BIOCHEMISTRY
AP BIOLOGY
I. Atoms in Organic MoleculeA. Organic = molecules with carbon and
found in living things
B. Common Atoms = C, O, H, N
C. Other Atoms = S, P
II. Importance of CarbonA. Valence number of 4 – forms four bonds
B. Backbone of all organic molecules
C. Functional groups attach to form specific properties
Four Valence electrons means four bonds…
Hydrocarbons Contain only carbon &
hydrogen atoms
Carbon can form an endless diversity of carbon skeletons
Large Hydrocarbons: Are the main molecules in the gasoline we
burn in our cars The hydrocarbons of fat molecules provide
energy for our bodies
Shape of Organic Molecules
Each type of organic molecule has a unique three-dimensional shapeThe shape determines its function in an organism
Functional Groups Groups of atoms that give properties to the
compounds to which they attach
Phosphate group Used to transfer energy
III. Bonding Organic Molecules Covalent bonds are used to form the
backbone of organic molecules Formed by dehydration synthesis (removal
of water to make room for new bonds) Broken by hydrolysis (replacing the water
as bonds are broken apart)
Giant Molecules - Polymers Large molecules are called
polymers Polymers are built
from smaller molecules called monomers
Biologists call them macromolecules
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Examples of Polymers
Proteins
Lipids
Starch
Nucleic Acids
Most Macromolecules are Polymers Polymers are made by stringing together many
smaller molecules called monomers
Nucleic Acid
Monomer
Linking Monomers
Cells link monomers in the process of dehydration synthesis (removing a molecule of water)
Remove H
Remove OH
H2O Forms
Breaking Down PolymersCells break down macromolecules by a process called hydrolysis (adding a molecule of water)
Water added to split a double sugar
IV. Types of Organic MoleculesA. Carbohydrates – energy formation –
sugars and starches
B. Lipids – storage and insulation – fats and oils
C. Proteins – enzymes run all body reactions
D. Nucleic acids – store genetic information – DNA and RNA
V. Carbohydrates
A. General Information1. Made of C, H, O
2. Basic shape is a ring of carbons with –OH and –H groups attached to the carbons
3. Isomers = same number of C, O, and H but arranged differently
4. Grouped based on number of rings in molecule
B. Monosaccharides1. Mono = one - one ring
2. Many isomers (glucose, alpha and beta; fructose; galactose) which react differently in the body
3. Function – used in energy releasing reactions
Glucose – the most common monosaccharide
Isomers
Glucose & fructose are isomers because they’re structures are different, but their chemical formulas are the same
Rings In aqueous (watery) solutions,
monosaccharides form ring structures
C. Dissacharides
1. Formed from two monosaccharides
2. Glycosidic bonds = covalent bonds in carbs formed by dehydration synthesis
3. Found mostly in plants – common example is sucrose – used as a transport sugar
+OH HO
+ H2O
D. Polysaccharides1. Many rings (100’s)
2. Purposes depend on way the rings are constructeda. Storage = starch in plants and glycogen in
animals
b. Structure = cellulose in plant cell walls and chitin in fungus cell walls or insect exoskeletons
Examples of Polysaccharides
Starch
Glycogen
Cellulose
Glucose Monomer
StarchStarch is an example of a polysaccharide in plants
Plant cells store starch for energy
Potatoes and grains are major sources of starch in the human diet
Glycogen
Glycogen is an example of a polysaccharide in animals
Animals store excess sugar in the form of glycogen
Glycogen is similar in structure to starch
Cellulose
Cellulose is the most abundant organic compound on Earth
It forms cable-like fibrils in the tough walls that enclose plants
It is a major component of wood
It is also known as dietary fiber
Cellulose
SUGARS
Dietary Cellulose
Most animals cannot derive nutrition from fiber
They have bacteria in their digestive tracts that can break down cellulose
Sugars in Water
Simple sugars and double sugars dissolve readily in water
They are hydrophilic, or “water-loving”
WATER MOLECULE
SUGAR MOLECULE
Lipids
VI. LipidsA. General Information
1. Fats and oils are triglycerides.
2. Constructed of a 3 carbon alcohol called glycerol and three long chains of hydrocarbons called fatty acids.
Lipid structure
H - C – O - fatty acid
H - C – O - fatty acid
H - C – O - fatty acid
H
H
Dehydration synthesis removed –OH and –H as bond forms
Fats Dietary fat consists largely of the molecule
triglyceride composed of glycerol and three fatty acid chains
Glycerol
Fatty Acid Chain
Dehydration links the fatty acids to Glycerol
B. Functions of Triglycerides1. Storage of chemical energy
2. Insulation
3. Padding
C. Types of Fatty Acids
Unsaturated fatty acids have less than the maximum number of hydrogens bonded to the carbons (a double bond between carbons)
Saturated fatty acids have the maximum number of hydrogens bonded to the carbons (all single bonds between carbons)
Single Bonds in Carbon chain
Double bond in carbon chain
Triglyceride
Glycerol Fatty Acid Chains
Fats in OrganismsMost animal fats have a high proportion of saturated fatty acids & exist as solids at room temperature (butter, margarine, shortening)
Saturated fats stack and block arteries.
