ch. 5 the molecules of life. 5.1 carbon is the main ingredient of organic molecules

Ch. 5 The Molecules of Life

5.1 Carbon is the main ingredient of organic

molecules

I. Carbon Skeletons and Functional Groups

A. Carbon is very common in living things

1. Carbon can form up to 4 bonds with other atoms due to 4 electrons in the outer shell

2. Carbon may bond with other carbon atoms

Carbon

Carbon Skeletons and Functional Groups

B. Carbon backbones

Carbon Skeletons and Functional Groups

C. Classification

1.Organic molecules- most molecules that are comprised of Carbon in various shapes (living)

2. Inorganic molecules- most non-carbon molecules (H2O, O2, and NH3) (non-living)

Carbon Skeletons and Functional Groups

D. Hydrocarbons- organic molecules composed of only Carbon and Hydrogen

1. Fuels such as methane CH4 as natural gas

Carbon Skeletons and Functional Groups

E. Functional Groups- group of atoms within a molecule that interacts in a predictable way; attached to a hydrocarbon skeleton

1.Hydroxyl group- polar hydrophilic – attract water around; also know as alcohols (like ethanol)

Carbon Skeletons and Functional Groups

• 2. Carbonyl group- polar hydrophilic; bonds with two other molecules or atoms. Oxygen end polar negative charge.

Carbon Skeletons and Functional Groups

a. If one or more of the bonds is connected to a hydrogen – it is called an aldehyde –polar hydrophilic (vanilla bean, lemon grass)

Carbon Skeletons and Functional Groups

b. If both bonds with carbon are other than hydrogen – it is called a ketone - polar hydrophilic (acetone, camphor-moth balls)

Carbon Skeletons and Functional Groups

3. Carboxyl group- polar, hydrophilic weak acid, (fatty acid chains, vinegar, niacin)

Carbon Skeletons and Functional Groups

4. Amino group- polar hydrophilic, weak base responsible for amino acid formation (proteins)

Functional Groups

II. Monomers and Polymers

A. Monomers- small molecular units

B. Polymers- large chains of monomers in various shapes

C. Life’s major Polymers: carbohydrates, lipids, proteins, and nucleic acids

III. Building and Breaking Polymers

A. Dehydration Synthesis- to lengthen a polymer chain

1. A hydrogen atom and a hydroxyl group from two monomers react

2. A new bond is formed and water is released.

Dehydration Synthesis

Building and Breaking Polymers

B. Hydrolysis- to shorten a polymer chain

1.A water molecule is added to a bond between two monomers

2. The bond is broken an a H is added to one monomer and a hydroxyl group to another monomer

Hydrolysis

5.2 Carbohydrates provide fuel and building material

I. Carbohydrates

I. Carbohydrates- organic compound made of a sugar molecule

A. Sugars contain C,H,O in a 1 carbon : 2 hydrogen : 1 oxygen ratio

1. Multiple of CH2O

2. Most are ring structures

II. Monosaccharides

II. Monosaccharides- one sugar unit molecule (end in –ose)

A.Glucose- both in straight chain and ring

1. Main fuel source for energy and to build other organic molecules

2. Molecules not used may be connected into larger molecules and stored for later use

Glucose

Glucose - monosaccharide

Isomers

• Different compounds having the same molecular formula are called isomers

• C4H8 hydrocarbons

Stereoisomers

• any of a group of isomers in which atoms are linked in the same order but differ in their spatial arrangement

• 1,2-dichlorocyclopentane

Stereoisomers of Glucose

Stereoisomers of Fructose

Isomers of C2H4O

III. DisaccharideIII. Disaccharide- a double sugar formed

from a dehydration reaction

A. Formation of Sucrose

1. Found in plant sap and table sugar – can be broken down easily for energy use

Glucose + Fructose Sucrose + water 

C6H12O6 + C6H12O6 C12H22O11 +  H2O 

Dehydration synthesis of sucrose

Disaccharide

Maltose (glucose + glucose)

