lecture 3: chemistry of life
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Lecture 3: Chemistry of Life
http://pearl1.lanl.gov/periodic/default.htmhttp://www.chemsoc.org/viselements/pages/pertable_fla.htm
Chemical Benefits and Costs
• Understanding of chemistry provides fertilizers, medicines, etc.
• Chemical pollutants damage ecosystems
Bioremediation
Use of living organisms to withdraw harmful substances
from the environment
ElementsElements• Fundamental forms of matter
• Can’t be broken apart by normal means
• 92 occur naturally on Earth
Less than 12 occur on the examLess than 12 occur on the exam
Most Common Elements in Living Organisms
Oxygen
Hydrogen
Carbon
Nitrogen
What Are Atoms?
• Smallest particles that retain properties
of an element
• Made up of subatomic particles:
– Protons (+)
– Electrons (-)
– Neutrons (no charge)
Fig. 2.3, p. 22
HYDROGEN HELIUM
electron
proton
neutron
Hydrogen and Helium Atoms Hydrogen and Helium Atoms
Atomic NumberAtomic Number
• Number of protons
• All atoms of an element have the same atomic number
• Atomic number of hydrogen = 1
• Atomic number of carbon = 6
Mass NumberMass Number
Number of protons
+Number of neutrons
Isotopes vary in mass number
Atomic MassAtomic Mass
IsotopesIsotopes• Atoms of an element
with different numbers of neutrons (different mass numbers)
• Carbon 12 has 6 protons, 6 neutrons
• Carbon 14 has 6 protons, 8 neutrons
RadioisotopesRadioisotopes• Have an unstable
nucleus that emits energy and particles
• Radioactive decay transforms radioisotope into a different element
• Decay occurs at a fixed rate
Radioisotopes as TracersRadioisotopes as Tracers• Example: Tracer Drug Study
– How long does a drug stay in the patient?– Determine dose guidelines
• Compound synthesized with a radioisotope
• Emissions from the tracer can be detected with special devices– Track levels in the blood, urine and feces
• Following movement of tracers is useful in many areas of biology
High SensitivityHigh Sensitivity
Very Low DoseVery Low Dose
Other Uses of RadioisotopesOther Uses of Radioisotopes• Drive artificial pacemakers• Internal structure
– Thyroid and bone scans
• Radiation therapyEmissions from some radioisotopes can destroy cells. Some radioisotopes are used to kill small cancers.
Thyroid ScanThyroid Scan
• Measures health of thyroid by detecting radioactive iodine taken up by thyroid gland
normal thyroid enlarged cancerous
What Determines Whether What Determines Whether Atoms Will Interact?Atoms Will Interact?
ElectronsElectrons
• Carry a negative charge
• Repel one another
• Are attracted to protons in the nucleus
• Move in orbitals - volumes of space that surround the nucleus
Z
X
When all p orbitals are full
y
Electron OrbitalsElectron Orbitals
• Orbitals can hold up to two electrons
• Atoms differ in the number of occupied orbitals
• Orbitals closest to nucleus are lower energy and are filled first
Shell ModelShell Model
• First shell
– Lowest energy
– Holds 1 orbital with up to 2
electrons
• Second shell
– 4 orbitals hold up to 8
electrons
CALCIUM20p+ , 20e-
Electron VacanciesElectron Vacancies
• Unfilled shells make atoms likely to react
• Hydrogen, carbon, oxygen, and nitrogen all have vacancies in their outer shells
CARBON6p+ , 6e-
NITROGEN7p+ , 7e-
HYDROGEN1p+ , 1e-
Chemical Bonds, Molecules, Chemical Bonds, Molecules,
& Compounds& Compounds• Bond is union between electron
structures of atoms
• Atoms bond to form molecules
• Molecules may contain atoms of only one element - O2
• Molecules of compounds contain more than one element - H2O
Chemical BondsChemical Bonds
Electrostatic
Covalent
Metallic
1. Ionic Bonding1. Ionic Bonding
• One atom loses electrons, becomes positively charged ion
• Another atom gains these electrons, becomes negatively charged ion
• Charge difference attracts the two ions to each other
Ion FormationIon Formation
• Atom has equal number of electrons and protons - no net charge
• Atom loses electron(s), becomes positively charged ion
• Atom gains electron(s), becomes negatively charged ion
