BIOCHEMISTRY AP BIOLOGY

I. Atoms in Organic Molecule Organic = molecules with carbon and found in living things Common Atoms = C, O, H, N Other Atoms = S, P

II. Importance of Carbon Valence number of 4 – forms four bonds Backbone of all organic molecules Functional groups attach to form specific properties

Four Valence electrons means four bonds…

Hydrocarbons Contain only carbon & hydrogen atoms

Carbon can form an endless diversity of carbon skeletons

Large Hydrocarbons: Are the main molecules in the gasoline we burn in our cars The hydrocarbons of fat molecules provide energy for our bodies

Shape of Organic Molecules Each type of organic molecule has a unique three-dimensional shape The shape determines its function in an organism

Functional Groups Groups of atoms that give properties to the compounds to which they attach

Phosphate group Used to transfer energy

III. Bonding Organic Molecules Covalent bonds are used to form the backbone of organic molecules Formed by dehydration synthesis (removal of water to make room for new bonds) Broken by hydrolysis (replacing the water as bonds are broken apart)

Giant Molecules - Polymers Large molecules are called polymers Polymers are built from smaller molecules called monomers Biologists call them macromolecules

Examples of Polymers Proteins Lipids Starch Nucleic Acids

Most Macromolecules are Polymers Polymers are made by stringing together many smaller molecules called monomers Nucleic Acid Monomer

Linking Monomers Cells link monomers in the process of dehydration synthesis (removing a molecule of water) Remove OH Remove H H2O Forms

Breaking Down Polymers Cells break down macromolecules by a process called hydrolysis (adding a molecule of water) Water added to split a double sugar

IV. Types of Organic Molecules Carbohydrates – energy formation – sugars and starches Lipids – storage and insulation – fats and oils Proteins – enzymes run all body reactions Nucleic acids – store genetic information – DNA and RNA

V. Carbohydrates

A. General Information Made of C, H, O Basic shape is a ring of carbons with –OH and –H groups attached to the carbons Isomers = same number of C, O, and H but arranged differently Grouped based on number of rings in molecule

B. Monosaccharides Mono = one - one ring Many isomers (glucose, alpha and beta; fructose; galactose) which react differently in the body Function – used in energy releasing reactions

Glucose – the most common monosaccharide

Isomers Glucose & fructose are isomers because they’re structures are different, but their chemical formulas are the same

In aqueous (watery) solutions, monosaccharides form ring structures

C. Dissacharides H2O + Formed from two monosaccharides Glycosidic bonds = covalent bonds in carbs formed by dehydration synthesis Found mostly in plants – common example is sucrose – used as a transport sugar + OH HO H2O

D. Polysaccharides Many rings (100’s) Purposes depend on way the rings are constructed Storage = starch in plants and glycogen in animals Structure = cellulose in plant cell walls and chitin in fungus cell walls or insect exoskeletons

Examples of Polysaccharides Glucose Monomer Starch Glycogen Cellulose

Starch Starch is an example of a polysaccharide in plants Plant cells store starch for energy Potatoes and grains are major sources of starch in the human diet

Glycogen Glycogen is an example of a polysaccharide in animals Animals store excess sugar in the form of glycogen Glycogen is similar in structure to starch

Cellulose Cellulose is the most abundant organic compound on Earth It forms cable-like fibrils in the tough walls that enclose plants It is a major component of wood It is also known as dietary fiber

Cellulose SUGARS

Dietary Cellulose Most animals cannot derive nutrition from fiber They have bacteria in their digestive tracts that can break down cellulose

Sugars in Water Simple sugars and double sugars dissolve readily in water WATER MOLECULE They are hydrophilic, or “water-loving” SUGAR MOLECULE

Lipids

VI. Lipids General Information Fats and oils are triglycerides. Constructed of a 3 carbon alcohol called glycerol and three long chains of hydrocarbons called fatty acids.

Lipid structure H H - C – O - fatty acid H - C – O - fatty acid Dehydration synthesis removed –OH and –H as bond forms H H - C – O - fatty acid H - C – O - fatty acid H - C – O - fatty acid H

Fats Dietary fat consists largely of the molecule triglyceride composed of glycerol and three fatty acid chains Fatty Acid Chain Glycerol Dehydration links the fatty acids to Glycerol

B. Functions of Triglycerides Storage of chemical energy Insulation Padding

C. Types of Fatty Acids Unsaturated fatty acids have less than the maximum number of hydrogens bonded to the carbons (a double bond between carbons) Saturated fatty acids have the maximum number of hydrogens bonded to the carbons (all single bonds between carbons)

Single Bonds in Carbon chain Double bond in carbon chain

Triglyceride Fatty Acid Chains Glycerol

Fats in Organisms Most animal fats have a high proportion of saturated fatty acids & exist as solids at room temperature (butter, margarine, shortening) Saturated fats stack and block arteries.

