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Get Ready for A & P!Get Ready for A & P!
Chemistry, DNA Transcription, Chemistry, DNA Transcription, Translation & Protein SynthesisTranslation & Protein Synthesis
ElementsElements
Fundamental forms of matterFundamental forms of matter
Can’t be broken apart by normal Can’t be broken apart by normal
chemical meanschemical means
92 occur naturally on Earth92 occur naturally on Earth
Most Common Elements in Most Common Elements in Living OrganismsLiving Organisms
OxygenOxygen
HydrogenHydrogen
CarbonCarbon
NitrogenNitrogen
Fig. 2-3, p.20
What Are Atoms?What Are Atoms?
Smallest particles that retain properties of Smallest particles that retain properties of
an elementan element
Made up of subatomic particles:Made up of subatomic particles: Protons (+)Protons (+)
Electrons (-) Electrons (-)
Neutrons (no charge) Neutrons (no charge)
Atomic NumberAtomic Number
Number of protonsNumber of protons All atoms of an element have the same All atoms of an element have the same
atomic numberatomic number Atomic number of hydrogen = 1Atomic number of hydrogen = 1 Atomic number of carbon = 6Atomic number of carbon = 6
Mass NumberMass Number
Number of protonsNumber of protons
++Number of neutronsNumber of neutrons
Isotopes vary in mass numberIsotopes vary in mass number
IsotopesIsotopes
Atoms of an element with different Atoms of an element with different numbers of neutrons (different mass numbers of neutrons (different mass numbers)numbers)
Carbon 12 has 6 protons, 6 neutronsCarbon 12 has 6 protons, 6 neutrons Carbon 14 has 6 protons, 8 neutronsCarbon 14 has 6 protons, 8 neutrons
RadioisotopesRadioisotopes
Have an unstable nucleus that Have an unstable nucleus that emits energy and particlesemits energy and particles
Radioactive decay transforms Radioactive decay transforms radioisotope into a different elementradioisotope into a different element
Decay occurs at a fixed rateDecay occurs at a fixed rate
Radioisotopes as TracersRadioisotopes as Tracers
Tracer is substance with a Tracer is substance with a radioisotope attached to itradioisotope attached to it
Emissions from the tracer can be Emissions from the tracer can be detected with special devices detected with special devices
Following movement of tracers is Following movement of tracers is useful in many areas of biology – useful in many areas of biology – Ex.: PET scansEx.: PET scans
Other Uses of RadioisotopesOther Uses of Radioisotopes
Drive artificial pacemakersDrive artificial pacemakers
Radiation therapyRadiation therapyEmissions from some radioisotopes can Emissions from some radioisotopes can destroy cells. Some radioisotopes are used to destroy cells. Some radioisotopes are used to kill small cancers.kill small cancers.
What Determines What Determines Whether Atoms Will Whether Atoms Will
Interact?Interact?
