Download Lecture 3 Chemistry

CHEMISTRY FOR BIOLOGIST
Relevance of Chemistry to biology “Natural Law”
Living Things are made up of Non-Living Components
To understand the way living things function, it is
necessary to understand basic chemical processes
BASIC CHEMISTRY
Living things had same materials (C,H,O) as many non-living
materials, but living material had a different organization
1821 Friedrich Wohler
Inorganic
NH4+NCO-
Organic
NH2CONH2
MATTER
Matter is anything that occupies space and has mass
Properties: Color, Texture, odor, Taste
Lattice –Repeat Units
Crystalline: regular Geometric shape
Amorphous- shapeless
chocolate
glass
soot
Physical Chemical Changes:
Physical – H20 3 phases(solid, liquid, and gas)
Chemical- composition Altered
CH4
CO2 + H20
Structure:
Elements of Life
Elements: made up of Atoms - 92 occur naturally
H- hydrogen
O- oxygen
Cl- chloride
Na- sodium (latin: natrium)
K- potassium (latin: kalium)
Fe- iron (latin: ferrum)
20 Essential for Life
CHOPKINS CAFÉ MIGHTY GOOD
TRACE ELEMENTS: Mn,Ca,Co,Zn,B, Mo, Cl, Si
Six elements comprise 99% of Bacterial dry weight
CHNOPS
ATOMS
Atoms: composed of subatomic particles
proton (+), neutrons, and electrons(-)
# protons = atomic number  defines atoms
C=6
N=7
protons + neutrons = atomic mass
protons + neutrons = atomic weight (Daltons)
C: 6+6=12
Isotopes
Isotopes are different Forms of Elements:
Atomic Number the same but Atomic Weights Different
(Neutrons greater Than Protons)
Hydrogen - 1 proton, 0 neutrons (Elemental State)
Deuterium - 1 proton, 1 neutron (Stable isotope)
Tritium -1 proton, 2 neutrons (Radioisotopes)
Radioisotopes are unstable and will degrade naturally
14C
32P
35S
3H
Electron Configuration
Atoms also have Electrons, negatively charged subatomic particles
Arrangement Two dimensionally vs 3-D
1st shell - 2 electrons
2nd Shell - 8 Electrons
3rd Shell - 8 Electrons
4th Shell - 18 Electrons
Outer shell 8 electrons *** Octet
Number of electrons in outer shell determines bonding properties
chemical behavior
Valence Electrons
Element
C
H
O
N
P
S
He
Ca
Na
Cl
# e6
1
8
7
15
16
2
20
11
17
shell #
2+4
1
2+6
2+5
2+8+5
2+8+8
2
2+8+8+2
2+8+1
2+8+7
valence
+4/-4
+1
-2
-3/+5
-3
+2/-6
0
+2
+1
-1
Molecules
Atoms with less than 8 e- in outer shell interact chemically or they
BOND To form molecules
The # and type of BONDS depends on # of electrons
Atoms share/lose or gain to reach stable state
Octet Rule –tendency of atoms to have 8 electrons in outer orbit
(unless the atom is H or P)
“FOOLS “ THE ATOM /THINKS CORRECT # e- for Stability
02
0:0
N2 N N
H2
H:H
Compounds: Atoms With more than one Element
2H+
+ 0-2-  H20
Types of Chemical Bonds
Covalent
Ionic
Hydrogen
Types of Chemical Bonds
Covalent Bonds- Shared Bonds- STRONG Bonds
Non-polar covalent Bonds - EQUAL SHARED ELECTRONS
•Hydrophobic Bonds
•van der Waals forces
Polar Covalent Bonds - UNEQUAL SHARED ELECTRONS
Hydrophilic bonds (likes water)
Some atoms attract electrons more strongly
Electronegativity
Fl
0
N
P
9p
8P
7P
15P
4.0
3.5
3.0
2.1
IONIC Bonds/Weaker than Covalent Bonds
VASTLY Different Electro negativity
ELECTRONS are COMPLETELY REMOVED
ELECTRONS ARE TRANSFERRED FROM 1 ATOM TO ANOTHER
NaCl placed in water
Compound is dissociated when “hydrated”
H20 + NaCl  Na+1
+ Cl-1
Ions (Ionization)
Cation Na+1
Anion Cl-1
Electrolytes
Opposites attract- Electrical Attraction Between atoms
Common Ions
Cations
monovalent: Na+, K+, H+, NH4+
divalent: Ca2+, Mg2+, Fe2+
Anions
Cl-, OH-, HC03-,N03CO32- S042P043-
Hydrogen Bonds
Hydrogen Bonds are much weaker bonds that form between molecules
Rather than within a molecule, e.g. H20
Biological molecules depend on H-Bonding to give shape &
function
DNA
Proteins
Bonds are individually weak but collectively “Strong”
H-Bonds gives water its important Properties
•Elements
•Atoms
•Molecules
•Compounds
•Bonds
•Covalent
•Electronegative
•Dipole Separation of partial Charges
•Ionic
•Hydrogen
Chemical Reactions
Making and Breaking Chemical Bonds
Reactants
Atoms/ions/molecules
Products
Atoms/ions/molecules
Speed of Chemical Reactions depend on:
• Reactants Concentration
• Temperature
• Random collisions
Types of Chemical Reactions
1. Synthesis / DEHYDRATION
2. Decomposition / hydration ADDS WATER
3. Exchange Reactions
Decomposition Chemical Reaction
CATABOLISM
Reverse of synthesis
Exothermic- Release energy
Break bonds of larger molecules to form smaller molecule
Hydrolysis- Water added to reactant
C12H22011 + H20  C6H1206
SUCROSE
GLUCOSE
+ C6H1206
FRUCTOSE
Synthesis
ANABOLISM
Dehydration Synthesis: Two small molecules are joined together
by covalent bonds and a water molecule is formed
Small-R-OH + H-R-Small-- large Molecule + H20
Energy input required: Endothermic Reactions
OH- removed form one Reactant
H- removed from another Reactant
Catabolic /Hydrolysis Reactions
Overall energy is released
X-Y +
H2O  X-H + OH-Y
Anabolic/Synthesis Reactions
Overall energy consuming reactions
X-H + OH-Y

