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Unit 1




Introduction
Objectives

1.   Enumerate the attributes of living matter.
2.   Distinguish between prokaryotes and eukaryotes.
3.   Identify the important organelles of the cell.
4.   Name the common elements and compounds required
     by living organisms.
What is a Biochemistry?

  Biochemistry   is the chemistry of biomolecules and their
                chemical reactions in living matter at the
                molecular and cellular level.
      biomolecules molecules involved in the survival of the

                       living organism.
      chemical reactions       changes within the organism’s
                       body usually referred to as biochemical
                       reactions or metabolism.
 Biochemistry   seeks to describe the structure, organization, and
 functions of living matter in molecular terms.
Level of Organization

1. Subatomic Paticles
    - an electron, proton, or neutron; three
      major particles of which atoms are
      composed.

2. Atom
    - smallest unit of an element that still
      remains the properties of that element.
3. Molecule
    - a unit of two or more atoms of the same
      or different elements bonded together.
4. Organelle
    - any various membraneous sacs or other
      compartments inside the cell that separate
      different metabolic reactions within the cellular
      space and in time.                                                    ribosome

5. Cell
    - smallest living unit; may live independently or may be part of a
      multicellular organism.
6. Tissue
    - a group of similar cells and intercellular substances
      functioning together in a specialized activity.                           red blood cell

7. Organ
    - one or more types of of tissues interacting as a structural,
      functioning unit.
                                                                jellyfish


                 brain
8. Organ system
    - two or more organs whose separate functions are integrated int the performance of a
      special task.
                                           • The heart is part of the circulatory system,
                                             which carries oxygen and other materials
                      heart                  throughout the body. Besides the heart, blood
                                             vessels are organs that work in your
                                             circulatory system.



9. Multicellular organism
    - individual composed of specialized,
      interdependent cells arrayed in tissues, organs,
      and other organ system.

 Biochemistry asks how the remarkable
  properties of living organisms arise
  from the thousands of different lifeless
  biomolecules.
   It can be divided into three principal areas:
          1. Structural and Functional Biochemistry: Chemical
              structures and 3D arrangements of molecules.
        2. Informational Biochemistry: Language for storing
            biological data and for transmitting that data in cells
            and organisms.
        3. Bioenergetics: The flow of energy in living organisms
            and how it is transferred from one process to another.
 When these molecules are isolated and examined individually,
  they conform to all the physical and chemical laws that
  describe the behavior of inanimate matter - as do all the
  processes occurring in living organisms.
 The study of biochemistry shows how the collections of
  inanimate molecules that constitute living organisms interact
  to maintain and perpetuate life animated solely by the physical
  and chemical laws that govern the nonliving universe.
   Physical and Chemical sciences alone may not completely
    explain the nature of life, but they at least provide the essential
    framework for such an explanation.

                       BIOCHEMISTRY
 Tools to study biochemistry:
    All   students of life must have a fundamental
     understanding of general chemistry, organic chemistry
     and biology.
    Know chemical structures and reactivities of molecules

     that participate in cellular reactions.
    Know biological functions of cellular molecules.

       Know how all of the pieces and different chemical
        reactions fit together.
Interweaving of the
historical traditions
  of biochemistry,
    cell biology,
    and genetics.
   Biochemistry draws its major themes from:
      1. Organic chemistry -       which describes the properties of
           biomolecules.
      2. Biophysics - which applies the techniques of physics to
        study the structures of biomolecules.
      3. Medical research -           which increasingly seeks to
          understand disease states in molecular terms.
      4. Nutrition - which has illuminated metabolism by describing
         the dietary requirements for maintenance of health.
      5. Microbiology - which has shown that single-celled
         organisms and viruses are ideally suited for the elucidation
         of many metabolic pathways and regulatory mechanisms.
6. Physiology - which investigates life processes at the tissue
   and organism levels.
7. Cell biology - which describes the biochemical division of
  labor within a cell.
8. Genetics - which describes mechanisms that give a
   particular cell or organism its biochemical identity.
Elements of Life

       Up to 99+% of the human body
        is made of the elements C
        (9.5%), H (25.2%), O (63%)
        and N (1.4%).




 Only 31 chemical elements occur naturally in plants and animals.
 99% of the mass of the human body is made up of only six
  elements: oxygen, carbon, hydrogen, nitrogen, calcium, and
  phosphorus.
 Every organic molecule contains carbon. Since 65-90% of
  each body cell consists of water (by weight), it is not surprising
  that oxygen and hydrogen are major components of the body.
Question

 What property unites H, O, C and N and renders these atoms
  so appropriate to the chemistry of life?
 Their ability to form covalent bonds by electron-pair sharing.

                  Bond           Energy (kJ/mol)
                  H-H              436
                  C-H              414
                  C-C              343
                  C-O              351
       The elements of Life
          C, the hybridizer                         Fe, the O2 carrier
          H, placeholder and water                  Na,K depolarizers
           builder                                   P, the energy carrier
          O, the oxidizer and hydrogen              Cl, the neutralizer
           bonder                                    S, the linker
          N, protein builder                        Mg, Zn, Cu, Ni, Mo
          Ca, the skeletizer
                                                      enzyme coordinators
                                                  Lithium, Strontium,
                                                         
        Oxygen (65%)          Sulfur (0.25%)    Aluminum, Silicon,
        Carbon (18%)          Sodium (0.15%)    Lead, Vanadium,
        Hydrogen (10%)        Magnesium (0.05%) Arsenic, Bromine
        Nitrogen (3%)                            (trace amounts)
        Calcium (1.5%)              Copper, Zinc, Selenium, Molybdenum,
        Phosphorus (1.0%)            Fluorine, Chlorine, Iodine, Manganese,
        Potassium (0.35%)            Cobalt, Iron (0.70%)
Biomolecules of Life

1. Proteins
     - these are polymers of amino acids linked by peptide
         bonds.
     - they are also called polypetides.
     - they function as transport proteins, structural proteins,
         enzymes, antibodies, cell receptors.

2. Nucelic acids
     - classified as RNA and DNA, are polymers of
       nucleotides linked by phosphodiester bonds.
- the nucleotide sequence in these polymers spells out
       the genetic information that directs growth,
       development and reproduction.
3. Carbohydrates
    - also known as polysaccharides which are polymers of
       monosaccharides.
    - function as storage sources of energy in plants (starch)
       and animals (glycogen) and as structural elements in
       plants.
    - function as storage sources of energy in plants (starch)
       and animals (glycogen), as structural elements in
       plants, supply carbon for synthesis of other
       compounds        and     used      in      intercellular
       communications..
4. Lipids
        - storage of energy in the form of fat
           - responsible for the integrity of cellular membranes
              (phospholipids), synthesis of hormones and
              vitamins, and act as insulator (thermal blanket).

 Livingthings are composed of lifeless molecules. When these
  molecules are considered individually, they are found to
  conform to all the physical and chemical laws that describe the
  behavior of inanimate matter.
 But   when put together in a particular manner, this collection of
  lifeless molecules start to exhibit the different attributes of life.
What is Life?

