Advanced Placement Biology

Advanced Placement Biology

Course Note Guide

Pinedale High School

2008-2009 School Year

Mr. Gregory

Phone: 367-2137 x 4311

Email: mgregory@sub1.k12.wy.us

Advanced Placement Biology

Introduction & Overview

The AP Biology course is designed to be the equivalent of a college introductory biology course found anywhere in the nation at any university. The content of the course is constructed based on the student having successfully completed Biology I and completion of or concurrent enrollment in Chemistry. It aims to provide all the instruction needed for the student to perform well on the AP Exam administered in early May. The expectation is that you are taking this course to prepare for and take the exam. In addition, the course provides a valuable framework for future biology-related studies. The curriculum of the course is based on current College Board directives for AP preparation and major unifying themes and concepts in biology.

The textbook used in the course is Biology (6th ed.) by Campbell and Reece. The text is arguably the most widely utilized collegiate general biology text in the nation (and has been for more than 10 years) and is endorsed by the College Board. It provides a thorough, clear, and concise explanation of the content, and is designed to supplement and guide study throughout the year. Along with the text and study materials is a series of 12 AP labs that make up the required lab component of the class (lab designed and published by the College Board). Other laboratories will be use to supplement the AP lab exercises. There are two major projects during the course that make up the bulk of the non-exam grade: a fall in-depth topic interest paper and the spring animal kingdom project. AKP materials/examples can be found at the end of this guide.

The course format is fairly simple. Students can expect 45-50 minutes of direct instruction per day followed by labs and activities designed to reinforce concepts and expose students to common biology lab techniques and protocols.

The three main areas of study in AP Biology are:

I. MOLECULES AND CELLS 25%

II. HEREDITY AND EVOLUTION 25%

III. ORGANISMS AND POPULATIONS 50%

Within these three major areas are concepts related to each topic as follows:

Molecules and Cells

A. Chemistry of Life - 7%

B. Cells - 10%

C. Cellular energetics - 8%

Heredity and Evolution

A. Heredity - 8%

B. Molecular genetics - 9%

C. Evolutionary biology - 8%

Organisms and Populations

A. Diversity of organisms - 8%

B. Structure and function of plants and animals - 32%

C. Ecology - 10%

Course Calendar

The calendar is based on approximately 33 weeks of instruction prior to the AP exam.

Starting with the first class day of the school year (not necessarily in this order):

LengthTopicChaptersAP LABS

2 weekschemistry of living things1 - 6none

3 weekscells - form and function7, 8 & 111 & 2

3 weekscell energetics and reactions9 & 104 & 5

2 weeksheredity and inheritance12 - 153 & 7

3 weeksmolecular genetics - DNA16 – 216

3 weeksevolution theory and mechanism22 - 258

2 weeksdiversity and speciation27 – 34none

1 week ecology (incl. behavioral ecology)50 - 5512

4 weeksplant form and function35 - 399

7 weeksanimal form and function40 - 4910 & 11

2 weekspre-testing & preparationnonenone

special* sections are independent sections in which no class instruction will take place and you are expected to learn the material on your own time. Study aids will be provided and an exam will cover these areas at the appropriate time.

Grading and Evaluation

Grades will be based and broken down as follows:

Tests and Quizzes 70 %

Labs and Projects 30 %

The standard break points will be used in assigning letter grades.

Note:

Within this grading system in very likely the most challenging aspect of the course (for some), there is no late work accepted at any point throughout the year. Late is defined as work that student is aware of and responsible for and is capable of completing prior to the due date but does not complete. Work missed as a result of class absences must be made up in a timely fashion = usually no more than 5 class days following the specific absence.

AP Biology – Chemistry review and Biochemistry basics

Biochemistry = that aspect of chemical science dealing specifically with the chemistry of the living world

We care about only a couple elements in biology: O, C, H, N, Ca, K, Na, P, and S

Atom = smallest unit w/ elemental properties

Atoms composed of proton, neutron, electron – our interest is proton and electron

Proton – minor but important!

1. charging of molecules = polarity (esp. in H2O)

2. a single proton is represented by _________________

Electron – major

1. mobile

2. energy carrier/transporter

3. cellular currency

Molecule = 2 or more atoms in a stable assembly

This is the standard area of interest in biology –

larger molecules = macromolecules

Compound = molecules resulting from chemical rxn

Major reaction types in biology are:

Synthesis/dehydration

Decomposition/hydrolysis

Bonding – affects biochem reactivity and shapes (functions)

· covalent

· ionic

· Van der Waals – weak temporary polarity based on e- mvmt

· HYDROGEN (H-bonds)

Water Chemistry

Simple molecular design – properties based on two things: polarity and H-bonding

SKETCH

Properties of H2O:

State density

Adhesion

Cohesion

Universal solvent

Specific heat – heat of vaporization

The pH scale is based on water in part conc. Of H+ ions (or OH- conc)

Buffers = hydrogen pullers/holders that keep H+ away form acid/base “makers”

we care because……..

AP Biology – Biomolecules

Bulleted items are FYI; all others are info or questions that pertain to major ideas in this section.

· Macromolecules are simply long chains of small molecules = polymers

· POLYMERIZATION = process of making polymers

· The term biomolecule refers to macromolecules of particular biological significance

· 35 simple molecules (=monomers or nonpolymers) combine in different ways to form virtually all of the biomolecules found in all living things; why so few?

What defines a sugar, lipid or nucleic acid?

Sugar monomers combine to form _________________.

Nucleotides form polymers called _________________.

List the characteristics of carbon that make it such a valuable element in forming a variety of compounds:

· R is the standard abbreviation for a functional group, or a group of atoms that give a special function, property or shape to a general type of compound (usually carbon-based) see top of p. 54 table 3-1

What special trait(s) do each of the following functional groups give to a compound?

Hydroxyl

Carbonyl

Carboxyl

Amino

Sulfhydryl

Phosphate

Lipids (aka fat)

You need to be able to distinguish between hydrophobic, hydrophilic and amphipathic as well as the difference between saturated and unsaturated fatty acids to fully understand why fat does it thing:

What is the process for making a triglyceride from glycerol and fatty acid? dehydration rxns to form ester linkages:

How does a phospholipid (or phosphatidylethanolamine) differ from a regular triglyceride?

most would argue that cholesterol is bad for you, we refute/counter that argument because its part of the animal cell membrane and the precursor to steroid hormone = sex hormones and other (like testosterone and estrogen).

Carbohydrates (AKA sugar & saccharide)

Sugars are for the most part based on a carbon ring structure of 5 or 6 carbon atoms. What are the differences between glucose (the most common energy molecule) and ribose (a building block of DNA)?

Sugars are held together by _______________ bonds that utilize an oxygen bridge to hold two monosaccharides together.

The general rxn looks like this:

Cellulose and starch are both polysaccharides of glucose only. Why is one a glucose source for most animals and the other an indigestible mass?

Nucleic Acids

We will deal with this group more extensively in the DNA unit

· Nucleic acids are made by polymerizing nucleotides. Nucleotides are made by combining a phosphate, a ribose or deoxyribose sugar and a nitrogenous base (one of the five letters A, C, T, G, U). It’s called a nitrogenous base because it has several nitrogen atoms in it and acts like a base (versus an acid)

· Two general types of nitrogenous base are present in living systems:

pyrimidines = 6-C ring (C, T, U)

purines = 6-C + 5-C ring (A and G)

· The difference between RNA and DNA is simply the type of sugar involved (ribose vs. deoxyribose = one oxygen removed) and the use of Uracil vs. Thymine

The nucleotides of DNA and RNA are very similar to ATP, but what is the difference that makes one suitable for building information storage molecules and the other a high energy molecule?

Proteins

The base molecule is the amino acid – 20 types in the living world

General structure of an amino acid (AA):

The functional ( R ) group determines behavior of each individual AA –

Hydrophobic vs. hydrophilic

(Value of each type:)

Acidic vs. basic

Polymerization of AAs yields chains known as polypeptides (or oligopeptides depending on length). The reaction process is pretty simple…it goes like this:

The key is the _______________ bond.

