CONCEPTS IN BIOLOGY
BSC 1005
FOR NON MAJORS
TABLE OF CONTENTS
1. CELLS:
A. SCIENTIFIC METHOD
B. STRUCTURE & ORGANELLES FUNCTIONS
C. MEMBRANES & TRANSPORT
D. CELL DIVISION
2. ENERGY & METABOLISM:
A. ORGANIC MOLECULES
B. ENERGY FLOW
C. PHOTOSYNTHESIS & RESPIRATION
3. GENETICS:
A. PATTERNS OF INHERITANCE
B. MEIOSIS
C. MOLECULAR GENETICS
D. GENETIC ENGINEERING
4. EVOLUTION:
A. NATURAL SELECTION
B. EVIDENCE OF EVOLUTION
C. SPECIATION
TOP
BSC1005 UNIT 1 - CELLS
KEY NOTE: All students must read each assigned chapter, note the meaning and the use of the words printed in bold dark letters in the texts before coming to class.
BIOLOGY: IS THE STUDY OF LIFE
CELL: Is the smallest organizational basic unit of life made up of a hereditary nuclear region surrounded by a cytoplasm, all kept in place by a phospholipid plasma membrane.
Simulation: A cell is like a boiled egg with the yolk as the nucleus, the white as cytoplasm and the shell as the plasma membrane.
SCIENTIFIC METHOD OR PROCESS
A philosophically organized way of arriving at conclusions using true observations (adequate evidence) as a test to either accept or reject a formulated hypothesis. This is limited to only the things we can see and measure,
TERMINOLOGIES: Students must find out the meaning and usage of the following:
INDUCTION HYPOTHESIS/ALTERNATIVE HYPOTHESIS
DEDUCTION PREDICTION
CFCs EXPERIMENTAL/CONTROL
OBSERVATION CONTROL EXPERIMENT
METABOLISM HOMEOSTASIS
TISSUE/ORGAN SPECIES/POPULATION
ORGANELLE/INCLUSION ECOSYSTEM/BIOMES/BIOSPHERE
EVOLUTION NATURAL/ARTIFICIAL SELECTION
CONCLUSIONS could be arrived at using A. Induction (from specific to general, 50/50 true)
OR B.Deduction(from general to specific, 100% true)
1. What will you call Newton's apple experiment?
2. Fe and Pb are metals, they sink in H2O therefore all metals will sink in water, what's that
called?
3. All birds have wings, Robin is a bird, then all Robins have wings is call -----?
4. If your sister is Robin and has no wings, how does that stand up to your #3 answer above?
In ozone (O3 ) destruction, Cl from CFCs was observed to split (O-O-O) to (O-O) + (O)
(O-O-O) filters out UV but not (O-O). The more (O-O-O) destroyed to (O-O) + (O) in the stratosphere, the wider the hole and the thinner the ozone layer. This increases the amount of UV on the earth, hence higher incidences of UV related health problems - skin cancer and the like.
STAGES OF SCIENTIFIC INVESTIGATION
1. OBSERVATION: Is the key to successful investigation. Good record keeping provide the evidence to conclusion. J. Farman would have got nothing to support the Ozone hole theory if he did not draw up a good set of data from his observations.
2. HYPOTHESIS: This is a guess that might be true of a particular situation, like in CFCs and ozone depletion. If there are more than one guess, then an Alternative Hypothesis will be made, like in ozone and convection - earth's spinning and sun spots. Null Hypothesis is a non true guess.
3. PREDICTIONS: They are expected consequences, e.g. the ozone hole and CFCs. If this is true then one should be able to find the source - CFCs and the chlorine they produce in th upper Antarctic atm.
4. TESTING: This is a set up of experiment to study or verify the situation. From this, observations will be made - good record keeping - (collection of data) as evidence for testing the hypothesis. In ozone studies, CFCs, Cl and fluorine were observed in the ozone layer.
5. CONTROLS: Factors than can influence the experiment are called Variables. The experiment is then set up with a group having all the variables in place, the Control. In the other set, only one variable is altered, the experimental group. In the ozone study, one group was set up with every variable in place and the other group had no CFC.
What do you call the underlined group?
6. CONCLUSION: Is hypothesis that has been tested and not rejected due to accumulated evidence (data). A collection of related tested hypotheses over time is the Theory, a unifying explanation for a multiple observations of principles that we are most certain.
A.Can you explain atomic theory, kinetic theory of gases, cell theory?
B. What does science discover, the truth or falsehood?
C. What does the future hold for a present day theory?
D. What does a theory mean to a scientist and the public?
E. Can science solve all the world problems, or force the public to implement solutions?
LIFE : Has no single definition but is studied under different properties.
PROPERTIES OR CHARACTERISTICS OF LIFE:
1. Cell Theory: All living things are made up of a cell or cells. (Pro- or Eu- karyotic in nature)
2. Metabolism: All living things use energy (EN) ATP for life processes. Source: The sun.
3. Homeostasis: Ability to maintain internal stable conditions such as body temp (98.6o F).
4. Reproduction: Ability to produce new ones of the same kind. (Asexual - mitosis or Sexual)
5. Heredity: During reproduction original or mutated genes in DNA are copied and handed
over to the young ones. Genes determine what an individual will be like.
6. Movement: Ability to show any form of change in location from one area or space to the
other, e.g. opening and closing of flowers, or locomotion, etc.
7. Response to Stimulus: Ability to show any form of reaction due to an administered action,
e.g. mimosa & touch, venus fly trap & insect landing, plants & light, roots and gravity, scare
or fright & flight/fight, hunger & eating, thirst & drinking, etc.
8. Evolution: Ability to change with the ENV for survival.
9. Death: Inability to exhibit the previous 8 qualities, but a disorganization back to chemical
level of atoms and molecules via bio or natural cycles. In some of these cycles,
decomposers
like fungi and bacteria(1ry decomposers) are involved. This is the cessation of life.
Question: If decomposers are involved in #9 above, it then means that decomposers do not die.
What is your opinion with respect to the above statement in red?
KINGDOMS: All living things are categorized into 6 main groups called Kingdoms.
Bacteria alone belong to 2 kingdoms
#1. Archeobacteria: e.g.. methane producing bacteria - (prokaryotic)
2. Eubacteria as in those soil bacteria that cause plant diseases (prokaryotic)
3. Fungi: e.g.. mushrooms, yeast
4. Protista: unicellular - e.g.. algae, amoebae
5. Animal: multicellular - lizards, you
6. Plantae: photosynthetic, multicellular - higher plants like rose, orange tree
THEMES IN THE LIVING SYSTEM
A. ORGANIZATION OF THE ECOSYSTEM (ES)
In the world, organisms interact at different levels for survival. The degree of complexity determines the level of interaction, the more the complexity, the more the interaction.
Level 1. Chemical level: atoms - C - and molecules - DNA
2. Cellular level: organelles - mitochondria
3. Tissue: similar cells together performing a function - muscle tissue
4. Organ: different tissues working together - the heart
5. Organ system: various organs that carry out functions - heart, blood and vessels form
the circulatory system
6. Organism: organ systems working together to form one coordinated functional unit as
in you, cow bird, worm, etc.
7. Population: one group of organisms, or gathering of one (species - can interbreed)
8. Community: all populations of an ES - human, cows, bacteria, fungi, birds, etc.
9. ES: community + physical Env. - Everglades, water, grassland, forest, etc.
10. Biome: similar ESs of the world - forest, desert, grassland, etc.
11. Biosphere: All living biomes and ESs of the world taken together.
12 Ecosphere: The Biosphere + all the physical Env.- the world
B. ENERGY (EN) FLOW: The ES is open to EN but closed to Mass.
Once radiant EN photons are converted to chem EN and stored as mass, the mass
can't leave or exit the ES any longer. That EN in the mass is transformed from one
kind and type to the other according to the laws of thermodynamics.
Source of EN:
The sun, (the photons in radiant EN of the sun - from gamma through white light to
microwaves) is only source of EN used by organisms.
Conversion of Photons:
Photosynthetic organisms (Producers) convert Rad. EN photons to chem EN (ATP
& (NADPH) and trap them in their masses for consumers that feed from these green
organisms. The EN now can flow through the ES via food chains (less stable) &
food webs (more stable) according to the laws of thermodynamics. EN flow shapes
the ES and determines the #s and kind of organisms per community.
