What’s the Matter?

• Matter: all things the have atoms and take up space

• Matter is made up of atoms• Atom: the smallest particle of an element that

has characteristics of that element

Atomic Structure

• Nucleus- the center of an atom, contains protons and neutrons

• Proton- positively charged particle• Neutron- particle with no charge

(neutral)• Circling around the nucleus are

electrons• Electrons- negatively charged particles• Protons and electrons attract since

they have opposite charges

Elements

• Everything is made of chemicals called elements

• Elements are substances that cannot be broken down into simpler chemicals

• Only about 25 elements are essential to life

Elements• Carbon, hydrogen, oxygen, and nitrogen make

up 96% of the mass of a human body• Other elements like copper and iron play an

important role in cells

• ?- Sodium’s atomic number is 11 and its atomic mass is 22.99. How many neutrons does it have? How many electrons?

Isotopes

• Atoms of the same element have the number of protons/electrons, but can have different numbers of neutrons

• Isotope- atoms of the same element, but with different numbers of neutrons

• Radioactive isotope- the nuclei of these atoms break down over time releasing radiation

• The release of radiation can be used to determine the age of rocks and fossils, and kill cancer cells

Compounds

• In nature, most elements are combined with other elements to be more stable

• Compound- a substance with atoms from two or more different elements

• Ex: water H20

Bonding

• Physical properties of elements change when they are in compounds

• Ionic bond- when one atom gives an electron and the other atom looses an electron to bond together to become more stable

• Ion- a charged particle due to loosing or gaining an electron• Electron shells- all atoms have various levels of electrons,

each wanting 8 electrons in their outer shells = octet of electrons

• Covalent bond- formed between two atoms that share electrons to become more stable

Ionic Bonding

Covalent Bonding

Chemical Reactions

• Chemical reactions occur whenever chemical bonds are broken or formed

• Substances that undergo chemical reactions are called reactants

• Substances created from chemical reactions are called products

• Atoms cannot be created or destroyed, but rather they are transformed into different chemicals

Water• Water is one of the most important

compounds to life• It has unique properties to it due to polarity• Polarity- when atoms in covalent

compounds do not share electrons• This creates a polar bond with a negative

and positive end due to where the electrons are

• Polarity in water causes a few unique properties

Water

• Water is called the universal solvent because it can dissolve many other compounds

• Water molecules attract other water molecules, called adhesion

• Water molecules attract to other surfaces, called cohesion

Water• Water resists changing temperature, requiring

energy to be used to heat it• Water expands when it freezes• Water forms hydrogen bonds (from the polar

+ and – end) between each other, causing cohesion

Mixtures

• Mixture: a substance composed of two or more elements that are physically mixed, but not chemically combined allowing each element to keep its properties

• Solution: a mixture in which the substances, called solutes, are evenly mixed into a liquid called a solvent

• Suspension: a mixture in which the substances are suspended in liquid

pH

• pH: the measure of how many H+ and OH- ions are formed when a substance mixes with water

• Acid- substance with lots of H+ and few OH-, 0-6.9• Base- substance with lots of OH-, and few H+, 7.1-14• Neutral- substance with equal H+ and OH-, 7.0• Buffer- a weak acid or base that reacts with a strong

acid or base to prevent sudden, sharp changes in pH

http://www.epa.gov/acidrain/education/site_students/images/phscale.gif

Biochemistry• Organic Chemistry- the study of all compounds

containing carbon• Biochemistry- the study of proteins, lipids,

nucleic acids, and carbohydrates in the body• Carbon has 4 electrons to go through bonding

Carbon

• Two carbon atoms can form covalent bonds with single, double, or triple bonds

• When carbon atoms bond, they can form chains or rings

• Carbon combines with hydrogen, oxygen, phosphorous, sulfur, and nitrogen in the body

Building Blocks

• Monomer- a small building block used to build larger molecules, linked by covalent bonds

• Polymer- molecules formed by linking two or more monomers, also called macromolecule

• Monomers link by polymerization to form polymers

• 4 types of macromolecules: carbohydrates, lipids, nucleic acids, and proteins

Carbohydrates

• Carbohydrate- a macromolecule made of carbon, hydrogen, and oxygen with 2 H and 1 O attached to each carbon

• Carbs are the main energy source for living things

Carbohydrates• Monosaccharide- the simplest type of carb, like glucose,

fructose, and galactose, made of one monomer• Disaccharide- made of two monosaccharides, like lactose• Polysaccharides- complex carbs made of several

monosaccharides– Starch- made of glucose monomers, energy storage for plants– Glycogen- made of branched glucose monomers, energy

storage for animals– Cellulose- made of linear chains of glucose, provides support

for plant cell walls, “fiber”

Lipids• Macromolecules made of carbon, hydrogen,

oxygen, and sometimes phosphorous• They are insoluble in water because their

molecules are nonpolar and repel water (hydrophobic)

• Monomers are glycerol and fatty acid chains

Lipids

• Fat- long term energy storage, saturated fat (many H’s) and unsaturated (less H’s)

• Wax- waterproof coverings on feathers, cuticles, and plants

• Phospholipid- makes up the cell membrane, contains phosphate

• Steroids- hormones – chemicals produced in one area of the body to control functions in another part of the body