**Properties of each AA in a chain gives the final protein its unique characteristics, shape and properties.

Shape – 4 levels of organization:

1o

2o

3o

4o

Denaturing a protein =

The many roles of Protein:

Structural components of cells/tissues

Cell membrane receptors

Chemical messengers

Enzymes

AP Biology - Cells

The microscope is the primary tool of cell study

· variations exist is type to maximize visible detail and resolution at various magnifications

Cell size – determined by a number of factors, but dominated by S : V ratio

Cell size analysis

AdvantagesDisadvantages

Starts with a membrane to hold the whole thing together – phospholipid bilayer with integrated proteins, carbs, and glycoproteins

SKETCH:

The Cell Membrane is detailed in the next noteguide section (Cell Membrane – Form and Function)

3 major cell types = Prokaryotic , Eukaryotic autotrophic, Eukaryotic heterotrophic

ALL HAVE: membrane, cytosol, DNA (chromosomes), and ribosomes

Differentiation found in TABLE 4-2 (see next page)

Functionally divided into areas of use

1. genetic function, regulation, and expression.

Includes:

2. endomembrane system.

Includes:

3. production organelles.

Includes:

4. microstructural areas = cytoskeleton.

Includes:

Reprint of a table (with permission) from:

Tobin & Duscheck, Asking about Life, HarcourtBrace Publishing 1998

AP Biology – Cell Membrane Form & Function

The special section of cell study focuses on membrane utility and fluid dynamics

A word on plant cells:

· Plant cell membranes are surrounded by a cell wall composed of cellulose (and lignin)

· Adjacent cells are cemented together but retain channels (called plasmodesmata) for fluid/material flow between

· Mature cells lay down additional wall material internally to create secondary walls. In time this buildup forms what we know as wood

Basic cell membrane architecture – see “cell” section

Advanced cell membrane architecture –

Extracellular matrix = space out side a cell

Contains proteins and glycoproteins that add strength and allow specialized communication between cells (e.g. cell migration and positioning)

Intercellular junctions – for communication or anchoring via one of three types of connection

1. tight junction =

2. desmosome =

3. gap junction =

Membrane composition = amphipathic phospholipids combined with integrated proteins and related molecules

FLUID MOSAIC MODEL states:

Membrane is selectively permeable system =

Along with the basic model is the role of integrated and associated protein molecules:

· attachment of cell to other cells or substances in extracellular space

· allow passage of material in and out of the cell

· transfer chemical signals from inside to outside of vice versa

· cell recognition (along with membrane carbohydrates)

· reaction centers (enzyme action)

Movement of material in and out of cell follows basic fluid dynamics =

concentration gradients

Forms of transport:

Passive diffusion (includes osmosis)

Facilitated diffusion

Active transport (includes cotransport)

Endocytosis and Exocytosis

AP Biology – Enzymatics and Cell Energy Basics

Chemical rxns come in two general varieties = catabolic (break down) and anabolic (put together)

Enzymes are specialized proteins that influence the rxn sequence and dynamics on most (if not all) biochemical rxns.

Free energy (delta G) is a key idea in enzymatics because it is free energy changes in a rxn that determines:

a.) whether or not the rxn can happen spontaneously

b.) if not, how much energy is needed to make it go

In terms of free energy, if the change in delta G is negative, then the rxn will happen spontaneously. If delta G is positive the rxn requires modification to happen.

Terms = exergonic – rxn releases free energy

endergonic – rxn consumes free energy

Key to things working in bioenergetic = energy coupling = putting a exergonic rxn with an endergonic one to make things happen.

The hydrolysis of ATP (Adenosine TriPhosphate) in the rxn ATP ADP + P is the most common exergonic rxn in all of biology in the area of energy coupling.

ATP rxn details (incl. intermediate)

Exergonic phase (delta G = -7.3)

Endergonic Phase (delta G = +7.3)

Factoids: in a muscle cell 10,000,000 ATP are used and recycled per second. If ATP was not regenerated, we would eat our body weight in pure ATP every day to stay alive.

Enzymes

Enzymes are specialized proteins that act to catalyze chemical rxns – they are not consumed during the rxn at any time.

Enzymes – how it works (diagram):

For a rxn to occur, a certain amount of energy (E) must be put in this is the activation energy (Ea) for the rxn.

Enzyme affect on rxn energy graph here:

Enzymes can be identified by:

· name ends is –ase

· name is written above the arrow in chemical rxns

· name often identifies function (e.g. synthase – synthesizes something)

The environment affects enzyme activity and efficiency of use

pH

temperature

concentration on substrate

concentration of enzyme

free space in rxn area

Enzyme regulation = controlling enzyme activity (DRAWINGS)

Competitive inhibitors

Noncompetitive inhibitors

Allosteric regulation (includes feedback inhibition)

AP Biology – Photosynthesis

Process = transformation of the energy contained within a photon of light into the bonds of ATP and various carbohydrates and lipids

Overall relationship:

Photosynthesis

CO2 + H2OO2 + Glucose

Cellular Respiration

ATP + heat

Anatomy of a chloroplast:

Two phases of photosynthesis = light-dependent and light-independent

Light –Dependent rxns

· Photons of light are absorbed in antenna complex which house chlorophyll = rxn centers:

· Two photosystems involved = PII (P680) and PI (P700)

PII donates e- to PI following light absorption and photolysis of H2O (releases e- from water)

KEY IDEA Oxygen from photolysis is released into cytoplasm to diffuse as waste into the air or to be used by mitochondria as needed

PI does one of the following two options based on conditions/needs:

1. Acyclical flow

2. Cyclical flow

Together they are able to accomplish:

· Pump H+ into thylakoid space from stroma (ATP production @ ATP synthase)

· Generate NADPH coenzyme (electron carrier) for use in L-I rxns (see below)

· Oxygen release

Light-Independent rxns = Calvin cycle = fate of e- from photosystems (NAPDH), CO2, and some ATP

E consumption from anabolic rxns

· Where?

Part #1 – carbon (from CO2) bonds to the 5-carbon

____________________________(RuBP) releasing ______________

Then to 2 molecules of 3-carbon _____________________________ (3-PG)

Then to 2 molecules of 3-carbon_____________________________ (G3P)

<> this part consumes 6 ATP and 6 e- (from NADPH) in the forming G3P

Part #2 – end product (G3P) can go one of two direction based on “need”

To Part #3 _____________________ (RuBP)used to synthesize glucose and other organics

Part #3 – regeneration of ______________________ uses three additional ATP per molecule

Importance of Rubisco enzyme (ribulose bisphosphate carboxylase) =

Net reactions

Totals for the day

· 6 CO2 for one Glucose (C6H12O6) molecule

· Six turns of the Calvin Cycle make 12 G3P 2 go to Glucose, 10 go to regenerating RuBP

· So to make one glucose you need 12 ATP + 12 NADPH (+6 ATP to get RuBP back)

18 ATP + 12 NADPH

· 48 photons of light needed to make 12 NADPH in PII and PI

can get 24 ATP made (by pumping H+ & ATP synthase activity)

AP Biology – Cellular Respiration

Process = Oxygen-dependent transformation of the energy from glucose (i.e. energy contained in its bonds) into the bonds of ATP

Overall relationship:

Photosynthesis

CO2 + H2OO2 + Glucose

Cellular Respiration

ATP + heat

Common to almost all forms of life (at least in part)

Aerobic vs. anaerobic

Facultative vs. obligate

Cell Respiration Big Ideas:

· Cell resp. starts with Glucose, so digestion of macromolecules (via enzymes and hydrolysis rxns) MUST preceed this process.

· Energy from glucose comes from the breaking of C-C bonds and moving that bond energy to the high-energy bonds of ATP

Anatomy of a Mitochondria

· Composed of three rxn sequences –

1. glycolysis

2. Kreb’s cycle (AKA citric acid cycle)

3. Electron transport

· Occur at three distinct location –

1. cytoplasm

2. matrix

3. inner membrane

STAGE 1 – Glycolysis

· Universal step – occurs in every living thing (incl. bacteria)

· Occurs in cytoplasm (cytosol)

· Starts with 1 molecule glucose----ends with 2 molecules of Pyruvate (AKA pyruvic acid)

· Generates 2 net molecules of ATP via substrate-level phosphorylation (= enzyme-driven phosphate transfer to ADP to form ATP)

· *2 ATP go into the early steps of the rxn sequence, but 4 come out later

· Also picks up 2 e- (NAD+ NADH)

· Produces a small quantity of H2O (metabolic water)

· Regulated via feedback inhibition (allosteric) – excess ATP clogs up Phoshofructokinase @ rxn #3 of the sequence

Net reaction of Glycolysis:

IF OXYGEN IS PRESENT PYRUVATE ENTERS STAGE 2, IF NOT IT STAYS IN THE CYTOPLASM AND ENTERS THE FERMENTATION PROCESS (see end notes of this guide)

STAGE 2 – Kreb’s Cycle

· NOTE: this cycle begin only once an intermediate step converts pyruvate into Acetyl-CoA during the transport of pyruvate into the mitochondrial matrix

· This subset of rxns creates some CO2 and an additional NADH (and an H+ that is released into the intermembrane space)

· It’s a cycle – you start and end with the same compound = ______________

Acetyl CoA gives C to _________________ citrate

Citrate moves H2O, loses CO2, and produces NADH a-ketoglutarate

a-ketoglutarate loses CO2, produces NADH & ATP Succinate

Succinate produces FADH2, adds H2O, produces NADH ___________

CYCLE DIAGRAM

· Net rxn provides e- (via carriers NAD and FAD) to stage #3 – these carrier MUST drop the e- or the system will shut down due to an overload of e- in this cycle and in glycolysis

STAGE 3 – Electron Transport Chain (ETC)

Highlights of the process (a walk-through)

· This stage uses only products from stages 1 & 2 – the electron carriers NADH and FADH, but Oxygen MUST be present for this process to work (if not = fermentation)

· The ETC is simply a chain of proteins of different types, most of which are classified as cytochromes, that are chemically capable of accepting then losing an e-.