Question: If green organisms produce foods for consumers, did the Incredible Hulk
make his own foods and gave some out to his friends especially during thanks
giving?
C. EVOLUTION: The change in species with the Env. over time.
Darwin in 1859 proposed that this change is due to a natural process called "natural
selection" (dub - only the strong survives), where nature selects the one (strong) that
well adapts to environmental challenges as the most common - and will reproduce
well adapted offsprings. This is increases the survival rate of the species.
Artificial Selection:
Qualities are passed on via DNA. Breeders manipulate DNA to achieve the
qualities and varieties they desire, these then can be transmitted to offsprings by
inbreeding or crossbreeding. This is artificial.
Coevolution: Two or more interdependent organisms change simultaneously as the
ENV changes so that the interdependency could continue. This exhibits
COOPERATION among or between species as could be seen in flowering plants
and insects and other symbiotic species, lichens, legumes/rhizobia, etc..
D. STRUCTURE & FUNCTIONS: Structure determines functions & biostructures
are well suited to their functions, e.g.. enzymes and their substrates, heart & blood
circulation, eyes & seeing, stomach and digestion, etc. These determine the
suitability and adaptability of individuals in the ES for survival via natural selection.
E. HOMEOSTASIS: Maintaining stable internal ENV - A state of internal balance.
This requires a complex of signaling back and forth using EN (ATP) and biomolecules.
BACK
UNIT II: ENERGY (EN) OF LIFE
CHEMISTRY OF LIFE
OUTLINE:
1. SIMPLE CHEMISTRY
2. WATER
3. MACROMOLECULES
4. ORIGIN OF THE FIRST CELLS
SIMPLE CHEMISTRY
All living things contain cells and cells are made-up of matter. All matter are made of atoms. All living things are atoms.
WHERE DID LIFE COME FROM? 3 Theories are considered.
1. Extraterrestrial Origin - Infection spores from another planet
2. Special Creation - The oldest believe in supernatural forces, rejected by scientist
3. Evolution - Life from association of inanimate matter, becoming more complex
via selection & molecular changes, hence prolonging existence. It permits
testable hypothesis. The 1st 2 do not.
The Theory of Evolution by Charles Darwin
Today's diversity came from natural selection for the more adapted ancestral forms
ATOMS:
The smallest particle of matter/element that represents that matter/element.
STR:- Nucleus (Protons and neutrons, (p+ = no mass = 1 amu) + many other subatomic particles) . Electrons ( negative charge, found outside the nucleus .
IONS: Ion/s are formed when an atom loses or gain/s an electron/s. There are (+) and (-) ions.
K+ is (+) & Cl- is (-). They are also called charges.
Electron Loss is OXIDATION, forms (+), and the # of (+s) = # of electron lost: and
Electron gain Is REDUCTION, # of charges = # gained.
Electrons carry EN and have mass - (Mass = 1/1840 amu) , some books report 1/1835 amu.
ISOTOPES: Atoms with the same at.#, but diff. neutron #.
126C 136C 146C
EN Levels: These are orbitals that electrons circulate around the nucleus. The pull by the nuc. on the electrons keeps the electrons from flying off their respective positions in the EN levels.
Molecules: the union of 2 similar atoms : like O + O = O2
If non similar atoms, then a compound is formed: like H + H + O = H2 O > in both cases the new substance formed is kept together by CHEM. BOND
Types of Chem bond: Bonds form to attain an octet to be more stable.
1. Ionic bond, formed by redox action that generates ions (+, -), which finally attract.
Relatively strong bond. There is a general attraction and repulsion among
participating atoms - non directional , so crystals form.
(Is James Bond a chem bond?)
Compounds form crystals, they are attracted to electrical fields, molten forms
conduct electricity, form electrolytes in water.
2. Covalent Bond: Formed by non-metallic atoms sharing electrons. Pure covalent
bond is a strong bond as in diamond. Bonds are directional among covalent atoms.
Water molecule contains 2 covalent bonds. Sometimes electrons spend more time
on one side of the atom, so this makes that side more (- ve, and the other side more
+ ve). This gives rise to a polar covalent bond, d + & d - ).
3. Hydrogen Bond: Weak intermolecular bonds, as in water , that exist due to polar
covalency. Very special weak bonds that give most biomolecules their shapes by
folding and are not effective over long distances. They are directional.
WATER
1. Powerful universal solvent, (bi polarity), the only natural compound at room temp.
2. Pure water is colorless, tasteless and odorless
3. Poor conductor, < 1% ionizes - H2O ---- -- > H+ + OH-
(+ & - in equal amounts) , Neutral pH.
(acid) (alkaline/ base)
pH: 0 -------------------- 7 -------------------- 14
high H+ H+ = OH- high OH-
4. Water attracts to each other (bipolarity) creating intermolecular forces called
cohesion. but water is not attracted to air. This internal forces, H-bonds, cause
surface tension - a thin film on the surface.
5. Water wets surfaces - adhesion. Both adhesion and cohesion give capillarity - the
ability for water to rise in small tubes. Apply: (Water and tall trees.)
BUFFER: Ability to resist drastic pH changes
Blood has a pH range of 7.25 to 7.4. This can be buffered by carbonic acid
H2CO3 ----------------> H+ + HCO3- If blood is acid HCO3- will be used
acid base If blood is alkaline, H+ will be used.
MACRO MOLECULES: (Organic Molecules - Carbon Compounds)
Organic Molecules: 1. Carbohydrates 2. Lipids 3. Proteins 4. Nucleic Acids
Made By: Removing water from the reacting groups. How are they broken down?
1. Carbohydrates Broken down to Disaccharides to Monosaccharides
a. maltose to glucose & glucose
(Polysaccharides) to b. sucrose to glucose & fructose
starches, glycogen c. lactose to glucose & galactose
cellulose, chitin
2. Lipids broken down to fatty acids & glycerol (Functional group - FG: R-COOH)
(Waxes, phospholipids, steroids/cholesterols, pigments, chloroplasts, eye retinal)
Can be sat. (hard) or unsaturated (liquid) at RT.
3. Proteins broken down to (21) AA - amino acids (FG : R - CNH2 -COOH)
(5 are polar; 6- non polar and uncharged; 6- non polar and ringed; rest have
groups used for linking and kinking to form diff, shapes); (Has 4 str. : 1ry, 2ndry,
3rdry, 4thry) (Denature: pH, heat, chemcals) .
(bond: peptide bond, forms poly peptide chains) (most important : enzymes)
4. Nucleic Acids broken down to AA, Pentose sugars, PO43-
RNA - blue print of hereditary info: (m,t, r - RNA) do not encode.
DNA - encode for hereditary info.: Z & B DNA. Z - no function, B - the encoder
Nucleotides: 1. Pentose Sugars
2. PO43-
3. N-Bases a. pyrimidines- 1 ring : cytosine C, thymine T, uracil U
b. purines- 2 rings : guanine G, adenine A
Paring: Chargaff's rule
A & T or T & A (2 bonds) ( Double Strands/Helix)
C & G or G & C (3 Bonds) These 4 base pairs are found in DNA, No "U" in DNA
In RNA, there is no T , T is replaced by U. In RNA there are G C AU sequence , No T
Each N-base, C, T, A G ,U is hooked to PO43- & Pentose sugar.
ORIGIN OF THE FIRST CELLS
What are in a cell? Macromolecules
Where did they come from? Not Understood but some scientists think "Spontaneously"
Suggestion: Ancient atm. was rich in H2S, NH3 and CH4 instead of O2 that attract e-s. High EN bombardment of these H-rich molecules released free e- s that helped form biomolecules of cells, (Miller & Urey) . These scientists found that a primordial soup of nucleotides and AA formed spontaneously under lab conditions. Tests show that UV destroys NH3 and CH4, and biomolecules do not form without them, so what do you think?
Bubble Theory: Biomolecules originated from bubbles on the ocean's surface. Water being polar attracts other polar units and concentrates them in the bubbles producing faster biomolecules spontaneously, also CH4 and NH3 needed for these biomolecules were protected from the UV. AAs form proteins and proteins break down to AAs by removing and adding water. So what is your opinion on that?