Formation of NaClFormation of NaCl
• Sodium atom (Na) – Outer shell has one electron
• Chlorine atom (Cl) – Outer shell has seven electrons
• Na transfers electron to Cl forming Na+ and Cl-
• Ions remain together as NaCl
7mm
SODIUMATOM11 p+
11 e-
SODIUMION
11 p+
10 e-
electron transfer
CHLORINEATOM17 p+
17 e-
CHLORINEION
17 p+
18 e-
Fig. 2.10a, p. 26
Formation of NaClFormation of NaCl
2. Covalent Bonding2. Covalent Bonding
Atoms share a pair or pairs of electrons to fill outermost shell
•Single covalent bond
•Double covalent bond
•Triple covalent bond
Two Flavors of Two Flavors of Covalent BondsCovalent Bonds
Non-polarNon-polar Covalent Covalent• Atoms share electrons
equally• Nuclei of atoms have
same number of protons
• Example: Hydrogen gas (H-H)
PolarPolar Covalent Covalent• Number of protons in
nuclei of participating atoms is NOT equal
• Molecule held together by polar covalent bonds has no NET charge
• Electrons spend more time near nucleus with most protons– Example: Water – Electrons more attracted
to O nucleus than to H nuclei
Example+
O
H H
slight negative charge at this end
slight positive charge at this end
molecule hasno net charge( + and - balanceeach other)
KEEP YOUR EYE ON THE ELECTRONS
Hydrogen BondingHydrogen Bonding
A bond by Hydrogen between two atoms
• Important for O and N
• Lets two electronegative atoms interact– The H gives one a net + and the other one
that is still – is attracted to it.
• The H proton becomes “naked” because its electron gets pulled away.
Hydrogen bond figure
- -
- + -
Like Charge Atoms Repel Each Other
Opposite Charge Atoms Attract Each Other
KEEP YOUR EYE ON THE ELECTRONS
onelargemolecule
anotherlargemolecule
a largemoleculetwistedbackonitself Fig. 2.12, p. 27
Examples of Hydrogen BondsExamples of Hydrogen Bonds
Properties of WaterProperties of Water
•Polarity
•Temperature-Stabilizing
•Cohesive
•Solvent
Water Is a Polar Water Is a Polar Covalent MoleculeCovalent Molecule
• Molecule has no net charge
• Oxygen end has a slight negative charge
• Hydrogen end has a slight positive charge
O
H H
O
H
HO
H
H
+ _
++
+
_
+
+
Liquid WaterLiquid Water
Hydrophilic & HydrophobicHydrophilic & HydrophobicSubstancesSubstances
• Hydrophilic substances– Polar– Hydrogen bond with water – Example: sugar
• Hydrophobic substances– Nonpolar– Repelled by water– Example: oil
Temperature-Stabilizing Temperature-Stabilizing EffectsEffects
• Water absorbs a lot more heat than oil before its temperature rises.
• Why?
• Much of the added energy disrupts hydrogen bonding rather than increasing the movement of molecules
Evaporation of WaterEvaporation of Water
• Large energy input can cause individual molecules of water to break free into air
• As molecules break free, they carry away some energy (lower temperature)
• Evaporative water loss is used by mammals to lower body temperature
Why Ice FloatsWhy Ice Floats
• In ice, hydrogen bonds lock molecules in a lattice
• Water molecules in lattice are spaced farther apart then those in liquid water
• Ice is less dense than water
Water CohesionWater Cohesion• Hydrogen bonding holds
molecules in liquid water together
• Creates surface tension
• Allows water to move as continuous column upward through stems of plants
Water Is a Good SolventWater Is a Good Solvent
• Ions and polar molecules dissolve easily in water
• When solute dissolves, water molecules cluster around its ions or molecules and keep them separated
Fig. 2.16, p. 29
Na+
Cl–
– –
––
––
–
––
– –
+ ++
+
+
+
+
+
+
+
+
++ +
+
+
+
+
Spheres of HydrationSpheres of Hydration
WaterWater
• Solvent- polar– Keeps ions in solution– Doesn’t dissolve membranes
• Heat management– Loosing heat– Holding heat– Density Changes
If it wasn’t ugly enough already: If it wasn’t ugly enough already:
Hydrogen Ions: HHydrogen Ions: H++
• Unbound protons
• Have important biological effects
• Form when water ionizes
The pH ScaleThe pH Scale
• Measures H+ concentration of fluid• Change of 1 on scale means 10X
change in H+ concentration
Highest H+ Lowest H+
0---------------------7-------------------14Acidic Neutral Basic