Maltose

IV. PolysaccharidesIV. Polysaccharides- long polymer

chains made up of simple sugars

A. Starch- polysaccharide found in plants made totally of glucose monomers

1. Found in potatoes, rice, and corn

Polysaccharides

B. Glycogen- polysaccharide found in animals made totally of glucose monomers that are highly branched

1. Stored as granules in muscle and liver – broken down when body needs energy

Polysaccharides

C. Cellulose- made up of glucose monomers that arrange in cable-like fibers in plants

1.Chains are linked by hydrogen bonds to form tough cell walls in plants like

broccoli stems

2. Human unable to digest – functions as fiber to help keep digestive system healthy

Polysaccharides

3. Cow and termites can break down cellulose due to organism in side them to get energy from it.

Polysaccharide- Cellulose

Polysaccharides

Properties of carbohydrates

IV. Properties of carbohydrates

• A. Hydrophilic – attract to water due to many hydroxyl groups

• B. Monosaccharides and Disaccharides dissolve readily in water

• C. Cellulose and some starches do not dissolve easily but are hydrophilic

5.3 Lipids include fats & steroids

I. Characteristics of Lipids

A. Hydrophobic- water avoiding or fearing molecules

B. Functions of lipids

1. Serves as a boundary that surrounds and contains aqueous contents of cells

2. Others serve as chemical signals or store energy as fats

II. Fats

II. Fats – consists of a 3 carbon backbone called glycerol (C3H8O3) attached to three fatty acids, that contain long hydrocarbon chains

A.Saturated fats- where all three fatty acid chains contain the maximum number of hydrogen atoms

Glycerol

• A trihydroxy sugar alcohol that is an intermediate in carbohydrate and lipid metabolism.

• It is used as a solvent, emollient, pharmaceutical agent, and sweetening agent

• Food, medicines, cosmetics,

Glycerol

Fats

1. All the carbon atoms form single bonds

a. Butyric acid- C4H8O2 (antihistamine properties)

2. Found in lard and butter – they are solid at room temperature

Butyric acid - C4H8O2

Fats

B. Unsaturated fats- contains less than the maximum number of hydrogen atoms in one or more fatty acid chain

1. Some of the carbon atoms are double bonded

2. Fats in fruits and vegetables and fish usually, corn, olive, other vegetable oils

Fats

3. Oleic acid- C18H34O2

a. Part of Lorenzo’s oil for clinical trial to treat childhood cerebral adrenoleukodystrophy (ALD), a degenerative myelin disorder

b. Used commercially in the preparation of oleates and lotions,

Oleic Acid – C18H34O2

Fats

4. Linoleic Acid - C18H32O2

a. Essential fatty acid in mammalian nutrition

b. Biosynthesis of prostaglandins (hormone) and cell membranes

Linoleic Acid – C18H32O2

Saturated fats

C. Saturated fats in high amounts may lead to plaque (lipid material) development in arteries

1. Can lead to decrease blood flow or complete blockage of blood to the heart or brain.

Phospholipids

D. Phospholipids- looks just like a lipid but has one of the fatty acid chains replaced with a Phosphate group (PO4)-

3 and then a R-group following the phosphate

1. Phosphates are a polar, hydrophilic, & acidic molecule

Phosphate

Phospholipids

2. Phospholipids are the key component of cell membranes

3. Phospholipids have a polar,hydrophilic head (phosphate region) and a nonpolar, hydrophobic tail (two fatty acid chains)

Phospholipid

Fats – simplified drawing

Unsaturated fats

Decanoic

acids

C18H34O2

Fat (unsaturated)• Palmitic acid - C16H32O2

• Stearic acid - C18H36O2

• Oleic acid - C18H34O2

Steroids

III. Steroids- lipid molecule where the carbon skeleton forms four fused rings

A.Lipid molecule where the carbon skeleton forms four fused rings; differ in functional groups and locations of functional groups