· NADH donates it e- to the first member of the ETC (flavin mononucleotide), while FADH drops in through a slightly later protein (iron-sulfur protein), but both give up the e- early in the chain – as you would expect.

· The movement of the e- depends on changes in ______________ ____________.

· During transport through the chain H+ pumping is enabled by the e- movement through the cytochromes – some act as both transporters and pumps. H+ is always pumped in the intermembrane space.

· The final e- acceptor is ______________ (which is why we need so much of it). Combining with H+ from the matrix further contributes to the gradient across the inner membrane we form ___________ in the end.

· The gradient across the inner membrane is the whole reason we go through all three stages

Using the H+ gradient to power oxidative phosphorylation is how we get all that ATP made

ATP synthase enzyme is where the key reaction happens – driven by the movement of

___________. The end result is H+ back in the matrix

ETC SKETCH / HIGHLIGHTS

The complete equation for cell respiration:

The final balance:

30-32 ATP produced (optimistic models give up to 38)

Glycolysis = 2 direct, 3-5 indirect

Krebs Cycle (incl. Acetyl-CoA formation) = 2 direct, 23 indirect

CELL RESPIRATION BIG IDEAS

Real life – sugar vs. fat vs. protein as energy:

Case study – ketosis

Control of the whole thing:

A few notes on fermentation:

· Organisms that have no mitochondria (bacteria) rely on fermentation for energy

· The inefficiency of fermentation limits the size and complexity of the cell due to a simple lack of energy for complex tasks

· It occurs in situations where cell respiration is either absent (bateria and some protists) or impossible due to the absence O2 (e.g. strenuous exercise)

· Fermentation occus in the cytoplasm – in anaerobic situations the pyruvate does not enter the mitochondria

· There are two forms of the fermentation reaction – one in simple, single-celled organisms, the other in organisms like us

· Both types start with the end products of glycolysis: pyruvate, NADH, and ATP

· The ATP is removed for use in the cell meet energy demand

Type 1 – them – alcohol fermentation:

Type 2 – us – lactic acid fermentation:

*both processes have the same goal – regenerate NAD to keep glycolysis going – some ATP is better than none at all!!

Eukaryotic cells that produce lactic acid convert it back to pyruvate for future use in the aerobic pathway through and extensive sequence of reactions = inefficient but vital

AP Biology – Cell Cycles – PART I

The section serves to explain how cells multiply, with emphasis on the nuclear cycles (mitosis and meiosis). Terminology is always a tough area here, so we start with major terms associated with this area.

· Genome

· Chromosome (SEE FIGURE 12.3)

· Chromatin

· Sister chromatids

· Homologous chromosomes (homologs)

· Somatic cells

· Reproductive cells

· Diploid (=2n)

· Haploid (=1n)

The typical cell cycle for plants an animals looks like this:

G1 =

S =

G2 =

M =

C =

G0 is a special case found only in some cell types. Its purpose is :

Distinction exist between Prokaryotic cell cycling and Eukaryotic cell cycling:

ProkaryotesEukaryotes

Sometimes the whole cycle is identified by phases. In this case we recognize five distinct phases:

Interphase (I), Prophase(P), Prometaphase (PM), Metaphase (M), Anaphase (A), and Telophase (T)

The goal of the cell cycle can vary –

1. autosomal cell cycles (includes mitosis) = 2 identical daughter cells from one original cell

Use:

2. reproductive cell cycles (includes meiosis) = not true cycles; 4 cells with ½ of the original genetic material as the one original cell

Use:

Mitosis = the subprocess in the cell cycle that is responsible for the distribution of genetic material to the two identical daughter cells

FIGURE 12.5 (pp. 218-219) PROVIDES EXCELLENT VISUAL REFERENCES FOR THESE PROCESSES

Keys to note: chromosome activity and separation, spindle fiber uses,

error avoidance measures

Reasons for each phase –

I = cell preparation, DNA replication, cell growth, organelle duplication, early chromatin condensation

P =

PM =

M =

A =

T =

Cytokinesis is the stage at which the cell actually splits into two daughter cells, but since the genetic material is already separated it is not considered part of mitosis, but since it starts before mitosis is finished it tends to get stuck in there.

Animal cells cytokinese through the use of a cleavage furrow and microtubule “pinching”. Why?

Plant cells cytokinese through the production of a cell plate that serves to divide each of the daughter cells without altering the existing wall structure. Why?

Regulation of the cycle – important because loss of control causes abnormal growth like CANCER!

· Cell cycle checkpoints = critical points in the cycle the determine if the cell proceeds to the next stage

· Chemical signals = cycling levels of signal molecules (e.g. cyclin, MDF)

· Growth factors = chemicals that stimulate cells to growth & divide

· Gene signaling and regulation = genes that regulate speed and frequency of the cycle

· Positional inhibition of growth =

AP Biology – Cell Cycles – PART II

Now that you hopefully have an understanding of the dominant cell reproduction system (mitotic cycles) we can move to the other less common, but arguably as important, one.

Comparatives –

MITOSIS CYCLESMEIOSIS CYCLES

Cell type involved

Location of process

Starting chr #

Ending chr #

# of division

The cell cycle of Meiosis:

- Male goal = 4 specialized haploid cells from 1 original cell sperm

- Female goal = 1 highly specialized haploid cell from 1 original cell egg

The sexual life cycle takes ALL plants and animal through an alternation of generations: sporophyte gametophyte sporophyte gametophyte

Meiosis = the subprocess in the cycle that is responsible for the distribution of genetic material to the four daughter cells

Meiosis I:

P I =

M I =

A I =

T I & C =

Meiosis II:

P II =

M II =

A II =

T II & C =

FIGURE 13.7 (pp. 240-241) PROVIDES EXCELLENT VISUAL REFERENCES FOR THESE PROCESSES

Keys to note: chromosome activity and separation, spindle fiber uses,

error avoidance measures

BIG IDEAS IN MEIOSIS:

1. Crossing over

Significance:

2. Reductional division

Significance:

AP Biology – Medelian (and non-Mendelian) Genetics

Genetics is divided into that area that stem from the work of Gregory Mendel and that which has been discovered that deviates from his classic model. As with the cell cycling sections, terminology is key to this section:

Phenotype

Genotype

Trait

Gene

Allele

Dominant / recessive

Homozygous

Heterozygous

P generation

F generation(s)

Cross

Mendels Big Ideas:

1. genes control physical traits

2. dominance and recessiveness

3. Law of Independent Assortment

4. Law of Segregation

Biology I reviews – The Punnett Square, Probability, and the Pedigree

Punnett Square:

A device used to predict the result of a single trait cross (monohybrid cross) assuming simple Mendelian relationships – EXAMPLES:

Probability:

In genetics the probability of two (or more) genetic combinations occurring based on the law of segregation follows the rule of multiplication – EXAMPLES:

Pedigree:

A chart designed to track genetic information through prior generations of a related group/family – EXAMPLES:

Non-Mendelian genetics = deviation from the Mendel model in real life. These are genetic situation that exist in various organisms and, in most cases, create greater genetic variety in a population

Atypical dominance =

Example:

Multiple Allele situations =

Example:

Pleitropy =

Example:

Epistasis =

Example:

Polygenics =

Example:

AP Biology – Additional Topics in Chromosomal Genetics

There are topics in genetics that are important, but do not fit neatly into the Mendelian section. These ideas create the link between the theoretical genetics of Mendel and the real world we see.

