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Cell Biology Lecture Notes 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. C) History: -Discovery of the cell followed by the development of the microscope A. 1665-Robert Hooke- observed cells from the fruiting bodies of fungi B. Anton van Leewenhoek- observed a variety of cells and called them "animalcules" C. 1830’s-Theodor Schwann and Matthias Schleiden developed the cell theory
- 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 D) Louis Pasteur -developed the theory of spontaneous generation that is that cells could develop from non-living matter -Also worked on problem associated with the fermentation of French wine -1857-developed a partial sterilization process called pasteurization- involves heating at a moderate temperatures to reduce the number of living microorganisms E) 1865 -Mendel -demonstrated that cellular traits (phenotypes) were inherited
- Seed shape and color in garden peas
- Named "Father of Genetics"
F) 1871- Johan Freidrick Miescher -isolated nucleic acids from cells "nuclein"
G) 1889- R.Altman -purified nucleic acids H) 1944- Oswald Avery , Colin MacLeod, and MacLyn McCarty- -Demonstrated that DNA was the heredity molecule -DNA could transform bacterial cells I) 1952-Alfred Hershey and Martha Chase -also demonstrated that DNA was the heredity molecule -Radioactive DNA from a virus was able to infect and transform bacterial cells J) 1953-James Watson and Francis Crick -developed the 3-D structure of DNA
K) 1958-Mattew Meselson and Frank Stahl -demonstrated that DNA replicated by a semi conservative method
L) 1961- Brenner, Jacob, Meselson -discovered RNA M) 1966- Nirenberg and Khorana -elucidated the chemical nature of the genetic code N) 1972-1973- Berg, Boyer, and Cohen - discovered gene cloning O) 1975- Gilbert and Sanger -developed chemical techniques to rapidly sequence DNA 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 um Metric system: -1 meter = 3.3 feet, 1 km = 10^3 m, 1cm = 10-2^ m, 1mm = 10-3^ m, 1um = 10-6^ m, 1nm = 10-9^ m, 1 A = 10-10^ m, 1pm = 10 -12^ m
Eukaryotic Cell - (eu=true karyon=nucleus)
- Possesses a complex membrane system
- Has a true nucleus
- Distinct membrane-bound intracellular compartments called organelles -Nucleus- dark-staining body within the cell by enclosed an intracellular membrane called the nuclear envelope -Nuclear envelope contains pores, which are filled with a ring of proteins called annulus -Contains DNA in the form of chromatin fibers -DNA is linear (linear DNA + proteins = chromosome) -Nucleolus- a cell organelle in the nucleus that disappears during part of cell division. Contains rRNA genes -Nucleus also contains RNA (mRNA, rRNA, and tRNA) -Transcription- conversion of genetic information from DNA to RNA occurs in the nucleus -DNA replication-duplication of genetic material
- Cytoplasm : major portion of the protoplasmic substance within the cell membrane a. Ribosomes-a cytoplasmic particle that contains RNA and protein and is involved in the process of protein synthesis -Translocation-process which takes place in the cytoplasm and converts genetic information in RNA into proteins -Ribosomes can either be freely suspended in the cytoplasm or attached to intracellular membranes a. Endoplasmic reticulum (ER)- a network of intracellular membranes where secreting proteins are synthesized -Rough ER- the ER + ribosom es -Smooth ER- the ER without ribosom es
Function
s in the breakdo wn 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 -Both (g and h) are involved in cellular movement 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 i. Specialized protozoan cell organelle: -Contractile vacuole- used to maintain proper osmotic pressure and secretes waste and excess H 2 O -Two types of nuclei
- Macronucleus- involved in asexual reproduction
Reactive Organic Molecules:
1. Hydroxyl group - strongly polar and highly reactive
- Carbonyl group - weakly polar and highly reactive
- Aldehyde
- Ketone
- Carboxyl group - strongly polar and acts as an acid
- Amino group - polar and acts as a base
- Phosphate group - acidic and polar
- Sulfhydral group - readily oxidized -Two sulfhydral groups can bond together to form a disulfide bond Carbohydrates: A. Function: 1. Store energy (starches in plants / glycogen in animals) 2. Provides rigidity to plant cells (cellulose) 3. 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 B- glucose 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
-A nonpolar side chain is attached at one end of the ring structure and a polar side group is attached to the opposite end of the ring structure -R’ is a polar unit and R is a nonpolar unit -The combination of polar and nonpolar side groups gives phospholipids dual solubility properties -An example of a sterol is cholesterol -Cholesterol is an important component of the cell membrane in all animal cells -Cholesterol also can be deposited inside arteries causing blockage, which contributes to the disease arteriosclerosis (hardening of the arteries) -Hormones are steroids and they play major roles in cell regulation, cell metabolism, and cell growth I. Proteins carry out many cellular functions:
