Warm up: Define biochemistry What does “Chemistry of Life” mean?
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Transcript of The Chemistry of Life. Basic Chemistry Matter has mass & takes up spaceElements 25 required for life...
The Chemistry of LifeThe Chemistry of Life
Basic ChemistryBasic Chemistry
MatterMatter has mass & takes up
space
ElementsElements 25 required for life C,H,O,N – make up
96% of living things P,S,Ca,K – most of
the remaining 4%
Trace ElementsTrace Elements Required but only in
minute amounts Some required by all
living things – Fe Others required only
by certain species – Iodine only for vertebrates
Goiters caused by iodine deficiency
www.pipevet.com/photos/goiter.htm
The thyroid gland requires iodine to produce one of it’s hormones.Without iodine, the gland swells. Iodized salt provides enough iodine to prevent this condition.
AtomsAtoms
Smallest units of matter
Composed of protonsprotons (+) and neutronsneutrons in nucleus and electronselectrons (-) in orbitals
www.phschool.com
Periodic Table InformationPeriodic Table InformationAtomic NumberAtomic Number Represents # of
protons Also # of electrons in
a stable atom of an element
Atomic MassAtomic Mass Sum of protons & neutrons Electron mass is small and almost negligible
www.sparknotes.com
Unstable AtomsUnstable AtomsIonsIons Different # of
electrons Atoms with a charge More electrons &
charge is negative Less electrons &
charge is positive
IsotopesIsotopes Different # of neutrons Often radioactive Used as diagnostic tracers
EX: barium, iodine
** The number of protons does not change! This would create an entirely different element.
Diagnostic Tracers
www.nature.com/gimo/contents/pt1/full/gimo29.html
http://student.bmj.com/issues/03/10/education/358.php
BondingBondingAtoms bond in order to fill their valence shell (outer energy level)
Octet RuleOctet Rule The idea that most atoms want 8 electrons
in their outer shell and will share, steal, or give away electrons in order to fill the valence shell
Exceptions are those who have less than 6 total electrons
Covalent BondingCovalent Bonding
Valence electrons (outer shell) are shared
Form molecules
Single, double or triple bonds are possible
www.school-for-champions.com
Types of Covalent BondsTypes of Covalent BondsNonpolar CovalentNonpolar Covalent Electrons are shared
equally EX: O2
Polar CovalentPolar Covalent Electrons are not
shared equally The more
electronegative atom exerts a greater pull on the electrons being shared
EX: H2O
academic.brooklyn.cuny.edu
Electrons are lost or gained from the outer shell in order to fulfill the octet rule
Ionic BondingIonic Bonding
www.school-for-champions.com
Hydrogen BondingHydrogen Bonding
Weak bonds formed between molecules that contain polar covalent bonds
http://trc.ucdavis.edu/biosci10v/bis10v/media/ch02/bond_types.html
Bonding animation: www.biology.arizona.edu
Molecular Molecular Structure vs. FunctionStructure vs. Function
Each molecule has a characteristic size & shape which determine its functionendorphins are brain signal molecules that
fit into specific receptors used in pain suppression & euphoria.
Morphine & heroin mimic the shape of endorphins and produce similar effects when they bind to receptors
www.charisma.org.uk/neuron-p.gif
Endorphin molecule
Morphine molecule
http://www.bio.davidson.edu/Courses/anphys/1999/Self/Ligands.htm
Earth’s Biological Earth’s Biological MediumMedium
PolarityPolarity
Slight charge on either end of the molecule due to the unequal electronegativities of hydrogen & oxygen
This leads to many other properties…
CohesionCohesion
http://www.arroyoseco.org/conservation.htmwww.biology.arizona.edu
AdhesionAdhesion
en.wikivisual.com www.ccs.k12.in.us
Surface TensionSurface Tension
http://faculty.vassar.edu/suter/1websites/bejohns/mateselection/files/female.htm
news.bbc.co.uk/.../photo_galleries/4670308.stm
www.ext.vt.edu
Specific HeatSpecific HeatAmount of heat that must be absorbed or lost for 1g of a substance to change by 1oCWater has high specific heat – it resists temperature changeThis keeps the earth
within viable temperature limits.
