Unit 2 (Biochemistry) Notes, Part 1: Atomic And Molecular Structure

Element A pure substance that is composed of only one type of atom; There are 92 natural elements Ex: Sodium (Na), Chlorine (Cl), Hydrogen (H), Lead (Pb)

Copyright Pearson Prentice Hall Atoms Basic unit of matter; smallest particle of element with all properties of that element Copyright Pearson Prentice Hall

Copyright Pearson Prentice Hall Placed side by side, 100 million atoms would make a row only about 1 centimeter long. Atoms contain subatomic particles that are even smaller. Copyright Pearson Prentice Hall

Copyright Pearson Prentice Hall The subatomic particles that make up atoms are protons neutrons electrons Copyright Pearson Prentice Hall

Copyright Pearson Prentice Hall Protons (+): positively charged particles in the nucleus Neutrons (0): neutral particles (no charge) in the nucleus Electrons (-): negatively charged particles outside the nucleus Helium atoms contain protons, neutrons, and electrons. The positively charged protons and uncharged neutrons are bound together in the dense nucleus, while the negatively charged electrons move in the space around the nucleus. Copyright Pearson Prentice Hall

Isotopes atom of same element w/ different number of neutrons (e.g., carbon-12, carbon-13, carbon-14)

Protons + Neutrons = Atomic Mass Drawing An Atom 1) All the mass of an atom is in the center or nucleus. 2) The mass of an atom can be calculated by adding the number of protons and the number neutrons. Ex: 6 C 12 (Atomic Mass) Protons + Neutrons = Atomic Mass

Atomic Number = The # of Protons Where can I find the number of protons? Ex: 6 (atomic number) C 12 Atomic Number = The # of Protons

Atomic Mass – Atomic Number = The # of Neutrons How do I find the number of neutrons? Ex: 6 C 12 12 – 6 = 6 Neutrons Atomic Mass – Atomic Number = The # of Neutrons

Copyright Pearson Prentice Hall Chemical Compounds A chemical compound is a substance formed by the chemical combination of two or more elements in definite proportions. Copyright Pearson Prentice Hall

Examples of Chemical Compounds Water H2O Table salt NaCl Carbon dioxide CO2 Sugar C6H12O6

Characteristics of Compounds Always formed from a specific combination of elements 2. Always formed in a fixed ratio Ex: H3O does not = water Ex: CO4 does not = carbon dioxide

Characteristics of Compounds Compounds are chemically and physically different from the elements they are made from: Ex: Water (H2O) has different properties than hydrogen (H) or oxygen (O)

Copyright Pearson Prentice Hall Chemical Bonds The atoms in compounds are held together by chemical bonds. The electrons that are available to form bonds are called valence electrons. Copyright Pearson Prentice Hall

Copyright Pearson Prentice Hall The main types of chemical bonds are: Ionic bonds Covalent bonds Copyright Pearson Prentice Hall

Copyright Pearson Prentice Hall Ionic Bonds force of attraction between oppositely charged ions (atoms that gain or lose electrons); electrons are transferred (e.g., NaCl) Copyright Pearson Prentice Hall

Copyright Pearson Prentice Hall The chemical bond in which electrons are transferred from one atom to another is called an ionic bond. The compound sodium chloride forms when sodium loses its valence electron to chlorine. Copyright Pearson Prentice Hall

Copyright Pearson Prentice Hall Covalent Bonds chemical bond formed when 2 atoms combine by sharing electrons (e.g., H2O) Copyright Pearson Prentice Hall

Copyright Pearson Prentice Hall The structure that results when atoms are joined together by covalent bonds is called a molecule. Copyright Pearson Prentice Hall

Copyright Pearson Prentice Hall One more bond type…Van der Waals Forces When molecules are close together, a slight attraction can develop between the oppositely charged regions of nearby molecules. Copyright Pearson Prentice Hall

Unit 2 (Biochemistry) Notes, Part 2: Properties of Water

Why do we study water properties in biology class? About 2/3 of the mass of a cell is water! Most life-sustaining reactions occur in water solutions

Water Molecule 2 atoms of hydrogen linked by covalent bonds to 1 atom oxygen (H2O) Polar Molecule: has positive hydrogen end and negative oxygen end

Water is Polar Polarity: The electrons are unevenly distributed between the Oxygen and the two Hydrogen atoms. Oxygen has 8 protons. Each hydrogen has 1.

