biochemistry unit 1. nucleus proton proton (positive charge) (positive charge) neutron neutron...

BiochemistryBiochemistry

Unit 1Unit 1

Nucleus

Proton Proton (Positive charge)(Positive charge)

Neutron Neutron (Neutral charge)(Neutral charge)

Shells outside NucleusShells outside Nucleus

Electron Electron (Negative charge)(Negative charge)

Arrangement of electrons determine reactions and nature of bonds

Atomic Structure

Ionic Bonds

One or more electrons completely One or more electrons completely transferredtransferred

Receiving atom gains negative chargeReceiving atom gains negative charge Donating atom gains positive chargeDonating atom gains positive charge ION=atom with a positive or negative ION=atom with a positive or negative

chargecharge Attraction between charges bonds Attraction between charges bonds

atomsatoms e.g. Nae.g. Na++ and Cl and Cl-- form NaCl form NaCl

Covalent Bonds

Electrons shared between atomsElectrons shared between atoms Single covalent bond shares 2 electronsSingle covalent bond shares 2 electrons Double covalent bond shares 4 electronsDouble covalent bond shares 4 electrons Triple covalent bond shares 6 electronsTriple covalent bond shares 6 electrons Nonpolar covalent bond = 2 eNonpolar covalent bond = 2 e-- shared shared

equallyequally Polar covalent bond = 2 e= 2 e-- shared differently shared differently

Larger nucleus pulls on eLarger nucleus pulls on e-- stronger stronger Creates charged poles in moleculeCreates charged poles in molecule

Covalent BondsCovalent Bonds

Polar Covalent Bond

Hydrogen Bonds Weak bond between oppositely charged Weak bond between oppositely charged

poles of different moleculespoles of different molecules e.g. Water moleculese.g. Water molecules

Properties of WaterProperties of Water

Hydrogen bonds give water special properties Excellent solventExcellent solvent High degree of cohesionHigh degree of cohesion Temperature is stableTemperature is stable

Water as a SolventWater as a Solvent

Ionic substances are soluble because of + Ionic substances are soluble because of + and – charges on water molecules’ polesand – charges on water molecules’ poles

Polar covalent substances are soluble Polar covalent substances are soluble because they have hydrogen bonding because they have hydrogen bonding with waterwith water Hydrophilic = water lovingHydrophilic = water loving

Nonpolar covalent substances do not Nonpolar covalent substances do not dissolve because the do not have charged dissolve because the do not have charged polespoles Hydrophobic = water hatingHydrophobic = water hating

Water Cohesion Strong surface Strong surface

tensiontension

Strong capillary actionStrong capillary action

Stable Temperature of Stable Temperature of WaterWater

Relatively large amount of energy to Relatively large amount of energy to warm (and boil) or cool (and freeze)warm (and boil) or cool (and freeze)

Removes a lot of heat when Removes a lot of heat when perspiration evaporatesperspiration evaporates

Oceans provide a temperature-Oceans provide a temperature-constant environmentconstant environment

Organic MoleculesOrganic Molecules

Based on Carbon (C)Based on Carbon (C) Has 4 eHas 4 e-- available for covalent bonding available for covalent bonding

Organic MoleculesOrganic Molecules Carbon chains form complex structuresCarbon chains form complex structures

Chains Chains Rings Rings


Other atoms add varietyOther atoms add variety Hydrogen (H)Hydrogen (H) Oxygen (O)Oxygen (O) Nitrogen (N)Nitrogen (N) Sulfur (S)Sulfur (S) Phosphorus (P)Phosphorus (P)

They form They form functional groups that give that give organic molecules specific propertiesorganic molecules specific properties

Functional GroupsFunctional Groups

PolarPolar HydrophilicHydrophilic


Weak acidWeak acid


Weak baseWeak base


AcidAcid


HydrophobicHydrophobic

Methyl


PolarPolar


Other atoms add varietyOther atoms add variety Hydrogen (H)Hydrogen (H) Oxygen (O)Oxygen (O) Nitrogen (N)Nitrogen (N) Sulfur (S)Sulfur (S) Phosphorus (P)Phosphorus (P)

