Chemistry of Life

What is Chemistry?

Study of composition of matterWhat is matter?

anything that takes up space and has massWhy mass? Not weight?

B/c weight changes but mass is constantWhat is an element?

a substance consisting of only one type of atom

On Earth, 92 elements occur naturally, and 25 of them are essential to living organisms

Ex: C, H, O, N, Ca, P, K, S, Na, Cl, Mg

What are 4 elements that make up >96% of mass of a human?

Carbon, Hydrogen, Oxygen, Nitrogen

Trace elements

essential elements that present in living things in very small amount (less than 0.01%)

What is an atom?

Nucleus (+ proton & 0 neutron) in center and – electron cloud out side

Compoundsa substance that contains 2 or more

elements into a fixed ratioex: water (H2O), glucose (C6H12O6)

Compounds are made by bonding elementsIonic bond

by mutual attraction of 2 ions of opposite chargeex: Sodium Chloride (Na+Cl-)

Covalent bondby sharing electronsex: H2, CH4, H2O

Hydrogen bondby attraction of opposite charge b/w Hydrogen and OxygenIt holds and stabilize many large biological molecules such as proteins and DNA

How do the unique chemical and physical properties of water make life on earth possible?

Water Structure

Held together by covalent bond

Neutral in charge as a whole

PolarUnequal distribution

of charge Is the basis for

hydrogen bond

Hydrogen Bond

Formed by attraction of opposite charge b/w hydrogen and oxygen

Important to properties of water and to DNA replication

Properties of WaterStrong Cohesion

Tendency of molecules to stick togetherHigh Surface Tension

A measure of how difficult it is to stretch or break the surface of a liquid

High Specific HeatAmount of heat that must be absorbed or lost to

change its temperatureHigh Heat of vaporization

Quantity of heat a liquid must absorb to be converted from the liquid to the gaseous state

Universal solventDissolving agent of a solution

Strong Cohesion (and adhesion)

High Surface Tension

Evaporative cooling

Density of Water

Ice less dense than liquid water Ocean and lakes don’t

freeze solid because ice floats

Ice protects the liquid water below from colder air

If liquid water were less dense tan ice Ice will sink and all

ponds, lakes and ocean would freeze solid

Life on Earth would not be possible

pHa measure of how acidic or basic a solution is. Scale of pH is 0-14Acids

any substances that form hydrogen ion (H+) in water pH below 7

Basesany substances that form hydroxide ion (OH-) in water pH above 7

Bufferssubstances that resist change in pH by accepting or donating hydrogen ionprevent sharp change in pHcontrolling pH is important for maintaining homeostasis

Acid Rainrain or snow with a pH below 5.6causes: air-pollutants; sulfur oxide and

nitrogen oxide from burning of fossil fuelEffects: damages forest, other lands,

lakes, and streams (kills trees and fish)

Biologically important macromolecules

How do structure of biologically important molecules (Carbohydrates, lipids, proteins, and Nucleic Acids) account for their functions?

PROPERTIES OF ORGANIC COMPOUNDS

Contains Carbon 4 electron in the outer shell of carbon allow

it to form complex structuresHydrocarbon

compound composed of only carbon and hydrogen Ex: methane, ethane, propane, etc.

Isomerscompounds that have same simple

(molecular) formula but different 3-d structuresEx: glucose & fructose (simple formula C6H12O6)

PROPERTIES OF ORGANIC COMPOUNDS

MacromoleculesMonomers

The fundamental molecular unit; building block of polymers

PolymersA large molecule formed by bonding many

smaller molecules ; usually in long chains

Therefore, cells build macromolecules by forming a chainEx: DNA, RNA, Protein, Polysaccharides

HOW DO CELLS COMBINE MONOMERS TO MAKE POLYMERS?By Dehydration Synthesis

Cells link monomers together to form polymers by removing a water moleculeEx: Glucose to StarchEx: Amino Acids to Proteins

HOW DO CELLS BREAK DOWN POLYMERS INTO MONOMERS?

By Hydrolysis“Breaking (lyse) apart with water (hydro-)”Cells break down macromolecules into

monomersex: Starch to glucoseex: ATP to ADP

CarbohydratesLipidsProteinsNucleic Acids

4 organic compounds

CARBOHYDRATES

Composed of Carbon, Hydrogen, and Oxygen

Categorized by size(A) Monosaccharides(B) Disaccaharides(C) polysaccharides

(A) MONOSACCHARIDES

Simple sugarsC:H:O::1:2:1Glucose (plants)Fructose (fruits)Galactose (milk)Functions

Readily available energy

(B) DISACCHARIDES

Double sugarsMaltose (glucose + glucose)Sucrose (glucose + fructose)Lactose (glucose + galactose)Functions

Transport form of sugars in plantsAvailable to be break down for energy

How would we combine glucose and fructose to make sucrose?

