Dark matter (23% of universe). Dark energy (73 ... Atkins

1
Why Study Cell Chemistry?

• Chemistry
• Atom smallest unit of matter (4 of universe).
• Quarks, quirks, strings,
• Dark matter (23 of universe).
• Dark energy (73) ? expanding universe ? end of
  life
• Cell
• Basic unit of life
• Suns Energy
• Light energy
• Stored and transferred in chemical bonds.
• Metabolism
• Chemical reactions in your cells.

2
Periodic Table Properties of Elements

• Elements basic substance of matter
• 103 elements
• 6 elements (CHNOPS) 95 of
  you
• others are Cl, Ca, Mg, Na, K
• Trace Fe, Zn, Co, I, Cu, F

See figure 2.3 page 21
3
Atoms Smallest Unit of Matter.

• Carbon Atom Example
• Three subatomic particles
• Electric
• Mass Charge
• Protons 1 1 atomic number 6
• Neutrons 1 0 mass atomic number
  6
• Electrons 0 -1 protons 6

12.01 in Periodic Table
C
Mass Number
12
Atomic Symbol
Atomic Number
6
4
Isotopes Atoms of an Element Differing in
Neutrons

• 126C 136C
  146C
• electrons 6 6
  6
• protons 6
  6 6
• neutrons 6
  7 8
• Radioactive Isotopes
• Uses
• Carbon Dating
• Medical and Plant Tracers
• Sterilize
• Mutagens

5
Bohr Models Location of Electrons. Shells
Energy Levels
See figure 2.6 page 22
Energy Increases with distance from nucleus.
M
L
K
Orbital Shells Octet (8) Rule

6
Atoms Pick Up and Give Off Energy
Energy released as chemical energy,
electron drops to lower orbit
Suns energy captured, pushing electron to outer
orbit.
Photosynthesis
Respiration
7
Atoms Form Molecules and Compounds

• Chemical bonds contain energy
• Molecule
• Compound
• Electron swapping or sharing is chemical bonding.
• Types of Bonds
• Ionic Bonds
• Covalent Bonds
• Polar Bonds
• Non-polar Bonds
• Hydrogen Bonds
• Peptide Bond

8
Ionic Bonds Transfer of Electrons
Very strong bonds Ions
Ions Transfer Electrons Na
Cl- neutrons 11
18 protons 11
17 electrons
11 ? 10 2 8 17 ? 18 2 8 8
How does salt dissolve in water?
See figure 2.7 page 24

9
Covalent Bonds Share Electrons Between Atoms
Key energy carrying bonds in living organisms.
Strong bonds
Polar Non-polar
See figure 2.8 page 25
3D shape determines functional role.
10
The Properties of Water Polar Covalent and
Hydrogen Bonds
Polar Covalent Bond larger oxygen dominates
smaller hydrogen

Hydrogen Bond Electronegativity
See figure 2.9 page 26
.
11
The Properties of Water Polar Covalent Bonds (P)
and Hydrogen Bonds (H)

• High Heat Capacity (H)
• High Heat of Vaporization (H)
• Solvent (P)
• Hydrophilic
• Hydrophobic
• Cohesive and Adhesive (H P)
• Cohesive
• Adhesive
• High Surface Tension (H)
• Solid Less Dense Than Liquid (H)

See text drawings page 28 29
Hill CD Basilisk Lizard
12
pH Scale (0 14) Measures Acid Base of
Solutions
pH negative log H. power of
hydrogen Each number 10x
greater pH 6 1 x 10-6
pH 7 1 x 10-7 Neutral solutions pH7
H OH- H2O ? H OH- ? H2O
Acid pH 0 to 6 Have more H than
OH-. HCL ? H CL- Base pH 8
to14 Have more OH- than H. NaOH ?
Na OH-
Blood pH 7.4 Tears pH 7.0 Cells pH 6.8
Acid Rain pH4 pH5
Figure 2.13 page 30
13
Buffers Maintain Your Body Homeostasis

• Buffers
• Homeostasis
• Acidosis pH lt 7.4
• Alkalosis ph gt 7.4
• Increased Acid
• C6H12O6 O2 ? CO2 H2O ? H2CO3 H2O ? H
  HCO3-
• 
  
• Increased Base
• C6H12O6 O2 ? CO2 H2O ? H2CO3 H2O ? H
  HCO3-
• Orange Juice increases acid
• HC6H7O6 ? H (blood) C6H7O6