Fats in Organisms Most plant oils tend to be low in saturated
fatty acids & exist as liquids at room temperature (oils)
D. Other types of LipidsFound in this group because they are insoluble in water.1. Phospholipids – a phosphate group
replaces one fatty acid. Found in cell membranes.
2. Terpenes = pigments such as chlorophyll
3. Prostaglandins = chemical messengers
4. Steroids = parts of hormones
SteroidsThe carbon skeleton of steroids is bent to form 4 fused rings
Cholesterol is the “base steroid” from which your body produces other steroids
Estrogen & testosterone are also steroids
Cholesterol
TestosteroneEstrogen
Synthetic Anabolic Steroids
They are variants of testosterone
Some athletes use them to build up their muscles quicklyThey can pose serious health risks
LipidsLipids are hydrophobic –”water fearing”
Nonpolar bonds on hydrophobic fatty acids.
Polar bonds on hydrophilic glycerol.
This means that lipids do not dissolve in water.
Includes fats, waxes, steroids, & oils
FAT MOLECULE
VII. Protein A. Building Blocks
1. Composed of chains of amino acids
H2N – C – COOH
H
R
2. Amino acids come in 20 types and only the R groups vary. R groups fall into three categories – nonpolar, polar, and ionized.
3. R groups interact and form bonds with one another.
Structure of Amino AcidsAmino acids have a central carbon with 4 things boded to it:Amino group -NH3Carboxyl group –COOH Hydrogen -H
Side group -R
Amino
group
Carboxylgroup
R group
Side groups
Leucine -nonpolar
Serine-polar
Linking Amino AcidsCells link amino acids together to make proteins
The process is called dehydration synthesisPeptide bonds form to hold the amino acids together
Carboxyl
AminoSide
Group
Dehydration Synthesis
Peptide Bond
Nonpolar(hydrophobic)
Polar(hydrophilic)
Charged(Negative/Positive)
B. How to build a protein1. PRIMARY STRUCTURE Straight chain of amino acids or a polypeptide (A peptide bond is a dehydration synthesis bond between two amino acids)
B. How to build a protein2. SECONDARY STRUCTURE - Chain forms helix or pleated sheet. (Motif = some parts are helix and some parts are sheet)
motif
B. How to build a protein3. TERTIARY STRUCTURE – Helix forms three dimensional shape as R groups interact.
Hydrophobic interactions
What holds the tertiary structure?1. Disulfide bridges
2. Ionic bonds
3. Hydrogen bonds
between polar R groups
4. Hydrophobic
interactions
4. QUATERNARY STRUCTURE – not always present – two or more tertiary structures bond together, usually with a metal atom as the center
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Types of Proteins
Structural
Contractile
Storage
Transport
Functions of Proteins1. Structural – support, tendons & ligaments
2. Storage – egg whites store amino acids
3. Transport – carry substances, hemoglobin
4. Hormones – coordinate body, insulin
5. Receptors – built into membranes
6. Contractile – movement, muscle fibers
7. Defensive – antibodies fight disease
8. Enzymes – accelerate reactions, digest molecules
Denaturating Proteins
Changes in temperature & pH can denature (unfold) a protein so it
no longer worksCooking denatures protein in eggs
Milk protein separates into curds & whey when it denatures
Denaturalization Proteins are denatured when their 3-D
shape changes. An incorrect shape can not bond with other molecules correctly and the enzyme does not function.
Denaturalization occurs by Temperature / heat pH changes Excessive salts
VIII. Nucleic AcidsA. General notes
1. Two basic types – DNA (long molecules which store all of our genetic information and never leave the nucleus) and RNA (short molecules that are copies of one gene of the DNA and used to direct protein synthesis)
2. The organelle chromatin is composed of DNA wrapped around proteins to form a double helix.
B. Structure1. A nucleotide has three parts – a sugar
(monosaccharide), a phosphate functional group, and a nitrogen base.
2. Nitrogen bases are rings of carbon, nitrogen, and hydrogen. They come in five major types (A, T, C, G, and U).
Nitrogenous base(A,G,C, or T)
Phosphategroup
Thymine (T)
Sugar(deoxyribose)
Phosphate
BaseSugar
Nucleic acids are polymers of nucleotides
Nucleotide
BasesEach DNA nucleotide has one of the following bases:
Thymine (T) Cytosine (C)
Adenine (A) Guanine (G)
–Adenine (A)
–Guanine (G)
–Thymine (T)
–Cytosine (C)
RNA – Ribonucleic Acid
Ribose sugar has an extra –OH or hydroxyl group
It has the base uracil (U) instead of thymine (T)
Nitrogenous base(A,G,C, or U)
Sugar (ribose)
Phosphategroup
Uracil
C. Functions1. Storage of genetic instruction
2. Using genetic instructions to create proteins.