 Hard to define!                   Let’s list some of its properties.
   Necessary Properties
        highly organized and complicated
          - all organisms are consist of one or more
            cells (atoms connect to form molecules,
            molecules make organelles, and
            organelles make cells. Cells make up
            tissue, tissues organized into organs,
            and organs into organ systems.
        uses energy
          - all organisms acquire and use energy to
            perform many kinds of work.
    sensitive (interacts with its environment)
         - plants grow toward light, an animal’s pupils dilate in darkness, amoeba and
           paramecia move toward food.
       metabolism
         - ability to change substances into different substances to get energy.
          evolutionary adaptation
             - all organisms interact with the environment and other organisms in ways that
               influence their survival to better adapt to their environment.
         homeostasis
            - all organisms maintain ‘relatively’ constant internal conditions like ion
              concentration, body fluid, temperature, glucose in the bloodstream, blood
              pH, blood pressure, etc.
         excretion
             - removal of waste products

   Likely (but maybe not be necessary) Properties
         grows and develops
            - normally, all forms of life must grow to allow development and reproduction
 reproduces
    - heriditary molecules (RNA and DNA) ensures production of offspring similar to
      previous generation.
 mutates and evolves

     - long term adaptation, new forms of life are formed from life itself
Requirements for Life

1. Energy (need food to function)
     a. Autotrophs = make their own food (plants are autotrophs)
       b. Heterotrophs = cannot make their own food (animals, people,
                         dogs, lizards, are heterotrophs).
2. Water – all living things need water to survive.

3. Living Space – need a place to get food, water, and shelter.

4. Homeostasis = Stable Internal Conditions – so when the temperature gets
                 too cold or hot, or too wet or dry where they live, their body
                 still stays the same inside.
The Cell

 All living organisms on earth are made of cells except viruses.
 The smallest unit that is capable of life.




                                             multicellur organism, Human
         one-celled organism, Bacteria            (at least 1014 cells)
 There are many different types of cells that are usually highly
 specialized. The differences could be according to shape and
 function.
Examples of Cells

             Amoeba Proteus


                              Plant Stem


Bacteria


                                           Red Blood Cell



           Nerve Cell
 All cells are relatively small. They vary in length from 2 µm to 30 µm.
Prokaryotic Cell

   Do not have structures surrounded by membranes
   Few internal structures
   No nucleus
• Nucleoid region contains the DNA
• Cell membrane and cell wall
• Contain ribosomes (no membrane)
  to make proteins in their cytoplasm
Eukaryotic Cell (Animal)

    Contain organelles such
     as a nucleus surrounded
     by membranes
    Most living organisms


    Contain 3 basic cell structures:
    • Nucleus
    • Cell Membrane
    • Cytoplasm with organelles
“Typical” Animal Cell
Eukaryotic Cell (Plant)


Contain 3 basic cell
structures:
  • Nucleus
  • Cell Membrane
  • Cytoplasm with
    organelles
“Typical” Plant Cell
Functions of Organelles
   Cell Membrane
   A lipid/protein/carbohydrate complex, providing a barrier and
   containing transport and signaling systems.
   (Serves as security guards or gate keeprs. Decides what can
   enter or leaves the cell. It lets in useful substances and lets out
   waste.)
   Cell wall
   Plants have a rigid cell wall in addition to their cell membranes
   Cytoplasm
   enclosed by the plasma membrane, liquid portion called cytosol
   and it houses the membranous organelles.
   Nucleus
   Double membrane surrounding the chromosomes and the nucleolus.
   Pores allow specific communication with the cytoplasm. The
   nucleolus is a site for synthesis of RNA making up the ribosome
   (Serves as the control center. All the activities inside the cell
   are controlled by instructions which comes from the nucleus.)
Mitochondrion
Surrounded by a double membrane with a series of folds
called cristae. Functions in energy production through metabolism.
Contains its own DNA, and is believed to have originated as a
captured bacterium.
(Serves as the power house of the cell. The mitochondira releases
energy from food.)


Chloroplasts (plastids)
Surrounded by a double membrane, containing stacked thylakoid
membranes. Responsible for photosynthesis, the trapping of light
energy for the synthesis of sugars. Contains DNA, and like
mitochondria is believed to have originated as a captured
bacterium.



Endoplasmic reticulum (RER)
A network of interconnected membranes forming channels within the
cell. Covered with ribosomes (causing the "rough" appearance) which
are in the process of synthesizing proteins for secretion or
localization in membranes.
 (Serves as the construction team of the cell.)
Golgi body
A series of stacked membranes. Vesicles (small membrane
surrounded bags) carry materials from the RER to the Golgi
apparatus. Vesicles move between the stacks while the proteins are
"processed" to a mature form. Vesicles then carry newly formed
membrane and secreted proteins to their final destinations including
secretion or membrane localization.
(Serves as the assembly and storage point of the cell. Some of the
substances made in the cells are assembled and stored in the Golgi
body.)

Lysosymes
A membrane bound organelle that is responsible for degrading
proteins and membranes in the cell, and also helps degrade materials
ingested by the cell.
(Serves as the waste disposal unit of the cell. The lysozomes eat
up waste materials and old worn out parts of the cell.)

Vacuoles
Membrane surrounded "bags" that contain water and storage
materials in plants.
Peroxisomes or Microbodies
Produce and degrade hydrogen peroxide, a toxic compound that
can be produced during metabolism.




 Cytoskeleton
 Arrays of protein filaments in the cytosol. Gives the cell its
 shape and provides basis for movement.
 E.g. microtubules and microfilaments.
Cell-Factory Analogy
Assignment

Purpose: To compare the structure and function of cells with a
         familiar system.
DIRECTIONS: You will create an analogy (comparison) for a cell
            using a factory.
Your analogy will include a

(1) drawing or model where you label each part of the city/house/
body/station and its corresponding cell part (organelle), and a

(2) written description of each city/house/body/station part and
how it is similar to its corresponding organelle.
Biomolecules in Cells
Biochemical Reactions

    • Metabolism - total sum of the chemical reaction happening in a living
                   organism (highly coordinated and purposeful activity)
         Anabolism – biosynthesis of small molecules to larger molecules
                         which requires energy.
         Catabolism - degradation of fuel molecules and the production of
                        energy for cellular function
   All biochemical reactions occur inside the cell and are catalyzed by
    enzymes.
   Both anabolism and catabolism may occur simultaneously not only
    because they involve different enzymes but also because they ma be
    separated in their location within the cell.
catabolic              • For example:
                                     the degradation of fatty acids to acetyl
                                    CoA occurs by way of exnzym located
                                    within the mitochondria, whereas the
                                    anabolic conversion of acetyl CoA to
            anabolic                fatty acids occurs in the cytoplasm by
                                    way oif a separate system.



   FUNCTIONS OF METABOLISM
      1. Acquistion and utilization of energy.
      2. Synthesis of molecules needed for cell structure and functioning
         (i.e., proteins, nucleic acids, lipids, etc.
      3. Removal of waste products.
Metabolic Pathway

   Metabolism generally occurs by orderly, stepwise, series or sequence of
    individual chemical reactions that are dependent on the basic laws of
    thermodynamics called as metabolic pathways.
 • Also called biochemical pathway, is a multistep reaction within a cell that is
   catalyzed by enzymes
 An example of a simple metabolic pathway is the single step

  conversion of a precursor A to a given product B.


                                              an enzymatic reaction
             A    enzyme         B             is reversible.
   In a multi-steps metabolic pathway, product B could become a
    substrate of the second reaction to yield product C and so on.

