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UNIT 1: BIOCHEMISTRY Chapter 2: Chemistry of Life

I. Atoms, Ions, and Molecules (2.1)

A. Living things consist of atoms of different elements

1. An atom is the smallest basic unit of matter

2. An element is one type of atom

3. An atom has a nucleus and electrons

a. The nucleus has protons and neutrons b. Electrons are in energy levels outside the nucleus

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4. A compound is made of atoms of different elements bonded together

a. Water (H20)

b. Carbon dioxide (CO2) c. Many other carbon-based compounds in living things.

B. Ions form when atoms gain or lose electrons 1. An ion is an atom that has gained or lost one or more electrons a. Positive ions -lost electron(s) b. Negative ions -gain electron(s) 2. Ionic bonds form between oppositely charged ions

1. A covalent bond forms when atoms share a pair of electrons

a. Multiple covalent bonds

b. Diatomic molecules

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2. A molecule is two or more atoms held together by covalent bonds

II. Properties of Water A. Life depends on hydrogen bonds in water

1. Water is a polar molecule

a. Polar molecules have slightly charged regions

b. Nonpolar molecules do not have charged regions

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c. Hydrogen bonds form between slightly positive hydrogen atoms and slightly negative atoms.

2. Hydrogen bonds are responsible for three important properties of water.

a. High specific heat b. Cohesion- attraction between molecules of the same substance (because of hydrogen bonds, water is very cohesive)

c. Adhesion- attraction between different substances. Adhesion between water and other charged or polar substances very important force. (responsible for capillary action)

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B. Many compounds dissolve in water

1. A solution is formed when one substance dissolves in another

a. A solution is a homogeneous mixture

b. Solvents dissolve other substances c. Solutes dissolve in a solvent

2. “Like dissolves like”

a. Polar solvents dissolve polar solutes b. Nonpolar solvents dissolve nonpolar solutes c. Polar substances and nonpolar substances generally remain separate

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C. Some compounds form acids and bases 1. An acid releases a hydrogen ion when it dissolves in water a. High H+ concentration

b. pH less than 7

2. A base removes hydrogen ions from a solution a. low H+ concentration

b. pH greater than 7

3. A neutral solution has a pH of 7

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III. Carbon-Based Molecules (2.3) A. Carbon atoms have unique bonding properties 1. Carbon forms covalent bonds with up to four other atoms, including other carbon atoms.

2. Carbon-based molecules have three general types of structures

a. Straight chain

b. Branched chain

c. Ring

B. Many carbon based molecules are made of many small subunits bonded together

1. Monomers are the individual subunits 2. Polymers are made of many monomers

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B. Four main types of carbon-based molecules are found in living things.

1. Carbohydrates are made of carbon, hydrogen, and oxygen

a. Carbohydrates include sugars and starches b.Monosaccharides are simple sugars. Includes glucose, fructose, and galactose (monomers)

c. Disaccharide- simple sugar, 2 sugar units bonded together. Three types:

•  Sucrose = glucose + fructose •  Maltose = glucose + glucose •  Lactose = glucose + galactose

d. Dehydration Synthesis- is the process of joining two molecules (or compounds) together following the removal of water. • Example: forming disaccharides by joining together monosaccharides

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e. Hydrolysis- is a reaction involving the breaking of a bond in a molecule using water. (breaking molecules apart) • Example: breaking apart a disaccharide into two monosaccharides.

f. Polysaccharides- complex sugar, repeating units of glucose bonded together d. Carbohydrates can be

broken down to provide energy for cells e. Some carbohydrates are part of cell structure

g. Polysaccharide- Three types: • Cellulose - makes up plant cell walls • Starch or Amylose - plants store glucose in this form •  Glycogen -glucose is stored in a branched form and stored in the liver and muscle cells for quick energy.

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2. Lipids are nonpolar molecules that include fats, oils, waxes and steroids

a. Many contain carbon chains called fatty acids b. Subunits: Fatty Acids (long chains of

carbon bonded to hydrogen) and Glycerol.

c. Triglycerides- 3 fatty acids bonded to glycerol. They make up fats and oils and function to store chemical energy in plants and animals.

d. Lipids have several different functions 1. Broken down as a source of energy 2. Make up cell membranes 3. Used to make hormones

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e. Fats and oils have different types of fatty acids

1. Saturated fatty acids (in animal fats)

2. Unsaturated fatty acids (found in plants- in vegetable oil)

f. Phospholipids make up all cell membranes

1. Polar phosphate “head” 2. Nonpolar fatty acid “tails”

g. Lipoproteins are clusters of lipids and proteins that travel in blood plasma. They carry lipids to the cells in the body and make membranes and steroids.

1. Low Density lipoproteins (LDL)- lethal cholesterol, clogs arteries.

2. High Density lipoproteins (HDL) –healthy cholesterol, remove cholesterol from arteries and return it to the liver.

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3. Proteins are polymers of amino acid monomers

a. 20 different amino acids. The body produces 12 and the rest come from diet

b. Amino acids contain a hydrogen atom, amine group NH2, carboxyl group (COOH) and a R side chain

•  The R side chain is the variable portion in an amino acid

c. Amino acids are linked by peptide bonds

d. Proteins differ in the number and order of amino acids 1). Amino acids interact to give a protein its

shape 2). Incorrect amino acids change a proteins

structure and function

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e. Protein Structure

f. Dehydration synthesis reactions bond amino acids together forming proteins (polypeptides) g. Hydrolysis reactions break proteins (polypeptides) into individual amino acids

4. Nucleic acids are polymers of monomers called nucleotides

a.  Nucleotides are made of sugar, phosphate group, and a nitrogen base.

b.  Dehydration synthesis reactions make the backbone of DNA

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b. DNA stores genetic information c. RNA builds proteins

IV. Chemical Reactions (2.4) A. Bonds break and form during chemical reactions.

1. Reactants are changed during a chemical reaction

2. Products are made by a chemical reactions.

C6H12O6 + 6O2 6CO2 + 6H2O

reactants products

B. Bond energy is the amount of energy that breaks a bond

1. Energy is added To break bonds

2. Energy is released when bonds form

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C. A reaction is at equilibrium when reactants and products form at the same rate. CO2 + H2O H2CO3

D. Chemical reactions release or absorb energy

1. Activation energy is the amount of energy that needs to be absorbed to start a chemical reaction.

2. Exothermic reactions release more energy than they absorb.

a. Reactants have higher bond energy than products b. Excess energy is released by the reaction

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3. Endothermic reactions absorb more energy than they release.

a. Reactants have lower bond energy than products

a. Energy is absorbed by the reaction to make up the difference.

V. Enzymes (2.5) A. A catalysts lowers activation energy 1. Catalysts are substances that speed up chemical reactions a. Decrease activation energy b. Increase reaction rate

B. Enzymes allow chemical reactions to occur under tightly controlled conditions.

1. Enzymes are catalysts in living things

a. Enzymes are needed for almost all processes

b. Most enzymes are proteins

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C. Disruptions in homeostasis can prevent enzymes from functioning.

1. Enzymes function best in a small range of conditions 2. Changes in temperature and pH can break hydrogen bonds. 3. An enzyme’s function depends on its structure

D. An enzyme’s structure allows only certain reactants to bind to the enzyme

1. Substrates

2. Active Site

E. The lock-and-key model helps illustrate how enzymes function

1. Substrates brought together 2. bonds in substrates weakened