The number and arrangement The number and arrangement of their electronsof their electrons
ElectronsElectrons
Carry a negative chargeCarry a negative charge Repel one another Repel one another Are attracted to protons in the nucleusAre attracted to protons in the nucleus Move in orbitals - volumes of space that Move in orbitals - volumes of space that
surround the nucleussurround the nucleus
Electron OrbitalsElectron Orbitals
First orbital can hold up to two First orbital can hold up to two electronselectrons
Atoms differ in the number of Atoms differ in the number of occupied orbitalsoccupied orbitals
Orbitals closest to nucleus are Orbitals closest to nucleus are lower energy and are filled firstlower energy and are filled first
Shell ModelShell Model
First shell First shell Lowest energyLowest energy
Holds 1 orbital Holds 1 orbital
with up to 2 with up to 2
electronselectrons
Second shellSecond shell 4 orbitals each 4 orbitals each
hold up to 8 hold up to 8
electronselectrons HYDROGEN1p+ , 1e-
HELIUM2p+ , 2e-
CARBON6p+ , 6e-
OXYGEN8p+ , 8e-
SODIUM11p+ , 11e-
CHLORINE17p+ , 17e-
HYDROGEN1p+ , 1e-
HELIUM2p+ , 2e-
CARBON6p+ , 6e-
OXYGEN8p+ , 8e-
SODIUM11p+ , 11e-
CHLORINE17p+ , 17e-
Fig. 2-6, p.23
NEON10p+ , 10e-
electron
proton
neutron
Electron VacanciesElectron Vacancies
Unfilled shells make atoms likely Unfilled shells make atoms likely to reactto react
Hydrogen, carbon, oxygen, and Hydrogen, carbon, oxygen, and nitrogen all have vacancies in their nitrogen all have vacancies in their outer shellsouter shells
Chemical Bonds, Molecules, Chemical Bonds, Molecules, & Compounds& Compounds
Bond is union between electron structures Bond is union between electron structures of atomsof atoms
Atoms bond to form moleculesAtoms bond to form molecules Molecules may contain atoms of only one Molecules may contain atoms of only one
element - Oelement - O22
Molecules of compounds contain more Molecules of compounds contain more than one element - Hthan one element - H22OO
Chemical BookkeepingChemical Bookkeeping
Use symbols for elements when writing Use symbols for elements when writing formulasformulas
Formula for glucose is CFormula for glucose is C66HH1212OO66
6 carbons 6 carbons
12 hydrogens12 hydrogens
6 oxygens6 oxygens
Molecular Mass & MolesMolecular Mass & Moles
1 mole of a pure substance has a mass 1 mole of a pure substance has a mass equal to its equal to its molecular mass (MM) in grams
Therefore, one mole of a compound, say CO (carbon Therefore, one mole of a compound, say CO (carbon monoxide) is equal to:monoxide) is equal to:
MM of C = MM of C = 1212
MM of O = MM of O = 16 16
MM of CO = MM of CO = 28 grams/ mole of CO28 grams/ mole of CO
So the molecular mass, MM, (molecular weight, MW) of a So the molecular mass, MM, (molecular weight, MW) of a compound is the sum of the atomic masses (atomic compound is the sum of the atomic masses (atomic weights) of the atomic species as given in the molecular weights) of the atomic species as given in the molecular formula. formula.
Chemical BookkeepingChemical Bookkeeping
Chemical equation shows reactionChemical equation shows reaction
Reactants ---> ProductsReactants ---> Products Equation for photosynthesis:Equation for photosynthesis:
REACTANTS PRODUCTS
6CO2
CARBONDIOXIDE
12H2O
WATER
+ C6H12O6
GLUCOSE
6H2O
WATER
+
6 carbons12 oxygens
24 hydrogens12 oxygens
6 carbons12 hydrogens
6 oxygens
12 hydrogens6 oxygens
6O2
OXYGEN
+
12 oxygens
sunlightenergy
Important Bonds in Important Bonds in Biological MoleculesBiological Molecules
Ionic BondsIonic Bonds Covalent BondsCovalent Bonds Hydrogen BondsHydrogen Bonds
Ion FormationIon Formation
Atom has equal number of Atom has equal number of electrons and protons - no net electrons and protons - no net chargecharge
Atom loses electron(s), becomes Atom loses electron(s), becomes positively charged ionpositively charged ion
Atom gains electron(s), becomes Atom gains electron(s), becomes negatively charged ionnegatively charged ion
Ionic BondingIonic Bonding
One atom loses electrons, One atom loses electrons, becomes positively charged ionbecomes positively charged ion
Another atom gains these Another atom gains these electrons, becomes negatively electrons, becomes negatively charged ioncharged ion
Charge difference attracts the Charge difference attracts the two ions to each othertwo ions to each other
Formation of NaClFormation of NaCl
Sodium atom (Na) Sodium atom (Na) Outer shell has one electronOuter shell has one electron
Chlorine atom (Cl) Chlorine atom (Cl) Outer shell has seven electronsOuter shell has seven electrons
Na transfers electron to Cl forming NaNa transfers electron to Cl forming Na++ and Cland Cl--
Ions remain together as NaClIons remain together as NaCl
Formation of NaClFormation of NaCl
electron transfer
sodiumatom11 p +
chlorineatom17 p +
17 e-
chlorineion
17 p +
18 e-
sodiumion
11 p +
10 e-
Covalent BondingCovalent Bonding
Atoms share a pair or pairs of electrons Atoms share a pair or pairs of electrons to fill outermost shellto fill outermost shell
•Single covalent bond
•Double covalent bond
•Triple covalent bond
molecular hydrogen (H2)H—H
Two hydrogen atoms, each with one proton, share two electrons in a single nonpolar covalent bond.