           E1             E2          E3           E4          E5
       A            B           C            D            E           Product
                   linear metabolic pathway
                   E’s are enzymes
                   B, C, D, E are intermediate substances also called metabolites.


                                      E5           E8          E11
                         E2     C            D           E            Product 1
           E1             E3          E6           E9          E12
       A            B           F            G            H           Product 2
                          E4
                                      E7           E10         E13
                                I            J           K            Product 3
                   branched metabolic pathway
Primary Metabolic Pathway

   A series of metabolism or biochemical reactions that encompasses
    reactions involving primary compounds which are formed as part of the
    normal anabolic and catabolic processes of plants and animals.
   Primary metabolites are compounds commonly produced from primary
    metabolic pathways such as proteins, carbohydrates, lipids, nucleic acid
    that are directly used for growth and devlopment.
   Absence of primary metabolites will cause cells and the whole organism
    to die.
   Examples:
        Glycolysis                 Electron Transport Chain

        Citric Acid Cylce          Oxydation of Fatty Acids
   GLYCOLYSIS
    reverse steps
    not shown
Secondary Metabolic Pathway

   A metabolism of secondary compounds or secondary metabolites other
    than primary compunds.
   A compound is classified as secondary metabolite if it does not seem to to
    directly function in the processes of growth and devlopment of the animal
    or plant.
   Even though secondary compounds are a normal part of the metabolism of
    an organism, they are often produced in specialized cells and tend to be
    more complex than primary compounds.
   Examples of secondary metabolites
        antibiotics      alkaloids
   Even though thousands of reactions sound very large and complex
    inside a tiny cell:
         1. The type of reactions are small.
         2. Mechanisms of biochemical reactions are simple.
         3. Reactions of central importance (for energy production and
            synthesis and degradation of major cell components) are
            relatively few in number.
   Frequent reactions encountered in biochemical processes:
         1. Nucleophilic substitution
               • one atom or group of atoms substituted for another.
         2. Elimination reactions
               • double bond is formed when atoms in a molecule is removed.
        3. Addition reactions
             • two molecules combine to form a single product.
             • hydration reactions - water added to alkene > alcohol
               (common addition reaction).
4. Isomerization reactions
       • involve intramolecular shift of atoms or groups
5. Oxidation-Reduction (redox) reactions
       • occur when there is transfer of electron from a donor to an
         electron acceptor.
6. Hydrolysis reactions
       • cleavage of double bond by water.
      Requirement for Life
    MATTER:
       PRODUCED IN BIG BANG (H & He) AND STARS
    (
    (HEAVIER ELEMENTS)
       ARE CERTAIN ELEMENTS NEEDED?
   STABLE ENERGY SOURCE:
       LOW MASS MAIN SEQUENCE STARS (OR SOMETHING
    E
    ELSE?)
   PROTECTED ENVIRONMENT:
       PLANETARY OR LUNAR SURFACES
       PLANETARY OR LUNAR INTERIORS
       THICK PLANETARY OR LUNAR ATMOSPHERES
   CHEMICAL SOLVENT (LIQUID):
        W
        WATER (OR SOMETHING ELSE?)
Secondary metabolism:
Metabolism of secondary compounds, defined simply as
compounds other than primary compounds. A compound is
classified as a secondary metabolite if it does not seem to
directly function in the processes of growth and
development. Even though secondary compounds are a
normal part of the metabolism of an organism, they are
often produced in specialized cells, and tend to be more
complex than primary compounds. Examples of secondary
compounds include antibiotics, and plant chemical
defenses such as alkaloids and steroids.

MetaCyc (www.metacyc.org)
Taiz, Lincoln, and Eduardo Zeiger. "Surface Protection and Secondary
Defense Compounds." Plant Physiology. New York: Benjamin/Cummings
Publishing Company, Inc., 1991: 320-345.
[item in sorceforge, should be readdressed via sourceforge]
Secondary metabolism:
Processes that result in many of the chemical changes of
compounds that are not required for growth and
maintenance of cells, and are often unique to a taxon. In
multicellular organisms secondary metabolism is generally
carried out in specific cell types, and may be useful for the
organism as a whole. In unicellular organisms, secondary
metabolism is often used for the production of antibiotics or
for the utilization and acquisition of unusual nutrients.


MetaCyc (www.metacyc.org)
Taiz, Lincoln, and Eduardo Zeiger. "Surface Protection and Secondary
Defense Compounds." Plant Physiology. New York: Benjamin/Cummings
Publishing Company, Inc., 1991: 320-345.
[item in sorceforge, should be readdressed via sourceforge]
   Metabolic Pathway Examples
    Glycolysis (Carbohydrate Metabolism): Glucose
    + 2 ADP + 2 Pi + 2 NAD+  2 Pyruvate + 2 ATP
    + 2 NADH + 2 H+ + 2 H2O
   Activation and Transport of Fatty Acids (Lipid
    Metabolism): Fatty Acid + ATP + Coenzyme A 
    Fatty Acyl-CoA + Pyrophosphate + AMP + H+
   Cholesterol Biosynthesis 1 (Lipid Metabolism):
    6 Acetyl-CoA + 6 Acetoacetyl-CoA + 14 NADPH
    + 14 H+ + 5 H2O + 18 ATP + O2  Lanosterol
    + 14 NADP+ + 12 CoA-S-H + 18 ADP + 6 Pi + 4 PPi
    + 6 CO2
   Shikimate Pathway (Amino Acid Metabolism): D-
    Erythrose-4-phosphate + 2 Phosphoenoylpyruvate
    + NAD+ + NADPH + ATP  Chorismate + NADH
    + NADP+ + ADP + 4 Pi
Metabolic Pathway (Glycolysis)




Glucose + 2 ADP + 2 Pi + 2 NAD+  2 Pyruvate + 2 ATP + 2 NADH
Main Players
   Enzymes: polymers of amino acids that
    act as catalysts that regulate speed of
    many chemical reactions in the
    metabolism of living organisms; ex.
    Phosphoglucoisomerase, aldolase
   Metabolites: substance involved or by-
    product of metabolism; ex. erythrose 4-
    phosphate, sedoheptulose 7-phosphate
Protein       Carbohydrates   Lipids



Amino Acids
.




    Ribosomes
    Protein and RNA complex responsible for protein synthesis

    Smooth endoplasmic reticulum (SER)
    A network of interconnected membranes forming channels within the
    cell. A site for synthesis and metabolism of lipids. Also contains
    enzymes for detoxifying chemicals including drugs and pesticides.