www.michigan.org
Evaporative CoolingEvaporative Cooling
www.doggonesafe.com/dog%20communication.htm
AP Photo/Darin Cummings
Density of IceDensity of IceSolid water is less dense than its liquid because as hydrogen bonds freeze, they force molecules further apart
In large bodies of water, a top layer of ice actually insulates the water below
4oC is when water is at its most dense
www.astrobiology.com/lter/album01/179.html
http://www.astrobiology.com/lter/album01/209.html
Universal SolventUniversal SolventWater dissolves many materials creating aqueous solutions (water is solvent, what’s being dissolved is solute)This property is the direct result of water’s polar structure HydrophilicHydrophilic – substances attracted to
water HydrophobicHydrophobic – repel water (or not
attracted)
Water & pHWater & pH
In pure water, even if dissociation occurs, the concentration of H+ and OH- ions is equalWhen acids or bases are added to water, these concentrations change quicklypH is a measure of hydrogen ion concentration on a scale between 0-14
AcidsAcidsChemical compounds that donate H+ ions as they dissociate in solution
EX: HCl H+ Cl-
The more acidic a solution,The higher the H+ concentrationThe lower the pH
Taste sourpH < 7
www.elmhurst.edu
BasesBasesCompounds that accept H+ ions and remove them from solution
Some donate OH- ions
The more basic a solution,The lower its H+ concentrationThe higher its pH value
Taste bitter
www.chemistryland.com
community.tvguide.com
BuffersBuffersSubstances that resist changes in pH
Many of these in the body since even minor changes can be life threatening EX: blood ph is 7.4 CO2 (carbonic acid when dissolved in water)
donates H+ to lower pH HCO3 (bicarbonate) binds excess H+ to raise pH
I am HI am H22OO
Organic CompoundsOrganic Compounds
Functional GroupsFunctional Groups
Parts of organic compounds most commonly involved in chemical reactions
Determine what bonds will be formed and functions of specific compounds
(Structure/Function)
Functional GroupsFunctional Groups
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCHEM2.html
Organic CompoundsOrganic CompoundsAll the compounds found in living things that contain CARBONCARBON
These compounds are divided into 4 families:CarbohydratesLipidsProteinsNucleic Acids
1.1. CarbohydratesCarbohydrates
Their main function is to provide energyenergy
Examples of “carbs” include candy, sugar, pasta, bread, etc.
All contain hydroxyl & carbonyl groups
There are 3 groups of carbohydrates:1. Monosaccharides
2. Disaccharides
3. Polysaccharides
A.A. MonosaccharidesMonosaccharides
Mono = single or simpleSaccharide = sugarThese are simple sugarsExamples are glucose & fructoseMonosaccharides always have the formula CH2O (they are a hydrate of Carbon)EX: glucose formula is C6H12O6
Glucose StructureGlucose Structure
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCHEM2.html
Examples of MonosaccharidesExamples of Monosaccharides
ResearchResearchers have found new evidence that soft drinks sweetened with high-fructose corn syrup (HFCS) may contribute to the development of diabetes, particularly in children. In a laboratory study of commonly consumed carbonated beverages, the scientists found that drinks containing the syrup had high levels of reactive compounds that have been shown by others to have the potential to trigger cell and tissue damage that could cause the disease, which is at epidemic levels. HFCS is a sweetener found in many foods and beverages, including non-diet soda pop, baked goods, and condiments. It is has become the sweetener of choice for many food manufacturers because it is considered more economical, sweeter and more easy to blend into beverages than table sugar. Some researchers have suggested that high-fructose corn syrup may contribute to an increased risk of diabetes as well as obesity
B. DisaccharidesB. Disaccharides
Double sugarsThese are things like sucrose, lactose, and maltoseThey are formed by removing a water to bond monosaccharides together GlycosidicGlycosidic linkage - bond formed between monosaccharides