Fig. 2-8b(1), p.25
Covalent BondingCovalent Bonding
molecular oxygen (O2)O=O
Two oxygen atoms, each with eight protons, share four electrons in a nonpolar doublecovalent bond.
Fig. 2-8b(2), p.25
Covalent BondingCovalent Bonding
Nonpolar Covalent BondsNonpolar Covalent Bonds
Atoms share electrons equallyAtoms share electrons equally
Nuclei of atoms have same Nuclei of atoms have same number of protonsnumber of protons
Example: Hydrogen gas (H-H)Example: Hydrogen gas (H-H)
water (H2O)H—O—H
Oxygen has vacancies for two electrons in its highest energy level orbitals. Two hydrogen atoms can each share an electron with an oxygen. The resulting two polar covalent bonds form a water molecule.
Fig. 2-8b(3), p.25
Covalent BondingCovalent Bonding
Polar Covalent BondsPolar Covalent Bonds
Number of protons in nuclei of Number of protons in nuclei of participating atoms is participating atoms is notnot equal equal
Electrons spend more time near Electrons spend more time near nucleus with most protonsnucleus with most protons
Water - Electrons more attracted to Water - Electrons more attracted to O nucleus than to H nucleiO nucleus than to H nuclei
Hydrogen BondingHydrogen Bonding
Molecule held together by polar covalent Molecule held together by polar covalent bonds has no bonds has no netnet charge charge
However, atoms of the molecule carry However, atoms of the molecule carry different chargesdifferent charges
Atom in one polar covalent molecule can Atom in one polar covalent molecule can be attracted to oppositely charged atom in be attracted to oppositely charged atom in another such moleculeanother such molecule
Water Is a Polar Water Is a Polar Covalent MoleculeCovalent Molecule
Molecule has no net Molecule has no net chargecharge
Oxygen end has a Oxygen end has a slight negative chargeslight negative charge
Hydrogen end has a Hydrogen end has a slight positive chargeslight positive charge
+ +
HH
O
Water Is a Good SolventWater Is a Good Solvent
Ions and polar molecules dissolve easily Ions and polar molecules dissolve easily in water in water
When solute dissolves, water molecules When solute dissolves, water molecules cluster around its ions or molecules and cluster around its ions or molecules and keep them separatedkeep them separated
The pH ScaleThe pH Scale
Measures HMeasures H++ concentration of fluid concentration of fluid Change of 1 on scale means 10X change Change of 1 on scale means 10X change
in Hin H++ concentration concentration
Highest HHighest H+ + Lowest H Lowest H++
0---------------------7-------------------140---------------------7-------------------14Acidic Neutral BasicAcidic Neutral Basic
Examples of pHExamples of pH
Pure water is neutral with pH of 7.0 Pure water is neutral with pH of 7.0 AcidicAcidic
Stomach acid: pH 1.0 - 3.0Stomach acid: pH 1.0 - 3.0 Lemon juice: pH 2.3Lemon juice: pH 2.3
BasicBasic Seawater: pH 7.8 - 8.3Seawater: pH 7.8 - 8.3 Baking soda: pH 9.0Baking soda: pH 9.0
Acids & BasesAcids & Bases
AcidsAcids Donate HDonate H++ when dissolved in water when dissolved in water
Acidic solutions have pH < 7Acidic solutions have pH < 7
BasesBases Accept HAccept H++ when dissolved in water when dissolved in water
Acidic solutions have pH > 7Acidic solutions have pH > 7
SaltsSalts
Compounds that release ions other than Compounds that release ions other than HH++ and OH and OH-- when dissolved in water when dissolved in water
Example: NaCl releases NaExample: NaCl releases Na++ and Cl and Cl––
Many salts dissolve into ions that play Many salts dissolve into ions that play important biological roles important biological roles
Organic CompoundsOrganic Compounds