    Golgi apparatus
    A series of stacked membranes. Vesicles (small membrane
    surrounded bags) carry materials from the RER to the Golgi
    apparatus. Vesicles move between the stacks while the proteins are
    "processed" to a mature form. Vesicles then carry newly formed
    membrane and secreted proteins to their final destinations including
    secretion or membrane localization.
Primary (1°) Metabolism
- Construct common biological macromolecules from simple
  building blocks found within every cell

- Typically a process of polymerization, stringing monomers
  together into a macromolecule that performs a cellular function

       sugars               polysaccharides

       amino acids          proteins

       fats                 phospholipid bilayers

- Block production: cell dies (primary metabolites are essential)
Metabolism and
Energy Production

            Citric Acid Cycle
       Electron Transport Chain
      ATP Energy from Glucose
       Oxidation of Fatty Acids
  Metabolic Pathways for Amino Acids
Cell Membrane


               Outer membrane of cell
                that controls movement
                in and out of the cell
               Double layer
Cell Wall
                                                         Most commonly
                                                          found in plant cells
                                                          & bacteria
                                                         Supports & protects
                                                          cells




http://library.thinkquest.org/12413/structures.html
Inside the Cell
Nucleus
   Directs cell activities
   Separated from cytoplasm by nuclear
    membrane
   Contains genetic material - DNA
Nuclear Membrane
                      Surrounds nucleus
                      Made of two layers
                      Openings allow
                       material to enter
                       and leave nucleus




http://library.thinkquest.org/12413/structures.html
Chromosomes
                                                         In nucleus
                                                         Made of DNA
                                                         Contain instructions
                                                          for traits &
                                                          characteristics




http://library.thinkquest.org/12413/structures.html
Nucleolus
                Inside nucleus
                Contains RNA to
                 build proteins




http://library.thinkquest.org/12413/structures.html
Cytoplasm
   Gel-like mixture
   Surrounded by cell membrane
   Contains hereditary material
Endoplasmic Reticulum
                 Moves materials around               

                                                          in cell
                                                         Smooth type: lacks
                                                          ribosomes
                                                         Rough type (pictured):
                                                          ribosomes embedded in
                                                          surface




http://library.thinkquest.org/12413/structures.html
Ribosomes
                Each cell contains
                 thousands
                Make proteins
                Found on ribosomes
                 & floating
                 throughout the cell



http://library.thinkquest.org/12413/structures.html
Mitochondria
    Produces energy through
     chemical reactions –
     breaking down fats &
     carbohydrates
    Controls level of water and
     other materials in cell
    Recycles and decomposes
     proteins, fats, and
     carbohydrates

http://library.thinkquest.org/12413/structures.html
Golgi Bodies
     Protein 'packaging
      plant'
     Move materials within
      the cell
     Move materials out of
      the cell




http://library.thinkquest.org/12413/structures.html
Lysosome

      Digestive 'plant' for
       proteins, fats, and
       carbohydrates
      Transports undigested
       material to cell
       membrane for removal
      Cell breaks down if
       lysosome explodes
http://library.thinkquest.org/12413/structures.html
Vacuoles
               Membrane-bound
                sacs for storage,
                digestion, and waste
                removal
               Contains water
                solution
               Help plants maintain
                shape

http://library.thinkquest.org/12413/structures.html
Chloroplast
               Usually found in
                plant cells
               Contains green
                chlorophyll
               Where
                photosynthesis takes
                place


http://library.thinkquest.org/12413/structures.html
What is Life Made of?
   Physical and Chemical sciences alone
    may not completely explain the nature
    of life, but they at least provide the
    essential framework for such an
    explanation.
   All students of life must have a
    fundamental understanding of organic
    chemistry and biology
Cell Structure
BOTTOM LINE:
THE ELEMENTS THAT MAKE UP TERRESTRIAL
 LIVING ORGANISMS ARE VERY COMMON IN
 STARS AND IN THE INTERSTELLAR
 MATERIAL FROM WHICH STARS AND
 PLANETS ARE FORMED.

IN LIVING THINGS, THE ATOMS OF THESE
  ELEMENTS ARE ORGANIZED IN ORGANIC
  MOLECULES, MANY OF WHICH ARE LARGE
  AND COMPLEX.
BASIC FACTS ABOUT LIFE ON EARTH
 LIVING ORGANISMS ON EARTH ARE MADE OF
  CELLS.
 EXCEPTION: VIRUSES

 A CELL IS TINY DROP OF WATER AND VARIOUS
   ORGANIC MOLECULES, SURROUNDED BY A
   MEMBRANE. SOME CELLS CONTAIN CERTAIN
   STRUCTURES, TO BE DISCUSSED LATER. SOME
   ORGANISMS (BACTERIA, FOR EXAMPLE) ARE
   SINGLE-CELLED, AND OTHER ORGANISMS
   (HUMANS, FOR EXAMPLE) ARE MULTICELLULAR. A
   CELL CAN DIVIDE, RESULTING IN TWO CELLS.
Bio-molecules
    Just like cells are building blocks of tissues likewise molecules are
     building blocks of cells.
    Animal and plant cells contain approximately 10, 000 kinds of
     molecules (bio-molecules)
    Water constitutes 50-95% of cells content by weight.

    Ions like Na+, K+ and Ca+ may account for another 1%
    Almost all other kinds of bio-molecules are organic (C, H, N, O, P, S)

    Infinite variety of molecules contain C.

     Most bio-molecules considered to be derived from hydrocarbons.
    The chemical properties of organic bio-molecules are determined by
     their functional groups. Most bio-molecules have more than one.
Major Classes of small Bio-molecules
                  •   Building blocks of proteins.
   1. Amino      •   20 commonly occurring.
    acids:        •   Contains amino group and carboxyl group
                      function groups (behavioral properties)
                  •   R Group (side chains) determines the
                      chemical properties of each amino acids.
                  •   Also determines how the protein folds and
                      its biological function.
                  •   Individual amino acids in protein connected
                      by peptide bond.

                  •    Functions as transport proteins, structural
                      proteins, enzymes, antibodies, cell
                      receptors.
Sugars
   Carbohydrates most abundant organic molecule
    found in nature.
   Initially synthesized in plants from a complex series
    of reactions involving photosynthesis.
   Basic unit is monosaccharides.
   Monosaccharides can form larger molecules e.g.
    glycogen, plant starch or cellulose.

Functions
 Store energy in the form of starch (photosynthesis in
  plants) or glycogen (in animals and humans).
   Provide energy through metabolism pathways and cycles.
   Supply carbon for synthesis of other compounds.
   Form structural components in cells and tissues.
   Intercellular communications
Fatty acids
   Are monocarboxylic acid contains even number C atoms
   Two types: saturated (C-C sb) and unsaturated (C-C db)
   Fatty acids are components of several lipid molecules.
   E,g. of lipids are triacylglycerol, streiods (cholestrol, sex
    hormones), fat soluble vitamins.

Functions
 Storage of energy in the form of fat
 Membrane structures
 Insulation (thermal blanket)
 Synthesis of hormones
Energy for Cells

   Living cells are inherently unstable.
   Constant flow of energy prevents them from
    becoming disorganized.
   Cells obtains energy mainly by the oxidation of bio-
    molecules (e- transferred from 1 molecule to another
    and in doing so they lose energy)
   This energy captured by cells & used to maintain
    highly organized cellular structure and functions
How do complex structure of cells maintain high internal order?



n   Synthesis of bio-molecules

2. Transport Across Membranes
-    Cell membranes regulate the passage of ions and molecules
     from one compartment to another.

3. Cell Movement
-    Organised movement- most obvious characteristics of living
     cells. The intricate and coordinated activities required to
     sustain life require the movement of cell components.

