Lamas Biology Notes

Unit 1-Most of 6

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Unit 1: Scientific Processes

I. An overview of life

a. Living things are organized

i. Organization of living things begin with the cell

ii. Cells combine to form tissue

iii. Different tissues combine to form organs

iv. Organs work together as organ systems

v. Multicellular Organisms may have many organs

vi. A species in a particular area is a population

vii. The populations in an area make up the community

viii. A community and its physical surroundings is an ecosystem

ix. The biosphere is that part of the earth which can support life; all the ecosystems

b. Living things acquire energy

i. Maintaining organization requires energy

ii. Food provides the nutrient molecules

iii. Energy is the capacity to do work

iv. Metabolism is all the chemical reactions that occur in a cell

v. The sun (photosynthesis) is the ultimate source of energy

vi. Homeostasis is trying to maintain a suitable environment

c. Living things respond

i. Response may result in movement

ii. Ability to respond helps organisms survive

iii. Behavior is all the responses to stimuli

d. Living things reproduce and develop

i. Reproduction is the ability to copy oneself

ii. Reproduction may be sexual or asexual

iii. Organisms develop as a result of instructions encoded in genomes

iv. Genes are long molecules of DNA

e. Living things have adaptations

i. Adaptations are modifications that make organisms suited to a lifestyle

ii. Natural selection is the process by which species become modified

iii. Descent with modifications is another term for evolution

Scientific Methods

I. Collecting Data

a. Data is information that is gathered

b. Observation is the basis for scientific understanding

c. Measuring involves quantitative data

d. Sampling is using a small part to represent a much larger group

e. Organizing data involves putting data in some logical order

i. Diagrams explain words and pictures

1. Are usually line drawings, but can be photographs

2. May tell more at a glance than written material

3. May show things that are not easily seen

ii. Tables show large amounts of data in an organized fashion

iii. Graphs show how one thing changes in relation to another

1. line graphs are the most common

a. easy to construct and east to read

b. line represents a relationship between 2 variables

c. the vertical line is called the y axis

d. the horizontal line is called the x axis

2. Bar graphs use bars to show differences in size or quantity

iv. Charts often show relationships between data

1. Pie charts show proportions of a whole

a. The whole is represented by a circle

b. Segments represent the components

2. Flow charts show a sequential flow of events

a. Describe events in words or simple diagrams with the use of arrows

b. Arrows mean it goes to or becomes

c. Arrows pointing away show diversions

d. An X through an arrow means the path is interrupted

e. Flow charts can be linear or cyclical

i. Linear flow charts begin at one point and end at a different point

ii. Cyclical flow charts begin and end at the same place

II. The Scientific Method

a. Scientific methods is a set of outline procedures to solve a problem

i. State the Problem

ii. Research the problem

iii. Form a hypothesis

iv. Test the hypothesis

v. Draw conclusions

1. If your hypothesis is correct, you have proven your point

2. If your hypothesis is incorrect, your experiment failed

a. Do more experiments

b. What was the procedure?

c. Was the experiment flawed?

d. Form another hypothesis

e. Test new hypothesis

III. Experimentation

a. Factors involved in a good experimental design

i. Proper controls must be included

ii. An experimental group with a variable

iii. A variable is a factor that causes an observable change

iv. The experimental variable is the factor being manipulated

v. The dependent variable is the result of the effects of the experimental value

vi. A control group receives the same treatment as the experimental group except for the variable

vii. Experiments must avoid biases

viii. Experiments must be repeatable

b. The scientific method does not always require experiments

c. Related Phenomena:

i. Phenomena refers to something that is not well understood

ii. Hypothesis is a statement which tries to support science

iii. Theory is a series of hypothesis which support a statement

iv. Inference- a statement supported by many facts; not testable

v. “Principle and Law”- refers to well established theory

1. Cell theory- living things are made up of cells

2. Evolution theory

3. Gene theory

Tools and Metrics

I. Microscopes

a. Compound light is what biologists typically use

i. Limited to about 20000x

ii. Beyond 2000x, resolution suffers

b. Electron Microscope

i. Beams of electrons, instead of light produce and image

ii. Type and use vary

c. Transmission electron microscopes (TEM)- magnify up to 200,000x

d. Scanning electron microscopes(SEM)

i. Provides a striking 3d image

ii. Can magnify 100,000x

e. Dissecting microscopes are commonly used for field biology

f. Other lab tools are mostly dissecting tools

II. Measurement

a. Scientists use the International System(SI) of measurement

b. Base units

i. Meter- length or distance (m)

ii. Gram- mass (g)

iii. Second- time (s)

iv. Ampere- electrical current (A)

v. Kelvin- temperature (k)

vi. Mole- amount of a substance (mol)

vii. Candela- light intensity; lumen (c)

c. Prefixes

i. Giga (g)- Billion

ii. Mega (m)- million

iii. Kilo (k)- thousand

iv. Hecto (h)- hundred

v. Deka (Dk)- 10

vi. Deci (d)- 1/10

vii. Centi (c)- 1/100

viii. Milli (m)-1/1000

d. Other prefixes and suffixes

Prefix	Meaning	Prefix	Meaning	Suffix	Meaning
a or an	not or non.	epi	above	-cyst	pouch
meso	middle	exo	outer, external	-derm	skin, layer
endo	inside, inner	gastro	stomach	-saccharide	sugar
aero	needing oxygen or air	hemo	blood	-itis	inflammation
anti	against.	hetero	different	-logy	study of
arth	joint, jointed	homo	same	-meter	measurement
auto	self	macro	large	-osis	condition
bio	related to life	micro	small	-phase	stage
chloro	green	multi	consisting of many units	-phage	eater
cyto	cell	photo	pertaining to light	-pod	foot
di	double	pre	before	-stasis	stationary condition
mono	singular or one	lipo	pertaining to fat	-lysis	to break
Geo	pertaining to the earth	poly	many	-synthesis	to build or make

e. S.I. derived units often used in biology

i. Area- square meters

ii. Volume- cubic meters

Classification

I. History of taxonomy

a. Aristotle used a two-kingdom system

i. Used common names for classification

ii. Rapid discovery of organisms made system inadequate

iii. Many of the names were misnomers (the name didn’t fit the creature

b. Linnaeus’s System

i. Carolus Linnaeus devised a 2 name system

ii. An organism’s morphology was the main criteria

c. Levels of Classification (taxa)

i. Kingdom- largest unit (Animalia)

ii. Phylum (called a division for plants)- Cordata

iii. Class- mammalian

iv. Order- primates

v. Family- hominidae

vi. Genus- Homo

vii. Species- Homosapiens

d. Catagories below the species

i. Subspecies- variations of a species usually separated geographically

1. Terrapene Carolina- eastern box turtle

2. Terrapene Carolina triunqui- variation of box turtle

ii. Varieties (in plants) breeds(in animals)- variations withing a species

1. Prunus persica- peach

2. Prunus persica nectarine- nectarine

iii. Strains are biochemically dissimilar groups within a species

1. Serrate marcescens D₁

2. Serrate marcescens 911

e. Binomal Nomenclature

i. Linnaeus devised a binomial system of classification

ii. The first part is the genus (capitalized); 2^nd part is the species identifier

iii. Usually describes, honors, or indicates a location

II. Modern Phylogenetic Taxonomy

a. Most taxonomists agree that classification should reflect phylogeny

b. Phylogeny is the evolutionary history of organisms

c. A phylogenic tree shows the relationships

d. The phylogenetic approach is called systematic

e. Systematic

i. Organizes living things in the context of evolution

ii. The fossil record

1. may provide clues to evolution

2. problem with incomplete parts

iii. Morphology

1. Homologous features suggest a common ancestor; same origin; different functions

2. Analogous features have same function; different origin

iv. Embryo development

1. Early patterns of development reflect relationships

2. Blastopore becomes the mouth in protestomes

3. Blastopore becomes the anus in deuterostomes

v. Chromosomes and Macromolecules

1. DNA and RNA nucleotide sequences can be compared

2. Karyotypes are used to study the bonding patterns

3. Amino acid (cytochrome c- protein found in aerobic animals) sequence

III. Cladistics

a. Cladistics uses derived characters to show relationships

b. A derived character is a characteristic that is found only in 1 group

c. Cladograms are ancestry diagrams

IV. The Six Kingdom System

a. Roger Whittaker developed the 5 kingdom system

i. Monera includes the prokaryotes

ii. Eukaryotes are divided into 4 kingdoms

b. The prokaryotes (bacteria) have been divided into 2 kingdoms

c. Archaebacteria

i. Unicellular prokaryotes with distinctive cell membranes

ii. Some are autotrophs which means they create their “food”