- Provide cellular support (cytoskeleton: microtubules – tubulin; microfilaments - actin)
- As enzymes, they catalyze cellular reactions
- Stabilize and control gene activity via interactions with other proteins and nucleic acids (DNA or RNA)
- Used in cell transport and cell recognition (cell membrane)
- Involved in cell-cell transport via secretory proteins and hormones 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 - commit to memory:
- Structure
- Name
- 3 letter abbreviation
- 1 letter abbreviation 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
6-aminopurine (adenine) 2-amino-6-hydroxypurine (guanine)
- Three common pyrimidine bases, cytosine, thymine, and uracil 4-amino-2-hydroxypyrimidine 2,4-dihydroxypyrimidine 2,4-dihydroxy-5-methyl pyrimidine (cytosine) (uracil) (thymine) II. Nucleoside - macromolecule composed of a nitrogenous base joined to a pentose III. Nucleotide - is a macromolecule composed of a nitrogenous base, a pentose, and linked (esterified) to one or more phosphate groups -5’-ribo(deoxyribo) - nucleotide
- Phosphate is linked to the 3’ OH of the pentose = 3’-ribo(deoxyribo) - nucleotide IV. Nomenclature of nucleosides: A-deoxyriboside = deoxyadenosine A-riboside = adenosine G-deoxyriboside = deoxyguanosine G-riboside = guanosine C-deoxyriboside = deoxycytidine C-riboside = cytidine T-deoxyriboside = deoxythymidine U-riboside = uridine V. Nomenclature of nucleotides in DNA base - deoxyribose - phosphate 5’-dAMP = deoxyadenosine-5’-PO 4 5’-dGMP = deoxyguanosine-5’-PO 4
5’-dTMP = deoxythymidine-5’-PO 4 5’-dCMP = deoxycytidine-5’-PO 4 VI. Nomenclature of nucleotides in RNA base - ribose - phosphate 5’-AMP = adenosine-5’- PO 4 5’-GMP = guanosine-5’- PO 4 5’-UMP = uridine-5’- PO 4 5’-CMP = cytidine-5’- PO 4 VII. Nomenclature of nucleoside triphosphates ATP = adenosine-5’-triphosphate dATP = deoxyadenosine-5’-triphosphate VIII. Nucleic acids RNA and DNA -Nucleotides held in chains by bridging a phosphate group that extends between the 5’-carbon of one sugar with the 3’-carbon of a second sugar (held together by a phosphodiester bond) -Produces a backbone chain of alternating sugar and PO 4 groups -DNA exists in a double helix that contains 2 intertwined chains of nucleotides -RNA is single-stranded Enzymes:
- Review 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
-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) -One way to supply energy is to heat the reactants -Second way is to add a catalyst -Catalyst forms a complex with the reactant, thus bringing the reactants closer together so they can react -In biological systems a catalyst is called an enzyme, which lowers the activation energy of the system -Graph: II. Three enzymatic mechanisms which can contribute to the formation of a transition state is a catalyzed biological reaction a) Enzyme brings reacting molecules into close proximity b) Enzyme orients reactants into positions to induce favorable interactions c) Enzymes alter the chemical environment of the reactants to promote interaction -E.g. is to create a nonpolar environment -Favorable condition for reactant nonpolar molecules III. Factors affecting enzyme activity
a) Substrate concentration b) Enzyme inhibition
- Competitive
- Noncompetitive c) Temperature - optimum temp. 40C -If temp. increases will denature the proteins d) pH - optimum pH 7 for most enzymes IV. Substrate concentration - reactants (substrates) products -As the reaction proceeds, the concentration of substrate decreases with time -If we increase the concentration of substrate, we will increase the rate of an enzymatic reaction to a point -From this point, if add more substrate, the rate of the reaction will not increase -The enzyme is said to be saturated with substrate -This effect is seen with all enzymes -Graph: -Phenomenon led Michaelis and Menten (1913) to the explanation that the enzyme (E) and the substrate (S) form a reversible complex ES. The ES then breaks down to give the product P and the free enzyme -They derived an explanation to describe enzyme reactions
- Derivation of the Michaelis Menten Equation:
-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 -Lineweaver-Burke plot:
- 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 -Lineweaver-Burke plot: 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 B C D 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 -Discovered by Tom Cech DNA structure: -Structure of DNA was deduced by x-ray diffraction and proposed by Watson and Crick 8 characteristics:
- Contains 2 nucleotide chains which wind into a right-handed double helix
- Backbone is composed of alternating sugar and phosphate groups separated by 1.1nn
- Space is filled by a purine: pyrimidine base pair, which lies in a flat, plane perpendicular to the backbone
- Each turn of the double helix is 10 bp
- The bp are held together by H-bonds
- There are 2 surface grooves on the helix, major groove and a minor groove