4. Waste Removal
-   Animal cells convert food molecules into CO2, H20 & NH3. If
    these not disposed properly can be toxic.
Thank you for your indulgence!
   Metabolic Pathway Examples
    Glycolysis (Carbohydrate Metabolism): Glucose
    + 2 ADP + 2 Pi + 2 NAD+  2 Pyruvate + 2 ATP
    + 2 NADH + 2 H+ + 2 H2O
   Activation and Transport of Fatty Acids (Lipid
    Metabolism): Fatty Acid + ATP + Coenzyme A 
    Fatty Acyl-CoA + Pyrophosphate + AMP + H+
   Cholesterol Biosynthesis 1 (Lipid Metabolism):
    6 Acetyl-CoA + 6 Acetoacetyl-CoA + 14 NADPH
    + 14 H+ + 5 H2O + 18 ATP + O2  Lanosterol
    + 14 NADP+ + 12 CoA-S-H + 18 ADP + 6 Pi + 4 PPi
    + 6 CO2
   Shikimate Pathway (Amino Acid Metabolism): D-
    Erythrose-4-phosphate + 2 Phosphoenoylpyruvate
    + NAD+ + NADPH + ATP  Chorismate + NADH
    + NADP+ + ADP + 4 Pi
Year




  1944                                                  Proteins were thought to
                                                        carry genetic information




 1897
       Mie s c he r d is c o ve re d D NA




 1828                                       Interweaving of the
                                            historical traditions
                                              of biochemistry,
                                                cell biology,
                                                and genetics.
   Living things are composed of lifeless molecules. When these molecules
    are considered individually, they are found to conform to all the physical
    and chemical laws that describe the behavior of inanimate matter.