The First Cells: Some scientist still believe in spontaneous generation, that C-rich molecules aggregated forming spheres like micro drops. Those that persisted and well adapted to EN functions were able to transfer these qualities to new ones, hence heredity and life. This is very hazy to me, I don't know about you. Read about SETI
BACK
CELL STRUCTURE & ORGANELLE FUNCTIONS
CELL - Different sizes & shapes -: Is the basic unit or living building block of life.
OUTLINE:
1. CELL GROUPS & CELL THEORY
2. CELL SIZES
3. CELL SURFACE
4. BACTERIA
5. STRUCTURE AND ORGANELLE FUNCTIONS
CELL GROUPS (2 Groups)
1. Prokaryotic Cell: Living functioning cell, but has no definite nucleus. It lacks internal membranes, e.g. bacteria and cyanobacteria.
2. Eukaryotic Cell: Living and functional with a definite area called nucleus. It has internal membrane structures called organelles, plus none membrane structures called inclusions.
CELL THEORY
The concept that all living things are made of cells is called the cell theory. Some organisms are made up of a single cell like in amoeba, paramecium and some algae, while others are made up of multiple cells like you (about 100 trillion cells), the tree, etc. Some are simple cells - bacteria, some are very complex - your cell. Robert Hooke 1st described cells in 1665 using self built microscope to observe compartments in a cork tissue. He called these honeycomb of compartments, "small rooms" or "cellulae", which we now call "cells".
THE MODERN CELL THEORY Includes:
1. All living things are made of one or more cells.
2. Cells are the smallest living things. Any thing smaller than a cell is considered non-living.
3. Biogenesis: Life evolved only once, living things today are continuous forms of early parents.
4. Cells arise only by division of existing parent cells.
CELL SIZES
Acetabularia cell is about 5 cm long, but your cell is about 5 - 20 micrometers across. bacterial cell is even smaller than you cell.
Why Are Cells so Small?
1. For efficiency in performing cell functions. The nucleus controls the cell's activities via communication. Communication with other parts of the cell must be fast. the smaller the cell the faster the communication, the more efficient the cell's activities.
2. Surface-to-volume ratio: The smaller the cells, the better the packing and the smaller the volume. More cells per volume, the more the surface area. Efficiency of cell's processes depends on surface area. The more the surface area for interactions, the more efficient the cell is.
CELL SURFACE: (The Plasma Membrane) Pile 10,000 of it = 1 paper thickness
PHOSPHOLIPID 0... Phosphate head (hydrophilic & polar)
Non polar hydrophobic lipid tails ..... /\ The membrane (both plant and animal) is made of a modified fat called Phospholipid (PL)
If PL is put in water, the fatty tails push away water , lines up in 2 layers or rows, exposing the P-heads to water and hiding the hydrophobic tails within the non polar bilayer excluding water.
ii !! ii ii <-- surface markers (can be any molecule, proteins, fats, sugars)
000000II00000000 <-- Polar hydrophilic P heads (1 layer top, one at the bottom
/\/\/\/\/\/\II/\/\/\/\/\/\/\/\
\/\/\/\/\/\/II\/\/\/\/\/\/\/\/ <-- Nonpolar hydrophobic fatty tails (2 layers)
000000II00000000
^ continuous proteins molecule
How does water soluble subs. pass through the membrane? Through the proteins that are inter spaced within the bilayer.
Some proteins extend up on the surface to generate surface proteins (name tags or markers) that help to identify the surface and control acceptance or rejection of incoming substances, e.g. the CD4 protein on WBC which the AIDS virus docks onto during infection.
Some proteins are continuous through the two layers (Transmembrane or Integral Proteins) .
The protein portion through the fatty layers is non polar in nature while the ends carry charges.
Some proteins are on one side only ( Peripheral Proteins)
Membrane Defects (Cystic Fibrosis CF)
In cf patients, the cf gene codes for defective membrane protein called chloride channel protein. This abnormal protein does not allow chloride to pass into the cf cell. This imbalance in Cl transport leads to a build up of chloride ions within the cells. This highCl-conc. withdraws water from the mucus causing the thickening and accumulation of thick mucus that blocks the airways and the ducts of other organs like pancreas, liver, kidney, causing organ failures. A 1-copy carrier does not show this effect but a 2-copy carrier, inherited from mom and dad, does.
BACTERIA
BACTERIA: The Simplest Cells ( Called Prokaryotes - before nucleus)
They lack internal membranes, definite nucleus and compartments. The genetic materials are found in the nucleoid region. Some bac. contain small round DNA called PLASMID used for biotechnological works.. Ribosomes (no memb. round them) are scattered in the cytoplasm. The whole cell is covered with plasma memb. and a cell wall of cross-linked carbohydrate molecules. Some bac have flagella, cilia or pilus - suspected to be used for genetic exchange during cell division.
TYPES: There three types.
1. Spherical forms, the coccus/cocci (can form chains) i.e.. strep causing bac.
2. The rods, spindle like, lots form plant diseases, i.e.. pseudomonas bac.
3. The spirilum, spring like, is a large bac., has flagella at each end
GROUPS:
There are : 1. Gram positive bac, (G+). Turns color with Iodine
2. Gram negative bac, (G-). No reaction with Iodine
CELL STRUCTURE AND ORGANELLE FUNCTIONS
Eukaryotic (true nucleus) cells are bigger and more complex than the prokaryotes. They have internal memb. structures like mitochondria and definite nuclei (organelles - can divide), but the non-membrane structures (proteins, fats etc.) are called (inclusions - can't divide).
Groups of Cells: 1. Plants 2. Animals
COMMON FEATURES IN BOTH GROUPS
1. Plasma memb.: (See above for str.) Is a boundary that keeps each cell as a unit.
It is also used for protection of the inner cell
Is a medium for cellular transport & communication
Also site for reactions
Produces enzymes for reactions and supports these reactions.
Temporary storage for substances
2. Cytoskeleton: Interior framework of protein fibers (diff. sizes):
Long slender micro filaments (proteins - actin)
Hollow micro tubules (proteins - tubulin)
And, thick intermediate fibers. They form and dissolve quickly. They are used:
For support and shape of the cell, also anchorage of some organelles to locations.
Provide "rail roads" for molecule trafficking where motor molecules transport
materials to locations in an ordered manner.
3. Centrioles (animals only) , an assembly of microtubule-triplets, forming a pair of
tubulin protein bundles at rt. Ls. one to the other close to the nucleus. They are very
complex containing c circular DNA used for making structural proteins. Cells with
flagella & cilia anchor these structures to basal bodies - a form of centriole.
Centrioles are used to move chromosomes (Xmosomes) during cell division and to
indicate the plane of cell division.
4. Flagella & Cilia: ( For Movement)
Flagella (many): -gellum (single): Long - 1 or 2 at most, slender organelle project-
ing from the cell surface from a basal body. Has a 9 + 2 arrangement, seen in
perm cell, euglena, organisms that cause red tide, etc.
Cilia (many) Cilium (for one): They are short and organized in dense rows. Have
the same 9 + 2 arrangement. Can be found on cells lining your breathing tubes, on
paramecium, etc.
5. Nucleus (Nuc) - The Control Center:
Could be found at the center in most animal cell, or displaced to the side in plants
cells due to large vacuoles. They contain DNA/RNA. The Nuc is surrounded by a
nuclear membrane that is punched out with nuclear pores. Xmosomes carry the
DNA and the proteins in the Xmosomes allow DNA to wind up into a tight unit esp.
during cell division. Genes are finally arranged in the DNA. Locus is the location
of a gene on DNA.
6. Ribosomes: Protein Manufacturing Centers:
They read copies of RNA and interpret it from gene language to protein language
so that proteins could be made. Ribosomes have 2 sub units - (large and small)
and are made of rRNA and a complex of different proteins. The nucleolus is the
center that the three RNAs - tRNA, rRNA, mRNA - are assembled.
7. Endoplasmic Reticulum (ER - rough with Ribosomes and smooth - none):
Tightly packed membrane system round the nucleus for transport purposes. They
also produce enzymes, support reactions and act as temporary storage systems
during high traffic times. They isolate some spaces as membrane-enclosed --vesicles.
8. The Golgies: a Delivery system and vesicle forming bodies.
A complex of 10 - 20 flattened sacks scattered in the cytoplasm - -all the Golgies
are called the Golgi complex.
The Golgies collect, process, package and distributes molecules made in the cells.