iii. Many live in harsh environments

d. Kingdom Eubacteria: used to be class or phylum

i. “true bacteria” that affects us

ii. short generation times allow for rapid change

e. Kingdom Protista

i. Variety of mostly single-celled organisms

ii. All eukaryotes, not plants or animals

iii. Some have both plant and animal characteristics

f. Kingdom Fungi

i. Heterotrophic eukaryotic organisms

ii. Absorb nutrients rather than ingest

g. Kingdom Plantae

i. Most are photoautotroph by photosynthesis

ii. Multicellular eukaryotic organisms

iii. Most live on land

h. Kingdom Animalia

i. Eukaryotic multicellular heterotrophic organisms

ii. Most have symmetrical body organization

iii. Almost all have sexual cycles

V. Three Domain System

a. Molecular biology has led to an alternative to the kingdom system

b. Sequences of ribosomal RNA are used to study relationships

c. Living things then to poing to 3 broad groups

d. Domain archaea- archeobacteria

e. Domain bacteria- eubacteria

f. Domain eukarya includes plants animals protista, and fungi

Unit 2: Energy Flow

Photosynthesis

I. Capturing light energy

a. Light absortion in the chloroplasts

i. The initial reactions of photosynthesis are the light reactions

ii. Thylakoids are the membranes with the pigments

iii. Grana are stacks of thylakoids

iv. Stroma is a protein rich solution where the grana are embedded

b. Light and pigments

i. To understand photosynthesis, you must understand the properties of light

1. Light travels in waves

2. Light can be measured in terms of wave lengths

3. Different colors in the spectrum have different wavelengths

4. A photon is a packet of energy

a. shorter wavelengths have more energy

b. longer wavelengths have less energy

ii. Chloroplast Pigments

1. A pigment is a compound that absorbs light

2. Chlorophyll is the most important pigment

3. Only “Chlorophyll A” is directly involved in the light reactions

4. Other Chlorophyll, and other pigments are called accessory pigments

a. Carotenoids provide the fall colors

b. Phycobilins in Rodophyla allow the red algae to survive at great depths

c. Electron Transport

i. Pigments are grouped in clusters (photosystems) in the thylakoids

ii. Photosystem II acts as an antenna

1. Accessory pigments channel the energy to chlorophyll a

2. Excited chlorophyll molecules lose electrons

iii. Electron transport chain is on the Thylakoid membrane

1. Act as runners in moving the chlorophyll

2. Electrons are moved to photosystem I

iv. Photosystem I

1. Receives electrons from photosystem II

2. Also processes light

3. Electrons from Photosystem I replace those from Photosystem II

4. A different electron transport chain is used

5. Protons are produced by the splitting of water inside the thylakoids; The protons are used to create a gradient

6. Molecules are transported to the inside of the thylakoids

7. ATP synthase forces the electrons out of the reaction center

d. The light reactions transform the light energy and produces energy in the form of ATP and NADPH

e. The energy stored in the bonds will produce glucose

II. The Calvin Cycle

a. ATP and NADPH will be used to produce organic compounds

b. In the Calvin cycle, atoms from CO₂ are fixed into organic compounds

c. Calvin Cycle occurs within the stroma

d. Carbon fixation by the Calvin cycle requires 3 steps

i. CO₂ diffuses into the stroma and produces a compound called PGA

ii. PGA is converted into PGAL

iii. Most of the PGAL will be used to power the Calvin Cycle

e. PGAL and other molecules in the Calvin Cycle will be built into a variety of compounds

III. Alternative Pathways

a. Calvin cycle is the most common pathway

b. Plants who use the Calvin cycle are called C₃ plants

c. C₄ Pathway

i. Fixes CO₂ into 4 carbon compounds

ii. C₄ plants partially close their stomata during the day

iii. Requires high temperature and high light intensity

iv. Corn, sugarcane, and crab grass are examples

d. Cam Pathway

i. Open their stomata at night, and close it during the day

ii. They grow fairly slowly

iii. They lose less water that the C₃ and C₄

iv. Cacti and pineapple are examples.

Cellular Respiration

I. Glycolysis and Fermentation

a. Harvesting Chemical Energy

i. Autotrophs convert light enerdy into chemical energy

ii. Both autotrophs and heterotrophs have a need for organic compounds

iii. ATP is the currency of the cell

iv. Glycolysis begins the process of respiration

v. Products of glycolysis may enter aerobic or anaerobic pathways

b. Glycolysis

i. In glycolysis, glucose is oxidized into pyrubic acid

ii. All of the reactions take place in the cytosol

iii. Glycolysis results in a net production of 2 ATP’s

iv. Glycolysis is an anaerobic pathway

c. Fermentation: anaerobic repiration

i. Occurs in the absence of Oxygen

ii. Fermentation pathways do not produce ATP

iii. Fermentation generate NAD

iv. Lactic acid fermentation converts pyrubic acid into Lactic Acid

1. NAD+ in lactic acid keeps the glycolysis going

2. Important in the production of yogurt and cheese

3. Also occurs in the muscles during strenuous exercise

a. Oxygen is not delivered fast enough to the cells

b. An oxygen debt develops

c. Muscle cells switch from aerobic to lactic acid fermentation

d. Acidity reduces the ability of the cells to contract

e. Results in fatigue, pain and cramps

v. In alcoholic fermentation, pyruvic acid is converted to Ethyl Alcohol

1. The basis of the wine and beer industry

2. Yeast cells are added to provide enzymes

3. Bread making depends on fermentation mostly

a. CO₂ produced by fermentation causes the bread to rise

d. Energy Yield

i. Anaerobic pathways are not efficient

ii. About 3.5% of the energy in glucose is used

iii. Anaerobic pathways probably evolved early in the history of the earth

iv. Organisms with this pathway have limited energy requirements

v. Large organisms need more efficient pathways

II. Aerobic Respiration

a. Summary of Aerobic Respiration

i. It occurs in 2 phases; KREBs Cycles and Electron Transport Chain

ii. Reactions take place in the mitochondria

iii. Pyruvic acid from glycolysis diffuses into the mitochondria

iv. The inner membrane of the mitochondria has folds called christae

v. The matrix is the space inside the folds

vi. The matrix has the enzymes needed for the KREBs cycle

b. The KREBs cycle

i. The oxidation of glucose is completed

ii. The NAD+ is reduced to NADH

iii. A small amount of ATP is produced

iv. All the reactions occur in the matrix

v. Only two net ATPs are generated

c. Electron Transport Chain

i. Most of ATP production occurs here

ii. Electrons from the KREB cycle are moved to the electron transport chain

iii. Process occurs in the cristae of the mitochondria

d. Energy Yield

i. 30-32 ATPs are produced

ii. About 50% efficiency

iii. Provide ATP’s for all cellular activity

iv. Also provides skeletons for larger molecules in the cells

Energy Transformations

I. Thermodynamics: Energy Laws

a. Thermodynamics is the study of the relationships of energy forms

i. Every reaction is accompanied by transformation of energy

ii. Kinetics is the study of the rates of reactions

iii. Thermodynamics tells us what a reaction will do

iv. The first law states that the amount of energy is constant

v. The second law states that energy available to do work decreases

b. Work

i. Work is the movement of an object against a force

ii. Work can be stored

iii. Work is stored as potential energy

iv. Kinetic energy is the energy of moving objects

v. Rearranging atoms in a reaction is work

vi. ATP has potential energy to do work

vii. Food energy is typically measured in calories

viii. Formation of chemical bonds releases energy

ix. Breaking of chemical bonds consumes energy

x. Free energy is available to do work

1. Exergonic reactions release energy

2. Endergonic reactions consume energy

3. Many reactions are coupled

xi. The splitting of ATP provides almost all cellular energy

xii. Entropy refers to organized energy

II. Metabolism and Enzymes

a. Metabolism refers to all the reactions in your cell

i. Activation energy is the minimum energy needed for a process to occur

ii. A catalyst is a substance that lowers activation energy

iii. An enzyme (usually a protein) is a biological catalyst

iv. Speeding up reactions is essential for life

b. How enzymes work

i. Enzymes bind to reacting molecules called substrates

ii. A substrate is the reactant being acted upon

iii. An active site is where the enzyme binds to the substance

iv. An induced fit is changes in the enzyme

v. Enzymes are highly specific

vi. Enzymes can be used over and over

c. Factors affecting enzymes

i. Enzymes work most efficiently at a certain pH

ii. A temperature increase will increase the rate of the reaction

iii. Too high a temperature can cass the protein denature (be unmade)

iv. Most human enzymes work at a pH of 6-8

v. Organisms adjust their metabolisms with the use of enzymes

III. Biomolecules of Life

a. Organic Compounds

i. Organic compounds refer to all carbon containing compounds

ii. Polymers are compounds made up of repeating units

iii. The repeating units are called monomers

iv. Most carbon based monomers are simple and universal

v. Most biological structures are made up of about 35 molecules

vi. The small number of molecule suggest a common origin

vii. Condensation is the process by which monomers form polymers

viii. Hydrolysis is the process of breaking a polymer into monomers

b. Functional Groups

i. Functional groups are clusters of atoms which have certain properties

ii. A small number of functional groups determine many properties

1. Hydroxyl Group (OH-)- very common; hydrophilic

2. Carboxyl group (COOH) found in amino acids and lipids

3. The amino group (NH₂) have bad smell

c. Carbohydrates (sugars)

i. Composed of carbon, hydrogen, and oxygen

ii. Important energy storage molecules

iii. Monosaccharide are monomers (simple sugars)