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Bio lec1

  • 2. Objectives 1. Enumerate the attributes of living matter. 2. Distinguish between prokaryotes and eukaryotes. 3. Identify the important organelles of the cell. 4. Name the common elements and compounds required by living organisms.
  • 3. What is a Biochemistry?  Biochemistry is the chemistry of biomolecules and their chemical reactions in living matter at the molecular and cellular level.  biomolecules molecules involved in the survival of the living organism.  chemical reactions changes within the organism’s body usually referred to as biochemical reactions or metabolism.  Biochemistry seeks to describe the structure, organization, and functions of living matter in molecular terms.
  • 4. Level of Organization 1. Subatomic Paticles - an electron, proton, or neutron; three major particles of which atoms are composed. 2. Atom - smallest unit of an element that still remains the properties of that element. 3. Molecule - a unit of two or more atoms of the same or different elements bonded together.
  • 5. 4. Organelle - any various membraneous sacs or other compartments inside the cell that separate different metabolic reactions within the cellular space and in time. ribosome 5. Cell - smallest living unit; may live independently or may be part of a multicellular organism. 6. Tissue - a group of similar cells and intercellular substances functioning together in a specialized activity. red blood cell 7. Organ - one or more types of of tissues interacting as a structural, functioning unit. jellyfish brain
  • 6. 8. Organ system - two or more organs whose separate functions are integrated int the performance of a special task. • The heart is part of the circulatory system, which carries oxygen and other materials heart throughout the body. Besides the heart, blood vessels are organs that work in your circulatory system. 9. Multicellular organism - individual composed of specialized, interdependent cells arrayed in tissues, organs, and other organ system.  Biochemistry asks how the remarkable properties of living organisms arise from the thousands of different lifeless biomolecules.
  • 7. It can be divided into three principal areas: 1. Structural and Functional Biochemistry: Chemical structures and 3D arrangements of molecules. 2. Informational Biochemistry: Language for storing biological data and for transmitting that data in cells and organisms. 3. Bioenergetics: The flow of energy in living organisms and how it is transferred from one process to another.
  • 8.  When these molecules are isolated and examined individually, they conform to all the physical and chemical laws that describe the behavior of inanimate matter - as do all the processes occurring in living organisms.  The study of biochemistry shows how the collections of inanimate molecules that constitute living organisms interact to maintain and perpetuate life animated solely by the physical and chemical laws that govern the nonliving universe.  Physical and Chemical sciences alone may not completely explain the nature of life, but they at least provide the essential framework for such an explanation. BIOCHEMISTRY
  • 9.  Tools to study biochemistry:  All students of life must have a fundamental understanding of general chemistry, organic chemistry and biology.  Know chemical structures and reactivities of molecules that participate in cellular reactions.  Know biological functions of cellular molecules.  Know how all of the pieces and different chemical reactions fit together.
  • 10. Interweaving of the historical traditions of biochemistry, cell biology, and genetics.
  • 11. Biochemistry draws its major themes from: 1. Organic chemistry - which describes the properties of biomolecules. 2. Biophysics - which applies the techniques of physics to study the structures of biomolecules. 3. Medical research - which increasingly seeks to understand disease states in molecular terms. 4. Nutrition - which has illuminated metabolism by describing the dietary requirements for maintenance of health. 5. Microbiology - which has shown that single-celled organisms and viruses are ideally suited for the elucidation of many metabolic pathways and regulatory mechanisms.
  • 12. 6. Physiology - which investigates life processes at the tissue and organism levels. 7. Cell biology - which describes the biochemical division of labor within a cell. 8. Genetics - which describes mechanisms that give a particular cell or organism its biochemical identity.
  • 13. Elements of Life  Up to 99+% of the human body is made of the elements C (9.5%), H (25.2%), O (63%) and N (1.4%).  Only 31 chemical elements occur naturally in plants and animals.
  • 14.  99% of the mass of the human body is made up of only six elements: oxygen, carbon, hydrogen, nitrogen, calcium, and phosphorus.  Every organic molecule contains carbon. Since 65-90% of each body cell consists of water (by weight), it is not surprising that oxygen and hydrogen are major components of the body.
  • 15. Question  What property unites H, O, C and N and renders these atoms so appropriate to the chemistry of life? Their ability to form covalent bonds by electron-pair sharing. Bond Energy (kJ/mol) H-H 436 C-H 414 C-C 343 C-O 351
  • 16. The elements of Life  C, the hybridizer  Fe, the O2 carrier  H, placeholder and water  Na,K depolarizers builder  P, the energy carrier  O, the oxidizer and hydrogen  Cl, the neutralizer bonder  S, the linker  N, protein builder  Mg, Zn, Cu, Ni, Mo  Ca, the skeletizer enzyme coordinators Lithium, Strontium,   Oxygen (65%)  Sulfur (0.25%) Aluminum, Silicon,  Carbon (18%)  Sodium (0.15%) Lead, Vanadium,  Hydrogen (10%)  Magnesium (0.05%) Arsenic, Bromine  Nitrogen (3%) (trace amounts)  Calcium (1.5%)  Copper, Zinc, Selenium, Molybdenum,  Phosphorus (1.0%) Fluorine, Chlorine, Iodine, Manganese,  Potassium (0.35%) Cobalt, Iron (0.70%)
  • 17. Biomolecules of Life 1. Proteins - these are polymers of amino acids linked by peptide bonds. - they are also called polypetides. - they function as transport proteins, structural proteins, enzymes, antibodies, cell receptors. 2. Nucelic acids - classified as RNA and DNA, are polymers of nucleotides linked by phosphodiester bonds.
  • 18. - the nucleotide sequence in these polymers spells out the genetic information that directs growth, development and reproduction. 3. Carbohydrates - also known as polysaccharides which are polymers of monosaccharides. - function as storage sources of energy in plants (starch) and animals (glycogen) and as structural elements in plants. - function as storage sources of energy in plants (starch) and animals (glycogen), as structural elements in plants, supply carbon for synthesis of other compounds and used in intercellular communications..
  • 19. 4. Lipids - storage of energy in the form of fat - responsible for the integrity of cellular membranes (phospholipids), synthesis of hormones and vitamins, and act as insulator (thermal blanket).  Livingthings are composed of lifeless molecules. When these molecules are considered individually, they are found to conform to all the physical and chemical laws that describe the behavior of inanimate matter.  But when put together in a particular manner, this collection of lifeless molecules start to exhibit the different attributes of life.
  • 20. What is Life?  Hard to define! Let’s list some of its properties.  Necessary Properties  highly organized and complicated - all organisms are consist of one or more cells (atoms connect to form molecules, molecules make organelles, and organelles make cells. Cells make up tissue, tissues organized into organs, and organs into organ systems.  uses energy - all organisms acquire and use energy to perform many kinds of work.
  • 21. sensitive (interacts with its environment) - plants grow toward light, an animal’s pupils dilate in darkness, amoeba and paramecia move toward food.  metabolism - ability to change substances into different substances to get energy.  evolutionary adaptation - all organisms interact with the environment and other organisms in ways that influence their survival to better adapt to their environment.  homeostasis - all organisms maintain ‘relatively’ constant internal conditions like ion concentration, body fluid, temperature, glucose in the bloodstream, blood pH, blood pressure, etc.  excretion - removal of waste products  Likely (but maybe not be necessary) Properties  grows and develops - normally, all forms of life must grow to allow development and reproduction
  • 22.  reproduces - heriditary molecules (RNA and DNA) ensures production of offspring similar to previous generation.  mutates and evolves - long term adaptation, new forms of life are formed from life itself
  • 23. Requirements for Life 1. Energy (need food to function) a. Autotrophs = make their own food (plants are autotrophs) b. Heterotrophs = cannot make their own food (animals, people, dogs, lizards, are heterotrophs). 2. Water – all living things need water to survive. 3. Living Space – need a place to get food, water, and shelter. 4. Homeostasis = Stable Internal Conditions – so when the temperature gets too cold or hot, or too wet or dry where they live, their body still stays the same inside.
  • 24.
  • 25. The Cell  All living organisms on earth are made of cells except viruses.  The smallest unit that is capable of life. multicellur organism, Human one-celled organism, Bacteria (at least 1014 cells)
  • 26.  There are many different types of cells that are usually highly specialized. The differences could be according to shape and function.
  • 27. Examples of Cells Amoeba Proteus Plant Stem Bacteria Red Blood Cell Nerve Cell