Hypoventilation
?
?
Acid
Base
?
?
Hyperventilation
14
Organic Molecules versus Inorganic Molecules

• Inorganic (non-living)
• Usually ions /-
• Usually ionic bonding
• Smaller molecule
• Examples
• Ca in bones
• P F for teeth
• Fe Cu blood hemoglobin
• K Na nerves
• Cl water balance
• Mg protein synthesis
• I in thyroid hormone

• Organic (living)
• Always C H
• Always covalent bonding
• Larger molecules
• Classes
• Carbohydrates
• Lipids
• Proteins
• Nucleic Acids

Biochemistry
15
Organic Molecules Contain Energy For Growth
Development

• Photosynthesis
• Solar Energy H2O CO2 ? C6H12O6 O2
• Respiration
• ATP H2O CO2 ? C6H12O6 O2
• How?
• Covalent Bonds
• glucose bonds formed
• glucose bonds broken
• WHY?

16
Carbon is the Key Element of LIFE.

• Diversity of molecules diversity of life
• 4 electrons in outer shell
• C - C backbone
• Isomers
• Functional groups (R)

See figures page 36
17
Functional Groups (R) Add Reactivity and Diversity

• How?
• Specific structure
• Specific reaction.
• Unique chemical characteristics.

See figures page 37
18
Four Classes of Organic Macromolecules
19
Four Classes of Organic MacromoleculesMacro
Large in size
Biological Compounds
Nucleic Acids
Proteins
Carbohydrates
Lipids
DNA, RNA, ATP
Fat, oil, wax or steroid
Simple Sugars
Amino acids
20
How Do You Make And Breakup Macromolecules?
Remove water to MAKE a polymer
See figure 3-5 page 38
Add water to BREAKUP a polymer
Polymer Macromolecules Monomer Building Blocks
H2O
H2O
21
Carbohydrates (-ose) Monosaccharides
Your Immediate Energy Source Hexoses glucose
(grapes blood) Glucose major
source of cellular energy for all living
things. Pentoses ribose (RNA), deoxyribose
(DNA), fructose (fruit, honey)
See figure 3.7 page 39
Disaccharides lactose (milk) glucose
galactose maltose (beer
) glucose glucose sucrose
(table sugar) glucose fructose (sugar cane
sugar beets)

22
Carbohydrates Polysaccharides Starch and
Glycogen Provide Short Term Energy.
Storage molecule large, not as soluble,
difficult passing through plasma membrane
Starch for plants amylose and amylopectin
See figure 3.8 page 40
Glycogen for animals in liver
23
Corn Seed Germination
Starch
Endosperm Aleurone Cells Storage Protein
Hydrolysis
Sugar

• Stored protein broken into
• amino acids by hydrolysis
• Amino acids produce
• amylase enzyme that
• breaks stored starch into
• glucose by hydrolysis.
• Glucose feeds the embryo
• during respiration.

Amylase
Hydrolysis
Amino Acids
DNA
Growth
GA3
H2O
24
Glucose As Your Source of Energy

• Provides energy to cells
• C6H12O6 O2 ? H2O CO2 ATP
• Glucose is blood sugar.
• Dont eat
• Hypoglycemia
• Diabetes

Raises Blood Sugar
High Blood Sugar
Promotes Insulin Release
Glucagon stimulates breakdown of glycogen
Liver
Pancreas
Glucose Glycogen
Formation of Glycogen
Insulin
Glucose uptake from blood
Promotes Glycogen release
Liver Fat Muscle
Tissue Cells
Lowers Blood Sugar
Low Blood Sugar
25
Diabetes (High Blood Glucose)

• Type 1
• Juvenile or insulin-dependent (5 10)
• Type 2
• Adult diabetes or non-insulin dependent (90 95
• Type 3
• Insulin problem in brain cells ? Alzheimer's?

Insulin rDNA technology production using E.
coli bacteria Humalog C257H383N65O77S6 788
atoms Lantus C267H404N72O78S6 827 atoms
26
Carbohydrates Polysaccharides Cellulose
(plants), Chitin (shell fish), Peptidoglycan
(bacteria) are for Structure.
Cellulose is most abundant organic molecule on
earth.
Strength due to hydrogen and covalent bonds
See figure 3.9 page 41
27
Lipids saturated bad, unsaturated better and
omega-3 best.
Monomer triglycerides Glycerol 3 fatty
acids Insoluble in water Provide long-term
energy.
See figure 3-11 page 43
Oils
Fats
28
The Skinny About DietsAtkins, South Beach,
Zone, Learn, Ornish

• Low Fat Diet
• Reduce fat ? reduce calories ? reduce weight.
• Low Carbohydrate
• Burn fat for energy instead of glucose reduce
  weight.
• Low Calorie
• Best approach is to eat less, reduce calories,
  reduce weight.