Proteins, lipids and sugars can be tagged together in the Golgies to form glyco-
lipids or glycoproteins that can be used as name tags on the membrane
surfaces. Processed molecules collect at the Golgi-folds as cisternae and finally
bud off or pinch of to designated areas.
9. Peroxisomes: Specialty Shops
They are ER-derived spherical vesicles carrying special enzymes that converts
fats to carbohydrates and also detoxifies harmful chemicals oxidants using O2 as
reactants. Reactions are confined to peroxisomes.
10. Lysosomes: Recycling Centers: (Animals only)
These are organelles with digestive enzymes that digest and recycle old worn out
tissues there by renewing the cell for longer life. Lysosomes do not digest them-
selves for it needs EN, but the mechanism is not known. Bac. have no lysosomes.
11. Mitochondria: Cell-like Structures nick named "Power Houses"
They have smooth outside memb and numerous folded internal memb called
cristae. The organelle has been suspected to have been derived from endosmy-
biosis of prokaryotes, thus they still contain small rounded DNA called
Mitochondrial DNA, for making some proteins essential for oxidative metabolism,
-EN release from foods through oxidation if these foods. Can't grow in the lab.
12. Chloroplasts: EN Traps. (Plants only)- Several Kinds, a, b, c, etc. - called
Plastids.
Thought to have come from endosymbiosis of green bacteria. Is like mitochondria.
Internal folded memb - thylakoids - are stacked on one another to form Grana that
are connected together by stroma lamella. Each granum is loaded in space called
stroma. They also contain large rounded DNA that code for proteins needed for
photosynthesis, the making of glucose, fats/oils & proteins. Can't grow in the lab.
Types: 1. Chloroplasts - green
2. Chromoplasts - colored
3. Leucoplasts - colorless
13. Vacuoles: Central storage; Large in plants; small in animals .
Its memb is called tonoplast. Vac contains water, minerals + other compounds
that important for the cell. It can also be used for elimination. The vac generates
internal pressure -turgor pressure- that helps the cell to expand to increase its
surface area for activities.
14. Cell Wall: Plants, Fungi and Bac. only; not in animals
In plants, is made of cellulose - complex carbohydrate -; in others made of other
biomolecules. They are used for support, strength and protection. The middle
lamella glues cells' 1ry walls together; 2ndry walls, when present are laid down
inside the 1ry wall.
BACK
THE LIVING CELL
Each student must read through the chapter and attempt the end of chapter questions before coming to class.
TRANSPORT:
1. CELL EATING & DRINKING
2. DIFFUSION
3. CELL DIVISION
4. COMMUNICATION
HOW DOES THE CELL EAT OR DRINK? by:
1. Water leaking through imperfections in the memb.
2. Food & water or liquids are engulfed by membrane folding around these particles
3. Proteins in the memb. act as doors for particles to move in & out- Diffusion/osmosis.
DIFFUSION: Is based on Kinetic Theory
KINETIC THEORY: Particles are in constant random motion due to the EN they
contain.
Where do they go? They move from where there is too much to where there is less # of them. This is called DIFFUSION.
Diffusion: Net movement of particles from high to low concentration (conc) area down the conc. gradient.
Osmosis: When this movement involves only WATER via semi permeable membrane, then it is called OSMOSIS.
Osmotic pressure: Pressure created inside a system due to water moving into that system .
It can cause that system to burst if the system is not built to withstand such pressure. It causes swelling. In plants, the outer wall is called cell wall made of cellulose to withstand these pressures.
Tonicity: Involves 2 solution systems. Soln. System #1 Soln. System #2
conc. = 5% salt conc. = 12% salt
Calculate the grams of water in each system. (Hypotonic to #2) (Hypertonic to #1)
Identify the direction of flow between #s 1 & 2.
What will happen if a cell from your body is placed in A. Distilled water & B. salty soln?
Endocytosis: Made of 1. Phagocytosis (eat) and 2. Pinocytosis (drink)
Cells bring in foods and fluids into the cytoplasm by forming false hands to encircle the part and then pulling it into the cytoplasm. This is Endocytosis. The opposite is exocytosis, out.
If the particle was food, then is called Phagocytosis - cell eating.
If the particle was fluid, what do you call that?
Types of Diffusion:
1. Simple diffusion, where particles move freely on their own along conc. grad. from high to low conc. with no help.
2. Facilitated Diffusion: Is like #1, only that the particles need memb. channels (help) to aid them to pass through.
3. Active Transport: Defies the rule of diffusion by going AGAINST the conc. grad. Particles are climbing the hill, so they can only go through a carrier or channel designed to open with EN supply to allow movement (one direction only) from low to high conc. e.g. the Na+ / K+ pump.
4. Coupled Transport: In the above pump, lots of sodium are outside the cell and they are trying to get back into diffusion, so as they do, they drag some other molecules along with them, e.g. sugars, proteins etc.
CELL COMMUNICATION
Chemical Sensing
All cells sense their env. via cell surface proteins or name "tags", these proteins are not used for diffusion of particles even though they stick out on both sides of the memb. They have receptor sites that bind to say, hormones that may finally trigger an action or a series of actions; e.g. insulin binding sites (IBS) on cell memb., the liver has the most IBS of all cells. WHY?
Electrical Sensing
Some memb prots. contain special central voltage sensitive AA (charged area, (+)
or -), when a voltage of opposite charge approaches, the door flips open to open up
the channel for ions (+ or -) to pass through, very important in the nervous system.
Self Info. Sensing
Internal communications go through the enormous net work of ER & Cytoskeletons. Motor molecules are also involved in this intracellular trafficking.
CELL DIVISION (reproduction)
CELL DIVISION: 1. MITOSIS 2. MEIOSIS (See Meiosis Chapter P125)
Mitosis: Cell division into 2 equal new ones called daughter cells. (Asexual reproduction
in prokaryotes but used for growth in eukaryotes).
Steps:
1. Genetic materials are copied to form 2 sets - REPLICATION: (Tetrads)
Copying starts from the ORIGIN and can move in both directions.
After copying, the genetic materials separate into 2 groups KARYOKINESIS
2. Cytokinesis: After genetic materials move apart in for 2 groups, the cytoplasm
divides at the center to form 2 new daughter cells exactly like the mother cell.
This is also referred to as BINARY FISSION, As seen in a bacterium cell
PHASES: 1. Pro - 2. Meta- 3. Ana- 4. Telo- phase
Interphase is not part of the phases of cell division.. It is the growth phase
where the cell grows & makes enough materials ready for the cell to divide
two or four.
Sub Phases of Inter phase:
G1: Proteins and other materials needed for cell division and growth are made.
S: Synthesis or the replication of identical DNA for cell division.
G2: Growth continues, materials for centrioles, mitochondria and other organelles are made, chromosomes start to condense.
MEIOSIS
Meiosis: A 2 step division that forms 4 daughter cells that contain half the Xmosome #
as mother cell. Division happens in only sexual organs of higher plants and animals.
The 4 daughter cells develop into eggs in females and pollen or sperms in males.
Sperm and egg are called GAMETES
The sperm fertilizes the egg to form a zygote, zygote develops into the young life.
Sequence: Meiotic Phases: Prophase I -> Metaphase I -> Anaphase I -> Telophase I
Prophase II -> Metaphase II -> Anaphase II -> Telophase II
Prophase I - Synaptic Phase:
In this phase, tetrads are formed and crossing over takes place.
GENETIC MATERIALS: Found in the nucleus as NUCLEIC Acid
Str. of Xmosome: (Use the Text)
Find out: Haploid Diploid nXmosome 2nXmosome Xmatid Cell Plate Centromere Kinetochore Histone Nucleosome Double Helix Homologues
How many chomatids have you per your cell?
Types of Nucleic Acid: 1. DNA (bDNA-genetic) 2. RNA (mRNA, tRNA, rRNA)
(zDNA- bDNAgenetic)
Do Cells Die?
Living cells contain hidden clocks that program the cells to divide a certain # 0f times and then the cell dies. Cell's activities wear down the cell's machinery and environmental conditions sometimes affect the timing of this internal clock in both ways.
1. Why don't you have webbed foot like the ducks?
2. "No food for the cell", which one will die 1st, human or bacterial cell?
BACK
EN & LIFE
OUTLINE:
1. CELL CHEMISTRY: REACTIONS
2. CELL-USE OF EN
3. PHOTOSYNTHESIS
4. RESPIRATION & FERMENTATION
CELL CHEM: REACTIONS
ALL LIVING CELLS USE CHEM EN, (ATP), from foods FOR LIFE'S ACTIVITIES.
