BIOCHEMISTRY AP BIOLOGY. I. Atoms in Organic Molecule A. Organic = molecules with carbon and found...

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.