Steroids

• B. Steroids are lipids due to their hydrophobic nature; however are different from fats structurally & functionally

C. Sex hormones

1. Testosterone- male hormone C19H28O2

2. Estrogen- female hormone C18H24O2

Steroids

Cholesterol

D. Cholesterol – essential material found in cell membranes and starting point for other Steroids (C27H46O)

1. LDL – low density cholesterol builds up in arteries to cause cardiovascular disease

2. HDL – high density cholesterol helps remove LDL cholesterol that clogs arteries

Cholesterol

5.4 Proteins perform most functions in cells

I. The Functions of Proteins

A. Protein- a polymer made from a set of 20 kinds of monomers called amino acids

B. Functions

1. Makes up structures hair, fur, muscle and long-term nutrient stores

2. Defend against foreign invader and serve as chemical signals

3. Controls chemical reactions

II. Amino Acids

A. Amino acid- monomer that consists of a carbon bonded to an amino group, carboxyl hydrogen and side chain (R)

1. Side group or R-group gives the amino acid its specific property and way interacts

2. Leucine is hydrophobic (CH3-CH3) 3. Serine is hydrophilic (OH)

Amino Acid Structure

• 20 different types based on R group

Properties of Amino Acids

• Properties of Amino Acids vary based on the R group– Non-polar, hydrophobic (8)– Polar,hydrophilic (7)– Acidic (Aspartic and glutamic acid)– Alkaline (Lysine, arginine, histidine)

Non-polar, hydrophobic amino acids

Polar, hydrophilic amino acids

Acidic Amino Acids

Alkaline Amino Acids

Zwitter ion

• The amino acid has performed an acid-base reaction on itself.

• pH affects charge of the amino acid

III. Building a Protein

A. Polypeptide- chain of amino acids created by dehydration reaction between each amnion and carboxyl group

B. Most polypeptide chains are at least 100 amino acids long

Peptide bonds

Polypeptide

• N-terminus and c-terminus

IV. Protein Shape

A. Influenced by the interaction between bonds between chains

B. The environment helps to determine shape like a aqueous (water) environment

1. Hydrophilic amino acids like water so will position on outside edge of protein

2. Hydrophobic amino acids repel water so they will cluster in center of protein

Primary Structure

• The sequence of amino acids forming a polypeptide chain.

Secondary Structure

• Coiling or folding of its polypeptide chain

Tertiary Structure

• Attraction between alpha and beta sheets

• Caused by interactions in R groups

Quarternary Structure

• Three dimensional structure of all polypeptide chains

5.5 Enzymes are proteins that speed up specific reactions in

cells.

I. Enzymes (proteins) and Activation Energy

A. Activation Energy- “start-up” energy needed to start the chemical reaction for the reactants

B. Catalysts- chemical compounds that speed up chemical reactions in the cell

C. Enzymes allow chemical reaction to occur without raising the cell’s temperature

D. Enzymes lower the activation energy in the body to allow certain products to be made

Activation Energy

Activation Energy

II. How Enzymes Work

A. Substrate- the substance or substances which the enzyme acts upon

B. Enzymes are substrate specific- fit like a lock and key

C. Induced fit model explains how enzymes work

1. Active site- location where substrate binds to an enzyme

D. Enzymes remained unchanged by the substrate in a chemical reaction

Enzymatic Reaction

E + S --> ES --> E + P

• E is the enzyme

• S is the substrate (reactant)

• ES is the enzyme-substrate complex

• P is the product

Induced-Fit Model

How Enzymes WorkE. Efficiency of enzyme is affected by

temperature and pH

1. Denature- enzymes lose their ability to catalyze when T> 104 F in humans

2. Excessive in pH can also cause denaturation

F. –ase is the standard suffix found on enzymes like

G. Enzymes can hold molecules in closer proximity – helps form larger molecules

Sucrase + Sucrose --> glucose and fructose