Download Lecture 3 Chemistry

Survey
yes no Was this document useful for you?
   Thank you for your participation!

* Your assessment is very important for improving the work of artificial intelligence, which forms the content of this project

Document related concepts

Atomic theory wikipedia, lookup

Molecular dynamics wikipedia, lookup

History of molecular theory wikipedia, lookup

IUPAC nomenclature of inorganic chemistry 2005 wikipedia, lookup

Computational chemistry wikipedia, lookup

Physical organic chemistry wikipedia, lookup

Biochemistry wikipedia, lookup

Unbinilium wikipedia, lookup

Ununennium wikipedia, lookup

Rutherford backscattering spectrometry wikipedia, lookup

Isotopic labeling wikipedia, lookup

Electrolysis of water wikipedia, lookup

Redox wikipedia, lookup

Chemical thermodynamics wikipedia, lookup

Radical (chemistry) wikipedia, lookup

Bohr model wikipedia, lookup

Atomic orbital wikipedia, lookup

Electron configuration wikipedia, lookup

Atomic nucleus wikipedia, lookup

Photosynthetic reaction centre wikipedia, lookup

Ion wikipedia, lookup

Electrochemistry wikipedia, lookup

Molecular orbital diagram wikipedia, lookup

Extended periodic table wikipedia, lookup

Chemical reaction wikipedia, lookup

Hypervalent molecule wikipedia, lookup

X-ray photoelectron spectroscopy wikipedia, lookup

Resonance (chemistry) wikipedia, lookup

Chemical bond wikipedia, lookup

Metallic bonding wikipedia, lookup

Bent's rule wikipedia, lookup

Metastable inner-shell molecular state wikipedia, lookup

Tennessine wikipedia, lookup

Homoaromaticity wikipedia, lookup

Electronegativity wikipedia, lookup

Bond valence method wikipedia, lookup

History of chemistry wikipedia, lookup

Coordination complex wikipedia, lookup

Chemistry: A Volatile History wikipedia, lookup

Inorganic chemistry wikipedia, lookup

Cocrystal wikipedia, lookup

Aromaticity wikipedia, lookup

Periodic table wikipedia, lookup

Livermorium wikipedia, lookup

Chemical element wikipedia, lookup

Oganesson wikipedia, lookup

Organic chemistry wikipedia, lookup

Adhesion wikipedia, lookup

Artificial photosynthesis wikipedia, lookup

Water splitting wikipedia, lookup

Hydrogen bond wikipedia, lookup

Transcript
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