two/more polypeptide chains aggregated into one functional macromolecule ex: hem + iron= hemoglobin, connective tissues (hydrophobic and hydrophilic interactions, & disulfide brid