FOODS (sugars) -----------------> EN + CO2 + H2O
(chem bonds broken) (CHEM REACTIONS)
EN + ADP + Pi ---------------------> ATP
ATP --------------------------------------> ADP + P + EN
(breaks down in cell) !
^ ^ This is the chem EN your cell uses to function
| Reactants | ^ ^
| Substrates | | Products |
More EN Lesser EN
Chem Reactions Can Be: 1. Exergonic /Exothermic : Heat given out, freezing water
2. Endergonic/endothermic: Heat absorbed, boiling water
Activation EN: EN that is added to a system to start a reaction. Reactions will not proceed if activation EN is not overcome. It is a chemical lock or barrier on exothermic reactions that keeps these reactions from going off spontaneously, nick named "a kick in the pants EN".
Catalysts: Biomolecules or Enzymes used to lay the foundation for "a kick in the pants" in chem reactions, for that reaction to start. This is called lowering the activation EN or catalysis. EN is still needed to be added to the system for the action to start. The process is like a sale sign on something you could not have been able to afford before the sale sign.
How do Enzymes (ENZ) Work?
1. They bind to the molecule - substrate- to create enzyme/substrate complex.
2. Bonding stresses the chem. bonds in the substrate to a point more likely for the
action to start. OR;
3. Encourages a bond to form between two reactants so that the action can set off.
4. To bind, enzymes must have binding sites that fit the substrate/s. To create stress
the enzymes must have active sites. Sites cause enzymes to posses specific shapes.
Some enzymes have shapes that can be altered. How?
These eznymes have another site on the surface - allosteric site - that signal molecule bind to changing the shapes.
When signal molecules change shapes like that, target molecules can't bind. This is called Allosteric Inhibition.
Other Inhibition: Competitive Inhibition, this is when decoy that looks like the real substrate binds to the active/binding site stopping the real substrate from having full access to the sites. This reduces or stops reaction. The more the competitor, the slower the rate of action.
Enzyme Helpers - Cofactors: Additional chem components that aid catalysis.
Coenzymes: Non protein organic cofactor, eg. NAD+
How do You recognize an Enzyme?
When called by its scientific name, an enzyme has an ....ase ending, as in:
1. ATP synthase, used in e- transport to make ATP from H-pump
2. Maltase, converts maltose to 2 glucoses
3. RuBP carboxylase, combines RuBP with CO2 to form PGA
One cell contains thousands of enzymes.
Factors Affecting Enzyme Activities:
1. Co Enzymes aid in actions
2. Temp: Enzymes do better at optimum temp , the bonds are flexible and weak to
enough to allow induced-fit activities.
3. pH: Structural bonds of enzymes are sensitive to H+ conc., it depends on the ENZ.
USE OF ENERGY BY CELLS
What's EN? The Ability to do work. All living things use ATP as the EN for activities,
.g. movements, etc.
ATP STR.
ATP contains 1. Adenine (protein) 2. Ribose pentose sugar 3. 3 PO43- (2 are active)
Adenine + pentose sugar = Adenosine (A)
A + PO43- (P) = AP or A - P; Adenosine Phosphate or Mono Phosphate (not
easily used or bond not easily broken).
AP + P = APP or A -P - P; Adenosine Di Phosphate (bond easier to break than in
A-P).
ADP + Pi + EN = ATP or A - P - P - P; Adenosine Tri Phosphate (P-P is High EN
bond, and the - P bond breaks easily to release the EN.
Breakdown: ATP ---------> ADP + P + EN (for doing work by the cell)
1 1 1
1 1 1
v v v
Recycled lost or lost as IR after work is done
recycled
PHOTOSYNTHESIS
Is the process used by all green living organisms to produce food (PE) from the sunlight and releasing O2 as a by product. How?
Chloroplasts capture light EN photons and change them to chem EN (ATP & NADPH), then stores these ENs in CO2 as foods (PE) , eg. glucose, other sugars/carbohydrates, lipids and proteins.
Chl + light EN + ENZs
Summary Equation: 6CO2 + 6H2O -----------------------------> C6H12O6 + 6O2
CHLOROPLAST: Contains chlorophyll. There are many types, eg. Chl a,b,c,d, etc. Only Chl a & b are used in capturing light for photosyn. These two are used in forming light harvesters called Photosystems (PS) I & II.
PS: There are: PS I or P700 Made up of Chl a, b + Proteins (Diff:- in proportion of)
PS II or P680 Made up of Chl a, b + proteins (Chls a & b )
Str. of Chloroplast: Folded membranes called thylakoids are stacked in groups called
grana. Grana are connected by stroma lamella and grana are loaded in the stroma.
PSs are located in the thylakoid membranes.
Phases of Photosynthesis: (2 Phases) (Another Diag)
1. Light Dependent (Light Phase): Rad. EN photons are transformed to 2 chem ENs.
a. ATP 2. NADPH
2. Light Independent (Dark Phase or Calvin/Benson Cycle or C3 path way): Glucose is
made from CO2
Light Phase (Cyclic) (Non Cyclic)
Here water is split by PSII to release O2. The hydrogen is shunted into a proton pump where H is pumped across the memb. into the inner memb. portion of the thylakoids. The excited electron goes through electron acceptors and carriers and coupled to the H+, Chemiosmosis takes place where the escaping H+ (by diffusion) via a proton channel generates ATP with the help of an enzyme - ATP synthase. At PSI, photon excited electrons passing through electron carriers generate a diff. chem EN NADPH from NADP. Two diff chem ENs , ATP & NADPH are formed.
Dark Phase:
Here CO2 is picked up by RuBP (RuBP Carboxylase must be present) and the ATP supplies the EN for H to be hooked onto C using NADPH so that glucose can be formed. One round uses only one CO2, so to form one glucose molecule, photosynthesis must go through 6 times.
Photorespiration + Rubisco
In the dark phase, RuBP + CO2 --------------------------> PGA is formed
(1 PGA has C - C - C back bone)
All plants that do this are called C3 Plants (most broad leaf plants).
But during hot dry periods, leaf stomata close to conserve water, so no air gets in. So oxygen from splitting water accumulates in the leaf. This oxygen turns around and breaks down RuBP, hence no PGA is formed. No PGA, no glucose, so photosyn. is less efficient in C3 plants.
C4 Pathway is like (CAM Cycle - Crassulacean Acid Metabolism) Both use PEP
PEP Carboxylase
CO2 + PEP --------------------------> Oxaloacetate ----------> malate or aspartate
( night stomata open, air is in) (both are C - C - C - C in the back bone)
Malate or Aspartate later breaks down to release CO2 to RuBP of C3 pathway. So all plants that do this are called C4 plants: eg. most narrow leaf plants -- grasses, corn, sugar cane, etc. Very efficient in photosyn. (Has both C3 & C4 paths.) There is no Photorespiration.
RESPIRATION - RESP. (ATP Made) (External & Internal)
The oxidation of food stuff, mostly glucose, to release EN is Cellular / Internal Resp.
This resp. requires molecular Oxygen O2 . From where?
From External Resp. : Breathing. The diaphragm lowers - (breathing in), air is pulled into the lungs space via the nose, O2 diffuses into the blood and CO2 in the blood diffuses out into lung space to meet other gases that did not get into the blood. Then, the diaphragm rises into the chest chamber, this causes the lungs to be squeezed and the gases in the lung space come out via the nose ( breathing out).
STEPS IN RESP.:
1. Glycolysis: Glucose split into 2 halves; needs 2 ATP, then 4 ATPs are produced at
the end. Also 2 pyruvates and NADHs are produced. Takes place in the cytoplasm .
Calculate net ATP.
2. Formation of Acetyl CoA from Pyruvates: 2Pyruvates lose (CO groups) and CoA are
hooked to the products to form 2 acetyl CoA. No ATP is formed, but NADHs and
CO2 are formed.
3. Krebs Cycle - TCA - Citric Acid Cycle - 2ice /glucose: 1Acetlyl CoA releases acetly
group to Oxaloacetate to form Citric Acid, this then breaks down totally to release
the oxaloacetate (recycled for the 2nd round), 1ATP, NADHs, FADH2s, CO2 /round.