They form They form functional groups that give that give organic molecules specific propertiesorganic molecules specific properties

Carbohydrates Monosaccharides are simplestMonosaccharides are simplest

Consist of one sugarConsist of one sugar Have formula (CHHave formula (CH22O)O)nn where where nn is between 3 and 8 is between 3 and 8

Glucose and fructose: and fructose: nn = 6 (i.e. C = 6 (i.e. C66HH1212OO66) but ) but configuration is differentconfiguration is different

Small changes in shape can cause dramatic chemical Small changes in shape can cause dramatic chemical changeschanges

CarbohydratesCarbohydrates

Disaccharides are two linked sugar Disaccharides are two linked sugar moleculesmolecules Sucrose is glucose and fructose linkedSucrose is glucose and fructose linked

CarbohydratesCarbohydrates Polysaccharides are a chain of monosaccharidesPolysaccharides are a chain of monosaccharides

Any molecule of repeating units is a polymerAny molecule of repeating units is a polymer Starch is a chain of thousands of Starch is a chain of thousands of αα-glucose units-glucose units

Food storage in plantsFood storage in plants e.g. Potatoese.g. Potatoes

Cellulose is a chain of thousands of Cellulose is a chain of thousands of ββ-glucose units-glucose units Storage and structureStorage and structure e.g. Wood and cell walls in plantse.g. Wood and cell walls in plants

LipidsLipids

Insoluble in water, but soluble in nonpolar Insoluble in water, but soluble in nonpolar substancessubstances

Fats, oils, and waxes have three fatty acids Fats, oils, and waxes have three fatty acids attached to a glycerolattached to a glycerol

LipidsLipids

Saturated fatty acids—carbons have Saturated fatty acids—carbons have single bonds between them with single bonds between them with hydrogens attachedhydrogens attached

Unsaturated fatty acids—carbons Unsaturated fatty acids—carbons have double bonds between themhave double bonds between them

Polyunsaturated fatty acids have Polyunsaturated fatty acids have multiple double bondsmultiple double bonds

Fatty acids differ by size of chain and Fatty acids differ by size of chain and number of double bondsnumber of double bonds

LipidsLipids

Phospholipids have Phospholipids have phosphate functional phosphate functional groupsgroups

Structural Structural foundation of cell foundation of cell membranesmembranes

Occur in double Occur in double membrane with membrane with hydrophilic heads hydrophilic heads outside and outside and hydrophobic tails hydrophobic tails insideinside

LipidsLipids

Steroids have a Steroids have a backbone of four backbone of four linked carbon ringslinked carbon rings CholesterolCholesterol Some hormonesSome hormones

ProteinsProteins

A variety of functionsA variety of functions Structural (hair, fingernails, eggs, Structural (hair, fingernails, eggs,

muscles, etc.)muscles, etc.) Enzymes (catalysts in biological Enzymes (catalysts in biological

systems)systems) Polymers of amino acidsPolymers of amino acids

Bonds between amino acids are called Bonds between amino acids are called peptide bondspeptide bonds

Proteins are polypeptidesProteins are polypeptides

ProteinsProteins

ProteinsProteins

Four levels of structureFour levels of structure Primary—order of amino acidsPrimary—order of amino acids Secondary—three-dimensional shape caused Secondary—three-dimensional shape caused

by hydrogen bonding (by hydrogen bonding (αα-helix or -helix or ββ-pleated -pleated sheet)sheet)

Tertiary—three dimensional shape caused by Tertiary—three dimensional shape caused by interaction of R-groups (forming globular interaction of R-groups (forming globular proteins)proteins)

Quaternary—two or more separate Quaternary—two or more separate polypeptides joining to form a larger proteinpolypeptides joining to form a larger protein

