Download Chemistry of Life biochemistry CHS

Chemistry of
Life
 What is Chemistry?
Study of composition of matter
 What is matter?
anything that takes up space and has mass
 Why mass? Not weight?
B/c weight changes but mass is constant
 What 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
 Compounds
a substance that contains 2 or more
elements into a fixed ratio
ex: water (H2O), glucose (C6H12O6)
Compounds are made by bonding
elements
Ionic bond
by mutual attraction of 2 ions of opposite charge
ex: Sodium Chloride (Na+Cl-)
Covalent bond
by sharing electrons
ex: H2, CH4, H2O
Hydrogen bond
by attraction of opposite charge b/w Hydrogen
and Oxygen
It 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
 Polar
Unequal 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 Water
Strong Cohesion
Tendency of molecules to stick together
High Surface Tension
A measure of how difficult it is to stretch or
break the surface of a liquid
High Specific Heat
Amount of heat that must be absorbed or lost to
change its temperature
High Heat of vaporization
Quantity of heat a liquid must absorb to be
converted from the liquid to the gaseous state
Universal solvent
Dissolving 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
pH
a measure of how
acidic or basic a
solution is.
Scale of pH is 0-14
Acids
any substances that
form hydrogen ion
(H+) in water
pH below 7
Bases
any substances that
form hydroxide ion
(OH-) in water
pH above 7
Buffers
substances that resist change in pH by
accepting or donating hydrogen ion
prevent sharp change in pH
controlling pH is important for maintaining
homeostasis
Acid Rain
rain or snow with a pH below 5.6
causes: air-pollutants; sulfur oxide and
nitrogen oxide from burning of fossil
fuel
Effects: 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 structures
Hydrocarbon
compound composed of only carbon and
hydrogen Ex: methane, ethane, propane, etc.
Isomers
compounds that have same simple
(molecular) formula but different 3-d
structures
Ex: glucose & fructose (simple formula C6H12O6)
PROPERTIES OF ORGANIC COMPOUNDS
Macromolecules
Monomers
The fundamental molecular unit; building block
of polymers
Polymers
A large molecule formed by bonding many
smaller molecules ; usually in long chains
Therefore, cells build macromolecules by
forming a chain
Ex: 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 molecule
Ex: Glucose to Starch
Ex: 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
monomers
ex: Starch to glucose
ex: ATP to ADP
4 organic compounds
Carbohydrates
Lipids
Proteins
Nucleic Acids
CARBOHYDRATES
Composed of Carbon, Hydrogen,
and Oxygen
Categorized by size
(A) Monosaccharides
(B) Disaccaharides
(C) polysaccharides
(A) MONOSACCHARIDES
Simple sugars
C:H:O::1:2:1
Glucose (plants)
Fructose (fruits)
Galactose (milk)
Functions
Readily available energy
(B) DISACCHARIDES
Double sugars
Maltose (glucose + glucose)
Sucrose (glucose + fructose)
Lactose (glucose + galactose)
Functions
Transport form of sugars in plants
Available 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 sugars
Glycogen
Starch
Cellulose
Chitin
Functions
Storage forms of energy
Structural molecules
LIPIDS
 Composed of carbon, hydrogen, and oxygen
 C:H:O::1:2:1
 Subunits
 triacylglycerol and 3 fatty acids
Triacylglycerol- 3 carbon alcohol
Fatty acids- chain of 16 or 18 carbons with a carboxyl group
 Hydrophobic nature
due 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 cholesterol
Functions
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
Subunits
Amino 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
PROTEINS
4 Levels of organization in proteins
1. Primary Structure
Linear sequence of amino acids
2. Secondary structure
Based on hydrogen bonding between
amino and carboxyl group
3. Tertiary structure
Based 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 polypeptide
 Denaturaton
The loss of protein conformation
 What 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 chemicals
Optimal condition for Enzyme activity
 Temperature 35-40 °C (close to our normal body
temperature)
 pH of 6-8
 Cofactor and coenzyme
Cofactor: non-protein helper
 ex: magnesium is a cofactor that is essential for the
proper functioning of chlorophyll
Coenzyme: organic cofactors (most Vitamins)
 Inhibitors
 Block substrate from entering active sites
 Ex: Penicillin
NUCLEIC ACIDS
 Composed of carbon, hydrogen, oxygen,
nitrogen, and phosphorus
 Subunit: Nucleotide
3 components of nucleotide
Pentose (5-carbon sugar)
Phosphate group
Nitrogen base
 2 types
DNA & RNA
DNA
RNA
 Double Helix
 Single Strand
 Master copy of an organisms’s
information (gene) code
 Process genetic instructions
to use in building proteins
 DNA nucleotide
 RNA nucleotide
1. Ribose
2. Phosphate group
3. Nitrogen base
1. Deoxyribose
2. Phosphate group
3. Nitrogen base
 Purines
 Adenine (A)
 Guanine (G)
 Pyrimidines
 Cytosine (C)
 Thymine (T)
 Purines
 Adenine (A)
 Guanine (G)
 Pyrimidines
 Cytosine (C)
 Uracil (U)