Water is Polar The atom with more protons (Oxygen) pulls electrons away from the atom(s) A diagram of what’s happening:

Water forms Hydrogen Bonds Hydrogen Bonds: Form due to attraction between water molecules. Not as strong as ionic/covalent bonds

Water forms Hydrogen Bonds Water can form up to 4 hydrogen bonds at once A diagram of what’s going on:

Water is Cohesive Cohesion: Water molecules are drawn tightly together (on the surface of a lake or a pond, this forms a film, which is called surface tension) Explains why: Water beads on a surface (like the lab table) Insects can walk on water http://www.youtube.com/watch?v=RphuMEUY3Og http://news.nationalgeographic.com/news/2003/08/0806_030806_skeeters.html

A Cool Example of Cohesion / Surface Tension: Water Strider Insect http://www.youtube.com/watch?v=RphuMEUY3Og http://news.nationalgeographic.com/news/2003/08/0806_030806_skeeters.html

Water is Adhesive = Adhesion = Water adheres (sticks) to different surfaces Ex: Measuring water in a graduated cylinder Water adheres (sticks) to the glass more than it adheres to itself. That’s why there is a dip in the water when you read the volume

Cohesion Adhesion Ex: Water Bubble Ex: Water and Paper Towels

Water can undergo Capillary Action Capillary Action= Water can flow up a tube, against gravity Ex: Plants absorbing water through their roots

Water is an Excellent Solvent Water often found as part of a mixture called a solution Solution: one substance (solute) dissolves into another (solvent); water is called the “universal solvent” Why is this important in humans? Salt (NaCl) in Water

Water Has a Neutral pH pH: measure of how acidic or basic a solution is scale is 0 to 14 If pH = 7, then substance is neutral (not acid or base)

Water Has a Neutral pH acid: forms hydrogen ions (H) in water; pH is less than 7 base: forms hydroxide ions (OH) in water; pH is greater than 7

Acid / Base Reactions pH level determines rate & types of reactions that can take place buffer: weak acid or base that can react with a strong acid or base to prevent sudden changes in pH Buffers help maintain a constant pH.  A change in pH in living cells could denature proteins, DNA and other important molecules resulting in the death of the cells.

Water is less dense in its solid form Water is less dense in its solid form than it is in its liquid form (Ice floats!) Why might it be a bad thing for ice to sink in a pond?

What does ice look like at the molecular level?

Water has a High Heat Capacity Water absorbs a lot of heat from the air without having a large temperature change So…lakes and oceans often stabilize air temperatures Water absorbs heat when it evaporates; this is why sweating helps us cool down!

So why does it take so much heat to increase the temperature of water?! You have to break the hydrogen bonds between water molecules first!

Unit 2 (Biochemistry) Notes, Part 3: Macromolecules

What elements are most common in our cells? Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, and Sulfur. Remember CHNOPS!

What have we already talked about? Water…which elements are found in water?

A carbon atom can form four covalent bonds with other atoms Carbon Compounds A carbon atom can form four covalent bonds with other atoms

Carbon Compounds Organic chemistry is the study of all compounds that contain bonds between carbon atoms. Lipids (Fats) Nucleic Acids (DNA) Carbohydrates Proteins

Carbon Compounds macromolecules: large molecules formed by process called polymerization polymer: forms when many smaller molecules (called monomers) bond together, usually in long chains

Building and Breaking Down Molecules 1) Dehydration/Condensation Reaction: monomers are joined to form a polymer; molecules of water are released

2) Hydrolysis: a polymer is broken into monomers when water molecules are added

Macromolecules in Living Things 4 Types 1) Carbohydrates 2) Lipids 3) Nucleic Acids 4) Proteins

1) Carbohydrates Functions: source of energy; also used to maintain plant structure Made of: Carbon, Hydrogen, Oxygen (1 C: 2H: 1O) Glucose

