biochemistry and the organization of cells chapter 1

Biochemistry and the Biochemistry and the Organization of CellsOrganization of Cells

Chapter 1Chapter 1

Levels of Structural Organization in the Levels of Structural Organization in the Human BodyHuman Body

Why is study of Biochemistry Why is study of Biochemistry important?important?

• Biochemistry describes life processes

• Multidisciplinary nature allows it use other sciences to answer questions about molecular nature of life processes

• Some biomolecules act in multiple ways and some take part in specific series of reactions

• More complex cells are found in larger organisms than simpler organisms

How is Biochemistry related to How is Biochemistry related to Organic Chemistry?Organic Chemistry?

• Organic Chemistry is study of compounds of carbon and hydrogen and their derivatives

• Biomolecules are made up of carbon• Many carbon compounds are not found in any

organism• Biomolecules of life can be synthesized in

laboratories (synthesis of urea from ammonium cyanate by Friedrich Wohler in 1828)

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

What makes biomolecules special?What makes biomolecules special?

• Biomolecules have important functional groups• Emphases 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?How and when did the Earth come to be?

• Big bang theory explains the origin of earth – formed from matter

• Due 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 planets

• Rest 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?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 sun

• Atmosphere of earth is always been debated

• Existence of Co2 from 3.8 billion years

• N2 in atmosphere – source for formation of proteins and nucleic acids

How were biomolecules likely to have How were biomolecules likely to have formed on the early earth?formed on the early earth?

• Miller-Urey experiment

• Occurred in earth’s early ocean

• Occurred on early earth’s clay particles

• Simple compounds can react (polymerize) abiotically to produce biologically important components of proteins and nucleic acids

Formation of biomolecules on early Formation of biomolecules on early earthearth

HCN present in nucleic acids and HCHO present in sugars

BiomoleculesBiomolecules

• Living cells include very large molecules, such as proteins, nucleic acids, polysaccharides, and lipids– these 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 MacromoleculesInformational Macromolecules

How is cellular activity determined?How is cellular activity determined?

• Enzymes:Enzymes: a class of proteins that are biocatalysts– the catalytic effectiveness of a given enzyme depends on its

amino acid sequence

• Genetic code: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 Which came first – the catalysts or the hereditary molecules?hereditary molecules?

• Cellular activity depends upon presence of catalysts and its synthesis by genetic code

• Discovery of enzyme ‘Ribozyme’ – RNA

• RNA has both catalytic and genetic coding properties

• Life originated from RNA

• Peptide bond formation is catalyzed by RNA portions of Ribosome

Stages in the Evolution of Self-replicating RNA Stages in the Evolution of Self-replicating RNA MoleculesMolecules

Vital importance of a cell membrane in Vital importance of a cell membrane in origin of lifeorigin of life

Assignment 1Assignment 1

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

Differences between prokaryotes and Differences between prokaryotes and eukaryoteseukaryotes

• Prokaryotes – before nucleus and absence of membrane bound organelles

• DNA is present in nuclear region and not separate from the cell

• Plasma membrane is present surrounding the cell

• Eukaryotes – true nucleus and presence of membrane bound organelles

• DNA is well defined

Differences between prokaryotes and Differences between prokaryotes and eukaryoteseukaryotes

• Mitochondria is absent and enzymes for oxidative reactions are located on plasma membrane

• Endoplasmic reticulum is absent

• Ribosomes are found freely floating in cytosol

• Chloroplasts are absent. Photosynthesis takes place in chromatophores which are extensions of plasma membranes

• Plasma membrane is present surrounding the cell

• Mitochondria is present• Endoplasmic reticulum is

present• Ribosomes are bound to

Endoplasmic reticulum• Chloroplasts present in

plants and absent in animals

Some more pointsSome more points

• Polysaccharide cellulose present in prokaryotic and eukaryotic cell walls (plant cells only)

• Some protists and all animal cells lack cell walls and chloroplasts

• Three important organelles – nucleus, mitochondria and chloroplast – separated from rest of the cell by double membrane

• Mitochondria and chloroplasts contain DNA- carry out transcription and protein synthesis

Five Kingdom classification of living Five Kingdom classification of living organismsorganisms

• Prokaryotes• Kingdom: Monera• Bacteria and Cyanobacteria

are members• Unicellular

• Eukaryotes• Kingdom: Protists, Fungi,

Plants and Animals• Unicellular protists are Euglena, Volvox, Amoeba and Paramecium

• Multicellular protists are algae

• Fungi, plants and animals are multicellular

• Fungi like yeasts and molds are unicellular

Three Kingdom classification of living Three Kingdom classification of living organismsorganisms

• Bacteria and Archaea form prokaryotes• Eukarya forms eukaryotes• Bacteria (true bacteria) and Archaea (early

bacteria) have different biochemical features – molecular structure of cell walls, membranes and some types of RNA

• Archaebacteria live in extreme environments – extremophiles – Methanogens, Halophiles and Thermoacidophiles

Did symbiosis play a role in development Did symbiosis play a role in development of eukaryotes?of eukaryotes?

• Theory of Endosymbiosis

• Proposal that eukaryotic organelles evolved through a symbiotic relationship

• One cell engulfed a second cell and a symbiotic relationship developed

• Mitochondria and chloroplasts are thought to have evolved this way

Evidence for EndosymbiosisEvidence for Endosymbiosis

Mitochondria 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?What is thermodynamics?

• Sun is ultimate source of energy on earth• Energy released or absorbed can be measured

in Biochemistry• Energy is converted from one form to another• Thermodynamics deals with changes in

energy that determine whether a process will take place

• Spontaneous reactions will take place without outside intervention

How can we predict what reactions How can we predict what reactions will happen in living cells?will happen in living cells?

• Spontaneity of reaction at a given temperature and pressure is decided by changes in free energy (ΔG)

• ΔG is negative, ΔG<0, spontaneous reaction, energy will be released

• ΔG is positive, ΔG>0, reaction is not spontaneous, energy will be required

• ΔG=0, reaction is in equilibrium

Is life thermodynamically possible?Is life thermodynamically possible?

Free energy: the energy available to do work

-denoted by the symbol G (Gibb’s free energy)

enthalpy: energy contained in a molecule’s chemical bonds

free energy = enthalpy – (entropy x temp.)

G = H - TS

Laws of ThermodynamicsLaws of Thermodynamics

First 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?Is life thermodynamically possible?

• In spontaneous reactions entropy of universe is always increasing

• Living organisms (local decreases) can reduce entropy with an increase in entropy of surroundings

Laws of ThermodynamicsLaws of Thermodynamics

Second Law of Thermodynamics: disorder is more likely than order

entropy: disorder in the universe

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

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