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ALL ABOUT CELLS
Introduction: A. Definition of a cell: fundamental structural and functional unit of all living organisms B. Characteristics of cells:
- Contain highly organized molecular and biochemical systems and are used to store information
- Use energy
- Capable of movement
- Sense environmental changes
- Can duplicate (transfer genetic information to offspring)
- Capable of self-regulation -Most cells are microscopic (invisible to the naked eye) and thus, a microscope is needed to view most cells. => Cell Theory states:
- All living organisms are composed of cells
- Cells are the functional units of living organisms
- Cells arise from preexisting cells via division
Cell Structure:
I. Most cells are microscopic and cannot be seen by the naked eye. II. Microscopes were developed to visualize cells. III. Resolution is the minimum distance where 2 objects can be visually separated -Unresolved -Partially resolved -Resolved -Depends on: a. Wavelength of light
b. Refractive index of the medium c. Of the light -The naked eye can resolve two separate objects separated by 200 Micrometers IV. Light microscope: -Can resolve two objects 100-200 Micrometers apart (including cells and large sub cellular organelles) -Uses different light sources and patterns of image formation a. Bright field d) differential interference b. Dark field e) fluorescence c) phase contrast V. Electron Microscope: -Uses a beam of electrons (e- ) rather than light as an illumination source A. Transmission Electron Microscope (TEM)
- Electrons forming the image focused through the specimen -Short wavelength of e- beam improves the resolution of TEM to 5 A (.5 micrometers) -Can resolve small sub cellular organelles and large proteins B. Scanning Electron Microscope (SEM) -Used to examine surfaces of cells or isolated cellular structures -e- beam "scans" the specimen -Resolution 5 to 10 micrometers
Prokaryotic Cells
โ small and primitive bacteria and blue-green algae (cyanobacteria) โ Lacks specialized internal membrane-bound compartments known as organelles โ Cell membrane- functions in transport, the movement of substances in and out of the cell, and in energy production (breakdown of large molecules, photosynthesis) โ Cell wall- gives structural strength (rigidity) to the cell โ Capsule- jelly-like substance which protects the cell wall from environmental damage
a. Endoplasmic reticulum (ER)- a network of intracellular membranes where secreting proteins are synthesized
- Rough ER the ER + riboso mes
- Smooth ER the ER without ribosomes
- Functions in the break down of fats attached to the rough ER in the Golgi complex a. Golgi apparatus -a membranous organelle that packages and sorts newly synthesized secretory proteins a. Lysosome - organelle which contains digestive enzymes e. Mitochondrion - semiautonomous eukaryotic cell organelle -Site of respiration -Consists of an outer membrane and a convoluted inner membrane -Site of ATP production within the cell a. Microbody -organelle within a cell containing specialized enzymes whose functions involve hydrogen peroxide (peroxisome) b. Microtubules-composed of tubulin h. Microfilaments-composed of actin a. Intercellular-includes flagella and cilia b. Intracellular- cytoplasmic streaming
Plant cell organelles:
-Chloroplast- involved in photosynthesis -Central vacuole- provides support to the plant via osmotic pressure -Cell wall- composed of cellulose, which provides extra strength and rigidity โ Specialized protozoan cell organelle: -Contractile vacuole- used to maintain proper osmotic pressure and secretes waste and excess H2O -
โ Two types of nuclei
- Macronucleus- involved in asexual reproduction
- Micronucleus- involved in sexual reproduction
Chemical Bonds:
I. 4 types of molecules make up cells:
- Carbohydrates
- Lipids
- Proteins
- Nucleic acids II. Biological macromolecules are held together by several different types of bonds:
- Ionic bond-a transfer of electrons
- Covalent bond-the sharing of electrons
- H-bonds-weak attraction when H+ serves as a bridge between 2 electronegative atoms by a covalent bond and electrostatic attraction
- Nonpolar associations-hydrophobic vs. Hydrophilic
- Van der Waals-a momentary dipole that will affect the electron distribution of neighboring molecules Acids and Bases:
- Acid-a substance that can take up an electron pair to form a covalent bond
- Base-a substance that can donate an electron pair to form a covalent bond
- H2O dissociates into H+ ions and OH
- [H+ ] + [OH- ] = 1x10-14 moles/liter (M)
- pH = -log10 [H+]
Carbohydrates:
A. Function:
- Store energy (starches in plants / glycogen in animals)
- Provides rigidity to plant cells (cellulose)
- Involved in cell-cell communication (glycoproteins) B. Structure -Carbohydrates have a characteristic content of C, H, O atoms in the ratio of 1C:2H:1O
- Monosaccharide is the subunit of a carbohydrate
- Disaccharide contains 2 monosaccharide subunits
- Oligosaccharide contains 2-10 monosaccharide subunits
- Polysaccharide contains >10 monosaccharide subunits C. Most carbohydrate subunits contains 3 carbons (triose), 5 carbons (pentose), or 6 carbons (hexose) glucose - glucose - glucose D. 2 common monosaccharides are: fructose and galactose E. Disaccharide = 2 monosaccharide subunits linked together -Ex: maltose = 2 glucose molecules linked together -Glycosidic bond = is the bond between 2 carbohydrate subunits formed by the eliminated of water F. Examples of Polysaccharides:
- Cellulose- comprises plant cell walls; molecule composed of repeating Bglucose units (monomers) held together by B 1=4 linkages
- Starch- (primary storage compound in plants) is a macromolecule composed of repeating - glucose units held together by 1=4 linkages