Examples of pHExamples of pHPure water is neutral with pH of 7.0
Acidic
Basic
Acids & BasesAcids & Bases
• Acids
– Donate H+ when dissolved in water
– Acidic solutions have pH < 7
• Bases
– Accept H+ when dissolved in water
– Acidic solutions have pH > 7
BuffersBuffersMinimize shifts in pH
• When blood pH rises, carbonic acid dissociates to form bicarbonate and H+
H2C03 -----> HC03- + H+
• When blood pH drops, bicarbonate binds H+ to form carbonic acid
HC03- + H+ -----> H2C03
AcidosisAcidosis
AlkalosisAlkalosis
Carbonic Acid-Bicarbonate Buffer SystemCarbonic Acid-Bicarbonate Buffer System
Lecture 2:Chemistry of Life
Part 2
Organic Compounds
Hydrogen and other elements covalently bonded to carbon
Carbohydrates
Lipids
Proteins
Nucleic Acids
Carbon’s Bonding Behavior
• Outer shell of carbon has 4 electrons; can hold 8
• Each carbon atom can form covalent bonds with up to four atoms
Bonding Arrangements
• Carbon atoms can form chains or rings
• Other atoms project from the carbon backbone
Functional Groups
• Atoms or clusters of atoms that are covalently bonded to carbon backbone
• Give organic compounds their different properties
Examples of Functional Groups
Hydroxyl group - OH
Amino group - NH3+
Carboxyl group - COOH
Phosphate group - PO3-
Sulfhydryl group - SH
Types of Reactions
Functional group transfer
Electron transfer
Rearrangement
Condensation
Cleavage
Condensation Reactions
• Form polymers from subunits
• Enzymes remove -OH from one molecule, H from another, form bond between two molecules
• Discarded atoms can join to form water
Fig. 3.4a, p. 37
enzyme action at functional groups
CONDENSATION
Hydrolysis
• A type of cleavage reaction
• Breaks polymers into smaller units
• Enzymes split molecules into two or more parts
• An -OH group and an H atom derived from water are attached at exposed sites
enzyme action at functional groups
HYDROLYSIS
Fig. 3.4b, p. 37
Carbohydrates
Monosaccharides(simple sugars)
Oligosaccharides(short-chain carbohydrates)
Polysaccharides(complex carbohydrates)
Monosaccharides
• Simplest carbohydrates
• Most are sweet tasting, water soluble
• Most have 5- or 6-carbon backbone
Glucose (6 C) Fructose (6 C)
Ribose (5 C) Deoxyribose (5 C)
Two Monosaccharides
glucose fructose
Disaccharides
• Type of oligosaccharide
• Two monosaccharides covalently bonded
• Formed by condensation reaction
+ H2O
glucose fructose
sucrose
Polysaccharides
• Straight or branched chains of many sugar monomers
• Most common are composed entirely of glucose– Cellulose
– Starch (such as amylose)
– Glycogen
Cellulose & Starch
• Differ in bonding patterns between monomers
• Cellulose - tough, indigestible, structural material in plants
• Starch - easily digested, storage form in plants
Cellulose and Starch
Glycogen
• Sugar storage form in animals
• Large stores in muscle and liver cells
• When blood sugar decreases, liver cells degrade glycogen, release glucose
Chitin
• Polysaccharide
• Nitrogen-containing groups attached to glucose monomers
• Structural material for hard parts of invertebrates, cell walls of many fungi
• Most include fatty acids– Fats– Phospholipids– Waxes
• Sterols and their derivatives have no fatty acids
• Tend to be insoluble in water
Lipids
Fatty Acids
• Carboxyl group (-COOH) at one end
• Carbon backbone (up to 36 C atoms)
– Saturated - Single bonds between carbons
– Unsaturated - One or more double bonds
Three Fatty Acids
stearic acid oleic acid linolenic acid
Fats
• Fatty acid(s)
attached to
glycerol
• Triglycerides
are most
common
Phospholipids
• Main components of cell
membranes
Sterols and Derivatives
• No fatty acids
• Rigid backbone of four
fused-together carbon
rings
• Cholesterol - most
common type in
animals
Waxes
• Long-chain fatty acids linked to
long chain alcohols or carbon
rings
• Firm consistency, repel water
• Important in water-proofing
•Omega-6 fatty acids are the predominant polyunsaturated fatty acids (PUFAs) in the Western diet.
•The omega-6 and omega-3 fatty acids are metabolically distinct and have opposing physiologic functions.