Dehydration SynthesisDehydration Synthesis
Dehydration SynthesisDehydration Synthesis
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCHEM2.html
Monomers Monomers Polymers Polymers
http://universe-review.ca/I11-10-reactions.jpg
C. PolysaccharidesC. Polysaccharides
Complex sugars
Breads, pastas
We break these down in order to get energy in our body. Water must be added to bust these apart –
HydrolysisHydrolysis
HydrolysisHydrolysis
www.biotopics.co.uk/as/disaccharidehydrolysis.gif
Indicators of CarbohydratesIndicators of Carbohydrates
Benedicts SolutionTurns from blue to orange in
a MONOSACCHARIDE
IodineTurns from amber to black in a
POLYSACCHARIDE
biology.unm.edu
iws.ccccd.edu
2. Lipids2. LipidsHydrophobic - little or no affinity for waterSmaller than true polymersHighly varied in form & functionTypes of lipids include
A. FatsB. PhospholipidsC. SteroidsD. Waxes & oils
A. FatsA. FatsMonomersGlycerolFatty acids
Ester linkageEster linkage - bond between fatty acids & glycerol formed by dehydration synthesis
Function in energy storage & protection
Dehydration SynthesisDehydration Synthesis of a fat- 3 waters removed between hydroxyl of glycerol and carboxyl of fatty acid to form ester linkages
io.uwinnipeg.ca/~simmons/cm1503/Image76.gif
Saturated vs. Unsaturated FatsSaturated vs. Unsaturated Fats
SaturatedSaturatedSolids @ room
tempAnimal fatsBuild up inside
vesselsNo double bonds
between carbons (saturated with hydrogens)
UnsaturatedUnsaturatedLiquids @ room
tempPlant oilsDouble bonds
between carbons (do not have max # of hydrogens
Unsaturated vs. SaturatedUnsaturated vs. Saturated
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCHEM2.html
FATSFATS
Which of these are saturated?
B. PhospholipidsB. Phospholipids
Similar to fats but with only 2 fatty acids rather than 3
The 3rd hydroxyl group of glycerol is joined to a phosphate group
Ambivalent behavior toward waterLipid tails are hydrophobicPhosphate heads have – charge and are
hydrophilic
Major component of cellular membranes
PhospholipidsPhospholipids
http://academic.brooklyn.cuny.edu/biology/bio4fv/page/phospc.gifwww.biologycorner.com/resources/lipidbilayer.gif
C. SteroidsC. SteroidsCarbon skeleton of 4 fused rings
Used in animal cell membranes & hormones
Extreme levels in the bloodstream may contribute to atherosclerosis
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCHEM2.html
3. Proteins3. ProteinsMonomers – amino acids
Contain both amino & carboxyl groups
Sophisticated in both structure & function
Used in support, storage, transport, signaling, immunity, metabolism
Account for more than 50% of dry weight of cells
PeptidesPeptidesPeptidesPeptides Individual amino
acids OR sequence of 2 or
more amino acids created by dehydration synthesis
Peptide bondPeptide bond – between amino acids
ghs.gresham.k12.or.us
ProteinsProteins
One or more polypeptides folded and coiled into specific conformations
www.biosci.ohio-state.edu
Levels of Protein StructureLevels of Protein StructurePrimary Structure (1Primary Structure (1oo))Unique sequence of amino acidsEX: Hemoglobin – normal vs. sickledEX: Insulin
http://academic.brooklyn.cuny.edu/biology/bio4fv/page/prot_struct-4143.JPG
Secondary Structure (2Secondary Structure (2oo)) Initial coiling and folding patterns that result
from hydrogen bondsEX: alpha helix – coils (alpha keratin in hair)EX: pleated sheet – folds (silk proteins of
insects & spiders
http://academic.brooklyn.cuny.edu/biology/bio4fv/page/prot_struct-4143.JPG
Tertiary Structure (3Tertiary Structure (3oo)) – secondary coiling and folding
Quaternary Structure (4Quaternary Structure (4oo)) – overall protein structure that comes from the way all the polypeptide subunits are situated
http://academic.brooklyn.cuny.edu/biology/bio4fv/page/prot_struct-4143.JPG
Protein StructureProtein Structure
Conformation & structure of proteins can be affected by pH, salt concentration, temperature and other environmental factors.
