CHEMISTRY

25 of the 92 natural elements are essential to life

4 of those 25 make up 96% of living matter they are Carbon (C), Oxygen (O), Hydrogen (H), Nitrogen (N)

Phosphorus (P), Sulfur (S), Calcium (Ca), Potassium (K) and a few others account for most of the remaining 4%

Energy levels- state of potential energy Electron shells- are where the electrons

are on the outside of the nucleus

Electron- negatively charged particle Proton- positively charged particle Neutron- neutral particle, no charge Elements- pure substances that consists

entirely of one type of atom Isotopes- an atom with extra neutrons Compound- is a combination of 2 or more

elements

Bonding Ionic Bond- are formed when 1 or more

electrons are transferred from 1 atom to another

Covalent Bond- formed when electrons are shared. There are 3 types single, double, and triple covalent bonds.

Hydrogen bond- Vander Waals

What bonds look like

Chemical bonding & equations

You can only have as many bonds as you have extra electrons in the outer most shield.

The making of bonds takes energy and the braking of bonds releases energy

6CO2 + 6H2O = C6H12O6 + 6O2 H

H-C=H H-C-H N=N H

Water Polarity (polar covalent) Cohesion- is the attraction between

molecules of the same substance Adhesion- the attraction between

molecules of different substances

Properties of water

Osmosis & diffusion

Osmosis is the movement of water from high concentration to low

Diffusion is the movement of any other substance besides water from an area of high concentration to low

Surface tension- is related to cohesion. It is a measure of how difficult it is to stretch or break the surface of a liquid.

Water has a greater surface tension than most other liquids.

A mol represents an exact number of objects -6.02x1023 which is called Avogardo’s number.

Molarity is the number of moles of solute per liter of solution. This is the unit most commonly used for aqueous solutions.

pH scale An acid is a substance that increases the

hydrogen ion (H+) concentration of a solution. A base is a substance that decreases the amount

of hydrogen ion concentration in a solution. pH= -log[H+] pH= -log10-7

The lower the pH number the more acid. The higher the pH number. the more basic.

Remember that each pH unit represents a tenfold difference in H+ and OH- concentration

Buffers are substances that minimize changes in the concentration of H+ and OH- in a solution

How pH works

Acid precipitation has lowered the pH of a lake to 4 what is the hydrogen ion concentration of the lake?

When writing pH it is always written as 10 –(H+) when talking about ion concentration

When

Organic Chemistry

Most organic compounds contain hydrogen and carbon atoms.

Everything depends on how the electrons are configured it determines the kinds and numbers of bonds an atom can form

Chemical reactions happen because of the movement of elections

Hydrocarbons are organic molecules consisting only of carbon and hydrogen (fossil fuels, fats, cell membranes)

Groups

Hydroxyl Group - have an OH bonded to a Carbon, these are called alcohols. Don’t get it confused with the hydroxide ion OH-

Carbonyl Group – this is a carbon atom double bonded to an oxygen. There are two group names Ketones (is when the carbonyl group is within) Aldehydes (when the carbonyl group is at the end)

Carboxyl Group- is a carbon double bonded to a O and single bonded to an OH (COOH). Carboxyic acid (organic acids)

Amino Group- has a nitrogen bonded to two hydrogen atoms. Name amines.

Sulfhydryl Group- consists of a sulfur bonded to a hydrogen.

Phosphate Group- has one phosphorus atom double bonded to one oxygen and then single bonded to 3 other oxygen atoms. 2 of those have a negative charge an one is bonded to a carbon.

Models

Isomers

Structural isomers Geometric isomers

Reactions and what happens

Dehydration Hydrolysis

ATP

ATP is energy The breaking of the bonds of one Phosphate group from another is what gives off energy

Macromolecules

4 major macromolecules: lipids (fats, oils), carbohydrates (breads, pastas), nucleic acids (DNA), protein (meats, nuts)

Lipids are hydrophobic and are a great place to store energy for long term

Carbohydrates short term energy Monomers- are short chains of molecules Polymers- are long molecules consisting

of many similar or identical building blocks of monomers

Condensation Reaction, dehydration reaction: are how monomers are connected covalently through a loss of water.

The cell must expend energy to carry out these dehydration reactions and to complete this process they need the help of enzymes.

Polymers are disassembled to monomers by hydrolysis ,which is the opposite of dehydration, bonds are broken with water

Carbohydrates

Monosaccharides-simple sugars. Glucose is the most common (C6H12O6)

Disaccharides- double sugars, consisting of two monosaccharides joined together most common is sucrose which is table sugar

Polysaccharides- polymers composed of many sugar building blocks, things like starch, cellulose, chitin. Major cellular fuel storage.