Lipids

• Dehydration synthesis to make a lipid• The glycerol and fatty acids come together,

water is formed and taken out to form a bond

Nucleic Acids• Macromolecules made of monomers called

nucleotides• Three parts to a nucleotide– 1. 5 carbon sugar: deoxyribe in DNA and ribose in

RNA– Nitrogenous base- adenine, thymine, guanine,

cytosine, uracil (RNA only)– Phosphate group

Nucleic Acids• Nucleotide monomers join by dehydration

synthesis combining the sugar of one to the phosphate group of another. These bonds are called phosphodiester bonds

Nucleic Acids• Hydrogen bonds form between the bases• This bonding allows for a spiral stair case

shape to form

Nucleic Acids

• DNA- forms a double stranded helix– Contains instructions to control cell’s activities and

heredity inside the cell’s nucleus– Sugar= deoxyribose Bases= A, T, C, G

• RNA– Forms a single stranded helix– Carries instructions from DNA to make proteins

and moves between the nucleus and cytoplasm– Sugar= ribose Bases= A, U, C, G

Proteins• Macromolecules made of carbon, hydrogen, oxygen,

nitrogen, and sulfur• Monomers are amino acids– Amine group NH2, carboxyl group COOH– Hydrogen, and “R” group which differs with each amino

acid– All these are attached to an “alpha” carbon

Proteins

• There are about 20 amino acids that form thousands of different proteins

• Amino acids link together by forming peptide bonds, a form of covalent bond through dehydration synthesis

• The specific sequence of amino acids determine what type of protein it forms

• If the temperature is too high or pH not neutral, proteins can denature or unravel and become useless

Proteins

Chemical Reactions

• Living things are made of chemicals• All growth, movement, and life functions

depend of chemical reactions• Chemical reaction- a process that changes one

set of chemicals into another set of chemicals– Slow- iron + oxygen -> rust– Fast- hydrogen gas + oxygen -> explosion

Chemical Reactions

• Reactants- elements going into the reaction• Products- elements formed by the reaction• Reactions always involve the breaking and forming of

bonds• When bonds break, energy is released in the form of heat

and when bonds form energy is absorbed in the form of cold

• Endothermic- reactions in which energy is absorbed, feels cold

• Exothermic- reactions in which energy is released, feels warm

Chemical Reactions

• We must obtain energy to be able to carry out reactions to live

• Animals get energy from food, plants get energy from the sun

• To make sure the body’s chemical reactions occur at the rate the body needs, cells have catalysts

Enzymes

• Catalyst- a substance that speeds up the rate of a reaction without being part of the reaction (stays the same)

• Enzyme- proteins that are catalysts, and are specific to which reactions they speed up

• Substrate- substances that need to be broken down or put together

Enzymes

• Active site- area on an enzyme that is specific for a substrate (like a lock and key)– Substrate combines with active site– Enzyme breaks down substrate into monomers – Hydrolysis, or adding water, breaks apart the

substrate– Enzymes can also take two substrates to bond

them together by dehydration synthesis

Enzymes

• Activity of enzymes depend on a very specific temperature and pH

• They can be denatured if temp or pH is off• If an enzyme is denatured, the shape of the

active site changes so the substrate will not fit

Rate of Reaction

• Partly a function of the initial concentration of a substrate

• More substrate = more frequently accessed active sites of enzyme

• Sometimes all enzyme are “busy”, enzyme is said to be saturated.

• Can be calculated by the disappearance of reactants and appearance of the product

Rate of Reaction

• Temperature- at first an increase in temperature will increase the reaction rate because of the kinetics, but after a certain high temperature is researched, the peptide bonds will fall apart and the enzyme will denature

• pH- Most enzymes work best at pH 6-8 but there are some exceptions such as pepsin, which works at low pH in the stomach

• If the environment changes too much from the optimum pH, the bonds are affected, denaturing the enyme

Rate of Reaction

• Enzyme Inhibitors- certain situations selectively inhibit the action of specific enzymes, slowing down the reaction– Competitive Inhibitors- a molecule that looks like

the substrate enough that it can bind to the active site in place of the substrate

– Noncompetitive Inhibitors- impede enzymatic reactions by binding to a part of the enzyme away from the active site (allosteric site) thus changing the enzyme shape

Rate of Reaction

• Allosteric site- a specific receptor site on some part of the enzyme remote from the active site to which the molecule regulates enzyme activity– Acts as a valve that controls the rate of reactions – Can switch by accepting activators or inhibitors – If an activator attaches to the allosteric site, the

shape of the active site is maintained– If an inhibitor attaches, the shape of the active site

changes so that the reaction is inhibited

Biochemical Pathways

• AKA- feedback pathways• A series of enzymes work together to create

one final product• The product of the first enzyme acts as the

substrate for the next enzyme, etc. all the way until the last enzyme creates the final product

Biochemical Pathways

• Feedback Inhibition– A pathway is switched off by its end product,

which acts as an inhibitor of the enzyme within the pathway

– When enough product is produced, the enzyme is inhibited. When the product runs out, the enzyme is reactivated

– Often, the product itself will bind to the enzyme as the inhibitor

– This is called negative feedback