**Since a gene is simply a specific piece of DNA with a specific job, it makes sense that genes are located at specific sites on specific chromosome.

EXAMPLE #1 –

EXAMPLE #2 – the work of Morgan (1920s) – the concept of ___________ chromosome linkage

Once the chromosome system and an understanding of the gene location idea are in place, major ideas become clear:

Linked genes –

Recombination and linked genes –

Sex chromosome genetics and linkages –

Gene maps –

Recombination frequencies –

The entire chromosome/gene management system is extensively error proofed, but errors do still occur:

The most common of these is a nondisjunction event during an Anaphase. SKETCH:

This type of error results in aneuploidy = a cell has an abnormal chromosome #

(this includes aneuploids for sex chromosomes)

The other class of errors involves parts of chromosomes instead of whole chromosomes. TYPES:

· Deletion

· Duplication

· Inversion

· Translocation

AP Biology – DNA Replication

DNA (DeoxyriboNucleic Acid) is of primary importance as it is the information molecule that controls all physical traits and process of all organisms.

Structure: composed of subunits called nucleotides (see biomolecule section) that form linear complexes with two distinct regions:

BackboneCoding

The backbone and the addition of an additional opposite section (antisense strand) achieve on simple, yet vital role: stabilizing the DNA code section

General ideas:

· the double helix occurs because it is this shape that provides for the greatest # of H-bonds within the molecule

· a purine always pairs with a pyrimidine

· nitrogenous base pairing rules:

· (See Figure 16.6)A always pairs with T (U if in RNA)

· C always pairs with G

DNA replication goal is ___________________________________________________

mechanism known as: ___________________ replication. It is the best system because it always uses an original DNA piece as a template for new DNA formation

DNA anatomy – 5’ and 3’ =

sense and antisense strands =

Replication Steps (common to prokaryotes and eukaryotes):

Goal: 2 exact copies of the original strand

prior to replication 2 steps:

gyrase

helicase

sense strandantisense strand

DIAGRAM OF PROCESS:

replication bubble/fork = points on DNA segment that are being replicated simultaneously

· bacteria possess one loop of DNA, so replication differs in:

Mutation =

result = different/altered protein (enzyme, hormone, etc.) based on the altered code

caused by mutagens (examples ____________________________________________________)

mutagens have predictable action of DNA

Rates and hot-spots important because:

Types of DNA mutations – known as point mutations:

substitution

insertion

deletion

Note: there are +/- 50 separate enzymes responsible for DNA integrity and repair processes

Simple example =

1. DNA nuclease identifies and removes damaged section

2. DNA polymerase encodes the new section (based on the opposite side)

3. DNA ligase seals the repair in place

pp. 300-301 contains some interesting detail on a special case in replication – telomeres. This area is of interest for 2 reasons – it has a link to aging and cell death and to possible cancer therapy.

AP Biology – DNA Transcription and Translation (from gene to protein)

With an understanding of DNA structure and its primary role, the “how’s that work” part is all that’s left.

gene (again) =

one gene-one enzyme concept:

one gene-one polypeptide concept:

problems with both concepts:

Two distinct processes take the DNA informational code and convert it into a functional product:

Transcription – converting the DNA code into a portable form (since DNA cannot leave the nucleus)

DIAGRAM:

Major steps: (the whole thing is enzyme driven)

1. a promoter region is present at the beginning of every gene in the DNA

2. transcription factors bind to promoter which binds RNA polymerase

3. RNA polymerase opens the DNA below the promoter and begins to synthesize mRNA based on the DNA sense sequence starting with a START code.

4. RNA polymerase works (elongation) until it hits a STOP code in the DNA

5. The new piece of mRNA is released from the enzyme and the whole complex breaks down – DNA rewind and everything returns to normal

A note on post-transciptional modification:

The newly made mRNA is modified is a couple ways following transcription –

· Segment protection

· Segment editing

Translation – creating a protein (amino acid sequence) based on the mRNA code

**this is where the code in DNA actually does its job (indirectly)

A Note On Coding:

One of the complex ideas in gene expression is how the code (in mRNA form) is translated to make protein. The whole thing works like reading a sentence composed of words with three letters. Each word represents a CODON, a 3 letter sequence of mRNA that corresponds to a specific amino acid during this process.

example: dog big eat cat red poo fur red

DIAGRAM:

Major steps: (players = mRNA, ribosomes, tRNA, and amino acids)

1. a ribosome (2 subunits) are attracted to the mRNA once it leaves the nucleus – the ribosome attaches to the start codon of the mRNA

2. the ribosome allows a specific tRNA to bind to the mRNA and release the amino acid it is carrying

3. Another tRNA comes in with a matching code – amino acid released following bonding to the first one (peptide bond)

4. the ribosome shift down the “reading frame” to release the first tRNA and allow binding of the next one

5. the ribosome reaches the STOP codon on the mRNA and stops – releasing the new polypeptide (protein)

6. the ribosome breaks apart, the mRNA is degraded by other enzymes (recycled) and the protein is shuttled to its final destination

Final Analysis

The whole system acts to take instructions and make something useful. Regulation and control is extremely dynamic and complex to keep at this working correctly hundreds and thousands of times every hour in each of your 10 trillion cells.

Why do we care??? – a couple of reasons:

**REVIEW FIGURE 17.25 – overall of entire process in visual form**

AP Biology – Unconventional Genetic Systems and Organelle Origins

Definition = genetic systems that are mobile within the genome or are not specifically in a nuclear genome.

= genetic systems that do not meet the conventional parameters of life, cannot be considered in

A bacterial domain but are part of the world biological system

important due to their roles / purposes and in providing evidence of early genetic evolution

Transposons

· genes integrated into host cell’s DNA

· their deal:

· the key to their ability is the _______________ enzyme

· insertion point can be good or bad, Why?

· Can be simple =

Or complex =

*evolutionary genetic recombination bacterial TB example

Plasmids

Small usually circular DNA or RNA w/ 3-300 gene; found in proks and some euks

Autonomous replication, which means:

Transmitted via “bacterial sex” = _________________

· Genetically engineered plasmids very important more in Ch. 13

Viruses

· Nonliving due to lack of energy process, metabolism

· Not all bad evolutionary tool for …

· Made up of protein = delivery systems and enzymes

nucleic acid (dsDNA, ssDNA, dsRNA, ssRNA) = directions for synthesis

capsid = host interaction/protection

or membrane envelope = host interaction/protection

· Two major shapes = ________________________ & ___________________, and others

· REPLICATION PROCESS – two types, same basic steps:

attachment – receptor recognition

entry – aided injection, endocytosis, membrane stealing

integration – enzyme driven

synthesis – make new viral parts

assembly – build the new virus particles

release – get em out of the host cell

· usually integrated replication =

*tumor viruses are special lysogenic types that have DNA that codes for proteins that disrupt the cell cycle control mechanisms (e.g. protooncogenes), leads to tumor cell formations

*What about ssDNA types? Use host machinery to get to translation process for their genetic material

*What about RNA viruses and plasmids? Either RNA-direct translation or make it into DNA via reverse transcriptase enzymes (called retroviruses, e.g. HIV)

Episomes = viruses or plasmids that can shift from autonomous to integrated replication and back

Lysogenic provirus –

Lysogenic viral phase –

Lytic viral phase –

Prions = proteins that can infect neighboring protein and change their conformation/shape, altering the other protein's function

Transmission somewhat unknown for most identified types

CWD discovered by Wyoming researcher in Laramie

Poorly understood type of infectious particle, but looks like a pre-virus type

Evolutionary Issues

Natural selection of host defense nat. sel. of virus attack host defense change etc.

In the end you get more efficient viruses with more efficient DNA (in terms of host useability) and DNA with less crap info in it and more effective host defenses

BIG PICTURE OF EVOLUTION: Transposons -------------------- plasmids ------------------------viruses

Eukaryotic systems

mitochondrial and chloroplast DNA & endosymbiosis theory

ii. Theory says: mito, chloro, and others are descended from prokaryotes that used to live alone then moved inside a “host” eukaryote see text for modern example of this

iii. Proof:

· Circular DNA in these organelles like prokaryotes

· DNA codes for components of their structures…some but not all (e.g. F0-F1 complex of ATP synthetase enzyme)

· Replication directed by nucleus and mito/chloro DNA

· Both have equipment for transcription and translation of their DNA inside

· Very distinct for regular eukaryotic DNA

· ALL mitochondria DNA shares some common characteristics all eukaryotic life is related

AP Biology – DNA technology (biotechnology) and Bioengineering

This is a special area of genetic study that is especially active in today’s society. Although there are a variety of concepts here, the basic idea is the same – study and/or modification of genetic material (i.e. DNA) for a specific reason

DNA / gene cloning =

DIAGRAM:

Restriction Enzymes & Mapping =

DIAGRAM:

Polymerase Chain Reaction (PCR) =

DIAGRAM:

DNA Electrophoresis =

-We do a lab on this one, so no diagram is necessary-

Genome Mapping (Human Genome Project) =

It’s complicated!