- Glycogen- (primary storage compound in animals) is a branched macromolecule composed of repeating 1=4 and 1=6 glycosidic linkages -Sucrose -Lactose -Most monosaccharides can exist in alternative forms when molecules, which are attached to the carbon chain, can be oriented in different positions -Stereoisomers - two molecules, which have the same molecular formula and the same chemical formula and physical properties, but are different in the spatial arrangement of atoms -Most carbohydrates exist in D and L forms Lipids: A. Definition- fats or fat-like substances that are insoluble in water and soluble in nonpolar solvents like acetone, ether, chloroform and benzene. B. Function:
- Primary component of cell membranes
- Store energy C. There are 3 types of lipids: neutral lipids, phospholipids, and steroids D. Neutral lipids (fats and oils)
- Composed of fatty acids and glycerol (alcohol)
- Fatty acid is a long, unbranched chain of carbon atoms attached by hydrogen and other groups and a terminal carboxyl group
- CH3(CH2)nCOOH saturated fatty acid since the carbons have the maximum possible # of H atoms
- CH3(CH2)nCH=CH(CH2)nCOOH unsaturated fatty acid because of the one double C-C bond.
- Structure of neutral lipids
- Glycerol has 3 OH groups each of which is attached to a fatty acid
II. Proteins are composed of subunit structures called amino acids A. 20 major biological amino acids B. General structure of amino acid C. 20 amino acids D. Amino acids can be linked together in chains of 2 or more units -Peptide bond - is a bond in which the carboxyl group of one amino acid is joined to the amino group of a second amino acid via a condensation reaction -Peptide - is a chain composed of 2 or more amino acids and contains one or more peptide bonds -Ex: dipeptide = chain composed of 2 amino acids -Tripeptide = chain composed of 3 amino acids -Polypeptide is an amino acid chain composed of 3 or more amino acids -The amino acid sequence of a polypeptide chain is called the primary structure of a protein E. Secondary structure of proteins - is the conformation imposed on the polypeptide chain by hydrogen bonding between amino acids
- There exists physical constraints on the rotation of the alpha carbon atoms that flank the peptide bond
- It has been determined that there are only 2 or 3 stable arrangements of amino acids which conform to these restraints
- Alpha helix
- Beta strands (sheets)
- Random coil
- These arrangements compose the secondary structure of a polypeptide chain -Secondary structure - is the arrangement of alpha helices, beta sheets, and random coils in a polypeptide chain
- Alpha helix - common structural motif of a polypeptide chain in which the linear sequence of amino acids folds into a right-handed helix -Helix is stabilized by internal hydrogen bonding between backbone atoms
- Beta sheet - common structural motif of a polypeptide chain, which is composed of beta, strands that are oriented in an antiparallel fashion -Stabilized by internal hydrogen bonds -Beta strand - is an extended zigzag arrangement of amino acids in a polypeptide chain -Beta barrel - is a cylindrical arrangement of beta sheets
-Example of a protein that is composed primarily of beta sheets is the silk protein secreted by silk worms (contributes to the high strength of silk fibers)
- Random coil - an irregular configuration of amino acids within a polypeptide chain
- Usually composed of proline
- cannot fit into an alpha helix or beta sheet
- Allows the protein to bend and flex -Allows the protein to compact into its most stable energetic structure F) Tertiary structure of proteins -The three-dimensional arrangement of a polypeptide chain within a protein (monomeric protein) G) Quaternary structure of protein -Three-dimensional relationship between 2 or more polypeptide chains within a complex protein -Ex: coiled coil & triple helix -Dimer = 2 subunits -Homodimer = identical subunits -Heterodimer = distinct subunits -Multimeric protein - composed of 2 or more subunits (identical or distinct)
Nucleic acids:
I. Definition - a large, chain-like macromolecule containing phosphoric acid, sugar, and a nitrogenous base -2 examples are deoxyribonucleic acid (DNA) & ribonucleic acid (RNA) a. Sugar is 5-carbon sugar called a pentose ribose deoxyribose b. Phosphoric acid is composed of one or more phosphate groups (PO4 - ) c. Nitrogenous base = 2 types purine pyrimidine
- Two common purine bases, adenine and guanine 6-aminopurine (adenine) 2-amino-6-hydroxypurine (guanine)
VII. Nomenclature of nucleoside triphosphates ATP = adenosine-5โ-triphosphate dATP = deoxyadenosine-5โ-triphosphate VIII. Nucleic acids RNA and DNA -Nucleotides held in chains by bridging a phosphate group that extends between the 5โ-carbon of one sugar with the 3โ-carbon of a second sugar (held together by a phosphodiester bond) -Produces a backbone chain of alternating sugar and PO4 groups -DNA exists in a double helix that contains 2 intertwined chains of nucleotides -RNA is single-stranded Enzymes:
- thermodynamics -First and second law of thermodynamics -Reversible reactions -Coupling reactions -Standard free energy change
- Definition of an enzyme - is a protein which increases the rate of a spontaneous reaction (catalyzes the reaction) a) Lowers the activation energy of the transition state b) Reaction would proceed without the enzyme c) Enzyme cannot make a reaction occur that would not proceed spontaneously without the enzyme d) Enzymes do not alter the equilibrium of a reversible reaction e) Enzymes increase the rate at which a reaction reaches equilibrium
Classification of enzymes:
- Oxidoreductases - catalyzes a reaction in which electrons are removed from the substrate are donated directly to molecular oxygen -Catalyzes oxidation-reduction reactions -Act on alcohols, ketones, aldehydes, amines, etc.