Hydrogen and other elements Hydrogen and other elements covalently bonded to carboncovalently bonded to carbon
Carbohydrates - C, H and OCarbohydrates - C, H and O Lipids - C, H, O and sometimes PLipids - C, H, O and sometimes P Proteins - C, H, O, N and sometimes SProteins - C, H, O, N and sometimes S Nucleic Acids - C, H, O, N, PNucleic Acids - C, H, O, N, P
Carbon’s Bonding Behavior Carbon’s Bonding Behavior
Outer shell of carbon Outer shell of carbon has 4 electrons; can has 4 electrons; can hold 8hold 8
Each carbon atom Each carbon atom can form covalent can form covalent bonds with up to four bonds with up to four atomsatoms
CarbohydratesCarbohydrates
MonosaccharidesMonosaccharides(simple sugars)(simple sugars)
OligosaccharidesOligosaccharides(short-chain carbohydrates)(short-chain carbohydrates)
PolysaccharidesPolysaccharides(complex carbohydrates) (complex carbohydrates)
Monosaccharides Monosaccharides
Simplest carbohydratesSimplest carbohydrates
Most are sweet tasting, water solubleMost are sweet tasting, water soluble
Most have 5- or 6-carbon backboneMost have 5- or 6-carbon backbone
Glucose (6 C)Glucose (6 C) Fructose (6 C)Fructose (6 C)
Ribose (5 C)Ribose (5 C) Deoxyribose (5 C)Deoxyribose (5 C)
Two MonosaccharidesTwo Monosaccharides
glucose fructoseFig. 3-7, p.38
DisaccharidesDisaccharides
Type of Type of oligosaccharideoligosaccharide
Two Two monosaccharides monosaccharides covalently bonded covalently bonded
Formed by Formed by condensation condensation reactionreaction
+ H2O
glucose fructose
sucrose
Fig. 3-7b, p.38
PolysaccharidesPolysaccharides
Straight or branched chains of many sugar Straight or branched chains of many sugar monomersmonomers
Most common are composed entirely of Most common are composed entirely of glucoseglucose CelluloseCellulose Starch (such as amylose)Starch (such as amylose) GlycogenGlycogen
Cellulose & StarchCellulose & Starch
Differ in bonding patterns between Differ in bonding patterns between monomersmonomers
Cellulose - tough, indigestible, structural Cellulose - tough, indigestible, structural material in plantsmaterial in plants
Starch - easily digested, storage form in Starch - easily digested, storage form in plantsplants
GlycogenGlycogen
Sugar storage form in animalsSugar storage form in animals
Large stores in muscle and liver Large stores in muscle and liver cellscells
When blood sugar decreases, When blood sugar decreases, liver cells degrade glycogen, liver cells degrade glycogen, release glucoserelease glucose
Fig. 3-9, p.38
Most include fatty acidsMost include fatty acids FatsFats PhospholipidsPhospholipids WaxesWaxes
Sterols and their derivatives have no fatty Sterols and their derivatives have no fatty acidsacids
Tend to be insoluble in waterTend to be insoluble in water
LipidsLipids
FatsFats
Fatty acid(s) Fatty acid(s)
attached to attached to
glycerolglycerol
Triglycerides Triglycerides
are most are most
commoncommon
Fig. 3-12, p.40
Fatty AcidsFatty Acids
Carboxyl group (-COOH) at one endCarboxyl group (-COOH) at one end
Carbon backbone (up to 36 C atoms)Carbon backbone (up to 36 C atoms)
Saturated - Single bonds between carbonsSaturated - Single bonds between carbons
Unsaturated - One or more double bondsUnsaturated - One or more double bonds
PhospholipidsPhospholipids
Main components of cell Main components of cell
membranesmembranes
WaxesWaxes
Long-chain fatty acids linked to Long-chain fatty acids linked to
long chain alcohols or carbon ringslong chain alcohols or carbon rings
Firm consistency, repel waterFirm consistency, repel water
Important in water-proofingImportant in water-proofing
Sterols and DerivativesSterols and Derivatives
No fatty acidsNo fatty acids
Rigid backbone of Rigid backbone of