Recombinant DNA - a how to guide

Practical Application of all this stuff:

· create transgenic animals or plants

· gene therapy

· Better drugs – bioengineered proteins (insulin)

· New form of identification of individuals

· Make study of genes/proteins easier with larger quantities

· Better understanding of where disease (and other) genes reside in the genome

· Define practical capability of gene modification (restriction capabilities)

AP Biology – Genetic Control of Development

At this point you have covered a number of different topics in molecular and cellular biology. This section serves as a transition between the microscopic world of biology and the macroscopic world we see around us.

3 processes get a single, fertilized cell to a completely developed organism:

1. cell division (cell cycle w/ mitosis)

2. cell differentiation (differential gene expression)

3. morphogenesis (blob to body)

Best to study organisms that have 4 general characteristics:

1. Easy to see _____________

2. _____________ generation time

3. ______________ genome

4. background genetic _______________________

Humans are, at present, to complex to study directly, so we use a modified reductionist approach (study the small then apply up) =

fly, nematode worm, mouse, fish, plants

Note: Plants are very similar to animals except: animals have cell movement and a limited embryonic stage

Totipotency =

Gene expression in the key to is the key to determination (which tissues produce what protein signals)

How does a cell know what to do and who to be?

· Positional information (juxtaposition)

· Cytoplasm determinant (compounds) cause _____________ events

· Cell environment

BIG IDEA = transcription factors cause transcription of specific genes = regulates

transcription = regulates gene activity = ____________________________________

Drosophilia genetics case study - most widely studied animal on the planet – gives us clues to how some of it works:

Gene type / classrole

Embryonic lethal

Establish body axes (N & S)

Morphogens

Direct segment formation along axes

Gap genes

Homeotic genes (homo box)direct the specific anatomy of as segments

Apoptosis genesprogrammed cell death (essential in development – webbing of hands/feet)

An extra word (or two) on plants:

· Plants possess embryo regions throughout life = meristems (i.e. buds)

· Also possess genes for the # or organs (flower parts) and organ identification

BIGGER IDEA = commonality within all life at a very fundamental level; leads to theories on the evolution of all life

AP Biology – Natural Selection as a mechanism for Evolution

Natural selection is the “how?” behind both major evolutionary processes (micro- and macroevolution)

Natural selection was proposed as the mechanism of evolution by Darwin (and Wallace) based on the research and theories of others and field research conducted by Darwin (1831-1836).

Natural selection, simply put, is the effect survival of the fittest has on a population / species

Fitness defined:

The contribution of a genotype (an individual) to the next generation compared to the contributions of alternate genotypes (other individuals)

· This process is based on mutation that leads to adaptation

Adaptation = directional process that leads to changes in genotype and phenotype in response

to mutation and the environment

Mutation = random, generally deleterious, genetic events that cause permanent change in an

organism’s DNA (genotype) __________________________________________

Highlights of mutation:

· _______% of DNA codes for protein

· many redundancies (protection of vital info)

· remnant DNA give clues to evolutionary sequences

· _____________________ and other enzymes are designed to repair damage

· Not all mutation are heritable

· 99.9% of all mutations are non-sense, bad, or have not effect (act on other______%)

How’d he do that? – look at what ideas he used:

Linnaeus – taxonomist who developed the naming system and started grouping

organisms by common characteristics

Lyell –

Malthus – superfecundity – organisms can produce more offspring than the environment

can support

Cuvier – old rocks vs. new rock (old on bottom)

Wallace –

Variety of evidences (see the micro / macroevolution section for additional details)

Natural Selection also came from artificial selection – selective breeding of animals for desired characteristics (chickens, cows, sheep, etc.)

Requirements for natural selection to work:

1. Genotypic variation between individuals of the same species:

2. Heritable traits (phenotype characteristics that can be inherited):

3. Superfecundity:

4. selective survival:

Natural Selection can act is several different “directions”:

Graphic representation of the three types

Directional Diversifying Stabilizing

AP Biology – Microevolution and Macroevolution

Microevolution = change in allele frequency (gene occurrence) in a species / population over time

Some terms first:

Species – a group of organisms that have strong genotypic and phenotypic similarities

and that can interbreed successfully but are reproductively isolated from all other groups

Population -

How it works:

1. a population of an species exists with some variation in genotypes (and phenotypes)

2. the environment places a selective pressure in this population

3. selective survival occurs – some phenotypes (and genotypes) are favored in this environment

4. superfecund survivors reproduce and increase the frequency of their specific alleles within the population, while those alleles that led indirectly to some dying are lost from the population

microevolution (shift / change in allele frequencies) has occurred

EXAMPLE for analysis: insecticide resistant insects

Macroevolution (AKA speciation) = creation of a new, distinct species as a result of microevolution over time in the presence of isolating barriers (see next page)

How it works:

1. a population of a given species contains genetic variations

2. an environmental event introduces a barrier within the population – separating the group into two or more smaller subgroups

3. each subgroup lives and reproduces isolated for the original – large amounts of time pass

4. selection microevolves each subgroup at different rates and in different directions – new isolations form

5. the two subgroups either remain isolated or come together again but are unable to successfully reproduce

a new species has formed = macroevolution

EXAMPLE for analysis: squirrels on the river

More on isolation types – remember, one (or more) must be present for macro to occur

· prezygotic barriers (prior to zygote in reproduction)

· habitat

· behavioral

· temporal

· mechanical

· gametic

· postzygotic barriers (after zygote has formed)

· reduced hybrid viability

· reduced hybrid fertility

· hybrid breakdown

Two versions of speciation (macroevolution) exist:

1. Allopatric

2. Sympatric

Speciation can cause macro to go in to distinct directions:

Convergent evolution

Divergent evolution

Science has never witnessed macroevolution first-hand, so we rely on other evidence:

Fossil Record – rock layering –

radioactive dating –

Pros = consistent distribution, sequence agreement, similarities over time

Cons = gaps (big ones) why?

Biogeography – multiple uses:

Taxonomy = artificial system – not useful in this context

Homology vs. Analogy – what is the difference?

Vestigial vs. rudimentary – different…but used the same –

Embryology – Haeckel and the current use

Molecular homologies:

Amino acids sequencing

DNA-DNA hybridization

The Molecular Clock concept

The speed of macroevolution over huge tracts of time is also arguable – two schools of thought exist on how it work (evidence exists to support both):

1. Gradualism (slow and steady)

2. Punctuation Equilibrium (stop-go-stop-go-stop-go)

In the end we must ask…CAN IT REALLY WORK LIKE THAT?

Additional support for species formation and macroevolution over time comes from our study of genetics and molecular biology –

· Allometric growth and hertrochoncy

· Paedomorphosis

· Homeotic gene systems

AP Biology - taxonomy and systematics

Systematics is:

Why does the binomial system exist?

Rules for scientific naming include:

1. genus + specific epithet = species name

2.

3.

The hierarchal system is based on separating organisms into different taxon =

the basic system starts at ______________________

and ends with ______________________

What is phylogeny?

A cladogram provides information on:

Molecular data allows us to assess phylogenic relationships that

______________________________________________________________________

How are differences in DNA sequences related to time since divergence?

= the ________________ ________________ idea

Occam’s razor states:

It applies to systematics how?

The molecular clock and HIV – an example of application of ideas

Molecular techniques – overall influence of systematics is to add precision.

AP Biology – Behavioral and Population Ecology – Ch. 51 & 52

Animal behavior is useful in:

· Understanding basic premises of an animal’s behavior helps us understand their biology

· Understanding simple behaviors can be extended to us

· Comparing behaviors of simple and complex life forms helps us see evolutionary progressions

Simplest forms include:

1. Kinesis

2. Taxis

3. FAPs

Energy needs drive behaviors optimum foraging strategy:

Learning in animals depends on neural complexity…bigger brain = _____________________

Examples:

Conditioning:

Play:

Cooperative behaviors:

Dominance

Hunting

Courtship

The biggest problem with understanding animal behavior is the complexity of _____________.