  • 28.  All cells are relatively small. They vary in length from 2 µm to 30 µm.
  • 29. Prokaryotic Cell  Do not have structures surrounded by membranes  Few internal structures  No nucleus
  • 30. • Nucleoid region contains the DNA • Cell membrane and cell wall • Contain ribosomes (no membrane) to make proteins in their cytoplasm
  • 31. Eukaryotic Cell (Animal)  Contain organelles such as a nucleus surrounded by membranes  Most living organisms Contain 3 basic cell structures: • Nucleus • Cell Membrane • Cytoplasm with organelles
  • 32.
  • 34. Eukaryotic Cell (Plant) Contain 3 basic cell structures: • Nucleus • Cell Membrane • Cytoplasm with organelles
  • 36. Functions of Organelles Cell Membrane A lipid/protein/carbohydrate complex, providing a barrier and containing transport and signaling systems. (Serves as security guards or gate keeprs. Decides what can enter or leaves the cell. It lets in useful substances and lets out waste.) Cell wall Plants have a rigid cell wall in addition to their cell membranes Cytoplasm enclosed by the plasma membrane, liquid portion called cytosol and it houses the membranous organelles. Nucleus Double membrane surrounding the chromosomes and the nucleolus. Pores allow specific communication with the cytoplasm. The nucleolus is a site for synthesis of RNA making up the ribosome (Serves as the control center. All the activities inside the cell are controlled by instructions which comes from the nucleus.)
  • 37. Mitochondrion Surrounded by a double membrane with a series of folds called cristae. Functions in energy production through metabolism. Contains its own DNA, and is believed to have originated as a captured bacterium. (Serves as the power house of the cell. The mitochondira releases energy from food.) Chloroplasts (plastids) Surrounded by a double membrane, containing stacked thylakoid membranes. Responsible for photosynthesis, the trapping of light energy for the synthesis of sugars. Contains DNA, and like mitochondria is believed to have originated as a captured bacterium. Endoplasmic reticulum (RER) A network of interconnected membranes forming channels within the cell. Covered with ribosomes (causing the "rough" appearance) which are in the process of synthesizing proteins for secretion or localization in membranes. (Serves as the construction team of the cell.)
  • 38. Golgi body A series of stacked membranes. Vesicles (small membrane surrounded bags) carry materials from the RER to the Golgi apparatus. Vesicles move between the stacks while the proteins are "processed" to a mature form. Vesicles then carry newly formed membrane and secreted proteins to their final destinations including secretion or membrane localization. (Serves as the assembly and storage point of the cell. Some of the substances made in the cells are assembled and stored in the Golgi body.) Lysosymes A membrane bound organelle that is responsible for degrading proteins and membranes in the cell, and also helps degrade materials ingested by the cell. (Serves as the waste disposal unit of the cell. The lysozomes eat up waste materials and old worn out parts of the cell.) Vacuoles Membrane surrounded "bags" that contain water and storage materials in plants.
  • 39. Peroxisomes or Microbodies Produce and degrade hydrogen peroxide, a toxic compound that can be produced during metabolism. Cytoskeleton Arrays of protein filaments in the cytosol. Gives the cell its shape and provides basis for movement. E.g. microtubules and microfilaments.
  • 41. Assignment Purpose: To compare the structure and function of cells with a familiar system. DIRECTIONS: You will create an analogy (comparison) for a cell using a factory.
  • 42. Your analogy will include a (1) drawing or model where you label each part of the city/house/ body/station and its corresponding cell part (organelle), and a (2) written description of each city/house/body/station part and how it is similar to its corresponding organelle.
  • 44. Biochemical Reactions • Metabolism - total sum of the chemical reaction happening in a living organism (highly coordinated and purposeful activity) Anabolism – biosynthesis of small molecules to larger molecules which requires energy. Catabolism - degradation of fuel molecules and the production of energy for cellular function  All biochemical reactions occur inside the cell and are catalyzed by enzymes.  Both anabolism and catabolism may occur simultaneously not only because they involve different enzymes but also because they ma be separated in their location within the cell.
  • 45. catabolic • For example: the degradation of fatty acids to acetyl CoA occurs by way of exnzym located within the mitochondria, whereas the anabolic conversion of acetyl CoA to anabolic fatty acids occurs in the cytoplasm by way oif a separate system.  FUNCTIONS OF METABOLISM 1. Acquistion and utilization of energy. 2. Synthesis of molecules needed for cell structure and functioning (i.e., proteins, nucleic acids, lipids, etc. 3. Removal of waste products.
  • 46. Metabolic Pathway  Metabolism generally occurs by orderly, stepwise, series or sequence of individual chemical reactions that are dependent on the basic laws of thermodynamics called as metabolic pathways. • Also called biochemical pathway, is a multistep reaction within a cell that is catalyzed by enzymes  An example of a simple metabolic pathway is the single step conversion of a precursor A to a given product B.  an enzymatic reaction A enzyme B is reversible.
  • 47. In a multi-steps metabolic pathway, product B could become a substrate of the second reaction to yield product C and so on. E1 E2 E3 E4 E5 A B C D E Product  linear metabolic pathway  E’s are enzymes  B, C, D, E are intermediate substances also called metabolites. E5 E8 E11 E2 C D E Product 1 E1 E3 E6 E9 E12 A B F G H Product 2 E4 E7 E10 E13 I J K Product 3  branched metabolic pathway
  • 48. Primary Metabolic Pathway  A series of metabolism or biochemical reactions that encompasses reactions involving primary compounds which are formed as part of the normal anabolic and catabolic processes of plants and animals.  Primary metabolites are compounds commonly produced from primary metabolic pathways such as proteins, carbohydrates, lipids, nucleic acid that are directly used for growth and devlopment.  Absence of primary metabolites will cause cells and the whole organism to die.  Examples:  Glycolysis  Electron Transport Chain  Citric Acid Cylce  Oxydation of Fatty Acids
  • 49. GLYCOLYSIS reverse steps not shown
  • 50.
  • 51. Secondary Metabolic Pathway  A metabolism of secondary compounds or secondary metabolites other than primary compunds.  A compound is classified as secondary metabolite if it does not seem to to directly function in the processes of growth and devlopment of the animal or plant.  Even though secondary compounds are a normal part of the metabolism of an organism, they are often produced in specialized cells and tend to be more complex than primary compounds.  Examples of secondary metabolites antibiotics alkaloids
  • 52. Even though thousands of reactions sound very large and complex inside a tiny cell: 1. The type of reactions are small. 2. Mechanisms of biochemical reactions are simple. 3. Reactions of central importance (for energy production and synthesis and degradation of major cell components) are relatively few in number.  Frequent reactions encountered in biochemical processes: 1. Nucleophilic substitution • one atom or group of atoms substituted for another. 2. Elimination reactions • double bond is formed when atoms in a molecule is removed. 3. Addition reactions • two molecules combine to form a single product. • hydration reactions - water added to alkene > alcohol (common addition reaction).
  • 53. 4. Isomerization reactions • involve intramolecular shift of atoms or groups 5. Oxidation-Reduction (redox) reactions • occur when there is transfer of electron from a donor to an electron acceptor. 6. Hydrolysis reactions • cleavage of double bond by water.
  • 54.
  • 55.
  • 56. Requirement for Life MATTER: PRODUCED IN BIG BANG (H & He) AND STARS ( (HEAVIER ELEMENTS) ARE CERTAIN ELEMENTS NEEDED?  STABLE ENERGY SOURCE: LOW MASS MAIN SEQUENCE STARS (OR SOMETHING E ELSE?)  PROTECTED ENVIRONMENT: PLANETARY OR LUNAR SURFACES PLANETARY OR LUNAR INTERIORS THICK PLANETARY OR LUNAR ATMOSPHERES  CHEMICAL SOLVENT (LIQUID): W WATER (OR SOMETHING ELSE?)
  • 57.
  • 58.
  • 59. Secondary metabolism: Metabolism of secondary compounds, defined simply as compounds other than primary compounds. A compound is classified as a secondary metabolite if it does not seem to directly function in the processes of growth and development. Even though secondary compounds are a normal part of the metabolism of an organism, they are often produced in specialized cells, and tend to be more complex than primary compounds. Examples of secondary compounds include antibiotics, and plant chemical defenses such as alkaloids and steroids. MetaCyc (www.metacyc.org) Taiz, Lincoln, and Eduardo Zeiger. "Surface Protection and Secondary Defense Compounds." Plant Physiology. New York: Benjamin/Cummings Publishing Company, Inc., 1991: 320-345. [item in sorceforge, should be readdressed via sourceforge]
  • 60. Secondary metabolism: Processes that result in many of the chemical changes of compounds that are not required for growth and maintenance of cells, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types, and may be useful for the organism as a whole. In unicellular organisms, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nutrients. MetaCyc (www.metacyc.org) Taiz, Lincoln, and Eduardo Zeiger. "Surface Protection and Secondary Defense Compounds." Plant Physiology. New York: Benjamin/Cummings Publishing Company, Inc., 1991: 320-345. [item in sorceforge, should be readdressed via sourceforge]