1. Glucose- most common simple sugar

2. Fructose- sweetest simple sugar

3. Galactose- simple sugar in milk

4. Ribose- simple sugar in RNA

5. Deoxyribose- simple sugar in DNA

6. Isomers- compounds with the same chemical formula, but different structural formula

iv. Disaccharides are double sugars

1. sucrose- sugar found in sugar cane

2. lactose- double sugar in milk (made of galactose and glucose)

3. Maltose- double sugar in grain

v. Polysaccharides are complex sugars

1. Starch- how plants store carbohydrates

2. cellulose- structural sugar in plants (make up the cell wall)

3. chitin- structural sugar in the exoskeleton of arthropods

4. glycogen- how animals store starch

d. Lipids

i. Main reservoirs of stored energy of animals

ii. Fatty acids are the monomers

iii. Generally they don’t dissolve in water

iv. In saturated fats, each carbon is bonded to its full potential

v. In unsaturated fats, carbon atoms are not bonded to the maximum

vi. Triglycerides are composed of 3 molecules of fatty acids

1. Fat (saturated triglycerides) is solid at room temperature

2. Oil (unsaturated triglycerides) is liquid at room temperature

vii. Phospholipids have 2 fatty acids joined by glysonal

1. Cell membrane is made up mostly of phospholipids

viii. Wax has a long chain of fatty acids

1. waxes are highly waterproof

2. form protective layers in plants and animals

ix. Steroids are composed of carbon rings

1. Sex hormones are steroid compounds

2. Cholesterol is needed for cells to function normally

3. Anabolic steroids can create problems

e. Proteins

i. 20 amino acids make up the monomers

ii. Proteins are the most diverse of organic compounds

iii. Peptide is a bond that forms between amino acids

iv. Enzymes are proteins that act as catalysts

v. Functions include:

1. Structural- feathers; webs; calogen

2. Transport- hemoglobin (carries oxygen through the blood)

3. Communication- hormones

4. Nutrition- milk, eggs

5. Weapons- antibodies

vi. Levels of Structure

1. Primary structure is the sequence of amino acids

2. Secondary structure has to do with the folding and bending of polypeptides

a. Alpha helix- coils

b. Folds

3. Tertiary structure is the 3d view of a polypeptide(at least 3 polypeptides can make up a protein)

4. Quartenary structure is the polypeptides which make up a protein

vii. Shape and structure determine the function of a protein

viii. Denaturing can destroy a protein

f. Nucleic Acids

i. Nucleotides are the monomers

ii. DNA and RNA are the basis for inheritance

iii. DNA is a double helix strand of nucleotides

1. Hydrogen bonding holds the bases together

2. Genetic information is coded in the base sequence

3. Sequence of bases is unique for each species

iv. RNA occurs as a single strand of nucleotides

1. There are different types

2. It is involved in protein synthesis

Unit 3: Cell Biology

Cell Structure and Function

I. Cell Theory

a. Cells conform to the definitions of life

i. Cells are highly organized

ii. Cells obtain energy in materials from food

iii. Cells change through time

iv. Cells respond to the environment

v. Cells reproduce

b. Cell Theory Statements

i. All organisms are made up of cells

ii. Cells are the basic unit of ogrinization

iii. All cells come from pre-existing cells

c. Contributions to the cell theory

i. Robert Hooke- gave us the word cell

ii. Leeuwenhoek- first to describe microorganisms

iii. Robert Brown- discovered nucleus

iv. Schleiden- said plants were made of cells

v. Schwann- said animals were made of cells

vi. Virchow said cells come from pre existing cells

d. Cell diversity

i. Size- cells are limited in size because the volume increases faster than the surface area

ii. Shape reflects the diversity and function

iii. Prokaryotes have different cell structure

1. no nucleus; just nucleoid

2. no membranes around the organelles

II. Eukaryotic cell structure

a. Cytoplasm is the area between the cell membrane and nucleus

i. Cytosol is the cytoplasm that is outside the organelles

ii. Cytosol makes up 50% of the cells volume

iii. Cytosol contains enzymes, glycogen, fat, etc

iv. Organelles, vesicles, and vacuoles are all embedded in the cytosol

b. The nucleus contains the genetic instructions

i. Nuclear envelope is a double membrane

ii. Nuclear pores form channels between the nucleoplasm and the cytoplasm

iii. Chromatin is a complex of DNA in proteins; Chromatin becomes chromosomes

c. Ribosomes are complexes if RNA in proteins

i. Involved in protein synthase

ii. Ribosomes in the cytoplasm are called free

d. Endplasmic Reticulum is a network of interconnected channels

i. The E.R. is made up of rough E.R. and smooth E.R.

ii. The E.R. membrane is a network of interconnected channels

iii. The E.R. makes up more than half of all the membrane in the cell

iv. The rough E.R. has many ribosomes

1. Mostly devoted to modifying proteins

2. Cells specialized for making proteins have a lot of rouch E.R.

v. Smooth E.R. has no ribosomes

1. Involved primarily in breaking down lipids

2. Also detoxifies substances in liver like alcohol

e. Golgi complex packages and labels proteins

i. Found near the nucleus

ii. Proteins are packaged in vesicles

f. Lysosomes contain enzymes for cell digestion

i. Vary is size, but all have enzymes

ii. Cells that perform phagocytosis(use white blood cells) have many lysosomes

iii. Lysosomes form in the golgi complex

g. Perioxisomes contain enzymes that break down Hydrogen Peroxide

i. Hydrogen Peroxide is very reactive and can damage the cell

ii. Catalase is perioxisomes break down Hydrogen Peroxide

iii. Abundant in cells that break down lipids

h. Mitochodria produces the energy and the cells

i. Have their own DNA

ii. ATP provides the energy for the cell

iii. It has internal and external membranes

1. The outer membrane is smooth

2. The inner membrane has folds called christae

iv. Cells that use lots of energy have many mitochondria

i. Plastids are organelles surrounded by double membranes

i. Chloroplasts is the place for photosynthesis

1. chloroplasts like mitochondria have their own DNA

2. Convert light energy in to chemical

3. Chlorophyll gives them their green color

ii. Chromoplasts contain the color pigments

1. Arise from chloroplasts- (began as chloroplasts)

2. Are revealed in autumn leaves when the chlorophyll breaks down

iii. Amyoplasts are placids that store starch

iv. Cell wall provides structural support

j. The cytoskeleton is the skeletal system for the cell

i. It is a complex of protein filaments

ii. It is constantly dissolving and reforming

iii. The cytoskeleton us made of 3 types of filaments

1. Microtubules are hollow cylinders that move DNA

2. Actin filaments are anchored to the cell surface and allow for flexibility

3. Intermediate filaments are fiberous protein

a. Keratin is found in hair, finger nails, and skin

b. All intermediate filaments are subject to mechanical stress

III. Cell structure Specializations

a. Plasmodesmata are the tiny channel that connect the cytoplasm of adjacent plan cells together

b. Tight junctions link the cells

i. Seal adjoining cells make them leak proof

c. Adhering junctions allow stretching to occur

d. Gap junction allow for cells to communicate

Homeostasis and Transport

I. Membrane Structure and Function

a. Membranes sever four basic functions

i. Boundaries that separate the inside and outside of the cell

ii. Regulate the contents of the space they enclose

iii. Serve as a “workbench” for reactions

iv. Participate in energy conversion

b. Cell membrane Composition

i. The fluid mosaic model describes the cell membrane

ii. The basic structure of membrane is a lipid bilayer

iii. The two layers differ slightly

iv. The lipid bilayer serves as a barrier to keep molecules inside the cell

v. Proteins are dispersed throughout the membrane

vi. Some membrane proteins help transport specific substances

vii. The membrane is fluid (lipids and proteins move around freely)