Because…

1. cost

2. benefit

Population Ecology = interactions between populations and their surroundings

**measured/categorized in numerous ways to determine the identity of a population:

1. Survivorship curves (x3 types)

2. reproductive productivity relationships

3. reproductive strategies (r and K) – see end of this section

Populations are viewed as snapshots and over time – time effects are influenced by many factors,

but __________________________ is one of the most important. The MATH of it:

Change in a specific interval of time ( N/t ) =

Rate of change over time ( r ) =

In an ideal world then, we get Exponential Growth:

Reality brings in the concept of environmental ability to sustain a population = Carrying Capacity (K):

This gives us things like r- and K-selected populations – Examples of each…

AP Biology– Community Ecology and Ecosystems – Ch. 53 & 54

Community definition and direction is based on species composition, which is influenced by:

1. Interspecific interactions

2. Energy structure

3. Disturbance

4. Biodiversity

INTERSPECIFIC INTERACTIONS

= interactions between species within a specific area

Types:

A. competition and response

i. exclusion

ii. niche development

iii. resource partitioning

iv. character displacement

B. predation and response evolutionary cause/effect scenario:

predator actions/responses

prey actions/responses

plant examples

animal examples

*parasitic interactions

C. Symbioses

Mutualistic

Commensalistic

ENERGY STRUCTURES

= energy flow through communities dictates all things

The major idea is loss from level to level the 10% rule:

Control is either bottom-up (most powerful) or top-down:

DISTURBANCE

The frequency and magnitude of disturbance affects stability, which affects composition.

Types of disturbance =

Disturbance often leads to __________________ (10 and 20 types)

Primary is most fundamental – greatest number of possibilities

Secondary is most common and predictable

BIODIVERSITY

· depends on size and geographic location of community

· Size affect

· Location affect

· +/- equal to species richness which =

Community + Abiotic Factors = ECOSYSTEM

**Ecosystems are defined by available resources = light and water temperature and precipitation

Available resources determine the primary productivity of an area, which directly influences all other levels of the “food chain” because of the _____________ rule.

Beyond available resources concept is the limiting nutrient concept, which states:

The efficiency of any trophic level within an ecosystem is dictated by the level directly above and directly below that level…EXAMPLE = herbivores:

Sustainability of a given ecosystem depends on efficiency of ______________ cycling.

EXAMLES:

Carbon

Nitrogen

AP Biology – Early Life and the Bacterial Domains

Since early life was prokaryotic, it only makes sense to start this section with a brief review of life history as we know it before diving into Domain Archaea and Domain Bacteria.

Major events in the pre-biotic and early prokaryotic world

For each of these events we will add rough dates and a word or two on their importance:

· Appearance of simple organic molecules – chemical evolution (Miller-Urey)

· Evolution of first genetic material – very likely ____________

· Protobionts appear

· Appearance of first prokaryotic life

· Cyanobacteria-like prokaryotes evolve and fill the early atmosphere with

· Oxygen

· Appearance of first primitive eukaryotic cells

· Multicellular eukaryotes appear

· Animals and plants diversify

Bacterial form and function – Domain Bacteria

Cell characteristics:

· Unicellular and very small (1-5 um diameter = 1/20th or smaller than eukaryote cell)

· No nucleus or other membrane-bound organelles

· Single circular piece of DNA + a few plasmids depending on species

· Ribosomes present – protein synthesis

· Cell membrane / cell wall / plasma membrane / capsule present

· Used extensively in bacterial ID and classification

· Contain a unique compound (=peptidoglycan) found only in prokaryotes – two types

· Gram positive = thick outer layer

· Gram negative = thin intermediate layer

· Shapes –

· Coccus (cocci) = round occur as single, chain, or cluster

· Bacillus (bacilli) = rod/pill occur as single or chain

· Helical = helix-shaped occur single

· Movement = flagellum (flagella) – simple machanics, corkscrew-like motion

Reproduction:

· Asexual = binary fission = simple mitotic-based system

· endospores – some possess the ability to produce “seeds” of sorts = a specialized cell within another cell surrounded by a stronger cell wall complex

· “sexual” = conjugation, transformation, and / or transduction

· Conjugation

· Transformation

· Transduction

Behavior and metabolism:

Bacteria possess simple taxis responses –

1. Chemotaxis – receptor-based responses to chemicals in the env.

2. Phototaxis – photosynthetic types respond weakly to light

3. Gravitaxis – some possess metallic substance that allow reponse to

4. magnetic field

Metabolic activity – bacteria utilize a variety of energetic pathways –

· photoautotrophic = use CO2 and light in photosynthesis

· chemoautotrophic= use CO2 and inorganic compounds (e.g. Sulfur)

· photoheterotrophic = use light and organic compounds

· chemoheterotrophic = use organic compounds

Environments:

Obligate aerobes =

Obligate anaerobes =

Facultative anaerobes =

Bacterial form and function – Domain Archaebacteria

This group is very similar to the other type listed above with a few important examples, the largest of which is in their ecology:

SEE TABLE 27.2 FOR A COMPARTIVE BETWEEN BACTERIA AND ARCHAEA

The archaea are know collectively as extremophiles – “lovers” of extreme environments – the idea is that this group, being the oldest, represents the primitive bacteria and thrive in the environments that have not changed much since the dawn of prokaryotic life. Examples:

· halophiles

· thermophiles

· methanogens

Bacteria and Us

Human have a love / hate relationship with bacteria:

Love –

Decomposers =

Nitrogen fixation in soil =

In the human (animal) body =

Digestion of cellulose =

Production of engineered drugs =

Genetically engineered bacteria (through the introduction of human genes into the bacterial genome) produce drugs in mass quantities for human medicine – insulin, antibiotics (ABx), hormones

Bioremediation =

Used to clean up toxic chemical spills and return fouled land (soil) to a productive state.

Hate –

Parasitize animals = 3 issues

1. cellular leaching

2. production of exotoxins

3. production of endotoxins

Antibiotics & and antibiotic resistance – how’s that work?

Background:

1928 – penicillin discovered

1928-1980’s – natural occurring ABx and derivatives used extensively

1990’s – resistances increase to noticeable levels

Present – extensive research and development in new ABx type

How ABx work:

· interfere with bacterial cell wall synthesis

· disrupt enzymes that build peptidoglycan

· interfere with bacterial protein synthesis

· disrupt mRNA and ribosomes

· interfere with bacterial DNA replication and repair

· target specific enzymes in process

How bacteria become resistant:

mutation and/or gene transfer between bacteria (sexual reproduction) create a specific mode of action

1. ABx efflux or blockage

2. ABx chemical modification

3. ABx target modification

Why does this matter?

It’s a model of microevolution that we really care about

Bacterial disease is one of two (the other is viruses) threats that are potentially lethal to humans on a global scale

The potential exists for global disease eradication – research and biotech in the future will show this to be possible of not

AP Biology – Kingdom Protista

Protists defined:

Plankton = protistans zooplankton = animal-like, phytoplankton = plant-like

Basis for classification = misfits – based on lifestyle, cellular characteristics, and reproduction

Motility – cilia or flagella sometime in life, others end up with pseudopodia

Importance = endosymbiosis theories:

= evolutionary systems:

Reproductive diversity – highly variable

· Haploid –

· Diploid w/ haploid gametes –

· Haploid but diploid zygote via cell fusion –

· Alternation of generations – haploid to diploid to haploid etc.

Common name-------------Characteristics----------------------------------------Repro

ALGAE (plant-like)

Dinoflagellata

Chrysophyta

Euglenophyta

Phaeophyta

Rhodophyta

Chlorophyta

PROTOZOA (animal-like)

Rhizopoda

Foraminifera

Sporozoa

Ciliophora

Zoomatigina

FUNGI-LIKE

Acrasiomycota

Myxomycota

Oomycota

AP Biology – Fungi and Plant Evolution

Some things need completion and there are several questions to answer:

PART I Fungi = Chapter 31

Fungi are a kingdom unto themselves because:

· Hyphae filaments – cell specializations in structure….collectively known as mycelium which makes up the bulk of the organism

So what is a mushroom then? (why is it necessary)

· Nuclei position variable based on the presence/absence of septum

· Immobile (mostly)

· Chitin in cell wall – unique to fungi and insects

· Sexual of asexual (some alt of gen) – hyphae budding or SPORES

Advantages of spores=

· No embryonic stage – plants and animals always have one

· External digestion = 1. invasive hyphae growth into food source – look at haustoria

2. excretion of digestive enzymes (expenzymes) = external digestion

3. absorption of nutrients – how?