  • 61. Metabolic Pathway Examples Glycolysis (Carbohydrate Metabolism): Glucose + 2 ADP + 2 Pi + 2 NAD+  2 Pyruvate + 2 ATP + 2 NADH + 2 H+ + 2 H2O  Activation and Transport of Fatty Acids (Lipid Metabolism): Fatty Acid + ATP + Coenzyme A  Fatty Acyl-CoA + Pyrophosphate + AMP + H+  Cholesterol Biosynthesis 1 (Lipid Metabolism): 6 Acetyl-CoA + 6 Acetoacetyl-CoA + 14 NADPH + 14 H+ + 5 H2O + 18 ATP + O2  Lanosterol + 14 NADP+ + 12 CoA-S-H + 18 ADP + 6 Pi + 4 PPi + 6 CO2  Shikimate Pathway (Amino Acid Metabolism): D- Erythrose-4-phosphate + 2 Phosphoenoylpyruvate + NAD+ + NADPH + ATP  Chorismate + NADH + NADP+ + ADP + 4 Pi
  • 62. Metabolic Pathway (Glycolysis) Glucose + 2 ADP + 2 Pi + 2 NAD+  2 Pyruvate + 2 ATP + 2 NADH
  • 63. Main Players  Enzymes: polymers of amino acids that act as catalysts that regulate speed of many chemical reactions in the metabolism of living organisms; ex. Phosphoglucoisomerase, aldolase  Metabolites: substance involved or by- product of metabolism; ex. erythrose 4- phosphate, sedoheptulose 7-phosphate
  • 64. Protein Carbohydrates Lipids Amino Acids
  • 65. . Ribosomes Protein and RNA complex responsible for protein synthesis Smooth endoplasmic reticulum (SER) A network of interconnected membranes forming channels within the cell. A site for synthesis and metabolism of lipids. Also contains enzymes for detoxifying chemicals including drugs and pesticides. Golgi apparatus A series of stacked membranes. Vesicles (small membrane surrounded bags) carry materials from the RER to the Golgi apparatus. Vesicles move between the stacks while the proteins are "processed" to a mature form. Vesicles then carry newly formed membrane and secreted proteins to their final destinations including secretion or membrane localization.
  • 66. Primary (1°) Metabolism - Construct common biological macromolecules from simple building blocks found within every cell - Typically a process of polymerization, stringing monomers together into a macromolecule that performs a cellular function sugars polysaccharides amino acids proteins fats phospholipid bilayers - Block production: cell dies (primary metabolites are essential)
  • 67. Metabolism and Energy Production Citric Acid Cycle Electron Transport Chain ATP Energy from Glucose Oxidation of Fatty Acids Metabolic Pathways for Amino Acids
  • 68.
  • 69. Cell Membrane  Outer membrane of cell that controls movement in and out of the cell  Double layer
  • 70. Cell Wall  Most commonly found in plant cells & bacteria  Supports & protects cells http://library.thinkquest.org/12413/structures.html
  • 72. Nucleus  Directs cell activities  Separated from cytoplasm by nuclear membrane  Contains genetic material - DNA
  • 73. Nuclear Membrane  Surrounds nucleus  Made of two layers  Openings allow material to enter and leave nucleus http://library.thinkquest.org/12413/structures.html
  • 74. Chromosomes  In nucleus  Made of DNA  Contain instructions for traits & characteristics http://library.thinkquest.org/12413/structures.html
  • 75. Nucleolus  Inside nucleus  Contains RNA to build proteins http://library.thinkquest.org/12413/structures.html
  • 76. Cytoplasm  Gel-like mixture  Surrounded by cell membrane  Contains hereditary material
  • 77. Endoplasmic Reticulum Moves materials around  in cell  Smooth type: lacks ribosomes  Rough type (pictured): ribosomes embedded in surface http://library.thinkquest.org/12413/structures.html
  • 78. Ribosomes  Each cell contains thousands  Make proteins  Found on ribosomes & floating throughout the cell http://library.thinkquest.org/12413/structures.html
  • 79. Mitochondria  Produces energy through chemical reactions – breaking down fats & carbohydrates  Controls level of water and other materials in cell  Recycles and decomposes proteins, fats, and carbohydrates http://library.thinkquest.org/12413/structures.html
  • 80. Golgi Bodies  Protein 'packaging plant'  Move materials within the cell  Move materials out of the cell http://library.thinkquest.org/12413/structures.html
  • 81. Lysosome  Digestive 'plant' for proteins, fats, and carbohydrates  Transports undigested material to cell membrane for removal  Cell breaks down if lysosome explodes http://library.thinkquest.org/12413/structures.html
  • 82. Vacuoles  Membrane-bound sacs for storage, digestion, and waste removal  Contains water solution  Help plants maintain shape http://library.thinkquest.org/12413/structures.html
  • 83. Chloroplast  Usually found in plant cells  Contains green chlorophyll  Where photosynthesis takes place http://library.thinkquest.org/12413/structures.html
  • 84.
  • 85. What is Life Made of?  Physical and Chemical sciences alone may not completely explain the nature of life, but they at least provide the essential framework for such an explanation.  All students of life must have a fundamental understanding of organic chemistry and biology
  • 87. BOTTOM LINE: THE ELEMENTS THAT MAKE UP TERRESTRIAL LIVING ORGANISMS ARE VERY COMMON IN STARS AND IN THE INTERSTELLAR MATERIAL FROM WHICH STARS AND PLANETS ARE FORMED. IN LIVING THINGS, THE ATOMS OF THESE ELEMENTS ARE ORGANIZED IN ORGANIC MOLECULES, MANY OF WHICH ARE LARGE AND COMPLEX.
  • 88. BASIC FACTS ABOUT LIFE ON EARTH LIVING ORGANISMS ON EARTH ARE MADE OF CELLS. EXCEPTION: VIRUSES A CELL IS TINY DROP OF WATER AND VARIOUS ORGANIC MOLECULES, SURROUNDED BY A MEMBRANE. SOME CELLS CONTAIN CERTAIN STRUCTURES, TO BE DISCUSSED LATER. SOME ORGANISMS (BACTERIA, FOR EXAMPLE) ARE SINGLE-CELLED, AND OTHER ORGANISMS (HUMANS, FOR EXAMPLE) ARE MULTICELLULAR. A CELL CAN DIVIDE, RESULTING IN TWO CELLS.
  • 89.
  • 90. Bio-molecules  Just like cells are building blocks of tissues likewise molecules are building blocks of cells.  Animal and plant cells contain approximately 10, 000 kinds of molecules (bio-molecules)  Water constitutes 50-95% of cells content by weight.  Ions like Na+, K+ and Ca+ may account for another 1%  Almost all other kinds of bio-molecules are organic (C, H, N, O, P, S)  Infinite variety of molecules contain C.  Most bio-molecules considered to be derived from hydrocarbons.  The chemical properties of organic bio-molecules are determined by their functional groups. Most bio-molecules have more than one.
  • 91. Major Classes of small Bio-molecules • Building blocks of proteins.  1. Amino • 20 commonly occurring. acids: • Contains amino group and carboxyl group function groups (behavioral properties) • R Group (side chains) determines the chemical properties of each amino acids. • Also determines how the protein folds and its biological function. • Individual amino acids in protein connected by peptide bond. • Functions as transport proteins, structural proteins, enzymes, antibodies, cell receptors.
  • 92. Sugars  Carbohydrates most abundant organic molecule found in nature.  Initially synthesized in plants from a complex series of reactions involving photosynthesis.  Basic unit is monosaccharides.  Monosaccharides can form larger molecules e.g. glycogen, plant starch or cellulose. Functions  Store energy in the form of starch (photosynthesis in plants) or glycogen (in animals and humans).  Provide energy through metabolism pathways and cycles.  Supply carbon for synthesis of other compounds.  Form structural components in cells and tissues.  Intercellular communications
  • 93. Fatty acids  Are monocarboxylic acid contains even number C atoms  Two types: saturated (C-C sb) and unsaturated (C-C db)  Fatty acids are components of several lipid molecules.  E,g. of lipids are triacylglycerol, streiods (cholestrol, sex hormones), fat soluble vitamins. Functions  Storage of energy in the form of fat  Membrane structures  Insulation (thermal blanket)  Synthesis of hormones
  • 94. Energy for Cells  Living cells are inherently unstable.  Constant flow of energy prevents them from becoming disorganized.  Cells obtains energy mainly by the oxidation of bio- molecules (e- transferred from 1 molecule to another and in doing so they lose energy)  This energy captured by cells & used to maintain highly organized cellular structure and functions
  • 95. How do complex structure of cells maintain high internal order? n Synthesis of bio-molecules 2. Transport Across Membranes - Cell membranes regulate the passage of ions and molecules from one compartment to another. 3. Cell Movement - Organised movement- most obvious characteristics of living cells. The intricate and coordinated activities required to sustain life require the movement of cell components. 4. Waste Removal - Animal cells convert food molecules into CO2, H20 & NH3. If these not disposed properly can be toxic.
  • 96. Thank you for your indulgence!
  • 97.
  • 98. Metabolic Pathway Examples Glycolysis (Carbohydrate Metabolism): Glucose + 2 ADP + 2 Pi + 2 NAD+  2 Pyruvate + 2 ATP + 2 NADH + 2 H+ + 2 H2O  Activation and Transport of Fatty Acids (Lipid Metabolism): Fatty Acid + ATP + Coenzyme A  Fatty Acyl-CoA + Pyrophosphate + AMP + H+  Cholesterol Biosynthesis 1 (Lipid Metabolism): 6 Acetyl-CoA + 6 Acetoacetyl-CoA + 14 NADPH + 14 H+ + 5 H2O + 18 ATP + O2  Lanosterol + 14 NADP+ + 12 CoA-S-H + 18 ADP + 6 Pi + 4 PPi + 6 CO2  Shikimate Pathway (Amino Acid Metabolism): D- Erythrose-4-phosphate + 2 Phosphoenoylpyruvate + NAD+ + NADPH + ATP  Chorismate + NADH + NADP+ + ADP + 4 Pi
  • 99. Year 1944 Proteins were thought to carry genetic information 1897 Mie s c he r d is c o ve re d D NA 1828 Interweaving of the historical traditions of biochemistry, cell biology, and genetics.
  • 100. Living things are composed of lifeless molecules. When these molecules are considered individually, they are found to conform to all the physical and chemical laws that describe the behavior of inanimate matter.