c. Passive Transport requires no energy

i. In simple diffusion, molecules go from a lighter to a lower energy

1. Movement is always in response to a gradient

2. Rate of diffusion will vary

3. Concentration gradients are temporary

ii. Osmosis is the movement of water through the membrane

1. The resulting force is called osmotic pressure

2. Physical pressure is exerted by the membrane counters the osmotic pressure

3. The difference between osmotic pressure and the physical pressure is called water potential

iii. Cells respond to environments created by the water potential

1. Isotonic- equal concentration of water inside and outside the cell

2. Hypotonic is the inflow of water molecules (There is more outside)

a. Cytosis is the bursting of an animal cell

b. Turgor pressure is the build up of water pressure against the cell wall

3. Hypotonic- outflow of water molecules (There is more water inside than outside)

iv. Facilitated diffusion accelerates passive transport

1. Carrier molecules bind with substances

2. Channel proteins form passage ways for certain molecules to go through

3. Receptor proteins form passageways for certain molecules to go through

4. Glycorecognition proteins supply tissues

d. Active Transport moves molecules against a gradient

i. The sodium potassium pump is an example of passive transport

1. Sodium ions are transported out

2. Potassium ions are transported in

ii. Uses ATP as energy

e. Membrane interaction

i. Membrane fusion allows the update of macromolecules

ii. In endocytosis, particles are brought into the cell

1. The membrane pinches and forms a vesicle

2. The vesicle travels into the cell’s interior

iii. There are three types of endocytosis

1. Phagocytosis- involves solid particles

2. Pinocytosis involves liquids

3. Receptor-mediated endocytosis takes up only specific substances

iv. In exocytosis, molecules are exported by the cell

1. Molecules exported are surrounded by vesicles

2. The then fuse with the plasma membrane

3. the vesicles (membranes) are provided by the golgi apparatus

Cell Reproduction

I. Chromosomes

a. Chromosome Structure

i. Rod-shaped structures made up of DNA and proteins

ii. Histones are proteins that provide the framework for chromosomes

iii. Nonhistones are involved in controlling specific areas of the DNA

iv. Chromatids?????

v. Centromere is the center which holds the chromatids together

vi. Prokaryotes have a single circular chromosomes

b. Chromosome Numbers

i. Each species has a characteristic number of chromosomes

ii. Sex chromosomes determine the sex of the organism

1. They may also carry other traits

2. Sex chromosomes are X&Y

iii. Autosomes are the non-sex chromosomes

1. Cells produced by asexual reproduction have 2 copies of each autosome

2. Homologous chromosomes(homologues)- a pair of identical chromosomes

iv. Karyotype is a map or picture of the chromosomes

v. Diploid refers to a cell with a full set of chromosomes

1. somatic (body cells) are diploid

2. 2n is an abbreviation for diploid

vi. Haploid refers to a cell with half of the chromosome number

1. Sperm and egg cells are haploid

2. 1n is the abbreviation of haploid

II. The Cell Cycle

a. Binary fusion us a diversion of a prokaryiotic cells

b. In eukaryotes, there are 2 types of cell division

i. Mitosis results in new cells that are identical

ii. Meiosis reduces the chromosome number to half

c. The cell cycle is the events in the life cycle of a cell

d. Interphase is where a cell spends most of its life

i. G₁ phase- the cells grow to their normal size

ii. S phase- DNA replication occurs

iii. G₂ phase- cells prepares for cell division

iv. G₀ phase- cells that don’t replicate spend their time here (muscles cells and nerve cells are examples)

III. Mitosis

a. Mistosis is the division of the nucleus

b. Mitosis is a continuous process

c. Prophase is the first phase

i. The chromatin is converted into chromosomes

ii. The mitotic spindle begins to develop

iii. Centrioles form at the poles

iv. Nuclear membrane disappears

v. Chromosomes attach to the spindle

d. Metaphase is when the chromosomes line up along the equator

e. Anaphase is when the chromosomes split in half

i. Each chromatid is attached to a kinetichore fiber

ii. The chromosomes move toward the poles

iii. The microtubules lengthen and shorten to pull the chromosomes

f. Telephase concludes mitosis

i. Chromosomes revert to chromatins

ii. Nuclear membranes form around the 2 daughter cells

iii. Nucleoli become visible

IV. Cytokinesis

a. Cytokinesis divides the cytoplasm

i. Actin filaments form a ring during anaphase

ii. A cleavage furrow forms

iii. By the end of telephase, the daughter cells are almost completely separate

b. Cytokines in plants utilizes a cell plate

i. The cell wall of plants prevents the cell from pinching into 2

ii. A new cell is built next to the cell plate

iii. The cell plate is produced during telephase

c. Cytokinesis is a distinct phase from mitosis

V. Meiosis

a. Meiosis enables sex cells to be produced

b. The first division is Meiosis I

i. Chromosomes are replicated in the S phase

ii. Prophase I is the most time consuming phase

1. chromosomes condense

2. nuclear membrane disappears

3. spindle apparatus forms

4. homologous chromosomes pair up

5. the four sister chromatids form a tetrad

6. crossing over occurs when you have an exchange of genes between chromatids

7. Chiasma is where the crossing over takes place

iii. In metaphase I, the tetrads gather at the equator

iv. In Anaphase I, the tetrads separate and chromosomes go to opposite poles

v. Telophase and cytokinesis occur rapidly

c. The second division is Meiosis II

i. Chromosomes are not replicated

ii. Prophase II is short since the chromosomes are already there

iii. In metaphase II, the chromosomes line up the equator

iv. In anaphase II, the chromosomes are split in half and go to opposite poles

v. In telophase II, the nuclear membrane reforms and 4 haploid daughter cells are produced

d. If chromosomes don not migrate properly in anaphase, you might have nondisjunction

e. Formation of gametes

i. Spermatogenesis is the production of sperm

1. A diploid reproductive cell divides and forms 4 haploid cells called spermatids

2. each spematid develops into a sperm cell

ii. Oogenesis is the production of egg cells

1. The diploid reproductive cells split and produce 1 egg

2. during cytokinesis I and II, the cytoplasm is unequally divided

3. Polar bodies are the egg cells that receive little or no cytoplasm

f. Asexual reproduction

i. Are genetically identical to the parent

ii. Mutations are the main source of variation

g. Sexual reproduction is favored since it gives your variety

Unit 4: Genetics

Gene Expression

I. Overview

a. DNA controls the production of proteins

b. Replication provides information for the cells

c. Mutations in DNA provide variety

d. DNA is the source for diversity

e. DNA serves as a template for RNA

f. The genetic codes is universal

g. The genetic code can be manipulated

II. The genetic material(DNA- RNA)

a. Structure of DNA

i. DNA is made up of subunits of nucleotides

ii. Each nucleotide is made up of 3 things

1. A phosphate group

2. Deoxyribose- 5 carbon sugar

3. 4 nitrogen bases

a. Adenine

b. Guanine

c. Cytosine

d. Thymine

4. The bases are complementary

5. A and G are purines

6. C and T are pyramides

iii. DNA is a double helix

b. How DNA is copied

i. Complementary strands of DNA serve as templates

ii. Replication is the duplication of DNA

iii. Enzymes called helecase unzip DNA

iv. Additional enzymes keep the strands open

v. A replication form is the point at which the double helix splits

vi. DNA polymerase (enzyme) helps new basis to unite

vii. The polymerase enzymes remain attached until the signal tells them to let go

viii. In the course of DNA replication, few errors are made

ix. DNA polymerase has a proofreading role

x. Proofreading prevents most errors

xi. An error in DNA occurs in about 1 nucleotide in a billion

xii. Replication is a simultaneous process

xiii. Human DNA is copied in segments of about 100,000 nucleotides

c. From Gene to Proteins

i. The path to get genetic information

1. Proteins are not built directly by genes

2. the working instructions are in RNA

ii. RNA, like DNA is a nucleic acid

1. RNA consists of a single strand

2. ribose is the 5 carbon sugar

3. Uracil is the base that replaces Thymine

iii. RNA is present in three forms

1. mRNA is involved in transcription

2. tRNA is involved in translation

3. rRNA makes up part of the ribose

iv. All 3 are involved in protein synthesis

v. Gene expression (making proteins) occurs in 2 stages

1. transcription is the copying of DNA by mRNA

2. translation is information in mRNA which is used to make proteins

d. Transcription: Making RNA

i. Transcription is the process of copying DNA

ii. Transcription begins with RNA polymerase

1. RNA polymerase binds to a piece of DNA

2. A promoter is a specific piece of DNA

3. the enzyme unwinds and separates the DNA

4. in transcription, only 1 strand is copied

5. RNA polymerase moves along like a train on tracks

6. Transcription proceeds at about 60 nucleotides

7. A terminator is a sequence of bases that stops the RNA polymerase

8. the promoter is further subdivided into codons

iii. Processing mRNA

1. mRNA must interprate from DNA

2. Introns and exons are coded into mRNA

a. Introns are non-coding areas of DNA

b. Exons are the coding regions

3. Before mRNA leaves the nucleus, the introns are deleted

4. The exons are joined together to make a single molecule of mRNA

iv. The genetic code:

1. after transcription, mRNA leaves the nucleus

2. the instructions are carried in codons

3. each codon represents amino acids

4. there are 64 possible codon combinations

5. there are 20 amino acids

6. the genetic code is universal

e. Translation: making proteins

I. Control of gene expression

a. Gene expression is the activation of a gene that results in a protein

i. A gene is expressed when transcription occurs

ii. Mechanisms have evolved to make sure the proteins are produced when needed

b. The genome is the complete genetic makeup of an organism

i. By regulating genes, the cell controls what part of the genome will be expressed

ii. Gene expression occurs in 2 parts

1. Transcription

2. Translation

II. Gene expression in prokaryotes

a. Gene expression was first studied in prokaryotes

i. Escherichia coli is an intestinal bacteria

ii. Lactose provides energy for E-Coli

iii. Three enzymes split lactose into glucose and galactose

iv. Three regulatory elements control enzyme production

1. structural genes- code for a polypeptide

2. promoter is a DNA segment that recognizes RNA polymerase

3. operator is a DNA protein that blocks transcription

v. Lac operon is the name of all 3 of these

vi. Activation of the segments control gene expression

b. Gene Expression (Lac operon) has 2 forms

i. Repression

1. In the absence of lactose, a protein attaches to the operator

2. A repressor protein inhibits a protein from being produced

3. the repressor on the operator keeps RNA polymerase from transcribing

4. this is called repression

5. a regulator gene makes repressors

ii. Activation

1. Where lactose is, it binds to the repressor

2. Removal of the repressor allows for the RNA polymerase to transcribe

3. Lactose acts as the inducer (gets the block out of the way)

4. An inducer is a molecule that starts gene expression

5. Activation is the initiation of transcription

III. Gene Expression in Eukaryotes

a. Eukaryotes have much larger genomes

b. Operons have not been found in Eukaryotes

c. In eukaryotes, gene expression is related to the coiling and uncoiling of DNA

i. Histones allow the DNA to form chromosomes

ii. Euchromatin is uncoiled DNA (site of transcription)

iii. Both introns and exons are transcribed

iv. Pre-mRNA includes the exons and introns

v. Called mRNA when the introns are deleted

d. Enhancer control

i. An enhancer is a non-coiling control sequence in a gene

ii. The enhancer must be activated for genes to be expressed

iii. Transcription factors are additional proteins that regulate transcription

Medelian Genetics

I. Objectives

a. Describe the blending theory

b. Describe Mendel’s work

c. Describe monohybrid and dihybrid crosses

II. Overview

a. Organisms produce their own kind

b. Offspring rarely resemble each parent exactly

c. Laws of heredity explain inheritance

d. Gregor Mendel discovered how traits were passed

e. Genetics is the study of inheritance

III. Introducing Gregor Mendel

a. He had a math and science background

b. The blending theory was the most believed

i. Both sexes contribute equally

ii. Offspring had an intermediate look

iii. Mendel’s work supported Darwin’s ideas of evolution

iv. Darwin was a contemporary of Mendel

c. Mendel used pea plants for his studies

i. Have a short generation time

ii. Can be cross-pollinated, or self-pollinated

iii. Mendel developed 14 pure lines

iv. He developed 7 contrasting traits

IV. Mendel did a monohybrid cross

a. Mendel preformed a cross between 2 pure lines

i. Called it a monohybrid cross; results are hybrid

ii. Crossed tall plants with short

iii. Mendel called this the F₁ generation

iv. The first generation were produced by cross pollination

v. Reciprocal crosses were performed

vi. All F₁ were tall

vii. Question: What happened to the short ones?

viii. F₁ were allowed to self pollinate

ix. F₂ had tall and short offspring

x. Resulted in Mendel’s laws/principles

1. Traits are inherited independently from each other

2. factors segregate during meiosis

b. Modern genetics has an answer for Mendel’s work

i. Each trait is controlled by 2 alleles

ii. An allele is an alternative form of a gene

iii. Dominant allele (T) is the dominant trait (it shows up)

iv. Recessive allele(t) is the masked trait

v. Gene locus is the location of a gene on a chromosome

vi. Process of meiosis may allow for genes to change locus

vii. Homozygous (TT or tt) 2 similar alleles form a trait

viii. Heterozygous (hybrid Tt)

1. the allele that is dominant will control the trait

2. the allele not expressed is recessive

c. Genotype vs. Phenotype

i. Genotype refers to the genetic make up of an organism

1. TT is the dominant genotype

2. tt is the recessive genotype

3. Tt will show the dominant phenotype

ii. Phenotype refers to the outward appearance

1. TT and Tt will show the dominant phenotype

2. tt shows the recessive phenotype

d. The punnet square is a diagram which shows probability

i. The sperm types are usually on the top

ii. The egg types are on the sides

	Tt	Tt
Tt	TT	TT
Tt	TT	TT

e. Mendel did a dihyrbid cross

i. Dihyrbrid crosses use two pairs of contrasting traits

ii. There are 16 boxes in the punet square

iii. Supports Mendel’s theory of segregation

iv. Incomplete dominance- 2 dominant alleles contribute to the phenotype

v. Codominance- both alleles are fully expressed

DNA Technology

I. The New Genetics

a. Manipulating Genes

i. DNA technology is genetic engineering

ii. DNA technology can be used to treat disease and improve crops

iii. DNA molecule is a sequence of nucleotides

iv. Restriction enzymes are bacterial enzymes that cut DNA

v. A cloning vector is a carrier used to take a gene from one organism to another

vi. A plasmid is a ring of DNA in a bacterium

1. A donor gene is spliced into the plasmid

2. Plasmid is returned to bacteria

3. A gene copy is produced

4. the plasmid can be used to transfer the gene again

b. Transplanting genes

i. Plasmids can be used to clone genes

ii. Insulin is an example

1. Restriction enzymes were used to cut the insulin proteins

2. genomic library is a our sets of DNA fragments

iii. Recombinant DNA is a combination of DNA from 2 or more sources

iv. Transgenic organism is the host receiving the recombinant DNA

c. Expression of Cloned Genes

i. Genes are often turned on and off until the proteins are needed

ii. The sequences (promoters) in the foreign gene are also transferred

II. DNA technology techniques

a. DNA fingerprints

i. A DNA fingerprint is a pattern of bonds made up of specific DNA fragments

1. may indicate is someone is related

2. Show if different species are related

3. May be used to solve a crime

ii. RFLP analysis is the process by which DNA fingerprinting is done

iii. Number and length of each fragment varies from person to person

iv. Gel electrophoresis is the technique that is used to provide the bonding

v. DNA fingerprinting (bands) can be analyzed visually or digitally

vi. Fingerprints are very accurate

vii. PCR can be used to make many copies of DNA when only a small sample is available

b. The Human genome Project

i. Goal is to determine nucleotide sequence in humans

ii. There are about 31,000 genes

iii. To see how genome is organized

iv. May help diagnosis treatment and cures

v. Gene therapy is introducing a gene to a cell to correct a defect

vi. Many ethical decisions will be involved

III. Practical uses of DNA technology

a. Producing Pharmaceutical Products

i. Many medicines use proteins

ii. Insulin is a product of DNA technology

iii. Interferon are used to treat viral infections

b. Genetically Engineered Vaccines

i. Vaccines are solutions that may contain a harmless form of a virus

ii. A virus’ surface protein can be put into a harmless virus to provide immunity

iii. The genome of a pathogen can be altered

c. Increasing agricultural yields

i. DNA technology can produce different strains

ii. Te help plants fertilize themselves

d. Safety and environmental issues

i. Several agencies regulate genetic engineering(i.e FDA, USDA, EPA, etc)