Calculate total ATP / Krebs cycle / glucose molecule.
4. Electron Transport System : Hs from NADHs & FADH2 are stripped off, electrons are also formed. Hs are used in proton pump sequence and 32 ATPs are produced here using ATP synthase. The electrons are transported to O2 (final e- acceptor) and the Hs+ used to form ATP combine with O2 and e- to form neutral water. #s 2,3,4 take
place in mitochon.
Calculate total ATP formed from 1glucose.
The amount of ATP in the body regulates the process of Respration.
FERMENTATION: ANAEROBIC IN NATURE , No oxygen is available.
There are 2: 1. Lactic acid fermentatiom : Pyruvate are converted to lactic acid and electrons and are stored in muscles - soreness. The liver breaks it down later. This is applied in food industries for manufacturing of fermented milk products.
2. Alcoholic Fermentation: Pyruvate is converted to alcohol - EtOH by yeast, as in the wine industries. So to make wine from grapes, crush and shut out O2.
BACK
ECOSYSTEMS (ES) & AND EN FLOW
OUTLINE
1. ES - MEANING
2. EN FLOW
3. NAT CYCLES
4. MAJOR ES
ES
ES is where living (community) & non living (abiotic) interact to perpetuate themselves.
Habitat: The place where individual species live.
Members of ES:
1. Producers, consumers and decomposers - microscopic or not - (living entity)
2. Soil particles, rocks and stones, water in all forms, air - (physical or non living
or abiotic entity)
ENERGY (EN) FLOW
EN flows through the Trophic Levels or food chains and webs, (Producers, Consumers, Decomposers). Ref. to your previous notes. Producers (all photosynthetic organisms)
trap the radiant EN as chem potential EN in biomolecules for the producers and consumers as well. Producers are the 1st trophic level. Ref. to your triangle.
EN Loss: As producers fix the sun's EN into PE biomolecules, EN is lost during
fixing consumption as IR, which heat is en example
Algae --------------> smelt ------------> trout -------------- > human
1 Kcal 150 cals 6 cals 1.2 cals
It takes 10 lb of grains ------------------------> 1 lb of human tissue, But
100 lb of grains --------------------> 1 lb of human tissue if we eat cows. Why?
Herbivores: Consumers that eat plants. They are the 1st consumer level, but 2nd
trophic level.
Carnivores: 2nd consumer level, eat herbivores.
Omnivores: Eat both plants and animals
Vegetarians: Human herbivores
Detritivores: Consumer-Decomposers (Bacteria & Fungi - are the 1ry decomposers) ; (2ndry decomposers are worms, ants, vultures).
Food chains can be long or short depending on the productivity of the ES. Most productive ES is the tropical rain forest - on land, the coral reefs in water, and the
least productive are the tundra and the desert on land and the open seas in water.
NATURAL CYCLES
All chemicals in biomolecules are recycled. We will look at H2O, C, N & P cycles only
(Use the Overheads) for the Cycles.
MAJOR ESs Land and Seas
1. Climate - (weather conditions) - determines the ESs. Water is a major factor in det.
the ESs but in the Tundra, the temp is the major factor.
2. Radiation differs decreasing from the equator (direct rays and warm rising air
producing high rains) to the poles ( oblique rays with cooler falling air and lower
rains).
3. Altitude also affect ESs simulating movement from the equator - forests -, to the
poles - tundra, P 563.
4. Also an elevation across the direction of the wind affects the ES. The windward will
be wet and forested while the lee will be dry and less forested.
5. Ocean currents - patterns of water circulation, clockwise in the north and anti clock-
wise in the south - also modify the ES. Winds over warm currents (El Nino) cause
rains on land but over cold currents (contain less water) generate deserts.
AQUATIC ES - Seas & Oceans : (Brackish & Salt Waters) and Fresh Waters
1. Shallow Waters: Contains more species (more productive) than the open seas due to light penetration for photosynthesis & nutrients from land.
Contain: 1. Intertidal zone (unstable zone), exposed and submerged with tide swings.
2. Estuaries - partially enclosed waters, brackish if formed from rivers, rich,
productive, used as nurseries, for shipping, polluted, dredged if for
shipping, stop point for migratory animals, forms deltas if not dredged.
2. Open Waters: Home for plankton - 100 meters deep - (phyto- {40% photosynthesis}
& zoo-) planktons. Also necktons are also found here.
3. Deep Sea: >300 meters. Less light penetration, less productive, less life, when
found, they are usually large. Some have bioluminescent structures for lighting,
communication and for hunting for preys. Any producer uses chemosynthesis for making food.
The benthose pop depend on drifts from the top eg. algae rains.
Fresh Waters: (rivers, streams, canals, lakes, ponds, marshes + swamps) are limited in area. These ESs are affected by local communities and organisms are adapted to strong currents in rivers and streams.
Zones:
Same as oceans, Shallow end, open surface and deep.
Thermal stratification exists in large lakes/ponds, thermocline separates the strata.
Turn overs (fall & spring) also exists in lakes/ponds.
Freshness:
1. Eutrophic waters have lots of minerals + OM in the waters, low oxygen content
2. Oligotrophic waters have very low levels of minerals + OM, high oxygen content
TERRESTRIAL ESs Form Biomes
Similar ESs over a broad area is Biome. A biome has similar climatic conditions and a defined group of organisms.
Type of Biomes: 1. Tropical rain forest 2. Temperate Deciduous forest
3. Savanna 4. Desert 5. Taiga 6. Tundra 7. Other Grasslands
1. TROPICAL Rain Forest: Richest ES, has >250 cm of rain (constant rain due to condensation of evapotranspirated waters); and contains 1/2 of the earth's species. Found in S America, Africa, S.E Asia . ES is lush due to mycorrhizal effect & 90% of the nutrients is in the standing crop, 10% is recycled. Has hot humid climate. Soils are poor and oxidized (Oxisols)
2. TEMPERATE Deciduous Forest: Rich hard wood forest, warm summers and cold winters, has 4 seasons with high rains. Found in Europe, Asia, N. USA + E. Canada. Trees lose their leaves and animals big and small are numerous. Species are abundant due to stable constant climatic conditions.
3. SAVANNA: World's great open grasslands of the tropics. Sparse trees and dominantly grass. Rains, 75 - 125 cm/yr. with huge range of migratory grazing African animals, active during the rains. Biome is a transition between the forest and the deserts. Many animals are endangered due to human activities and desert encroachment. Most of the soils are oxisols.
4. DESERT: Dry lands of the interior - the Sahara of Africa, the Gobi of Asia, the great sandy desert of Australia. Rains are < 25 cm/yr. Vegetation is sparse and survival of both plants and animals depend on water conservation and modifications for adaptat- ions. Animal activities are restricted to cool periods and moisture conditions. Day time activities are rare, animals spend more time in burrows , cracks and caves. Camels drink a lot of water when available and can survive long arid conditions. Some animals migrate via the desert for seasonal abundance. Grasses are bunch grasses. Soils are Aridisols high in minerals. Why?
5. TAIGA: The Temperate or Northern Evergreens - The Conifer or Pine Cone Forests, covers about 9 % of the earth, found only in the North. Have long cold winters and summer rains (50 cm/yr), 4 seasons are prominent but short except winters, hence, not good for agriculture, but lumbering. Topography is flat and sometimes rolling. Ponds and lakes, marshes and rarely bogs are present. Permafrost is not common, soils are acidic due to piney conditions. Vegetation is mostly pine trees (in dense stands of one or more species) or in with some deciduous species. Animals are large and they migrate to the tundra for free meals. Hunting and trapping are extensive.
6. TUNDRA: A Desert < 25 cm of rain per yr. Most water is in the solid state. Found in the North, open, wind swept and boggy. The soils are permafrost (about 1 meter deep even in summer) and the winters are long and harsh. Summers are very short ( land of the midnight sun) and crops must be adapted to the short growing season. ES is fragile and trees are short and confined to stream beds. Large animals live there and migratory ones from taiga visit the tundra in the summers. Bugs are abundant. Soil is low in OM. Why?
7. OTHER GRASSLANDS: The Temperate Grasslands - Seas of Grass found in N. America - Prairies, S. America - Pampas, and Eurasia, S. Africa and Australia. Soils are deep dark and rich (Mollisols) and good for agriculture. Rains (25 - 75 cm/yr) are common and the 4 seasons are prominent. Numerous grazing herds populate the ES. The Es is highly modified by man's actions that threaten lots of the species like bisons pronghorns.
