Proteins Made of amino acids in a specific sequence attached by peptide bonds. Consist primarily of carbon, hydrogen, oxygen, and nitrogen, but may include a few other elements. Proteins can be enzymes or structural building blocks. Proteins can vary from organism to organism. They are what make you unique.

Amino Acids Amino acids ~ building blocks of proteins; contains an amino group (-NH2), a carboxyl group (-COOH), a central carbon, a Hydrogen, and an R group. The R group is unique for the different amino acids There are 20 different types of amino acids. A protein may contain as few as 50 or as many as several thousand amino acids. All proteins in all living things consist of these same 20 different amino acids, but the combination of the amino acids is unique for different living things.

Polypeptide Chain Peptide bond ~ a bond that links the carboxyl and the amino groups of two amino acids. Dehydration synthesis occurs in peptide bonding. Polypeptide chain ~ many amino acids joined together by peptide bonds, forming proteins.

Synthesis ~ process that forms a new substance Dehydration/Condensation and Hydrolysis Reactions (Making and Breaking Polymers) Monomers are linked together to form polymers through dehydration synthesis aka condensation reactions, which remove water Synthesis ~ process that forms a new substance Polymers are broken apart by hydrolysis, the addition of water

Unlinked monomer Short polymer Figure 3.3A_s1 Figure 3.3A_s1 Dehydration reaction building a polymer chain (step 1) 7

Dehydration reaction forms a new bond Figure 3.3A_s2 Unlinked monomer Short polymer Dehydration reaction forms a new bond Figure 3.3A_s2 Dehydration reaction building a polymer chain (step 2) Longer polymer 8

Figure 3.3B_s1 Figure 3.3B_s1 Hydrolysis breaking down a polymer (step 1) 9

Hydrolysis breaks a bond Figure 3.3B_s2 Hydrolysis breaks a bond Figure 3.3B_s2 Hydrolysis breaking down a polymer (step 2) 10

Protein Folding Four Levels of Protein Structure: 1. Primary structure ~ the sequence of amino acids in a single polypeptide chain. If even one amino acid is missing or out of place the protein will not function properly. 2. Secondary structure ~ the polypeptide chain forms either alpha helixes or beta pleated sheets. This is caused by hydrogen bonds that form at set intervals within the chain. Tertiary structure ~ the alpha helixes or beta pleated sheets fold. Due to interactions between the R groups Quaternary structure ~ Proteins that are composed of multiple polypeptide chains, called subunits. Denatured- when a protein unfolds. If a protein isn’t folded right it won’t function right. Extreme heat and change in pH are a couple things that can denature proteins.

Enzymatic Function of Proteins Enzyme ~ organic catalysts. They speed up a reaction but are not changed in the reaction. Most are proteins. Substrate- the compound the enzyme is affecting Active site ~ the area of the enzyme that combines with the substrate. The active site fits with the shape of the substrate like a lock and key. When the enzyme binds to the substrate it changes shape and weakens some of the chemical bonds in the substrate This lowers the activation energy which is the energy necessary to start a reaction, so it speeds up the reaction. Specific enzymes only work for specific substrates and specific reactions. Some enzymes in your body cause reactions to occur 1 million times faster. Cold temperatures don’t denature a protein but they do cause molecules to move around slower so the enzyme and the substrate are less likely to come in contact with each other.

Enzyme available with empty active site Figure 5.14_s1 1 Enzyme available with empty active site Active site Enzyme (sucrase) Figure 5.14_s1 The catalytic cycle of an enzyme (step 1) 16

Enzyme available with empty active site Figure 5.14_s2 1 Enzyme available with empty active site Active site Substrate (sucrose) 2 Substrate binds to enzyme with induced fit Enzyme (sucrase) Figure 5.14_s2 The catalytic cycle of an enzyme (step 2) 17

Enzyme available with empty active site Figure 5.14_s3 1 Enzyme available with empty active site Active site Substrate (sucrose) 2 Substrate binds to enzyme with induced fit Enzyme (sucrase) H2O Figure 5.14_s3 The catalytic cycle of an enzyme (step 3) 3 Substrate is converted to products 18

Enzyme available with empty active site Figure 5.14_s4 1 Enzyme available with empty active site Active site Substrate (sucrose) 2 Substrate binds to enzyme with induced fit Enzyme (sucrase) Glucose Fructose H2O Figure 5.14_s4 The catalytic cycle of an enzyme (step 4) 4 Products are released 3 Substrate is converted to products 19

Activation energy barrier Figure 5.13A Activation energy barrier Enzyme Activation energy barrier reduced by enzyme Reactant Reactant Energy Energy Figure 5.13A The effect of an enzyme in lowering EA Products Products Without enzyme With enzyme 20

Activation energy barrier Figure 5.13A_1 Activation energy barrier Reactant Energy Figure 5.13A_1 The effect of an enzyme in lowering EA (part 1) Products Without enzyme 21

Activation energy barrier reduced by enzyme Figure 5.13A_2 Enzyme Activation energy barrier reduced by enzyme Reactant Energy Figure 5.13A_2 The effect of an enzyme in lowering EA (part 2) Products With enzyme 22

Progress of the reaction Figure 5.13Q a b Energy Reactants c Figure 5.13Q Activation energy with and without an enzyme Products Progress of the reaction 23