Biochemistry and the Organization of CellsChapter 1

Levels of Structural Organization in the Human Body

Why is study of Biochemistry important?Biochemistry describes life processesMultidisciplinary nature allows it use other sciences to answer questions about molecular nature of life processesSome biomolecules act in multiple ways and some take part in specific series of reactionsMore complex cells are found in larger organisms than simpler organisms

How is Biochemistry related to Organic Chemistry?Organic Chemistry is study of compounds of carbon and hydrogen and their derivativesBiomolecules are made up of carbonMany carbon compounds are not found in any organismBiomolecules of life can be synthesized in laboratories (synthesis of urea from ammonium cyanate by Friedrich Wohler in 1828)

Functional group: an atom or group of atoms that shows characteristic physical and chemical properties

What makes biomolecules special?Biomolecules have important functional groupsEmphases of functional groups differ in Organic chemistry (alkyl halides and acyl chlorides) and in Biochemistry (carbonyl groups, hydroxyl groups, carboxyl groups, amines, amides and esters).Derivatives of phosphoric acid such as esters and anhydrides are also important (in Biochemistry)ATP contains both ester and anhydride linked by phosphoric acid (in Biochemistry) (figure 1.2)

How and when did the Earth come to be?Big bang theory explains the origin of earth formed from matterDue to explosion (released Hydrogen, Helium and some Lithium), temperature of Universe raised to (15 billion K) Decrease in temperature led to formation of stars and planetsRest of chemical elements i) by thermonuclear reactions that take place in stars, ii) in explosions of stars, iii) by the action of cosmic rays outside the stars

How did elements arise from stars?Age of earth 4 to 5 billion years ago Second generation of stars formed from supernovas led to formation of sunAtmosphere of earth is always been debatedExistence of Co2 from 3.8 billion years N2 in atmosphere source for formation of proteins and nucleic acids

How were biomolecules likely to have formed on the early earth?Miller-Urey experiment Occurred in earths early oceanOccurred on early earths clay particlesSimple compounds can react (polymerize) abiotically to produce biologically important components of proteins and nucleic acids

Formation of biomolecules on early earthHCN present in nucleic acids and HCHO present in sugars

BiomoleculesLiving cells include very large molecules, such as proteins, nucleic acids, polysaccharides, and lipidsthese biomolecules are polymers (Greek: poly + meros, many + parts)they are derived from monomers (Greek: mono + meros, single + part) --amino acids --> proteins --nucleotides --> nucleic acids --monosaccharides --> polysaccharides --glycerol and 3 fatty acids --> lipids

Informational Macromolecules

How is cellular activity determined?Enzymes: a class of proteins that are biocatalyststhe catalytic effectiveness of a given enzyme depends on its amino acid sequence

Genetic code: the relationship between the nucleotide sequence in nucleic acids and the amino acid sequence in proteins

Which came first the catalysts or the hereditary molecules?Cellular activity depends upon presence of catalysts and its synthesis by genetic codeDiscovery of enzyme Ribozyme RNARNA has both catalytic and genetic coding propertiesLife originated from RNAPeptide bond formation is catalyzed by RNA portions of Ribosome

Stages in the Evolution of Self-replicating RNA Molecules

Vital importance of a cell membrane in origin of life

Assignment 1

Write down the structure and function of all organelles in eukaryotes.

Differences between prokaryotes and eukaryotes

Prokaryotes before nucleus and absence of membrane bound organellesDNA is present in nuclear region and not separate from the cellPlasma membrane is present surrounding the cell

Eukaryotes true nucleus and presence of membrane bound organellesDNA is well defined

Differences between prokaryotes and eukaryotesMitochondria is absent and enzymes for oxidative reactions are located on plasma membraneEndoplasmic reticulum is absentRibosomes are found freely floating in cytosolChloroplasts are absent. Photosynthesis takes place in chromatophores which are extensions of plasma membranesPlasma membrane is present surrounding the cellMitochondria is presentEndoplasmic reticulum is presentRibosomes are bound to Endoplasmic reticulumChloroplasts present in plants and absent in animals

Some more pointsPolysaccharide cellulose present in prokaryotic and eukaryotic cell walls (plant cells only)Some protists and all animal cells lack cell walls and chloroplastsThree important organelles nucleus, mitochondria and chloroplast separated from rest of the cell by double membraneMitochondria and chloroplasts contain DNA- carry out transcription and protein synthesis

Five Kingdom classification of living organismsProkaryotesKingdom: MoneraBacteria and Cyanobacteria are membersUnicellularEukaryotesKingdom: Protists, Fungi, Plants and AnimalsUnicellular protists are Euglena, Volvox, Amoeba and ParameciumMulticellular protists are algaeFungi, plants and animals are multicellularFungi like yeasts and molds are unicellular

Three Kingdom classification of living organismsBacteria and Archaea form prokaryotesEukarya forms eukaryotesBacteria (true bacteria) and Archaea (early bacteria) have different biochemical features molecular structure of cell walls, membranes and some types of RNAArchaebacteria live in extreme environments extremophiles Methanogens, Halophiles and Thermoacidophiles

Did symbiosis play a role in development of eukaryotes?Theory of EndosymbiosisProposal that eukaryotic organelles evolved through a symbiotic relationship One cell engulfed a second cell and a symbiotic relationship developedMitochondria and chloroplasts are thought to have evolved this way

Evidence for EndosymbiosisMitochondria and chloroplasts:-have 2 membranes-possess DNA and ribosomes-are about the size of a prokaryotic cell-divide by a process similar to bacteria

What is thermodynamics?Sun is ultimate source of energy on earthEnergy released or absorbed can be measured in BiochemistryEnergy is converted from one form to anotherThermodynamics deals with changes in energy that determine whether a process will take placeSpontaneous reactions will take place without outside intervention

How can we predict what reactions will happen in living cells?Spontaneity of reaction at a given temperature and pressure is decided by changes in free energy (G)G is negative, G0, reaction is not spontaneous, energy will be requiredG=0, reaction is in equilibrium

Is life thermodynamically possible?Free energy: the energy available to do work-denoted by the symbol G (Gibbs free energy)enthalpy: energy contained in a molecules chemical bondsfree energy = enthalpy (entropy x temp.)G = H - TS

Laws of ThermodynamicsFirst Law of Thermodynamics energy cannot be created or destroyed-energy can only be converted from one form to another

For example:sunlight energy chemical energy photosynthesis

Is life thermodynamically possible?In spontaneous reactions entropy of universe is always increasingLiving organisms (local decreases) can reduce entropy with an increase in entropy of surroundings

Laws of ThermodynamicsSecond Law of Thermodynamics: disorder is more likely than orderentropy: disorder in the universe

The 2nd Law of Thermodynamics states that entropy is always increasing.

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*****Genetic code determines the information to be passed from generation to generation for structure and function of all living things. *