Dehydration Synthesis

By removing a water molecule and bonding them together

How do we digest or break down lactose into glucose and galactose?

Hydrolysis

To break down a disaccharide, add the water back

(C) POLYSACCHARIDES

Many sugarsGlycogenStarch Cellulose ChitinFunctions

Storage forms of energyStructural molecules

LIPIDS

Composed of carbon, hydrogen, and oxygenC:H:O::1:2:1Subunits

triacylglycerol and 3 fatty acids Triacylglycerol- 3 carbon alcohol Fatty acids- chain of 16 or 18 carbons with a carboxyl group

Hydrophobic naturedue to nonpolar C-H bonds in the hydrocarbon chains of fatty acids

BIOLOGICALLY IMPORTANT LIPIDS

(A) Fats and oils(B) Waxes(C) Steroids(D) Phospholipids

(A) FATS AND OILS

Saturated fatty acids

Animal fats

single bond between the carbon atoms of hydrocarbon chain

Unsaturated fatty acids

Vegetable oils

one or more double bonds, formed by the removal of hydrogen atoms from the carbon skeleton

(A) FATS AND OILS

Formed by which process?

Dehydration Synthesis

Functions

1. Storage form of energy

2. insulation (fat)

3. Cushioning (fat)

(B) WAXES

Where are they naturally found? coats on leaves, fruits, animal skin,

feather, fur

Function

prevent water loss

(C) STEROIDS

Are based on cholesterolFunctions

1. Components of animal cell membrane and myelin sheaths

2. metabolic regulation

(a) makes hormones

(b) sex hormones are steroids

(D) PHOSPHOLIPIDS

Function

1. A major component of cell membrane

2. Affects transport across the membrane

Characteristics Hydrophilic heads

Hydrophobic tails

PROTEINS

Composed of carbon, hydrogen, oxygen, nitrogen, and sulfur

SubunitsAmino Acids

Formed by peptide bond between amino acids by dehydration synthesis

Involved in almost everything organisms do

TYPES OF PROTEINS

1. Structural proteins- collagen

2. Storage proteins- albumin

3. Transport proteins- hemoglobin

4. Defensive proteins- antibodies

5. Contractile proteins- actin, myosin

6. Receptor proteins- neuro-receptors

7. Hormonal proteins- insulin

8. Enzyme/Biocatalysts- gastrin

PROTEINS4 Levels of organization in proteins 1. Primary Structure

Linear sequence of amino acids

2. Secondary structureBased on hydrogen bonding betweenamino and carboxyl group

3. Tertiary structureBased on bonding between R group

4. Quaternary structure Results from intertwining 2 or more amino acid chains

PROTEINS

What determines Protein Conformation?

The sequence of the polypeptideDenaturaton

The loss of protein conformationWhat causes the denaturation?

Physical & Environmental alteration such as pH, temperature, salt concentration

How do enzymes regulate the rate of chemical reactions?

Enzyme is a catalyst; a protein that speeds up a chemical reaction

(without itself being changed into a different molecules in the process) by lowering the required activated energy

How does the specificity of an enzyme depend on its structure?

Enzymes are substrate-specific (Key-lock relationship)

How does the activity of an enzyme regulated?

Temperature, pH, and some chemicalsOptimal condition for Enzyme activity

Temperature 35-40 °C (close to our normal body temperature)

pH of 6-8Cofactor and coenzyme

Cofactor: non-protein helperex: magnesium is a cofactor that is essential for the

proper functioning of chlorophyllCoenzyme: organic cofactors (most Vitamins)

InhibitorsBlock substrate from entering active sitesEx: Penicillin

NUCLEIC ACIDS

Composed of carbon, hydrogen, oxygen, nitrogen, and phosphorus

Subunit: Nucleotide3 components of nucleotidePentose (5-carbon sugar)Phosphate groupNitrogen base

2 typesDNA & RNA

DNA

Double Helix

Master copy of an organisms’s information (gene) code

DNA nucleotide

1. Deoxyribose2. Phosphate group3. Nitrogen base Purines

Adenine (A)Guanine (G)

PyrimidinesCytosine (C) Thymine (T)

RNA

Single Strand

Process genetic instructions to use in building proteins

RNA nucleotide1. Ribose2. Phosphate group3. Nitrogen base Purines

Adenine (A)Guanine (G)

PyrimidinesCytosine (C)Uracil (U)