four fused-together four fused-together
carbon ringscarbon rings
Cholesterol - most Cholesterol - most
common type in common type in
animalsanimals
Fig. 3-14, p.41
Amino Acid StructureAmino Acid Structure
aminogroup
carboxylgroup
R group
Properties of Amino AcidsProperties of Amino Acids
Determined by the “R group”Determined by the “R group”
Amino acids may be: Amino acids may be: Non-polar Non-polar
Uncharged, polar Uncharged, polar
Positively charged, polarPositively charged, polar
Negatively charged, polarNegatively charged, polar
Protein SynthesisProtein Synthesis
Protein is a chain of amino acids linked Protein is a chain of amino acids linked
by peptide bondsby peptide bonds
Peptide bondPeptide bond Type of covalent bondType of covalent bond
Links amino group of one amino acid with Links amino group of one amino acid with
carboxyl group of nextcarboxyl group of next
Forms through condensation reactionForms through condensation reaction
Fig. 3-15b, p.42
Primary StructurePrimary Structure
Sequence of amino acidsSequence of amino acids
Unique for each proteinUnique for each protein
Two linked amino acids = dipeptideTwo linked amino acids = dipeptide
Three or more = polypeptideThree or more = polypeptide
Backbone of polypeptide has N atoms:Backbone of polypeptide has N atoms:
-N-C-C-N-C-C-N-C-C-N--N-C-C-N-C-C-N-C-C-N-
one peptide group
Primary structure influences shape in Primary structure influences shape in two main ways:two main ways: Allows hydrogen bonds to form between Allows hydrogen bonds to form between
different amino acids along length of chaindifferent amino acids along length of chain Puts R groups in positions that allow them Puts R groups in positions that allow them
to interactto interact
Primary StructurePrimary Structure & Protein Shape & Protein Shape
Secondary StructureSecondary Structure
Hydrogen bonds form between different Hydrogen bonds form between different parts of polypeptide chainparts of polypeptide chain
These bonds give rise to coiled or These bonds give rise to coiled or extended patternextended pattern
Helix or pleated sheetHelix or pleated sheet
Examples of Secondary Examples of Secondary StructureStructure
Tertiary StructureTertiary Structure
Folding as a Folding as a
result result
of interactions of interactions
between R between R
groupsgroups
heme group
coiled and twisted polypeptide chain of one globin molecule
Quaternary StructureQuaternary Structure
Some proteins Some proteins
are made up of are made up of
more than one more than one
polypeptide polypeptide
chainchain
Hemoglobin
heme alpha globin alpha globin
beta globin beta globin
Fig. 3-17, p.44
DenaturationDenaturation
Disruption of three-dimensional shapeDisruption of three-dimensional shape Breakage of weak bondsBreakage of weak bonds Causes of denaturation:Causes of denaturation:
pHpH TemperatureTemperature
Destroying protein shape disrupts Destroying protein shape disrupts functionfunction
SugarSugar Ribose or deoxyriboseRibose or deoxyribose
At least one phosphate groupAt least one phosphate group
BaseBase Nitrogen-containingNitrogen-containing
Single or double ring structureSingle or double ring structure
Nucleotide StructureNucleotide Structure
Composed of nucleotidesComposed of nucleotides Single- or double-strandedSingle- or double-stranded Sugar-phosphate backboneSugar-phosphate backbone
Nucleic AcidsNucleic Acids
AdenineCytosine
Structure of Nucleotides Structure of Nucleotides in DNAin DNA
Each nucleotide consists ofEach nucleotide consists of Deoxyribose (5-carbon sugar) Deoxyribose (5-carbon sugar)
Phosphate groupPhosphate group
A nitrogen-containing baseA nitrogen-containing base