- Transferase - catalyze the transfer of functional groups -Sulfhydral, glycosyl, aldehyde, acyl, etc.
- Hydrolases - catalyze hydrolysis reactions -Glycosidic bonds -Peptide bonds
- Lyases - catalyze the addition of groups to double bonds
- C=C, C=N, C=O -Ex: AP lyases involved in repairing DNA
- Isomerases - catalyze an intramolecular rearrangement -Catalyzed isomerization reaction - Isomerization - rearrangement of atomic group within the same molecule without any loss or gain of atoms
- Ligases - a group of enzymes that catalyze reactions in which a bond is formed between 2 substrate molecules using energy (ATP) obtained from the cleavage of a pyrophosphate bond -Ex: DNA ligase & RNA ligase Characteristics of enzymatic proteins: -Enzymes combine briefly with reactants during an enzyme-catalyzed reaction (enzyme-substrate complex) -Enzymes are released unchanged after catalyzing the conversion of reactants to products -Enzymes are specific in their activity; each enzyme catalyzes the reaction of a single type of molecule or a group of closely related molecules -Enzymes are saturated by high substrate concentrations -Many enzymes contain nonprotein groups called cofactors -Inorganic cofactors = metal ions -Organic cofactors = coenzymes (ex: vitamins) I. Activation energy: the energy in excess of the ground state that must be added to a molecular system to allow a chemical reaction to start (e.g. rock on a cliff must be pushed to roll down the hill)
Enzyme inhibition: -Model for an enzyme-catalyzed reaction requires that the enzyme and substrate form a recognizable chemical complex ES (transition state) -In general, enzymes are much larger in size than substrate molecules -Portion of the enzyme that complexes with the substrate are called the active center (site) of the enzyme -It is not known exactly how enzymes lower the energy required to form the transition state or ES complex -A good amount of chemical information concerning the active sites of enzymes has been obtained by studying enzyme inhibitors -Chemical inhibitor - is a substance that represses or stops a chemical reaction -Inhibition - reduction in the rate of enzymatic activity E + S โ โ ES โ โ + P E + I โ โ EI โ no products a) Competitive inhibition b) Noncompetitive inhibition
1. Competitive inhibition - the inhibition of enzyme activity caused by the competition of an inhibitor with a substrate for the active (catalytic) site on the enzyme; impairment of the function of an enzyme due to its reaction with a substance chemically related to its normal substrate -Very common situation in the study of drug action -Many drugs work by competing with the normal substrate molecules for the active site of enzymes 2. Noncompetitive inhibition
- inhibition of enzyme activity by a substance that does not compete with the normal substrate for the active site and thus cannot be reduced by increasing the substrate concentration Regulation of Enzymatic Activity: -In living cells, chemical equilibria for reactions are seldom, if ever, reached
-Due to the fact that cellular chemical reactions are coupled to form metabolic pathways A โ โ B โ โ C โ โ D โ โ E -Three major known mechanisms by which enzyme activities appear to be regulated: a) Change in the rate of synthesis of the enzyme -Induction of the enzyme & repression of the enzyme contribute to gene regulation b) Feedback inhibition of the enzyme
- cellular control mechanism by which the end product of a series of metabolic reactions inhibits the activity of an earlier enzyme in the metabolic pathway; thus, when the end product accumulates, its further production ceases c) Allosteric regulation (inhibition): -Occurs by reversible combination of substances with sites on the enzyme other than the active site -Enzyme is called an allosteric enzyme
- an enzyme whose active site can be altered by the binding of a small molecule at a non-overlapping site -Enzyme can be activated by this binding = allosteric activation -Enzyme can be inhibited by this binding = allosteric inhibition RNA based enzymes (ribozymes): -First discovered in the protozoan Tetrahymena -RNA molecule involved in splicing (or modifying) RNA intermediate structures