29
Human Energy Storage

• Energy Amount
  Miles Traveled
• Source per Kg Kcal
  at 3 mph
• ATP 0.1 10
  0.2
• Glycogen 0.4 1,700
  0.3
• Fat 15.0 135,000
  2,015.0

30
Lipids Phospholipids Plant and Animal Cell
Membrane
Consists of phosphate glycerol polar head 2
fatty acid non-polar tail.
Phospholipids make up the bulk of the plasma
membranes in the cell.
See figure 3.12 page 44
Essential for cell structure and
function. Determine what enters and leaves the
cell.
Hydrophilic
Hydrophobic
31
Lipids Steroids and Waxes
Steroids 4 fused rings plasma membrane and sex
hormones
Steroid medicines.
Male sex hormone testosterone produced in testes.
Female sex hormone estrogen progesterone produce
d in ovaries.
See figure 3.13 page 45
Waxes solid, hydrophobic, fatty acid chain
alcohol chain (beeswax) Protective coating for
plants (apple) and animals (ear wax)
32
Proteins 20 Amino Acids
Importance in structure and function of cells (8
are essential). 100,000 proteins 50 cell
weight Function 1. Support 2.
Enzymes 3. Transport
4. Defense
5. Hormones
6. Motion Amino Acid amino (NH2)
acidic (-COOH) R (remainder of
molecule).
See figure 3.15 page 46
Peptide Bond
Peptide Polypeptide
33
Proteins Four Levels of Protein Structure
Protein shape (structure) determines protein
function.
Peptide Bonds amino acid sequence chain (egg
white 400 amino acids)
See figure 3.17 page 48
Peptide Bonds Hydrogen Bonds fibrous proteins
Peptide Bonds Hydrogen Bonds Covalent Bonds
Ionic Bonds 3D globular proteins
All bonds chaperone proteins Misfolded
Proteins Prions
34
Nucleic Acids Five Nucleotide Monomers Your
Genetic Code is a Nucleotide Polymer
Nucleotide phosphate 5 carbon sugar
nitrogen base
Inorganic ATP has 3 phosphates -P-P-P
See figure 3.19 page 50
DNA Pairing A-T and C-G RNA Pairing A-U and
C-G ATP A
Complementary Base Pairing
35
Nucleic Acids Key Characteristics
36
ATP The Energy Currency () or Carrier in Cells

• ATP Function
• Chemical work
• Transport work
• Mechanical work

Temporary storage of energy in bond between 2nd
3rd P.
See figure 6.3 page 104
37
Metabolism is a Series of Energy Transformations
or Reactions

• Coupled Reactions
• Occur simultaneously
• Exergonic energy released
• ATP drives other reactions
• Endergonic require ATP energy ? muscle
  contraction
• 
  

See figure 6.4 page 105
38
Metabolic Pathways

• Metabolism
• Metabolic Pathway
• A B ? C D ? E F ? G
  
• E1 E2 E3
  
• Each cell regulates which enzymes are present
  activated
• Metabolic reaction
• Linear or Circular
• Substrate
• Enzymes
• Energy (ATP)
• Product produced

Enzymes
AB
CD
G
EF
39
Enzyme Activity

• Proteins initiate speed reactions
• Energy of Activation
• Energy needed for molecules to react.
• Enzymes reduce energy needed

Saltine cracker tastes Sweet in your
mouth. Starch ? Sugar
Se figures 6.5 page 106 and figure 6.6 page 107
40
Speed of Enzyme Reactions

• Increasing speed by increasing enzyme / reactant
  collisions
• 1) Substrate
• 2) Temperature
• Cold slows
• Warm speeds
• Hot kills
• Denatured changes enzyme
• shape
• 3) pH
• 4) Enzyme

See figure 6.8 page108 and Figure 6.10 page 109
41
Enzyme Inhibition Slows or Stops ReactionLock
Key Model
Competitive
Noncompetitive Feed
back Inhibition
Examples Poison Penicilli
n Mercury and Lead
See figure 6.11 page 109