8. OTHER BIOMES:
Chaparral: Winter rains and summer droughts - prone to fires. Found in the Mediterranean regions, CA, Aust., S. Africa. Trees are spiny, short and conditioned to fires. Is an area for fruits and veggies.
Read on Polar Ice, Semi Deserts, Tropical Monsoon Forests and the Alpines.
BACK
GENETICS - (THE STUDY OF INHERITANCE)
OUTLINE:
MENDEL'S WORK
GENOTYPE / PHENOTYPE
MEIOSIS
PATTERNS OF INHERITANCE
MENDEL'S WORK
An Austrian Monk , Gregor Mendel studied pea crossings (like British farmers) and finally came up with a series of rules that shed light on the puzzle about inheritance, indicating that traits are written in genes that are housed in DNA. Mendel chose peas because there were previous info. on peas, like many varieties, they grow faster, are self pollinated, and traits appear and disappear.
He grew peas that self fertilized (pure breed) or parental P generation and then crossed the Ps to get F1 generation - dominant trait always shows (expressed trait) eg, purple vs white flowers ;- all purple , Purple- dominant D & white - recessive R (not expressed). He then allowed F1 to self fertilize to get F2 generation - the recessive trait came back in a 3 D ::1 R ratio. In each situation, he counted the #s that showed certain qualities. More breeding showed that in crossing different traits, the pop. will turn out to be: 1 true breed D, 2 non -true breed, 1 true bred R .
MENDELE'S THEORY: (From a set of rules to explain his theory) (Simplified)
1. Parents transmit trait information (merkmal or factors) now - genes - that act later to produce the trait (in the offspring) to their offsprings.
2. Each parent contain 2 (similar or dissimilar) copies of these trait factors . Two similar factors encoding for the same thing - say white (ww)- are homozygous, but heterozygous (Ww) if one codes for White (w) and the other Purple (W).
3. Alternative form of a factor is an allele. W, he called "Dominant, w, Recessive. The appearance of an individual due to a trait (say white flowers) is Phenotype
4. The white color is determined by which allele of color GENE (genotype) the plant received from the parents. For example in a pea plant with phenotype "white flowers and genotype of ww", ( w) came from Dad - male - and the other (w) from Mom and do not affect each other, each allele is passed on unchanged.
5. The presence of an allele is not an assurance of trait expression as inWw, where the W achieved expression - Purple, (w )recessive , not express .
PUNNETT SQUARES
This determines the possible genotypic out come of a particular crossing.
1 Homozygous (purple) all dominant
| W | w__
W | WW | Ww 2 Heterozygous (purple) W = dominant
| |_______
w | Ww | ww 1 Homozygous (white) recessive
Test Cross: Used by Mendel to determine an individual's genetic composition, eg. is the genotype WW or Ww? Ans.: Cross it with a white, of course white = ww.
If WW If Ww
All Purple
| W | W | W | w 50% white
----------------------------- -------------------------------
w | Ww | Ww w | Ww | ww
----------------------------- -------------------------------
w | Ww | Ww w | Ww | ww
----------------------------- --------------------------------
EPISTASIS: Phenotypes that result as a reaction of 2 or more genes acting together.
It occurs in that one gene blocks the expression of the other (when
acting alone): ie. BB or Bb produces colored pigments - bb , no production .
AA or Aa allows pigment to be deposited - aa , no deposit .
Individuals with BB/Bb and aa will be white even though it has the ability to produce
colored pigment: (No pigment deposit); the same will hold for the opposite.
| BA | Ba
-----------------------------
BA | BBAA | BBAa
-----------------------------
Ba | BBAa | BBaa <---------White + ability to produce colored pigment
-----------------------------
MENDEL'S LAWS OF HEREDITY:
1. The Law of Segregation: Gametes combine randomly to form offspring and only
one allele that specifies an alternative trait can be in a particular gamete.
2. Law of Independent Assortment: Genes located on different chromosomes are
inherited independently of one another.
FACTORS THAT AFFECT GENOTYPIC EXPRESSION (PHENOTYPES)
1. Multiple alleles, as seen in I-gene (I i) alleles for the ABO blood groups. Major gps. are A & B. Gp. O = ii, is a result of i & i allele interaction . Segregation
looks like this:
IA or IB and i. +ing will give the A, B, AB & the O blood gps.
2. Interaction between the products of 2 genes where only one of the genes modifies
the phenotypic expression produced by the other, gene blocking the expression of
the other. (See Epistasis above)
3. Continuous Variation: Multiple genes act together to influence a trait.
4. Pleiotrophy: One gene affects more than one trait.
5. Incomplete Dominance: Heterozygous individuals do not resemble any of the
parents due to codominant alleles contributed by the parents.
ALTERATION OF CHROMOSOMES:
Nondisjunction: Homologous chromosomes fail to move apart properly at meiosis I or
sister chromatids fail to separate at meiosis II
This creates more or less than 2 chromosomes in the fertilized nucleus if these cells unite to cause pregnancy (ANEUPLOIDY).
Trisomy: If 3 chromatids ( Down Syndrome = Trisomy in # 21 Xmosome.
Monosomy: If 1 chromatid More than 2n chromosomes, is, polyploidy
Tetraploidy: If 4 chromatids (XX & XXY - Klinefelter syndrome: cause sterility
(XXY will have more female characteristics than XY)
(XO - Turner syndrome: 1 copy of X, cause sterile
females
(XYY are fertile males and anti social (controversial)
MEIOSIS (See Mitosis too)
Sex Chromosome, XY: An egg with the "X" from the father is a female & Y is the male. Y chromosome is said to contain no genes that are used. So genes that function on X chromosome have no partner on Y. Autosomes: are the remaining non sex chromosomes
Activity : In all female cells except the ovarian cell, only one "X" of 23rd Xmosome is active, the other or (Barr body ) condenses to an inactive form. Any genetic problem associated with this XY chromosome is said to be sex linked.
HUMAN HEREDITY DISORDER
Gene encoded proteins work precisely to promote normality, but sometimes mutation (all are recessive) cause genes to encode abnormal proteins causing genetic disorders. Some of these disorders could be seen in:
Cystic fibrosis - failure of Cl- transport system
Sickle-cell : - abnormal hemoglobin
Tay-Sachs: - defective form of enzyme hexosaminidase
Hemophilia: - defective for of blood clotting factor VIII
Hutington's - production of brain cell metab. inhibitor
Muscular dystrophy: - destruction of the myelin layer of nerve stmulating muscles
Hypercholesterolemia: - abnormal cholesterol cell surface receptor
Phenylketonuria: - defective phenylaline hydroxylase.
GENETIC COUNSELING & THERAPY:
The identification of parents at risk of producing F-1 with genetic defects. Generally if one of your relatives is affected, there is a possibility that others in the family are carriers. AMNIOCENTESIS can be used to identify some of these defects during pregnancies and proper treatments could recommended.
BACK
HOW GENES WORK OR FROM DNA TO PROTEINS
OUTLINE
GENES & DNA
DNA REPLICATION
TRANSCRIPTION
TRANSLATION
REGULATING GENE EXPRESSION
GENE TECHNOLOGY
GENES & DNA
GENE: A set of instructions in living things that determine what the individual is and looks like. Gene pool is genotype.
1. Genes are in and made of DNA, DNA contains nucleic acid.
2. DNA is in or forms the core of chromosomes.
3. Chromosomes are in the nucleus.
4. Chromosomes contain 2 macromolecules: A. Proteins (AA)
B. Deoxyribonucleic acid nucleotides .
Which of the 2, A or B carry the information for activities? ANSWER: B, based on
Griffith-Avery work on Streptococcus pneumoniae in 1928:
Virulent form - kills mice Non Virulent form - no killing
Has slimy coat or covering (coat - not poison) No slimy coat
Heat killed slimy forms, (harmless to mice) Heat killed + non slime, killed
mice
Transformation took place.
The non slime acquired slime gene from the dead bac. and becomes slime bac. The gene now instructs the non-slime how to make slime and become a killer. Oswald in 1944 isolated DNA.
VIRUSES: Are not living, but pieces if DNA or RNA protected with organic molecules.