ProteinsProteins

Nucleic AcidsNucleic Acids

Nucleic acids store and transmit Nucleic acids store and transmit hereditary informationhereditary information

GenesGenes Are the units of inheritanceAre the units of inheritance Program the amino acid sequence of Program the amino acid sequence of

polypeptidespolypeptides Are made of nucleotide sequences on Are made of nucleotide sequences on

DNADNA

The Roles of Nucleic The Roles of Nucleic AcidsAcids

There are two types of nucleic acidsThere are two types of nucleic acids Deoxyribonucleic acid (DNA)Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA)Ribonucleic acid (RNA)

36

Deoxyribonucleic AcidDeoxyribonucleic Acid

DNADNA Stores information for the synthesis of Stores information for the synthesis of

specific proteinsspecific proteins Found in the nucleus of cellsFound in the nucleus of cells

DNA FunctionsDNA Functions Directs RNA synthesis (transcription)Directs RNA synthesis (transcription) Directs protein synthesis through RNA Directs protein synthesis through RNA

(translation)(translation)

1

2

3

Synthesis of mRNA in the nucleus

Movement of mRNA into cytoplasm

via nuclear pore

Synthesisof protein

NUCLEUSCYTOPLASM

DNA

mRNA

Ribosome

AminoacidsPolypeptide

mRNA

Figure 5.25

3’C

5’ end

5’C

3’C

5’C

3’ end

OH

Figure 5.26

O

O

O

O

The Structure of Nucleic The Structure of Nucleic AcidsAcids

Nucleic acidsNucleic acids Exist as polymers called Exist as polymers called

polynucleotidespolynucleotides

(a) Polynucleotide, or nucleic acid

O

O

O

O

Each polynucleotideEach polynucleotide Consists of monomers called nucleotidesConsists of monomers called nucleotides Sugar + phosphate + nitrogen baseSugar + phosphate + nitrogen base

Nitrogenousbase

Nucleoside

O

O

O

O P CH2

5’C

3’CPhosphate

group Pentosesugar

(b) NucleotideFigure 5.26

O

Nucleotide MonomersNucleotide Monomers

Nucleotide Nucleotide monomersmonomers Are made up of Are made up of

nucleosides (sugar nucleosides (sugar + base) and + base) and phosphate groupsphosphate groups

(c) Nucleoside componentsFigure 5.26

CHCH

Uracil (in RNA)U

Ribose (in RNA)

Nitrogenous bases Pyrimidines

CN

NC

OH

NH2

CHCH

OC

NH

CHHN

CO

CCH3

N

HNC

C

HO

O

CytosineC

Thymine (in DNA)T

NHC

N C

CN

C

CH

N

NH2 O

NHC

NHH

C C

N

NH

CNH2

AdenineA

GuanineG

Purines

OHOCH2

HH H

OH

H

OHOCH2

HH H

OH

H

Pentose sugars

Deoxyribose (in DNA)Ribose (in RNA)OHOH

CH

CH

Uracil (in RNA)U

4’

5”

3’OH H

2’

1’

5”

4’

3’ 2’

1’

Nucleotide PolymersNucleotide Polymers

Nucleotide polymersNucleotide polymers Are made up of nucleotides linked Are made up of nucleotides linked

by the–OH group on the 3´ carbon by the–OH group on the 3´ carbon of one nucleotide and the phosphate of one nucleotide and the phosphate on the 5´ carbon on the nexton the 5´ carbon on the next

GeneGene

The sequence of bases along a The sequence of bases along a nucleotide polymernucleotide polymer Is unique for each geneIs unique for each gene

The DNA Double HelixThe DNA Double Helix

Cellular DNA moleculesCellular DNA molecules Have two polynucleotides that spiral Have two polynucleotides that spiral

around an imaginary axisaround an imaginary axis Form a double helixForm a double helix

The DNA double helixThe DNA double helix Consists of two antiparallel nucleotide Consists of two antiparallel nucleotide

strandsstrands3’ end

Sugar-phosphatebackbone

Base pair (joined byhydrogen bonding)