ii. Some people worry that genetically produced food may be harmful

iii. Genetically engineered tomatoes have a gene that prolongs their shelf life

iv. Fears of genetically engineered crops wiping out native plant species

IV. Human Genetics

a. Work done on other organisms have relevance to us

b. Understanding human genetics is important to your children

c. Counting chromosomes

i. Nondisjunction causes abnormalities

1. Nondisjuntcion is whent eh homologues don’t separate properly

2. Many trisomies and nearly all monosomies are fatal

a. Trisomy 18 (Edward’s syndrome)- heart and nervous disorders

b. Trisomy 21- Down’s Syndrome

i. Three copies of chromosomes 21

ii. Chances of death inclease drastically till the age of 40

iii. Translocation 21 is not related

iv. Characteristics include round face, slanting eyelids, and mental retardation

ii. X and Y numbers also change

1. Sex chromosome abnormalities may occur

2. XYY (males) with 24 chromosomes

a. Taller than average and suffer persistent acne

b. Have barely normal intelligence

c. Suggested that they are chemically aggressive

3. XO (female) Turner Syndrome

a. Has only 1 sex chromosome

b. Short and have a broad chest

c. The ovaries never become functional

d. Do not undergo puberty

4. XXY (male) Klinefelter’s syndrome

a. Has two or more X chromosomes

b. Sterile males with underdeveloped testes

c. Abnormalities are not apparent until puberty

5. XXX (female) Metafemale

a. More than 2 X chromosomes

b. Would seem to be very feminine

c. May have menstrual irregularities

d. Considering autosomal traits

i. Individuals receive pairs of chromosomes

ii. Individuals also receive pairs of alleles

iii. Many common traits are controlled by dominant alleles

iv. There are patterns of inheritance

1. An AA or Aa will have this disorder

2. If the disorder is recessive, aa will have it

v. Genetic counselors construct pedigree charts to find certain traits

1. pedigree charts show the pattern of inheritance

a. Males are designated by squares

b. Females are designated by circles

c. Shaded circles and squares

i. Half shaded are the heterozygous (carriers)

ii. Full shaded have the traits

d. A line between a square and circle represent a union

e. A vertical line down represents a single child

f. If more than one child, they are placed on a horizontal line

2. Females are usually carriers

vi. Some disorders are dominant

1. Neurofibromatosis (1:3000)

a. Have large spots on skin

b. Gene is on chromosome 17

2. Huntington disease (1:20000)

a. Neurological disorder

b. Leads to progressive degrading of the brain

c. Symptoms normally appear at middle age

d. No effective treatment

e. Gene is located on chromosome 4

3. Sickle cell is partially dominant

a. Disorder is controlled by incomplete dominant alleles

i. AA- normal red blood cells

ii. AA’- both type of red blood cells

iii. A’A’- have only sickle cells

b. Adaptation to malaria

Unit 5: Evolution

Overview of Evolution

I. Evidence for Evolution

a. Darwin called evolution descent with modification

b. Darwin’s ideas were based on 4 principles

i. The world is old an always changing

ii. Recognized that species change

iii. Said species were made up of populations of individuals

iv. Argued that every species descended from a common ancestor

c. Darwin believed many changes were adaptive

d. Not everyone agrees with Darwin’s theory

i. In conflict with biblical accounts

ii. Conflicted with Plato’s view of the world

e. Evolutionary ideas were not unique to Darwin

i. Linnaeus’s system of Taxonomy supports evolution

ii. Darwin’s grandfather proposed evolution

iii. Cuvier proposed extinction as the reason for diversity

iv. Lamarck proposed the inheritance of acquired traits

v. Wallace developed a theory based on natural selection

II. Fossils and Geologic time

a. Terms and concepts

i. Fossils are evidence of past life

ii. Fossil record provides an evolutionary view string of the world

iii. Geologic time divides the history of the earth into units of time

iv. Units of geologic time

1. Eras are the largest; there are 4 of them

2. Periods are intermediate units

3. Epochs are the smallest units of time

v. Fossil dating is used to construct geologic time

1. Relative age is the position of the fossil in sedimentary rock

2. absolute age is the approximate age of the fossil

vi. Radioactive isotopes are used to determine absolute age

1. Carbon-14 is used to date young fossils (14-50 thousand years)

2. Uranium-238 is used to very old fossils

vii. Microevolution refers to changes in a species over a brief period of geologic time

viii. Macroevolution is revolutionary events which occur to a group of species over a longer period of time

b. Geologic time

i. Precambrian (570-4600 million years ago)

1. Largest era: 90% of the history of the earth

2. Prokaryotes appear about 3.8 billion years ago

3. First eukaryotes appear about 2 billion years ago

4. Multicellular organisms appear by the end of the era

5. Few fossils because of the soft body parts

ii. Paleozoic Era (245- 570 million years ago)

1. Cambrian period

a. Marine algae flourish

b. Invertebrates dominate

c. Fungi evolve

2. Ordovician Period

a. Marine algae continue to flourish

b. Invertebrates radiate and diversify

c. Jawless fish are the first vertebrates to appear

3. Silurian Period

a. First evidence of life on land

b. Vascular plants appear

c. Mass extinction of intertebrates

d. Jawed fish appear

4. Devonian Period (Age of Fish)

a. Seed ferns appear

b. Jawed fish flourish

c. First insects appear

d. First amphibians appear

e. Mass extinctions occur

5. Carboniferous Period (Age of Amphibians)

a. Great coal-forming forests flourish

b. Amphibians diversify

c. First reptiles appear

d. Great radiation of insects

6. Permian period

a. Conifers appear

b. Reptiles diversify

c. Amphibians decline

d. Mass extinctions

iii. Mesozoic Era (Age of Reptiles) 66- 245 million years ago

1. Triassic period

a. Gymnosperms and ferns dominate

b. First dinosaurs appear

c. First mammals appear

d. Corals and mollusks dominate the seas

e. Mass extinctions

2. Jurassic Period

a. Cycads and other gymnosperms flourish

b. Dinosaurs flourish

c. Birds appear

3. Cretaceous Period

a. Flowering plants spread

b. Conifers decline

c. Placental mammals appear

d. Modern insect groups appear

e. Mass extinction of dinosaurs

iv. Cenozoic Era (Age of Mammals) present to 66 million years ago

1. Paleogene Period

a. Paleocene Epoch

i. Angiosperms diversify

ii. Primitive primates appear

iii. Herbivores, carnivores, and insectivores appear

b. Eocene Epoch

i. Subtropical forests thrive

ii. All modern orders of mammals are present

c. Oligocene Epoch

i. Modern flowering families evolved

ii. Monkeylike primates appear

2. Neogene Period

a. Miocene Epoch

i. Grasslands expand and forests contract

ii. Apelike mammals flourish

iii. Insects flourish

b. Pliocene Epoch

i. Herbaceous angiosperms flourish

ii. First hominids appear

c. Pleistocene Epoch (The Ice Age)

i. Herbaceous plants radiate

ii. Modern humans appear

d. Holocene Epoch (Age of Human Civilization)

i. Destruction of tropical rain forest

ii. Acceleration of extinctions by men

III. Lines of Evidence

a. The evolutionary events portrayed by fossils are supported by other fields

b. Biogeography is the distribution of species

i. Similarity in species on islands and on continents

ii. Convergent evolution is when unrelated species look more and more similar

iii. Divergent evolution is when related species are looking more and more dissimilar

c. Taxonomy confirms evolutionary relationships

i. Species in similar groups have resemblances

ii. Variation still exist within species

d. Comparative anatomy reveals relationships in structures

i. Homologous structures came from a common ancestor, but have different uses

1. Humans use 4 limbs to write

2. Bats use 4 limbs to fly

3. Moles use 4 limbs to dig

4. Whales use 4 limbs to swim

ii. Analogous structures have different origin, but the same function

iii. Vestigial structures don’t have an apparent function

e. Comparative embryology reveals similarity

i. All vertebrate embryos have tails and gill slits

ii. Early structures later differentiate into different structures

f. Comparative biochemistry confirms the hereditary record

i. All cells use DNA and RNA and the same genetic code

ii. Cytochromosome C is used to establish relationships

iii. DNA- DNA hybridization reveals when species diverged

IV. Natural Selection

a. Natural selection is the mechanism for evolution

b. Darwin believed natural selection occurs because population growth is limited

i. Individuals that survive pass on traits

ii. More offspring are born than survive

iii. Change in a population depend on the intensity of selection

c. Evolution by Natural selection requires this:

i. Variation- difference

ii. Inheritance- genetic differences must be inherited

iii. Differential adaptedness- differences affect how well organisms adapt

iv. Differential reproduction- the better adapted are more likely to reproduce and make a bigger contribution to the gene pool