Four basesFour bases Adenine, Guanine, Thymine, CytosineAdenine, Guanine, Thymine, Cytosine
DNADNA
Double-stranded Double-stranded Consists of four Consists of four
types of types of nucleotidesnucleotides
A bound to TA bound to T C bound to GC bound to G
RNARNA
Usually single strandsUsually single strands Four types of nucleotidesFour types of nucleotides Unlike DNA, contains the base Unlike DNA, contains the base uraciluracil in in
place of place of thyminethymine Three types are key players in protein Three types are key players in protein
synthesissynthesis
base pairing during transcription
DNA
RNA
DNA
DNA
base pairing during DNAreplication
Fig. 14-2c, p.220
Base Pairing Base Pairing during during
TranscriptionTranscription
newly forming RNA transcript
DNA template unwindingDNA template winding up
DNA template at selected transcription site
b All through transcription, the DNA double helix becomes unwound in front of the RNA polymerase. Short lengths of the newly forming RNA strand briefly wind up with its DNA template strand. New stretches of RNA unwind from the template (and the two DNA strands wind up again).
Fig. 14-3b, p.220
Gene TranscriptionGene Transcription
direction of transcription3´
growing RNA transcript
5´
5´ 3´
c What happened at the assembly site? RNA polymerase catalyzed the assembly of ribonucleotides, one after another, into an RNA strand, using exposed bases on the DNA as a template. Many other proteins assist this process.
Fig. 14-3c, p.221
Adding NucleotidesAdding Nucleotides
Three Classes of RNAsThree Classes of RNAs
Messenger RNAMessenger RNA Carries protein-building instructionCarries protein-building instruction
Ribosomal RNARibosomal RNA Major component of ribosomesMajor component of ribosomes
Transfer RNATransfer RNA Delivers amino acids to ribosomes Delivers amino acids to ribosomes
tRNA StructuretRNA Structure
codon in mRNA
anticodon
amino acid OH
amino-acidattachment site
Figure 14.7Figure 14.7Page 223Page 223
funnel
small ribosomal subunit
large ribosomal subunit
intact ribosome+
Fig. 14-8, p.223
RibosomesRibosomes
Genetic CodeGenetic Code
Set of 64 base Set of 64 base tripletstriplets
CodonsCodons 61 specify amino 61 specify amino
acidsacids 3 stop translation3 stop translation
Fig. 14-6, p.222
DNA
mRNA
mRNAcodons
threonine proline glutamate glutamate lysine
amino acids
Fig. 14-5, p.222
Genetic CodeGenetic Code
Three Stages of TranslationThree Stages of Translation
InitiationInitiation
ElongationElongation
TerminationTermination
InitiationInitiation
Initiator tRNA binds to small Initiator tRNA binds to small ribosomal subunitribosomal subunit
Small subunit/tRNA Small subunit/tRNA complex attaches to mRNA complex attaches to mRNA and moves along it to an and moves along it to an AUG “start” codonAUG “start” codon
Large ribosomal subunit Large ribosomal subunit joins complexjoins complex
ElongationElongation
mRNA passes through ribosomal subunits mRNA passes through ribosomal subunits tRNAs deliver amino acids to the tRNAs deliver amino acids to the
ribosomal binding site in the order ribosomal binding site in the order specified by the mRNAspecified by the mRNA
Peptide bonds form between the amino Peptide bonds form between the amino acids and the polypeptide chain growsacids and the polypeptide chain grows
ElongationElongation
TerminationTermination
Stop codon into placeStop codon into place No tRNA with anticodonNo tRNA with anticodon Release factors bind to Release factors bind to
the ribosomethe ribosome mRNA and polypeptide mRNA and polypeptide
are releasedare released
new polypeptide chain
mRNA
OverviewOverview
Transcription
Translation
mRNA rRNA tRNA
Mature mRNA transcripts
ribosomal subunits
mature tRNA