Fats They have a fatty acid tail which makes

them hydrophobic and a glycerol head that is hydrophilic.

Phospholipid are similar to fats but instead of having 3 glycerol’s they only have 2. Phospholipid bilayer

is what makes up the membrane of a cell.

Saturated vs. Unsaturated

Protein Proteins make up more than 50% of a cells

dry mass. Proteins make up enzymes Catalysts help to speed up chemical reactions Enzymes can be used over and over again. Proteins are made up of amino acids

-they help carry out chemical reactions, transport small molecules, regulate cell processes- transport things in and out of cells-helps fight disease

Polymers of amino acids (20) are called polypeptides

A protein consists of one or more polypeptides folded and coiled into specific conformations Enzymes are specific When amino acids arebonded together by the use of enzymes, a peptidebond is formed and a dehydration reaction occurs (loss of water)

Enzyme – substrate complex- is enzymes that have binding sites where reactants can be brought together to react. These sites reduce the energy needed for

reactions to occur The reactants (the things being put in the

complex) are called substrates

Levels of Protein Structure

Primary Structure- sequence of amino acids

Secondary Structure-folded or coiled amino acids, resulting from hydrogen bonds between amino acids α helix- coiled, formed by

hydrogen bonds between every 4th amino acid

β pleated sheet- folds, formed by interactions between two amino acid chains

Tertiary Structure- formed by interactions between side chains (R groups)

Quaternary Structure- over all structure resulting from the interactions

Nucleic Acids- contain hydrogen, oxygen, nitrogen, carbon, and phosphorus- they store and transmit hereditary or genetic information-there are 2 types RNA and DNA-Adenine (A), Thymine (T),

Cytosine (C), Guanine (G), and Uracil (U)

The polymers are called polynucleotides. The monmersof these are called nucleotidesand they consist of a base, sugar,and a phosphate

Nucleic Acids

Enzymes Active site- is where the substrate

(reactant) binds to Induced Fit- brings chemical groups of the

active site into positions that enhance their ability to catalyze the chemical reaction

An enzyme can catalyze both the forward and the reverse reactions

Enzymes can only speed up reactions that would occur any way

Heat speeds up reaction, but it denatures proteins and kills cells

Cofactors- are nonprotein helpers for catalytic activity. These can either be permanent residents, or they may bind loosely and reversibly along with the substrate.

Coenzyme- are organic cofactors Competitive inhibitors- they reduce the

productivity of enzymes by blocking substrates from entering active sites

Noncompetitive inhibitors- they do not directly compete with the substrate to bind to the enzyme at the active site. Instead they bind to another part of the enzyme and change the shape of the active site.

If the inhibitor attaches to the enzyme by covalent bond inhibition is usually irreversible

Allosteric regulation- is the term used to describe any case in which a protein’s function at one site is affected by the binding of a regulatory molecule to a separate site. It may result in either inhibition or stimulation of an enzyme’s activity

Energy

Catabolic Pathways - are pathways that breakdown complex molecules into simpler compounds (cellular respiration)

Anabolic Pathways (biosynthertic) – these consume energy to build complicated molecules from simpler ones

Pathways can have more than one starting molecule and/or product

Potential energy-is energy that matter possesses because of its location or structure

Kinetic Energy- is the energy associated with the relative motion of objects

Chemical energy-refers to the potential energy available for release in a chemical reaction

1st law of thermodynamics- energy can be transferred and transformed but it cannot be created or destroyed

2nd Law of Thermodynamics- energy transformed or transferred increases the entropy of the universe

Entropy is the measure of disorder and randomness of the universe

Spontaneous reactions are reactions that occur without the input of energy

Free energy – measures the portion of a system’s energy that can perform work when temperature and pressure are uniform throughout the system as in a living cell

Enthalpy-is total energy Spontaneous reactionsalways have a –G (H decrease or TS increase) Systems tend to change to a more stable state untilthey reach equilibrium

Free Energy Reaction

Endergonic reaction –energy is put in to make the reaction occur. Stores energy in the molecules

Exergonic- energy is released at the end of the reaction. These are spontaneous reaction.

Activation Energy- the energy need to be reached before a reaction can occur

The key of metabolic reaction not reaching equilibrium is that the product of one reaction does not accumulate but becomes the reactant in the next step

AB + CD = AC + BD

A-BC-D

A-BC-DTransition State

A-CB-DProducts

Energy Coupling- is a key feature in how cells manage their energy resources to do work and use the exergonic process to drive an endergonic one.

ATP is responsible for mediating most energy coupling in cells and in most cases it acts as the immediate source of energy.

The release of energy during the hydrolysis of ATP comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves

ATP releases so much energy because of how the phosphate groups are bonded together because of the negative charge on the oxygen