•The increased omega-6/omega-3 ratio in Western diets most likely contributes to an increased incidence of heart disease and inflammatory disorders.
•Omega-3 PUFAs suppress cell mediated immune responses and reduce inflammation
Polyunsaturated Fatty Acids
Omega-3
Omega-6
•Bioactive Lipids•Made in all cells•Short range signaling•Eicosanoids?
•Prostaglandins•Inflammation and Pain Perception•Kidney Function•Bone Development•Reproductive Process
•Commercially Important•$4 BILLION/ Year spend on drugs to inhibit prostaglandin synthesis•Vioxx, Celebrex, Ibuprofen, Asprin
Lipids in Cell Signaling
PGE2
Amino Acid Structure
aminogroup
carboxylgroup
R group
Properties of Amino Acids
• Determined by the “R group”
• Amino acids may be:
– Non-polar
– Uncharged, polar
– Positively charged, polar
– Negatively charged, polar
Protein Synthesis
• Protein is a chain of amino acids linked
by peptide bonds
• Peptide bond
– Type of covalent bond
– Links amino group of one amino acid with
carboxyl group of next
– Forms through condensation reaction
Primary Structure
• Sequence of amino acids
• Unique for each protein
• Two linked amino acids = dipeptide
• Three or more = polypeptide
• Backbone of polypeptide has N atoms:
-N-C-C-N-C-C-N-C-C-N-
Protein Shapes
• Fibrous proteins
– Polypeptide chains arranged as strands or sheets
• Globular proteins
– Polypeptide chains folded into compact, rounded
shapes
• Primary structure influences shape in two main ways:– Allows hydrogen bonds to form between
different amino acids along length of chain
– Puts R groups in positions that allow them to interact
Primary Structure & Protein Shape
Secondary Structure
• Hydrogen bonds form between different parts of polypeptide chain
• These bonds give rise to coiled or extended pattern
• Helix or pleated sheet
Examples of Secondary Structure
Tertiary Structure
Folding as a
result
of interactions
between R
groups
heme group
coiled and twisted polypeptide chain of one globin molecule
Quaternary Structure
Some proteins
are made up of
more than one
polypeptide
chain
Hemoglobin
Polypeptides With Attached Organic Compounds
• Lipoproteins
– Proteins combined with cholesterol, triglycerides,
phospholipids
• Glycoproteins
– Proteins combined with oligosaccharides
Denaturation
• Disruption of three-dimensional shape
• Breakage of weak bonds
• Causes of denaturation:– pH
– Temperature
• Destroying protein shape disrupts function
A Permanent Wave
hair wrapped around cuticles
differentbridges form
bridgesbroken
• Sugar
– Ribose or deoxyribose
• At least one phosphate group
• Base
– Nitrogen-containing
– Single or double ring structure
Nucleotide Structure
Nucleotide Functions
• Energy carriers
• Coenzymes
• Chemical messengers
• Building blocks for
nucleic acids
ATP - A Nucleotide
three phosphate groups
sugar
base
• Composed of nucleotides
• Single- or double-stranded
• Sugar-phosphate backbone
Nucleic AcidsAdenineCytosine
DNA
• Double-stranded • Consists of four
types of nucleotides
• A bound to T• C bound to G
RNA
• Usually single strands
• Four types of nucleotides
• Unlike DNA, contains the base uracil in place of thymine
• Three types are key players in protein synthesis
• Normal metabolic products of one
species that can harm or kill a different
species
• Natural pesticides
– Compounds from tobacco
– Compounds from chrysanthemum
Natural Toxins
Synthetic Toxins
atrazine DDTmalathion
Negative Effects of Pesticides
• May be toxic to predators that help fight pests
• May be active for weeks to years
• Can be accidentally inhaled, ingested, or absorbed by humans
• Can cause rashes, headaches, allergic reactions
Producers Capture Carbon
Using photosynthesis, plants and other producers turn carbon dioxide and
water into carbon-based compounds
Atmospheric Carbon Dioxide
• Researchers have studied concentration of CO2 in air since the 1950s
• Concentration shifts with season– Declines in spring and summer when
producers take up CO2 for photosynthesis
CO2 and Global Warming
• Seasonal swings in CO2 increasing
• Spring decline starting earlier
• Temperatures in lower atmosphere increasing
• Warming may be promoting increased photosynthesis
Humans and Global Warming
• Fossil fuels are rich in carbon
• Use of fossil fuels releases CO2 into atmosphere
• Increased CO2 may contribute to global warming
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