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