If the shape of a protein is changed, it is DENATURED and becomes inactive.
EnzymesEnzymesProteins that lower the amount of activation lower the amount of activation energy neededenergy needed to start reactions
CatalystsCatalysts that speed up reactions without being consumed or changed by the reaction
Has a specific active sitespecific active site that fits a specific substrate
Rate at which they work depends on things like temperature, pH, amount of substrate and temperature, pH, amount of substrate and amount of enzyme presentamount of enzyme present
Metabolism, Energy & Metabolism, Energy & EnzymesEnzymes
Chapter 6
MetabolismMetabolism
The total amount of an organism’s chemical processes and reactions
Metabolism = catabolic + anabolic Metabolism = catabolic + anabolic reactionsreactions
Catabolic ReactionsCatabolic Reactions
Chemical reactions that break down molecules
Release energy
EX: cellular respiration where glucose is broken down and ATP is released
Anabolic ReactionsAnabolic Reactions
Reactions that build complex molecules from simpler ones
Requires energy input
EX: synthesis of proteins from amino acids
Energy TransformationsEnergy Transformations
11stst Law of Thermodynamics Law of ThermodynamicsEnergy can be transferred and
transformed, but it can be neither created nor destroyed ~ Conservation of Energy
22ndnd Law of Thermodynamics Law of ThermodynamicsEvery energy transfer makes the universe
more disordered (Entropy)EX: heat is energy in its most random state
Free EnergyFree Energy
Portion of a system’s energy that can perform work when temperature is uniform throughout the system
“free” because its available for work
Represented by G
Energy ReactionsEnergy ReactionsExergonic ReactionExergonic ReactionHas a release of free energy - ΔGCatabolic reactions are also exergonic
EX: cellular respiration
Endergonic ReactionEndergonic ReactionAbsorbs free energy +ΔGAnabolic reactions are also endergonic
EX: photosynthesis
Cellular WorkCellular Work3 main kinds of work done by a cell
1.1. MechanicalMechanicalMovement
EX: muscle contraction; cilia beating
2.2. TransportTransportPumping of substances across membranes
3.3. ChemicalChemicalPushing of endergonic reactions that d not occur spontaneously
EX: dehydration synthesis
ATPATP
Adenosine TriPhosphateAdenosine TriPhosphate Energy molecule used to power cellular work Adenine, ribose sugar & 3 phosphate groups Hydrolysis of the last phosphate group causes the
release of free energy Renewable molecule regenerated by the addition
of a phosphate group to ADP (phosphorylation)
ATP Animation
biology.clc.uc.edu www.theory-of-evolution.net
www.biochem.arizona.edu
InhibitionInhibition
Competitive InhibitionCompetitive InhibitionWhen another molecule competes directly
for the active site of an enzyme and blocks it so the substrate cannot attach
Noncompetitive InhibitionNoncompetitive InhibitionWhen a molecule attaches to the enzyme
somewhere other than the active siteThis changes the shape of the active site
preventing attachment to the substrate
4. Nucleic Acids4. Nucleic AcidsStore & transmit hereditary informationEX: DNA & RNAMonomers are nucleotidesEach nucleotide contains a sugar,
phosphate group and nitrogen base (A, T, G, C)
Sugars – DNA has deoxyribose sugarsRNA has ribose sugars
http://www.csb.yale.edu/userguides/graphics/ribbons/help/dna_rgb.html