GROUPS: 1. DNA viruses (Strept.. pneumonia) 2. RNA viruses (HIV, TMV, HRV)
PHAGE: Virus that can kill a bac., also called bacteriophage.
Viral Infection: After a virus lands on the correct host's membrane, viral DNA is injected into the host and the viral jacket is left outside. In some cases, the whole virus gets into the host before injection takes place. This injected viral DNA now takes over the command of the host, instructing the host to manufacture materials needed to form new viruses. Then the Viral DNA replicates. The replicates then collect the host's manufactured materials and build new viruses as the host is now dead. Finally The new viruses break up the host's membrane and move out for more infections.
(See Hershey-Chase exp.)
IF RNA virus, then the RNA does exactly as above, but if the RNA must insert itself into DNA, the RNA must first be converted from RNA to DNA using reverse transcriptase before insertion.
Structure of DNA: DNA (also RNA) contains 3 nucleotides. (Ref to notes from CHEM of LIFE)
1. DNA is anti parallel (anti //) 3' _____________ 5' Is made up of 2 sides twisted to
_____________ form the double helix str..
5' 3'
2. Each side is complementary to the other and and each side carries genes -gene pool.
3. DNA winds 2 ice round histone protein (to form nucleosome), these are now stacked
on one another to form the complex DNA design .
4. DNA (copies itself) replicates semi conservatively during S-phase of the interphase.
5. DNA is used as a foundation for making RNA - transcription.
DNA REPLICATION: Making copies of the same DNA
1. Forking enzymes move to the replication forks (about 100,000 nucleotides/fork) to
destroy the H-bonds between the N bases.
2. RNA primer forms and binds to the 3' ends and makes a short RNA piece.
3. Then DNA polymerase binds to this complex (of #2) and starts copying or making
the complements of each strand. Corrections are made (if any - proof reading) by
the DNA polymerase. Proof reading is not perfect, mistakes leads to variation &
evolution
4. Then the short RNA piece is replaced with the correct DNA complement
5. The old strand is now joined to the new strand - semi conservative.
RNA TRANSCRIPTION: Making RNA from DNA so that proteins could be made.
(Transcription Happens in the nucleus)
CENTRAL DOGMA: Path of info. (DNA ---> RNA ---> Proteins) used by DNA to make Proteins or for gene expression.
When the cell needs proteins, the genes responsible (coding) for these proteins will be required to form the RNAs that will be used to manufacture these proteins. These genes have promoter sites associated with them.
1. Forking enzyme binds at the promoter region and breaks the N-bases bonds. The DNA strand coding for the proteins is called the coding or "+ve" strand, or, template strand.
2. Transcription factors bind to the 3' end at the promoter site of the split DNA
3. This complex attracts RNA polymerase to the promoter site at the 3' end.
4. The RNA poly-ase then reads and makes the complements of the strand replacing all "Ts" with "Us". All the 3 RNAs are made the same way from the same coding strand.
5. Corrections are made by cutting out the (introns - mistakes or non coding junk) and rejoining (exons - about 10% in humans ) the true codes together, becomes a shorter piece. This is the codon or mRNA. tRNA or the anti codon carries the opposite codes of the codon.
6. The 3 RNAs move out of the nucleus into the cytoplasm for translation for protein building.
TRANSLATION: Building Proteins . It Happens in the Cytoplasm
Types of RNA: 1. mRNA - codon or messenger RNA, carries genetic codes from DNA
2. tRNA - anti codon, recognizes codes on codon and then transfers the AA that the codes represent. Aminoacyl-tRNA synthases energize the AA to bind
the AA binding onto the attachment site found on the tRNA end.
3. rRNA - ribosomal RNA, used for making ribosomes that translate
the mRNA form DNA language to protein language, thus, making
proteins.
TRANSLATION STEPS:
1. Initiation : The building of ribosomes from rRNA. Ribosome has 2 sub units, the large and small sub units. LSU has 3 rRNA + > 34 diff. proteins
SSU has 1 rRNA + 21 - 36 diff proteins. Both stay separated
when not in use .
Ribosomes also have 3 binding sites: (a). mRNA binding site,
(b). A- site, amino acyl site, AA are brought here by tRNA.
(c). P- site, protein chains are built here
2. Elongation: After mRNA binds to its binding site, ribosome starts to read in triplets, the codes on the codon with the anti codon recognizing and bringing the corresponding AA into the A-site. The AAs are now joined into a poly peptide chain by
using a peptide bond between each AA. Proteins are made only when the ribosome reads an "AUG" triplet. Many ribosomes can hook onto a single mRNA, thus making lots of the same protein .
3. Termination: (Protein making stops) When ribosomes reach any of the 3 triplets;
(triplets: UGA, UAA and UAG), elongation stops and the protein is sent to GOLGIES
for processing and distribution.
REGULATING GENE EXPRESSION: (Self Control)
Each cell must be able to regulate when genes are used for expression in order to effect a controlled growth and development processes, for there would be chaos if all the genes were used at the same time for expressions. This control is from a score code written in the genes that regulate proteins needed to bind on the regulatory sites of each gene in order to turn the gene on and (off- negative control), for effective expressions.
Enhancer, repressor and activator proteins are used for these processes.
DNA
______________________________ When repressor protein binds,
|___|__________|__gene__________ then expression is not possible till
promoter regulatory it is removed for the promoter
site site or operator site site to be activated.
RNA- repressor protein
Poly-rase binds here
binds here
Transcription has many levels of controls, so most genes have the same structure like the text book that has front matter before the real chapters. So genes have:
Enhancers ---- Activators ---- Promoters --- Repressors --- before the real Gene.
Cells regulate Genes by binding enhancer or inhibitor proteins to that DNA
Multigene Families: Multiple copies or clusters of almost identical genes on DNA.
Transposons: Jumping Genes - Similar genes repeated and scattered around the
chromosome, have the ability to move from one point to another in the
chromosome.
GENE TECHNOLOGY
Genetic Engineering: Moving genes from one organism to another.
Gel Electrophoresis: Technique that electricity is used to separate & move gene fragments.
Movement is due to size and wt of the fragments
Plasmid: Small round DNA in bacteria used for inserting other pieces of DNA of choice:
they are a means of transferring DNAs.
Restriction Enzymes: Are like surgical knives used for cutting DNA at specific sites for the desired quality (usually 4 - 6 nucleotide sequences). The cut leaves sticky ends that can be reglued into another DNA using a glue or sealing enzyme called LIGASE.
STAGES OF GENETIC ENGINEERING
1. Cleaving or cutting the req. DNA (vector)
2. Recombination or putting the cut piece into a carrier that can infect target cells.
3. Cloning or infecting target and allowing the infected cells to reproduce.
4. Screening or selecting the infected cells carrying the needed DNA. Sometimes they
use tags to probe for the gene of interest.
Some technique called PCR Amplification (Gene multiplication) is also used in biotechnology. DNA of interest is obtained and primers synthesized. Both are heated to about 95o C to unwind the DNA to single strand. Cooling allows primers to bind to the strands at the region of interest. Heat stable DNA (Taq Polymerase) polymerase is added, this then adds nucleotides to the strand changing the primers to to complementary fragments. Finally two copies of the the original fragments are formed. Process can be repeated.
cDNA:
Transcription produces mRNA that introns have been cut out. mRNA are found in cytoplasm. Reverse transcriptase can be used to reverse MRNA to DNA. This is called copy DNA or cDNA. This new DNA can then be a template to produce a complement to form a double stranded DNA.
APPLICATION OF GENE TECH:
1. FORENSICS - DNA Finger Printing:
Samples are collected, DNA extracted and and DNA restriction endonuclease (enzyme) is used to fragment the DNA into pieces. Gell electrophoresis is used to separate the pieces; pieces move according to size forming bands, the smaller ones faster than the bigger pieces. Gell can be stained and viewed or processed onto micrographs.
2. Making cDNA
3. Medicine: Making insulin, anticoagulants, factor III blood clotting agents, vaccines, human gene therapy (transferring effective genes to replace defective ones), etc.
4. Agriculture: Plant transformations using Ti plasmids, herbicide resistant plants,
pest resistance - corn, N- fixation in other plants, animal farms - bovine growth
hormones (BHG), cloning, etc.
5. Sequencing the whole or entire human genome - (3000 million base pairs),
fragment by fragment.
Concerns? Playing GOD?? Consumption dangers??? Impacts on the ES???? etc.