Fats in Organisms Most plant oils tend to be low in saturated fatty acids & exist as liquids at room temperature (oils)

D. Other types of Lipids Found in this group because they are insoluble in water. Phospholipids – a phosphate group replaces one fatty acid. Found in cell membranes. Terpenes = pigments such as chlorophyll Prostaglandins = chemical messengers Steroids = parts of hormones

Steroids The carbon skeleton of steroids is bent to form 4 fused rings Cholesterol Cholesterol is the “base steroid” from which your body produces other steroids Estrogen Testosterone Estrogen & testosterone are also steroids

Synthetic Anabolic Steroids They are variants of testosterone Some athletes use them to build up their muscles quickly They can pose serious health risks

Lipids Lipids are hydrophobic –”water fearing” Nonpolar bonds on hydrophobic fatty acids. Polar bonds on hydrophilic glycerol. This means that lipids do not dissolve in water. Includes fats, waxes, steroids, & oils FAT MOLECULE

VII. Protein H H2N – C – COOH R Building Blocks Composed of chains of amino acids H H2N – C – COOH R

2. Amino acids come in 20 types and only the R groups vary 2. Amino acids come in 20 types and only the R groups vary. R groups fall into three categories – nonpolar, polar, and ionized. 3. R groups interact and form bonds with one another.

Structure of Amino Acids Amino acids have a central carbon with 4 things boded to it: Amino group Carboxyl group Amino group -NH3 R group Carboxyl group –COOH Hydrogen -H Side group -R Side groups Serine-polar Leucine -nonpolar

Linking Amino Acids Cells link amino acids together to make proteins Carboxyl Side Group The process is called dehydration synthesis Dehydration Synthesis Peptide bonds form to hold the amino acids together Peptide Bond

Nonpolar (hydrophobic) Polar (hydrophilic) Charged (Negative/Positive)

B. How to build a protein 1. PRIMARY STRUCTURE Straight chain of amino acids or a polypeptide (A peptide bond is a dehydration synthesis bond between two amino acids)

B. How to build a protein 2. SECONDARY STRUCTURE - Chain forms helix or pleated sheet. (Motif = some parts are helix and some parts are sheet)

motif

B. How to build a protein 3. TERTIARY STRUCTURE – Helix forms three dimensional shape as R groups interact. Hydrophobic interactions

What holds the tertiary structure? Disulfide bridges Ionic bonds Hydrogen bonds between polar R groups Hydrophobic interactions

4. QUATERNARY STRUCTURE – not always present – two or more tertiary structures bond together, usually with a metal atom as the center

Types of Proteins Storage Structural Contractile Transport

Functions of Proteins Structural – support, tendons & ligaments Storage – egg whites store amino acids Transport – carry substances, hemoglobin Hormones – coordinate body, insulin Receptors – built into membranes Contractile – movement, muscle fibers Defensive – antibodies fight disease Enzymes – accelerate reactions, digest molecules

Denaturating Proteins Changes in temperature & pH can denature (unfold) a protein so it no longer works Cooking denatures protein in eggs Milk protein separates into curds & whey when it denatures

Denaturalization Proteins are denatured when their 3-D shape changes. An incorrect shape can not bond with other molecules correctly and the enzyme does not function. Denaturalization occurs by Temperature / heat pH changes Excessive salts

VIII. Nucleic Acids General notes Two basic types – DNA (long molecules which store all of our genetic information and never leave the nucleus) and RNA (short molecules that are copies of one gene of the DNA and used to direct protein synthesis) The organelle chromatin is composed of DNA wrapped around proteins to form a double helix.

B. Structure A nucleotide has three parts – a sugar (monosaccharide), a phosphate functional group, and a nitrogen base. Nitrogen bases are rings of carbon, nitrogen, and hydrogen. They come in five major types (A, T, C, G, and U).

Nucleic acids are polymers of nucleotides Nitrogenous base (A,G,C, or T) Phosphate group Thymine (T) Sugar (deoxyribose) Phosphate Base Sugar Nucleotide

Bases Each DNA nucleotide has one of the following bases: Adenine (A) Thymine (T) Cytosine (C) Adenine (A) Guanine (G) Thymine (T) Cytosine (C) Adenine (A) Guanine (G)

RNA – Ribonucleic Acid Ribose sugar has an extra –OH or hydroxyl group Nitrogenous base (A,G,C, or U) Ribose sugar has an extra –OH or hydroxyl group Uracil Phosphate group It has the base uracil (U) instead of thymine (T) Sugar (ribose)

C. Functions Storage of genetic instruction Using genetic instructions to create proteins.