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McMillan preAP Biology Ch. 2 Biomolecules

Notes
by

Kathy McMillan

on 14 January 2013

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Transcript of McMillan preAP Biology Ch. 2 Biomolecules

Chapter 2-4 Chemical Reactions and Enzymes
A. Chemical Reactions – process that changes one set of chemicals into another set of chemicals
1. reactants → products
2. breaking of bonds in reactants and forming new bonds in products 4 levels of organization of proteins
Primary- sequence of amino acids in a protein chain
Secondary- amino acid within a chain is twisted or folded
Tertiary- the chain itself is folded
Quaternary- if a protein has more than one chain Lipids
not soluble in water
fats, oils, and waxes
C,H,O (glycerol + fatty acid) much greater than a 2:1 ratio of H:O
Example: C18H34O3
saturated (max # of H bonds) and unsaturated (at least one double bond=) B. Macromolecules – “giant molecules”
1. Connecting monomers to make polymers
2. 4 groups of macromolecules
a. Carbohydrates
carbon, hydrogen, oxygen – 1:2:1 ratio
main source of energy for organisms
starch – storage molecule
monosaccharides (ex. Glucose) and polysaccharides (glycogen and cellulose) C. Acids and Bases
1. pH Scale – indicates the number of H+ ions in a solution. (Ranges from 1-14)
2. Acids – Contain a higher concentration of H+ ions than pure water and pH values below 7
3. Bases – Contain a lower concentration of H+ ions than pure water and pH values above 7. They also produce OH-
4. Buffers – weak acids or bases that can react with strong acids or bases to prevent sharp, sudden changes in pH B. Solutions and Suspensions
1. Mixture – material composed of two or more mixed compounds that are physically mixed together but not chemically combined.
a. Solutions – all components are evenly distributed (ex: salt water)
1. solute – what is being dissolved
2. solvent – substance in which the solute dissolves
b. Suspensions – mixture with non-dissolved particles (ex: blood)
3. Radioactive Isotopes
a. Geologists determine age of rocks
b. Radiation for cancer
c. Used as tracers to follow substances in organisms
Chemical Compounds
1. A compound is a combination of two or more elements in definite proportions
2. Use chemical formula 2-1 The Nature of Matter
A. Atom – The basic unit of matter
1. 3 types of subatomic particles in an atom
a. proton (+ charge)
b. neutron (no charge)
c. electron (- charge)
Protons and neutrons are in the NUCLEUS
Electrons are in constant motion around the nucleus.
---Atoms have a neutral charge!-- 2. Regulation of Enzyme Activity
a. pH values
b. temperature
c. cells regulate - proteins turn enzymes “on” or “off” D. Enzyme Action
1. Enzyme-Substrate Complex
a. substrates – reactants of enzyme-catalyzed reactions
active site – where substrates bind to enzyme (lock and key)
Catalase. It catalyzes the decomposition of hydrogen peroxide into water and oxygen.
2H2O2 -> 2H2O + O2
One molecule of catalase can break 40 million molecules of hydrogen peroxide each second C. Enzymes – (Proteins)
1. Are biological catalysts
2. Catalyst – speed up RXN by lowering activation energy
3. Very specific – only one reaction Catalyzed vs. Uncatalyzed
Reaction B. Energy in Reactions – released or absorbed
1. RXNS (reactions) that release energy are spontaneous – produce heat light and sound
2. RXNS that absorb energy must have a source of energy – plants (sunlight) and animals (food)
3. Activation Energy – energy needed to get reaction started Protein structure

