Biochemistry

A. Basic Chemistry1. Atom – smallest particle of an element that has the characteristics of that element

3 partsa. protons (+) inside theb. neutrons (0) nucleusc. electrons (-) orbiting nucleus

2. Element – substance that cannot be broken downa. ex : C, H, O, Na

3. Compound (com = with/together) – substance composed of 2+ elements chemically combineda. ex : H2O (water), C6H12O6 (glucose), NaCl (salt)

B. Bonds – 4 main kinds

1. ionic bonds – forms when electrons are transferred between atoms

2. covalent bonds (com = with/together) – forms when atoms share electrons

3. hydrogen bonds – a weak bond formed between a H+ and a (-) atom

4. peptide bonds – forms between amino acids to form a protein

C. Properties of Water1. water is Polar – has unequal charges

2. water has a High Specific Heat Capacity – resists temperature change

3. water is Cohesive – water molecules stick to each other to create surface tension

4. water is Adhesive – water molecules stick to other surfaces

5. water is the Universal Solvent – dissolves other particles (solutes)

D. Acids and Bases

1. Acid – pH below 7

2. Base – pH above 7

3. Neutral – At pH 7

4. Buffers – solutions added to maintain a pH level

a. if a solution becomes too acidic, a basic solution will be added

b. if a solution becomes too basic, an acidic solution will be added

E. Definitions

1. Monomor- (mono = 1 ) - single unit

2. Polymer (poly – many) – large molecule made up of monomer units bonded together

F. Making and Breaking Bonds

1. Condensation Reaction (aka Dehydration Synthesis)

a. bonding of 2 monomers together

b. whenever a bond is formed water is formed

c. one molecule releases an –OH while the otherreleases an –H

2. Hydrolysis (hydro = water, lysis = to break/dissolve)

a. breaking of bonds within a polymer

b. water is absorbed

c. one molecule gains an –OH while the othergains an -H

G. Organic Chemistry

1. Organic – contains C and found in living things(CO2 – exception to this rule)

2. Most common elements in living things : C, H, O, N, P, and S

3. 4 kinds of organic compounds : carbohydrates, lipids, proteins, and nucleic acids

H. Carbohydrates

1. contains C, H, and O in a 1:2:1 ratio

2. monomer unit : monosaccharides (mono = 1, saccharo – sugar) –short-term / primary energy source

Examples:a. glucose - C6H12O6 – short term energy in all living things

b. fructose - C5H10O5 – found in fruit

c. ribose / deoxyribose - C5H10O5 - found in RNA and DNA

d. drawing of glucose –

3. disaccharides (di = 2, saccharo – sugar) - contains 2 monosaccharides combined together through condensation reaction

a. chemical formula : C12H22O11- explanation : C6H12O6 + C6H12O6 = C12H24O12

– H2O C12H22O11

Examplesb. sucrose – table sugar = glucose + fructose

c. lactose – milk sugar = galactose + glucose

d. maltose = glucose + glucose

4. polysaccharides – (poly = many, saccharo = sugar) – contains many monosaccharides bonded together through condensation reaction

Examplesa. starch – how plants store glucose after photosynthesis

b. glycogen – how animals store glucose in the liver

c. cellulose – makes up plant cell wall – not digested by animals

d. chitin – makes up cell wall in fungi

5. indicators – a chemical used to test the composition of another substance

a. iodine – changes from yellowish to dark blue in the presence of a starch

b. Benedict’s solution – changes from blue to orange in the presence of a monosaccharide

I. Lipids

1. contains C, H, and O

2. examples : fats, oils, and waxes

3. lipids are insoluble in water (hydrophobic, hydro = water, phobia = fear of))

4. Functions of lipids

a. insulation

b. long term energy storage

potato with iodine

Sol’n must be heated to work!

Sucrose did not turn colors - it is a disaccharide, not a monosaccharide

5. Monomer units : 1 glycerol and 3 fatty acids

6. Drawing of a lipid

7. Steroid – lipid in a double ring structure

a. function in gender hormones, metabolism, muscle and bone synthesis

8. Phospholipids – lipids with phosphates attached that make up the cell membrane

9. Indicator – paper becomes translucent in the presence of lipids

Saturated fatty acids - contain no double bonds

Unsaturated fatty acid – contain double bonds

Condensation reaction must occur 3 times in order for 1 lipid molecule to be made

- 3 molecules of water are given off

Conversely – 3 molecules must be absorbed for the hydrolysis of 1 lipid molecule

J. Proteins1. contains C, H, O, N

2. monomer unit : amino acids

3. amino acids

a. only 20 different kinds of amino acids

b. different arrangement of amino acids in a chain produces different proteins

c. amino acids are bonded together with peptide bonds

d. drawing an amino acid

4. functions of proteins

a. growth and repair of cells

b. make antibodies that fight disease (immune support)

c. make up hormones

d. facilitate heredity

e. speed up chemical reactions (only special proteins called enzymes)

5. Examples of proteins

a. melanin – protein responsible for skin and hair pigmentation

b. hemoglobin – protein in blood that carries oxygen

c. insulin – protein responsible for maintaining glucose levels in the blood

d. amylase – protein in saliva that breaks down starch

Each oval represents 1 amino acid

They are bonded together to make a protein

Proteins are also called polypeptides

6. folding of protein structure is related to the function of protein

7. Indicators - Biuret solution changes from blue to orange in the presence of a protein

K. Enzymes

1. specific type of protein that acts as a catalyst (speeds up chemical reactions)

2. enzymes lower the activation energy (amount of energy required for a reaction to begin)

3. each enzyme is specific and works on only one kind of substrate

4. active site of the enzyme must match the shape of the substrate (lock and key model)

5. Steps in enzyme functioninga. substrate attaches to enzyme at active site forming enzyme-substrate complex

b. enzyme completes the reaction – breaking down substrate or building up substrate

c. enzyme release products and is ready to be reused

A – substrateB – enzymeC – enzyme-substrate complexD – enzyme ready to be reusedE - products

6. enzymes are reusable

7. enzymes names end in –ase and are usually named after substrate (ex : lipase – enzyme,

lipids – substrate)

8. 3 factors that affect enzyme functioning :a. temperature

b. pH

c. substrate concentration

9. Extreme temperatures or pH can cause enzymes to change shape of the active site = denaturation

Each enzyme has an optimal (best) temperature and pH.

For substrate concentration – any number of substrates present over the number of enzymes is past the point of saturation. For example, if I have 10 enzymes and 15 substrates, there will be 5 substrates that will not be in use at the time. These five substrates are past the point of saturation and do not increase the rate of enzyme reaction.

L. Nucleic Acids

1. Contain C, H, O, N, and P

2. Ex : DNA (D = deoxyribose) and RNA (R = ribose)

3. monomer unit – nucleotides

4. nucleotides – 3 parts

a. 5 carbon sugar

b. phosphate (PO4)

c. Nitrogen Base

1. DNA : A-T, G-C

2. RNA : A – U, G-C

5. drawing of a nucleotide

6. Drawing of a DNA strand

If the active site changes shape, the enzyme is no longer able to bond with the substrate

7. DNA shape is really a double helix – twisted ladder

8. function of nucleic acids

a. DNA and RNA carry genetic information to codefor proteins

In DNA – A always pairs with T

G always pairs with C

The backbones (red and purple lines) represent the phosphates and sugars