5 major taxons of fungi (COMPLETE AS SHOWN FOR #1 BELOW):

1. Chytridiomycota – simple fungi (some don’t even consider these fungi)

aquatic

flagellated spores

earliest type and likely major player fungi/plant land move

2. Zygomycetes – conjugation fungi (fill in rest on own)

3. Ascomycetes – sac fungi

4. basidiomycetes – club fungi

5. deuteromycetes – imperfect fungi

Importance: Decomposers, Parasites (30% of 100,000 known species), Lichens, Mycorrhizae

What is mycosis?

Which has it worse in terms of fungal parasites, plants or animals? Why?

Lichen are symbionts, but who needs who worse in this relationship? Why?

What is so special about mycorrhizae in terms of plant evolution (move onto land)?

How are we related to fungi?

PART II Early Plants = Chapter 29 & 30

Plants = multicellular photosynthetic organisms derived from an embryo

Bryophytes vs. vascular plants – what’s the difference?

Compare and contrast gymnosperms and angiosperms in 4 distinct ways.

What are the 3 major advantages to life on land??

3 major disadvantages: buoyancy issues

non-aquatic reproductive problems

water supply and retention issues

Solutions to the problems of land are ??:

Evolution of plants – lots of evidence, logical and sequential – simple to complex anatomy, physiology, lifestyles, and reproductive strategies

go from asexual to spore formers that alternate generations to naked seeds to flowers and fruits

go from being predominantly haploid throughout life to dominantly diploid with only a short haploid stage (=gametes)

Evolution of land plants = list and briefly describe the evidence presented in the text that argues that green algae evolved into land plants

How is a seed different than a spore (look at seeds p. 599)??

What does the reduction of the gametophyte tell us in terms of explaining what we see and how it evolved?

Gymnosperms = naked seed – conifers

Angiosperms = covered seed – flowering plants

Physiologic differences between the two groups include:

Reproductive system/cycle –

Vascular system – gymnosperm xylem is tracheid-based

Angiosperms also contain fiber cells for support and vessel elements which are more efficient at water transport than tracheids

Angiosperms are divided into dicot and monocot types (list the differences)

What are the parts of the basic flower and what are their functions:

StructureFunction in Reproduction

What is a fruit and why does the existence of this specialized structure support coevolutionary ideas?

in your opinion, will the value of plant diversity to human civilization go up, go down, or stay relatively the same? Explain you rationale as if talking to an idiot.

NOTE: We will cover more specifics of anatomy, physiology, and reproduction in these groups later

AP Biology – Plant Morphology and Function

How is gravity in plant cells overcome? 2 major ways =

Plants deal with the gaseous CO2 via _____________, that do what?

Differences between shoot and root systems:

Plant Tissues are divided into 3 categories/types – here’s the deal:

Parenchyma

Collenchyma

Sclerenchyma

Structure and arrangement of vascular system = xylem and phloem arrangement

Xylem:

Phloem:

Major characteristics (cell types and growth aspects) of the three tissue systems: dermal, ground, vascular

Dermal:

Ground:

Vascular:

Transport occurs in three levels:

1. uptake of water and solutes by individual cells

2. short-distance transport or substances from cell to cell

3. long-distance transport of sap in xylem and phloem

Transport of water – how does it work? (important structures and overall process)

Transport of nutrients – how does it work? (important structures and overall process)

Monocot vs. dicot, the difference is:

Roots obtain water from soil by the following processes:

C4 plants, what is their specialization and why do they do it?

Defense – the selective pressure is herbivory, the results are mechanical, chemical, and other weird, yet fascinating stuff.

Mechanical = pointy things that irritate/harm herbivores to discourage predation

Chemical = production of substances that disagree with predator’s body in several ways:

Examples of 2o compounds:

Terpenes =

Phenolics =

· Lignin

· Tannin

· Alkaloid

Canavanine =

Weird, yet fascinating stuff = genetic responses to pathogens the plant immune system

gene 4 gene

HR (hypersensitivity response)

SAR (systemic acquired response)

AP Biology – Plant Reproductive Anatomy & Physiology

The bullets are general information of importance…the questions designate the most important ideas and information in the chapter:

· Probably the most unique quality of modern corn is its inability to reproduce without human assistance due to its compact seed arrangement and morphology = “natural” corn cannot exist in its current state unique result of artificial selection.

What is the difference between sporophytes and gametophytes? What do these two stages look like in the average plant?

· *the mechanism of egg and sperm formation are unimportant…the bottom line is the efficiency of the end result.

What is the vital importance of endosperm?

How would a deficiency in endosperm formation affect the embryo?

Levels of gene expression is the key difference between meristem cells and their neighbors.

Why might imbibition and scarification be so vital to stimulating embryo development once it has entered dormancy?

How does gibberellin initiate the embryonic nutritional system?

· Consider for a minute what the metabolic processes of a seed must be like to allow it to stay alive during a dormancy period of 10,000 years. (how long can you go between meals?)

How would plants that are under constant pressure from herbivores adapt to preserve their vital meristems?

· Shoot meristems and root meristems are almost identical in gene expression; both radiate from the embryo but follow opposite gravitational pathways.

What root adaptations would a plant need to be successful in rocky or very dense soil?

· Flowers can be thought of as simple modifications of leaves, with extreme cell specializations for sexual reproduction.

Why is the homeotic selector gene, first found in plants, so important to all of biology?

Why are cork and vascular cambium so darn important and what is their product?

YOUR NOTES ON TOPIC:

AP Biology – Plant Regulation & Control

Plants control themselves through a very simple system based on hormones and environmental cues.

The key to everything in plants is signal transduction pathways – getting certain cells to do certain things by exposing them to certain substances / signals

the signal causes gene expression which creates a product (protein) which makes the cell capable of specific actions

Hormones

Compounds that attach to specific receptors on or in a specific cell to stimulate a specific response

DIAGRAM:

Major hormone classes & actions

Growth–stimulating classesFunction

Auxincell elongation/growth(see next page), root growth, branching and differentiation, fruit development, apical dominance,

Giberellin

Cytokinin

Growth-inhibiting classesFunction

Ethylenethe triple response to obstacles, cell death, leaf ascission, and fruit ripening

Abscisic acid

Brassinosteroidsinhibit root growth and leaf abscission

Cell Elongation in detail = DIAGRAM:

Special classes of hormones also exist in certain plant types –

e.g. salicyclic acid

Found only in thermogenic plants, this hormone stimulates mitochondria activity to supply additional ATP for the production of _______________ (increase as much as ________oC)

Other plant compounds that affect behavior:

Amyloplasts/statoliths – gravitropic responses

The settling of the amyloplasts cause a secondary signal to the cell giving direction to cell orientation and target areas for auxin action

Phytochromes – phototropic and photoperiodic responses

Pr and Pfr reactions

Short-day vs. long-day vs. day-neutral

AP Biology – Animal Kingdom Basics

Kingdom Animalia:

multicellular, eukaryotic heterotrophs that develop from an embryo with very short gametophyte stages

Hypotheses suggest animals evolved for _________________ _________________.

Animals evolved extensively and proliferated during the Cambrian period (543-525 million years ago)

this event in evolutionary history is often referred to as the

_____________________ _____________________

Current Classification of Animals

Divided into two groups (subkingdoms) based on symmetry and embryo development = Parazoans – radial symmetry

Eumetazoans – bilateral symmetry

we focus on the Eumetazoans because they make up the bulk of the animal kingdom

3 body plans exist within animals:

1. Acoelomate – lack a body cavity between the gut and the outer body wall

2. Pseudocoelomate – partial body cavity

3. Coelomate –

Coelomates are further divided based on gut development in the embryo:

1. protostomes – mouth is first gut structure to develop

EXAMPLES:

2. deuterostome – anus is the first gut structure to develop

EXAMPLES:

AP Biology – Animal Body Design, Organization, and Rationale

Driving force behind all animal forms = homeostasis =

Two distinct areas – Anatomy

Physiology

Organization (& function) is based on cell specialization into _____________, and tissue orientations

Tissues are:

Do specific cellular jobs as a group on a macro level division of labor concept

Typeexamplesform/function relationship

Epithelialstratified epitheliallayers of the skin = rapid growth, living to dead

Glandular epithelialsecrete a product = mucous, sweat, etc.

