Biological Chemistry

Macromolecules Large organic molecules Basic Structure POLYMERIZATION!

Macromolecules Carbohydrates Lipids Proteins Nucleic Acids

Proteins

Proteins Chains of amino acids Basic structure below: Basic amino acid structure shown above Alpha-carbon 5

Proteins Amino acid in solution Structure shown: aldosterone 6

Proteins 20 amino acids Differ only in their side chains, R. Structure shown: aldosterone 7

Condensation!

Proteins: Primary Structure Order of amino acids Protein made depends on Kind: which amino acids are present? Amount: how many amino acids? Sequence: what’s the order they are arranged? Amino acid sequence 9

Proteins: Secondary Structure Folding & coiling form pleated sheets and helixes Stabilized by hydrogen bonds Sequence of amino acids are linked by hydrogen bonds 10

Proteins: Tertiary Structure Long coils fold among themselves Occurs when certain attractions are present between alpha helices and pleated sheets Disulfide bonds Hydrogen bonds 12

Proteins: Quaternary Structure separate amino acid chains fit together to make the final structure of a protein i.e., hemoglobin has 4! Protein consisting of more than one amino acid chain 13

Overview Conformation, or shape, of protein is basically the 2˚, 3˚, & 4˚ structure Sequence controls 2˚, 3˚, & 4˚ structure. Therefore, primary structure controls conformation.

Proteins: What do they do? Structural: collagen, elastin Oxygen-carriers: hemoglobin, myoglobin Forms parts of cell membranes: channels, receptors Allow muscle contraction Enzymes 15

Proteins: Enzymes Protein catalysts that speed up important biological chemical reactions All reactions require a certain activation energy (Ea) in order to happen. In many reactions, few reactant molecules possess enough energy to react, so only those that do possess enough energy react. The result is a very slow reaction rate. HOWEVER, catalysts lower the activation energy that is required and makes the reaction much faster. 16

Proteins: Enzymes How do they work? substrates Each enzyme (protein) has a very specific shape, due to primary  quaternary structure. The total confirmation (shape) of some enzymes is spherical or globular. Only a certain part of the enzyme molecule acts as the catalyst (active site). The reactants (now called substrates) are held by the enzyme so they can react easily. The only substrates held are those that fit the active site. 17

Proteins: Enzymes How does environment affect its activity? Things to consider: Temperature pH 19

Proteins: Enzymes How does environment affect its activity? If the enzyme does not have exactly the right conformation (shape), it can’t hold the substrate and won’t work. If the conformation changes at any structural level, the protein breaks down and the enzyme becomes denatured (inactive). 20

Pepsin: works in stomach, where pH is very low, very acidic, so this environment is good -- digests other proteins Trypsin: works in intestine at higher pH

Prosthetic group=bound covalently Coenzyme= bound by hydrogen or ionic

allosteric site:  a site on a multi-subunit enzyme that is not the substrate binding site but that when reversibly bound by an effector (inhibitor) induces a conformational change in the enzyme, altering its catalytic properties.

Nucleic Acids

Nucleic Acids DNA: deoxyribonucleic acid RNA: ribonucleic acid ATP: adenosine triphosphate 25

Nucleic Acids Monomers are called nucleotides Each nucleotide has 3 parts nitrogen-containing base monosaccharide ribose phosphate Nitrogen-containing bases are either Adenine, Guanine, Thymine, & Cytosine. C & T are categorized as pyrimidines (single ring) G & A are categorized as purines (double ring) FYI… nitrogenous base shown is adenine 26

Nucleic Acids Five kinds of bases Adenine Guanine Thymine (in DNA only) Cytosine Uracil (in RNA only) 27

U Base-pairing rules; slightly different in DNA & RNA since there is no thymine in RNA, adenine will form a bond with uracil Notice that there is a pyrimidine matched with a purine!

Nucleic Acids Carbon-4 is missing the oxygen in deoxyribose. (de-= without, oxy-= oxygen… DUH!) 30

DNA & RNA form the genetic material of an organism

ATP carries energy and provides to help many reactions in the cell