X-Y + HOH
Exchange Reactions
A + BC  AB
+
C
+ CD  AD
+
BC
AB
C6H1206 +
Glucose
A-P-P-P
ATP

C6H1206-P + A-P-P
Glucose-6P
ADP
Sum of Catabolic + Anabolic Rxn = METABOLISM
PROPERTIES OF WATER
1) Water has Thermal Stability (HIGH SPECIFIC HEAT)
2) The High Heat Capacity which causes Evaporative Cooling
3) Due to Polarity & COHESIONESS, Water is an Excellent
Solvent for Polar Compounds
4)Water Molecules are attracted to each Other giving Cohesion
and Adhesion-Surface Tension
5) Solid Water Floats??
Acids, Bases and pH
H+ = Minus an electron is a Proton
H20 ---------- H+
+
OH-
SOLUTIONS WITH > H+ THAN OH- (Hydroxyl) is Acidic
SOLUTIONS WITH > 0H- THAN H+ is Basic
ACID: HCL----- H+
COOH--- H+
BASE: NaOH--- Na+
NH2----- NH3+
+ Cl+ COO+ OH-
pH Scale
Measures Whether Solution is Acidic, Basic or Neutral
pH= -log[H+]
Neutral is pH 7, or [H+] Concentration of 10-7
Higher [H+] gives lower pH value
[H+] = 10-3, pH = 3 Acidic
[H+] = 10-12, pH = 12
BUFFERS
BUFFERS CONSIST OF AN ACID AND ITS CORRESPONDING
BASE
Buffers Minimize Changes in pH by Absorbing or releasing H+
K2HP04
+ H+---------- KH2P04
KH2P04
+ OH+---------- K2HP04
Organic Compounds
Carbon Skelton: C-C-C
Hydrocarbon – Saturated-All H’s
HYDROPHOBIC/NON POLAR
Function Groups Added-Unsaturated
Hydrophilic
Contains Electronegative Elements
O/N/P/S
Carbon
Building block of life
Component of every organism
Component of daily diet, fuel, clothing
6 million cps/1000/yr new
250,00 inorganic cpds
Organic cpds- C-C covalent bondingSTABLE
Inorganic cpds NO C-C Ionic bonding
UN-Stable
Organic Chemistry
Biochemistry
Hydrocarbons
Alcohol
Aldehyde
Ketone
Organic acid
Carbon dioxide
Stoichiometry of REDOX Processes
• Oxidation Level, OX, Imaginary Charge of
an Element being stabilized in a molecule
compared with corresponding low stability
of the single atom
• Major elements in OM: C, O, H, N, S
• ED Not EA
Valence Electron Orbit
N=2n2
• shell: 2
• 2nd shell:8
• 3rd shell: 18
st
1
Atomic #
1
6
7
8
11
12
15
16
17
Element
H
C
N
O
Na
Mg
P
S
Cl
1st
1
2
2
2
2
2
2
2
2
2nd
3r
4
5
6
8
8
8
8
8
1
2
5
6
7