Human Evolution

I. The Evolution of Primates

a. Primates are a mammalian order in which the members live in trees

b. Primates include monkeys, apes, humans, and prosimians

c. Evolved 2 distinct anatomical structures

i. Development of grasping fingers and toes

ii. Position of eyes in front of head

d. Most primates are diurnal

i. Primates developed cone cells for color vision

ii. Gestation is lengthy; allows for big brains

iii. Single birth and extended period of care

e. Primates are diverse

i. Prosimians were the first primates

1. Include tarsiers, lorises, and lemurs

2. Many are in danger of extinction

ii. Anthropoids include monkeys, apes, and humans

1. The hominoids include apes and humans

2. Hominids are the family of man

iii. Apes and humans probably share an ancestor line

iv. Human and chimpanzee DNA differ only by 1.6%

v. Hemoglobin, a protein with 573 amino acid differs by only 1 amino acid

vi. Proconsul may be the ancestor to today’s hominoids

II. The Hominids break away

a. The hominid line of decent begin with Australopithecus

b. Australopithecus is our earliest known direct ancestor

c. Australopithecines traits

i. Were sexually dimorphic

1. Females were about 4 ft tall; weighed about 38 kg

2. Males about 5 ft tall; weighed about 45 kg

ii. Were bipedal

iii. Had larger brains than apes

d. Australopithecas anamensis is the oldest hominid

e. A. afarensis (3.4 mya) Lucy is the best known

f. A. africanus (2.5 mya) called the manlike ape

g. A. robustus- stocky species called the nutcracker man

III. The Human Line

a. Homo habilis (2 mya) was the first member of our genus

i. Names H. habilis because the use of tools

ii. About the size of Lucy, but had a larger brain

iii. Lived in Africa for about 500,000 years

iv. Seems to have had an omnivorous diet

b. Homo erectus replaced H habilis

i. much taller than former hominids; 6 ft male; 5 ft female

ii. first hominid to use fire

iii. produced efficient stone tools

iv. probably migrated into Europe and Asia

v. Probably the direct ancestors of our species

IV. Origin of Modern Humans

a. Modern humans are Homo sapiens

b. Evolved from Homo erectus

c. Most people accept out of Africa hypothesis

d. Homo sapiens migrate into Europe (130,000 years ago)

e. Neanderthals were early Homo sapiens in Europe

i. Short stocky and very powerfully built

ii. The Neanderthals’ brains were larger than modern man’s

iii. Sturdy build was probably absorption for cold

iv. Cared for sick and buried dead

v. Used and controlled fire

vi. Cro-magnons replaced the Neanderthals

f. Cro-magnons has a modern appearance

i. Taller and not as stocky

ii. Made advanced tools; probably first to use spears

iii. Had a sophisticated culture

iv. Probably had language capabilities

v. Many have been responsible for the extinction of some large mammals

V. Humans are one species

a. Humans interbreed and bear fertile offspring

b. DNA variation is about the same with any ethnic group

c. Generally accepted that climate affects phenotype

d. Humans are unique

i. Ability to walk and use tools

ii. Language allows transmission of experiences

iii. Change and mold their environment to their needs

Process of Evolution

I. Genetic Differences Powers Evolution

a. When a gene mutates, alleles are created

b. Chromosome mutations tend to be lethal

c. Most traits are polygenic

d. Genetic variability is determined by the mutation rate

i. Most mutations are damages

ii. Some mutations are neutral or positive

iii. Without randomly occurring mutations, evolution would stop

iv. Rate of population evolution is a function of mutations

e. Only variations that affect an individual’s ability to survive, are subject to natural selection

II. The Hardy- Weinberg Principle

a. The Hardy-Weinberg Principle states that alleles will remain the same if certain conditions are met

i. No mutations- no changes in alleles

ii. No gene flow- no immigrants or emigrants

iii. Random mating

iv. No genetic drift- no different frequencies in alleles

v. No selection

b. In real life, this can’t occur

c. Evolution can be detected by any deviation

III. What causes Evolution

a. Gene Mutate: genes are the raw material for change

i. Mutation rates are very slow

ii. Each organism has many genes and a population has many individuals

iii. Raw material are for change

iv. Mutation are common no trace

b. Nonrandom Mating

i. Random mating occurs by chance

ii. Inbreeding or mating between relatives is non-random

iii. Inbreeding increases the frequency of recessive abnormalities

iv. Assertive mating occurs when individuals tend to mate with a certain phenotype

c. Gene flow is the movement of alleles among populations by migration

d. Genetic drift refers to changes in allele frequency in a gene pool

i. Genetic Drift

ii. Founder’s effect- rare alleles occur at a high frequency

1. Amish in Lancuster PA carry an allele for dwarfism

2. Population at large is 1/1000 dwarfish

3. All Amish with this syndrome can be traced back to a single couple

iii. Bottleneck effect- a large population is reduced to very few individuals, but then the population rebounds

IV. Adaptations occur naturally

a. Natural selection is the process by which populations adapt

b. Evolution by natural selection requires the following

i. Variation

ii. Inheritance

iii. Differential adaptedness

iv. Differential reproduction

c. Three types of natural selection have been described

i. Directional selection occurs when an extreme phenotype is favored

1. Typical of a changing environment

a. The peppered moth changed to black

b. Same bacteria are very powerful

2. Man may be responsible for some of this

ii. Stabilizing selection- an intermediate phenotype is favored

1. Babies of average weight is favored

2. The average is favored against the extreme

3. It is characteristic of stable environments

iii. Disruptive selection

d. Variations are maintained

i. Populations always show variations

ii. Some variations may be detrimental to a population overtime

iii. Sickle cell anemia is an example of this

1. AA is normal red blood cells

2. A’A – is both regular and sickle cell

3. A’A’ only has sickle cells

V. Considering Speciation

a. Speciation is the splitting of a species into two

b. Members of a species interbreed and share a common gene pool

c. The biological concept is a tricky definition

i. Does not apply to asexual organisms

ii. Does not apply easily to extinct organisms

d. Many species have races or subspecies

e. Incipient species are subspecies that may be in the process of separating

f. Species rarely hybridize in nature

g. Reproductive Isolating Mechanisms

i. Premating isolation- mechanisms prevent reproductive attempts

1. Habitat isolation- species in the same area have different habits

2. Temporal isolation- reproduce at different times of the year

3. Behavioral isolation- the courtship behaviors differ

4. Mechanical isolation- the genetalia don’t fit

ii. Post mating isolating- prevent hybrid offspring

1. Game isolation- sperm can’t fertilize the egg

2. Zygote mortality- the zygote doesn’t survive

3. Hybrid sterility- the offspring is sterile

4. F₂ Fitness- the hybrid is fertile by the F₂ generation is not

h. How species arise

i. Whenever reproductive isolation develops, speciation has occurred

ii. Allopatric speciation occurs when a population is separated by a physical barrier

iii. Sympatric speciation occurs when members of a population develop a genetic difference

i. Adaptive radiation produces many species

i. Adaptive Radiation is the rapid development of many species of one species

ii. Finches on the Galapagos Islands

iii. Hawaiian Honeycreepers

Unit 6: Microorganisms

Viruses

I. Structure

a. History

i. By the late 1800’s people suspected the presence of viruses

ii. In 1935, Stanley isolated the 1^st virus (tobacco mosaic virus)

iii. Virology provides clues

b. Characteristics of a Virus

i. Among the smallest biological particles

ii. Made of compound associated with cells, but not living

iii. Can replicate by infecting cells only

iv. Viral Structure:

1. Capsid- protein coat on the virus

2. Viral nucleic acid- DNA or RNA

3. Envelope- membrane around the capsid

4. Enveloped viruses- influenza; chicken pox; herpes syntax; HIV

5. Glycoproteins- allow the virus to recognize certain cells

c. Grouping viruses

i. Grouped based on shape and structure

ii. DNA and RNA viruses differ in how they infect the host

iii. Retroviruses- RNA viruses with an enzyme called reverse transcription

iv. Viroids are short single strands of RNA without a capsid

1. Can disrupt plant cells

2. infect potatoes, cucumbers, and oranges

v. Priones are polypeptides of about 250 amino acids

1. Affect the nervous system

2. scrapie is a disease that affects sheep and goats

3. Mad Cow Disease (BSE) is a fatal brain disease

II. Viral replication

a. Viruses are called obligate intercellular parasites

b. Bacteriophages are viruses that affect bacteria

c. The T phages are the most studied bacteriophages; they are found in E-coli

d. Infect Escherichia coli- which is an intestinal acid

e. Bacteriophage structure

i. Head with nucleic acid

ii. Tail- helps to inject the nucleic acid

iii. Tail fibers- help the virus to attach to the host

f. The Lytic cycle

i. The lytic cycle is the life cycle of virulent viruses

ii. A virulent virus causes disease

iii. Lytic cycle consists of 5 phases

1. Attachment

a. Phage attaches the tail fibers to the receptor site

b. Receptor sites are the specific area recognized by the virus

2. Entry- phage releases an enzyme to weaken the cell wall and then releases the DNA

3. Replication is when the virus takes over the cell and makes its own viral particles

4. Assembly- viral particles are put together

5. Release- enzymes call the cell wall to break down and viral particles are released

iv. In enveloped viruses, the cell membrane becomes the envelope

g. The Lysogenic Cycle

i. Some viruses can stay with the host for a long period of time

ii. Temperate viruses replicate using the Lysogenic cycle

iii. Steps in the Lysogenic cycle

1. Attachment of the virus to the host

2. injection of viral DNA

3. Integration of viral DNA with that of the host genome

4. Cell multiplication of the host and viral DNA

iv. Prophage refers to a virus that has a DNA integrated with the host’s

v. Radiation or chemicals may cause a virus to become virulent

h. Evolution

i. Probably evolved from the prokaryotic cells

ii. Mutations may allow viruses to evade the immune system

iii. Flu and HIV viruses mutate rapidly

iv. Flu vaccines target a specific strain each year

III. Viruses and Human Disease

a. Infectious Diseases

i. Many viruses affect humans

ii. Viral infections can effect various organs

1. Rabies- transmitted in saliva; affect nervous system

2. Chicken Pox- highly contagious; affects skin

3. Colds represent more than 200 different viruses

4. Others include measles, polio, and Hepatitis

b. Prevention and Treatment

i. Antiviral drugs interfere with nucleic synthesis

1. Acyclovir is a drug that treats herpes and chicken pox

2. Azidothymidine (AZT) inhibits reverse transcriptase in HIV

3. Protease inhibitors interfere with synthesis of the capsid

4. Antibiotics are no use to treat viruses

ii. Viral Vaccines

1. Pathogen is a disease causing agent

2. Vaccines stimulate the immune system

a. Inactivated viruses don’t replicate in the host

b. Attenuated viruses have been genetically altered so they don’t cause disease

iii. Smallpox once killed 40% of all infected people

1. Vaccinations helped to eradicate smallpox

2. In 1980 it was officially eradicated

3. In 1977 the last case of smallpox was found (Somalia, Africa)

c. Emerging Viruses

i. Exist in isolated habitats

1. Hantavirus cases pneumonia

2. HIV came from Africa

3. Ebola virus came from Africa

ii. Viruses and Cancer

1. Cancer genes may be triggered by some Lysogenic viruses

2. Examples of cancers that may be caused by viruses include leukemia, liver cancer, and cervical cancer

Bacteria

I. Evolution and Classification

a. Evolution

i. Fossils indicate bacteria is about 3.5 billion years old

ii. Have evolved into many different forms

iii. Survive in places most organisms can’t

b. Classification

i. Prokaryotes are divided into 2 kingdoms

ii. Archaea (Archaebacteria) live in harsh environments

iii. Archaea consists 3 phyla

1. Halophiles are salt loving bacteria

2. Thermoacidiophiles inhabit hot springs

3. Methanogens produce methane and CO₂ from Hydrogen Gas

a. Live in guts of animals, swamps, and sewage

b. Recycle carbon from organisms back into the air

4. Eubacteria are classified by how the get food

a. Photoautotrophs use light energy

b. Chemoautotrophs get energy by oxidizing inorganic compounds

c. Heterotrophs derive energy from other organisms

5. Prokaryotes use oxygen differently

a. Obligate aerobes require O₂

b. Obligate anaerobes can’t live with O₂

c. Facultative anaerobes can live with or without O₂

II. Characteristics of Prokaryotes

a. DNA is in the nucleotide

i. Have single circular chromosomes

ii. Plasmids are accessory DNA outside the main chromosome

iii. Lack membrane bound organelles

b. No sexual reproduction in bacteria buy 3 forms of genetic recombination

i. Transformation- bacteria pick up DNA from the environment

ii. Conjugation- exchange of genes through a conjugation tube

iii. Transduction- transfer of genes between 2 bacteria via a virus

c. Prokaryotes come in 3 basic forms

i. Bacilli are rod shaped

ii. Spirillia are spiral shaped

iii. Cocci are spherical shaped

d. Bacteria possess a cell wall

i. Provides structure and support

ii. Polysaccharides and other compounds make up the cell wall

iii. The gram- stain uses dyes to stain the cell wall

1. Gram- positive stain purple; this means that there are lots of antibiotics

2. Gram- negative stain pink; more difficult to control

iv. Pili are protein strands used for attachments and conjugation

v. Capsule is a covering over some bacteria

vi. Endospores allow bacteria to stay dormant for a long time

III. Bacteria and Humans

a. Bacteria can be helpful

i. Help to recycle organic matter

ii. All life depends on bacteria

iii. Bacteria assists in many commercial products

Algae

I. Overview of Algae

a. Characteristics

i. Algae are autotrophic protists

ii. Used to be classified with the plants

iii. Most algae are aquatic and flagella

iv. Pyrenoids- organelles that make and store starch

b. Structure

i. Thallus is the body of an Algae

ii. Thalli come in 4 forms

1. Unicellular Algae

a. Consist of a single cell

b. Most are aquatic

c. Comprise the phytoplasm

d. Examples: Chlamydomonas, diatoms, Euglena

2. Colonial Algae

a. Groups of cells that act as a group

b. Some cells become specialized

c. Examples: Volvox

3. Filamentous algae: somium

a. Have slender, rod shaped thallus

b. Holdfast anchor the thallus

c. Examples: spirogyra, oedogonium

4. Multicellular Algae

a. Have a large complex thallus

b. Macrocystis (giant kelp) is the largest algae

c. Has many plantlike characteristics

c. Classification

i. Classified into 7 phyla

ii. Criteria for classifying

1. Primary pigments

2. Type of chlorophyll and accessory pigments

3. Their food storage substance

4. Composition of cell wall

d. Reproduction

i. Most reproduce both sexually and asexually

ii. Sexual reproduction is triggered by environmental stress

iii. Zoospores are haploid flagellated cells

iv. A zygospore is a zygote with a protective covering

v. Alternation of generation involves 2 phases

1. gametophyte- haploid

2. sporophyte- diploids

II. Algal Diversity

a. Phylum Chlorophyta

i. Called for the green algae

ii. All four thyla occur in this phylum

iii. Probably gave life to plants

1. Chloroplasts contain chlorophyll a and b

2. both have accessory pigments called caretinoids

3. store their food in the form of starch

4. cell wall is made of cellulose

b. Phylum Phaeophyta

i. Called the brown algae

ii. Fucoxanthin is their primary pigment

iii. Laminarin is their food storage material

iv. Macrocystis (kelp) lives in the inner tidal zone (area between low and high tide)

1. Holdfast- anchors the thallus

2. stipe- stemlike area

3. blades- leaf like area for photosynthesis

v. Alginate is found on the cell wall and used for cosmetics, drugs, and ice cream

vi. Way to remember: “Laminate the Brown X” (The food storage sounds like laminate; they are brown algae; The pigment has an X in it)

c. Phylum Rhodophyta

i. Called red algae and most are marine

ii. Phycobilins are pigments that allow red algae to survive at great depths

iii. Carrageen (polysaccharide)- used in cosmetics, capsules, and cheese

iv. Agar is a gel forming base for culturing microbes

v. Way to remember: “GRRRR!!!! Regis Philbin care-a gene red.” (GRRR==Agar; Regis Philbin== Phycobilin; Care-a gene== carrageen)

d. Phylum Bacillariophyta

i. Diatoms is the name for the members

ii. Valves are the cell wall

iii. Centric diatoms have circular valves and are marine

iv. Pennate diatoms have rectangular valves and are fresh water

v. Diatomaceous Earth is used for detergents, toothpaste, fertilizers, and paint removers

vi. Leucosin is their food storage material

vii. Cell wall has pectin and silicon dioxide

viii. Way to remember them: I HAVE NO CLUE!!!!

e. Phylum Dinoflagellata

i. Most dinoflagellates have two flagellas

ii. Cellulose plates look like armor

iii. Bioluminescence (Noctiluca)- displayed by some of the members

iv. Red tide is a bloom of dinoflagellates

v. Way to remember: What is there to remember?

f. Phylum Chrysophyta

i. Called the golden algae

ii. Have large amounts of caretenoids

iii. Important in the formation of petroleum deposits

iv. Way to remember: “Golden gas goes in the car te no?

g. Phylum Euglenophyta

i. Euglenoids have plant-like and animal- like characteristics

ii. Euglena is the most familiar fresh water species

iii. Has a pellicle instead of a cell wall

iv. Good indicator of polluted water

v. Way to remember: “Euglena: More than Pelicans and Plants”(pelicans for pellicle and animals)

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