Old strands

Nucleotideabout to be added to a new strand

A

3’ end

3’ end

5’ end

Newstrands

3’ end

5’ end

5’ end

Figure 5.27

A,T,C,GA,T,C,G

The nitrogenous bases in DNAThe nitrogenous bases in DNA Form hydrogen bonds in a Form hydrogen bonds in a

complementary fashion (A with T only, complementary fashion (A with T only, and C with G only)and C with G only)

DNA and Proteins as DNA and Proteins as Tape Measures of Tape Measures of

EvolutionEvolution Molecular comparisons Molecular comparisons

Help biologists sort out the Help biologists sort out the evolutionary connections among evolutionary connections among species species

The Theme of Emergent The Theme of Emergent Properties in the Chemistry of Properties in the Chemistry of

Life: Life: A ReviewA Review

Higher levels of organizationHigher levels of organization Result in the emergence of new Result in the emergence of new

propertiesproperties OrganizationOrganization

Is the key to the chemistry of lifeIs the key to the chemistry of life

Chemical Reactions in Chemical Reactions in Metabolic ProcessesMetabolic Processes

ATP provides the chemical energy for ATP provides the chemical energy for many metabolic reactionsmany metabolic reactions


Reaction needs to reach activation Reaction needs to reach activation energyenergy

Catalyst accelerates reaction by Catalyst accelerates reaction by lowering required activation energylowering required activation energy

Catalyst does not change during the Catalyst does not change during the reactionreaction


Reactions in biological systems are Reactions in biological systems are part of the metabolismpart of the metabolism Catabolism breaks downCatabolism breaks down Anabolism or synthesis builds upAnabolism or synthesis builds up Energy is transferred from one Energy is transferred from one

substance to anothersubstance to another


Net direction of Net direction of reaction is reaction is determined by determined by concentrations of concentrations of reactants and end reactants and end productsproducts

Chemical equilibrium Chemical equilibrium occurs when occurs when concentrations of concentrations of both reactants and both reactants and end products are the end products are the samesame


Enzymes are catalysts in biological Enzymes are catalysts in biological reactionsreactions Enzymes are globular proteinsEnzymes are globular proteins Specific to one reactionSpecific to one reaction Enzymes are named with “ase” suffixEnzymes are named with “ase” suffix Enzymes act on the substrateEnzymes act on the substrate


Induced fit model—active site of enzyme attaches to substrate changing its shape for easier reaction


Enzymes operate at optimum Enzymes operate at optimum temperature and pHtemperature and pH

If temperature or pH is off, the If temperature or pH is off, the enzyme’s structure can denatureenzyme’s structure can denature If denatured, it does not revert to If denatured, it does not revert to

original structureoriginal structure


Cofactors are nonprotein molecules Cofactors are nonprotein molecules that assist enzymes in lowering the that assist enzymes in lowering the activation energyactivation energy MineralsMinerals

Organic cofactors are called Organic cofactors are called coenzymescoenzymes VitaminsVitamins


Reactions are regulated byReactions are regulated by Allosteric enzymesAllosteric enzymes Feedback inhibitionFeedback inhibition Competitive inhibitionCompetitive inhibition


Allosteric enzymes Allosteric enzymes have two binding have two binding sitessites One for substrateOne for substrate One for allosteric One for allosteric

effectoreffector Effector can either Effector can either

activate or inhibit activate or inhibit reactionreaction


Feedback inhibitionFeedback inhibition End product serves as an allosteric End product serves as an allosteric

effector to shut down reactioneffector to shut down reaction Competitive inhibitionCompetitive inhibition

A substance other than the substrate A substance other than the substrate occupies the active site and keeps the occupies the active site and keeps the reaction from happeningreaction from happening

biochemistry unit 1. nucleus proton proton (positive charge) (positive charge) neutron neutron...

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chain of thousands

single bonds

e strongercreates

e available

size of chain

glucose unitsstorage

negative chargedonating

charges bonds atomse