1. Carbohydrates (Sugars) monosaccharide: carbohydrate monomer, simple sugars Example: glucose and fructose disaccharide: 2 monosaccharides form 2-sugar carbohydrate Example: sucrose

1. Carbohydrates polysaccharide: carbohydrate polymer (forms when sugars join together in a long chain) Examples: 1) starch: used as food storage by plants 2) glycogen: form in which animals store food 3) cellulose: cell walls in plants

2. Lipids (Fats) Made of: Carbon and Hydrogen (with a few Oxygens) Functions: long-term energy storage, insulation, protective coatings (Some lipids are important parts of biological membranes and waterproof coverings.) Examples: fats, oils, and waxes - insoluble in water Steroids are also lipids. Many steroids serve as chemical messengers.

2. Lipids Structure: Usually 3 fatty acids (carbon-hydrogen chains) bonded to 1 glycerol molecule

Saturated Fat (Butter) 2. Lipids Saturated vs. Unsaturated Fat…which is “worse” for you and why? Saturated Fat (Butter) Unsaturated Fat (Oil)

3. Nucleic Acids Made of: C, H, O, N, and P Functions: store & transmit information in cells in form of a code Nucleotide: monomer of a nucleic acid ; 3 parts (nitrogen base, 5 carbon sugar, and phosphate group) DNA or RNA: polymers made by linking nucleotides in a chain

3. Nucleic Acids Nucleotide DNA

3. Nucleic Acids DNA : deoxyribonucleic acid; master copy of organism's genetic code RNA: ribonucleic acid; forms copy of DNA; used to make proteins (protein synthesis)

4. Proteins Made of: C,H,N,O and sometimes S Functions: 1) Structure (hair, nails) 2) Transport (hemoglobin in blood) 3) Movement (muscle fibers) 4) Defense (antibodies) 5) Regulating Cell Functions (hormones and enzymes)

4. Proteins Amino Acids : Monomers of proteins; 20 common amino acids ; Consists of a central Carbon atom bonded to 4 groups 4 Groups 1) Hydrogen Atom 2) Amino Group 3) Carboxyl Group 4) R group (changes in each Amino Acid!)

4. Proteins Polypeptide: polymer; one chain of amino acids Proteins: several polypeptides folded into complex structures.

4. Proteins Four Levels of Protein Structure 1) Primary 2) Secondary 3) Tertiary 4) Quaternary ..\..\..\Downloaded Videos\Protein Structure.avi

Unit 2 (Biochemistry) Notes, Part 4: Enzymes

Why do we study chemical reactions in biology? Chemistry isn’t just what life is made of, chemistry is also what life does Everything that happens in an organism is based on chemical reactions (growth, response to environment, etc.)

Chemical Reaction A process that changes reactants into products. Slow Reactions vs. Fast Reactions

Chemical reactions  breaking bonds in reactants and forming bonds in products

Energy Changes Some reactions release energy and some absorb energy Activation Energy: the energy required to start a reaction

Speeding up Reactions Slow reactions or reactions with high activation energies need a catalyst Catalyst = any substance that lowers the activation energy of a reaction to “speed it up” Enzymes are catalysts that are protein molecules.

Enzymes Enzymes provide a site where reactants can be brought together to react. In an enzyme-catalyzed reaction, the reactants are called substrates. Each enzyme has a specific shape and a specific portion called the active site, where substrates bind.

The substrates must fit exactly into the active site The substrates must fit exactly into the active site. This is called the lock and key model. Once the reaction is complete, the enzyme releases the products of the reaction. Enzymes can join or break substrates into products.

G:\Teacher Resources\Downloaded Videos\Enzyme Action.avi Breaking 1 Substrate into 2 Products G:\Teacher Resources\Downloaded Videos\Enzyme Action.avi

Joining 2 Substrates into 1 Product

Enzymes can break or join substrates into products. Enzymes work best at a certain pH and temperature. Roles of Enzymes: 1) regulating chemical pathways 2) making materials 3) releasing energy 4) transferring info