http://www.youtube.com/watch?v=lijQ3a8yUYQ Protein Structure Amylase- starts process of breaking down starch in the mouth
Hemoglobin- carries oxygen in our blood
Collagen-gives structure and support to our skin, tendons, and even bones
Insulin-regulates the amount of sugar in the blood
Fibrin- forms a scab to protect cuts as they heal
Actin-one of the major proteins in a muscle
Luciferase (in plants)-catalyzes the reaction that makes fireflies glow Examples d. Proteins
N, C, H, O
Polymers of amino acids
Amino group- NH2 and a carboxyl group – COOH
Proteins control rate of cell reaction(rxn),
regulate cell processes,
form bones and muscles,
transport into and out of cells, and
some fight diseases c. Nucleic acids
H, O, N, C, P
Polymers of nucleotides – sugar, phosphate, and nitrogen base
Store and transmit hereditary or genetic information
RNA and DNA Figure 4.5 The role of hydrocarbons in fats Chapter 2-3 Carbon Compounds
What is a Valence Electron?
What is an Organic Compound?
A. Carbon
1. 4 Valence Electrons
Ability to bond with other elements and itself – millions of structures
Compounds containing carbon are considered ORGANIC 2. Hydrogen Bonds - attraction between the partial positive and the negative charges of atoms. These bonds are not as strong as ionic or covalent bonds. (EX: Water)
a. Cohesion – attraction between molecules of the same substance
b. Adhesion - attraction between molecules of different substances. 2-2 Properties of Water

A. Characteristics of Water
- It is the single most abundant
compound in most living things
- A water molecule is neutral
1. Polarity –
the oxygen end of the molecule has a slight neg (-) charge and the hydrogen end has a slight pos(+) charge.
There is an uneven distribution of e- between O and H Draw a pH scale. Then place the following substances on the scale in the appropriate location according to their pH values.
Dr. Pepper
Fantastik cleaner
Water
Answer:
0 7 14
Dr.P water Fantastik Warm-up D. Chemical Bonds
1. Ionic – valence electrons are transferred (ex: NaCl)
2. Covalent – valence electrons are shared (ex: H20)

3.Van der Waals Forces – When molecules are close together they can develop a slight attraction to the oppositely charged regions of nearby molecules B. Elements and Isotopes
1. Element - is a pure substance that consists entirely of one type of atom.
a. Atomic number- number of protons in an atom (C- Carbon 6)
An atom has the same number of protons and electrons.

2. Isotopes – Atoms of the same element that differ in the number of neutrons.
a. Mass number- sum of protons and neutrons
b. Isotopes are named by their mass number Chapter 2
The Chemistry of Life Feedback Inhibition
If the product of a series of enzymatic reactions, e.g., an amino acid, begins to accumulate within the cell, it may specifically inhibit the action of the first enzyme involved in its synthesis (red bar). Thus further production of the enzyme is halted. Figure 5.15 The 20 amino acids of proteins: polar and electrically charged Figure 5.10 The synthesis and structure of a fat, or triacylglycerol Figure 5.11 Examples of saturated and unsaturated fats and fatty acids  Figure 5.5 Examples of disaccharide synthesis Figure 5.3 The structure and classification of some monosaccharides 1. How do you know whether a sample is a mixture(physical) or a compound (chemical)?
Answer: a mixture can easily be separated into the component parts
2. Are solutions only in the liquid state?
Answer: No, solutions can be solids, liquids, or gases Questions Look at the following words. Place each one in the table below and define if you think you can.
atom proton neutron
electron nucleus element compound Warm-Up Competitive inhibition
The necessity for a close, if brief, fit between enzyme and substrate explains the phenomenon of competitive inhibition.

One of the enzymes needed for the release of energy within the cell is succinic dehydrogenase. It catalyzes the oxidation (by the removal of two hydrogen atoms) of succinic acid (a). If one adds malonic acid to cells, or to a test tube mixture of succinic acid and the enzyme, the action of the enzyme is strongly inhibited. This is because the structure of malonic acid allows it to bind to the same site on the enzyme (b). But there is no oxidation so no speedy release of products. The inhibition is called competitive because if you increase the ratio of succinic to malonic acid in the mixture, you will gradually restore the rate of catalysis. At a 50:1 ratio, the two molecules compete on roughly equal terms for the binding (=catalytic) site on the enzyme. Competitive Inhibition Figure 4.3 Valences for the major elements of organic molecules
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