Connectiveadipose tissuefat = specialized for storage (expandable)

Cartilageprotects bone surfaces @ contact points (= joints)

Boneendoskeletal structure and storage of key minerals

Nervousneurons

Muscleskeletal muscle

Tissues grouped together in a common area/position = ORGAN organs with a common task set = ORGAN SYSTEM

11 organ systems in the animal body work together to provide all vital function related to homeostasis – see TABLE 40.1

Why have tissues into organs and organs into organ systems? ______________________

Physical constraints on Body plans and organization of these systems = environmental/ecological survival strategy

Examples:

Gravity

S-V ratio

Hydrodynamics

Tissue Specializations

Exposures/Protective Needs

Bioenergetic Needs

Bioenergetics in depth

Energy Budgeting = allotments of energy expenditure related to cost – benefit system

Ectotherms

Endotherms

BMR = Basal Metabolic Rate:

BMR + daily expenditure for survival = energetic need leads to prioritization system:

Feeding

Escape

Reproduction (most variable)

Nutritional needs = essential nutrients required to meet energetic demand

Macronutrients = amino acids and fatty acids

Micronutrients = vitamins and mineral

*differ in amount needed (macro vs micro)

Process (general) = ingestion digestion (mech and chem enzyme hydrolysis/catabolism) absorption elimination

Diets – dictate physiologic and anatomic design to maximize food resource exploitation

1. herbivory

2. carnivory

3. omnivory

Specializations = mutations favored by the environment/available food situation

Dentition:

Digestive tract design (increasing complexity with exceptions):

a. external digestion = excretion or simple absorption from environment

b. internal digestion (simple) = used by unicells, whole-cell system

c. internal digestion (complex) = tube within a tube

length

Compartmentalization

Symbionts (ruminants)

AP Biology – Homeostasis and the Animal Body

Homeostasis is the simple idea that every cell’s primary goal is to maintain a stable internal environment so that collectively the organisms can also maintain stability.

Animals come if two forms depending on the environment they reside in and their basic body system plan:

Regulators

Conformers

*Both groups must balance the energy gain – energy loss equation for their particular lifestyle, such that a deviation from complete balance will cause cell and organism death at a certain point.

Another way to think of energy control is the energy budget – where cost and benefit are weighed throughout the animal’s life

EXAMPLES:

The field mouse - a regulator

The rattlesnake - A conformer

Thermoregulation – an example of the homeostatic process in action

There are two pathways animals have taken in the area of thermoregulation:

Exotherms

[e.g. American alligator (80kg) 60 kcal / day base need]

Endotherms

[e.g. human (80 kg)1300-1600 kcal / day base need]

All biological life has an ideal temperature for function that the individual organisms tries to maintain. To do so they must deal with heat loss / gain from several areas in the environment:

Radiation

Conduction

Convection

Evaporation

Behavioral and physiological adaptations exist in all animals for the sole purpose of thermoregulation – some EXAMPLES are:

Diurnal / nocturnal = heat based behaviors

Vasodilation & vasoconstriction =

Counter-current exchange =

Heat-shock proteins =

Torpor (estivation) =

Hibernation = a long-term torpor

Characteristic of both endo and exotherms that live on cold climates throughout a significant portion of the year:

Metabolic rate drops – as low as 1% of normal, active metabolic rate

Body temp drops – extreme examples are to 1-2 oC

Control of thermoregulation = negative-feedback system:

AP Biology – Skeletal, Muscular, and Digestive Systems

Skeletal types:

Hydrostatic – fluid pressure based continuous support system

Drawbacks =

Exoskeleton – chitin based external support system

Drawbacks =

Endoskeleton – mineral based internal support system

Drawbacks =

· Each provides the support for organs and fixed anchor points for muscle attachment

· Skeletal features must work against tension,compression, and sheer forces to adequately meet the needs of an organism

· The endoskeleton is a result of specialized cells called osteoblasts that, along with osteoclasts, build and mold bone for specific tasks/situations

· Muscles anchor to bones via dense connective tissue – tendons and ligaments

YOUR NOTES ON TOPIC:

Muscle stuff:

Three types of muscle = cardiac (heart), smooth (internal organs), and skeletal (movement)

· Muscle cell anatomy holds the key to its function:

elongated cells containing a complex system of fixed (thin) and mobile (thick) filaments and specialized receptors allow muscle cells to respond to nerve impulses and contract along the long axis

· Muscles pull (shorten) against the anchor (e.g. tendon) to create movement – pairs of muscles create reversible movement (e.g. flexing and extending the arm)

· The sliding filament mechanism/model describes how muscle contraction works

· The entire contraction process is driven by ATP, which allows the filaments to move past one another. The breakdown of ATP produces large amounts of waste head that is used by some vertebrates to regulate body temperature.

YOUR NOTES ON TOPIC:

Digestive Review:

The need for food is driven by the need for an energy source

· The minimum food requirement is based on an organism’s basal metabolic rate (BMR), which is the minimal energy level required to keep the organisms functioning normally.

· Basic diet variety provides the necessary amino acids, carbohydrates, fats, and vitamins & minerals for meeting all of an animal’s metabolic needs; no matter whether it is herbivorous, omnivorous, or herbivorous.

One hole vs. two hole digestive system – advantages /disadvantages

The “disassembly line” idea – 4 processes at work = movement, secretion, digestion, and absorption

Overall the same for vertebrates; specialization for those with unique dietary situations:

e.g. birds – needs to break down seeds crop and gizzard added

cows – need to break down plant cells ruminant stomach system

anteaters (and others) – need to get specific food in specialized mouthparts

KEYS

Enzymes drive the digestive process by catabolizing large molecules of carb, prot, and lipid

Surface area makes system useable and highly efficient

Each segment has a specific role, so no part can work alone in the process (and if one fails = trouble)

Nervous system, via impulses and hormones, controls digestive system directly

YOUR NOTES ON TOPIC:

AP Biology – Endocrine, Circulatory, and Nervous Systems

Endocrine and Nervous systems are the major homeostatic regulators of the body endocrine is chemical, nervous in electrochemical.

Endocrine stuff:

· Hormones exert effects on cell(s) by initiating chemical/metabolic changes in the target cell(s).

· Pheromones exert effect on cell(s) of another organism, usually of the same species.

· Glands are specialized groups of tissues that secrete a chemical product in response to nervous system of other body cues.

· There are two general classes of hormones: releasing and inhibiting, what is the difference in action?

· **Make sure you understand the negative feedback system and examples of how it works

· Hormones can go directly to the nucleus of the target cell to cause change (lipid-soluble) or use a second messenger system to get the job done (water-soluble); the cell membrane is the key barrier.

· Hormones attach to the binding site of the hormone receptor in the nucleus or on the cell membrane.

· No matter what the system (direct or secondary messenger) the goal is to stimulate a metabolic response in the target cell example = growth hormone, causes target cell to initiate mitosis and divide = growth in that tissue (e.g. bone or muscle)

YOUR NOTES ON TOPIC:

Circulatory tidbits:

Design goals include getting oxygen-poor (waste-laden) blood to the lung for clearing while getting oxygen-rich blood to all cells of the body without mixing the two. Solution, separate circulation systems using a common pumping organ with separate compartments.

· Compare the three heart designs found in the text, note the differences and the evolutionary path taken to get to where we are today why the changes?

· What is blood made of and what do the different components do? You need to know this one to explain why blood exists in the first place.

· Blood vessels (i.e. veins and arteries) are active participants, constricting and contracting to help meet blood circulation needs. They are regulated by the nervous and endocrine systems, find an example of each.

YOUR NOTES ON TOPIC:

Nervous Goodies:

Goal = to get a basic grasp on how neurons get the job of signal transmission done; this is the biggest concept to grasp in the nervous system. Work through Chapter diagrams to see if you can follow the process.

· Nerve cells get signals from the end of one to the beginning of another via neurotransmitters, specialized chemical compounds (like hormones) like acetylcholine (Ach).

· The key of communication between neurons (and getting signals from one body part to another) is the chemical jump = getting Ach from one side of the gap to the other – its all about diffusion of molecules

· Nerves sense the environment and conditions within the body, a brain integrates those signal and creates a motor response to them.

· Animals that lack a brain use a neuron network throughout the body to sense the environment. Response to that environment comes as a reflex action – conscious decisions are not made.

· The general plan for the animal brain is three parts: forebrain, midbrain, hindbrain the development of each influences neural complexity and ability (worms versus apes)

· The ear, eye, nose, and tongue are specialized sensory organs designed to receive specific stimuli and send it to the brain complex for processing what survival advantages do these specialization give to an animal?

· For an example of sensory integration read the section on the eye-brain connection

YOUR NOTES ON TOPIC:

AP Biology – Topics in Animal Development

The whole thing starts with fertilization initiates sequence of events resulting from sperm-egg fusion

Basic ideas = how it works:

1. sperm enzymes from acrosome released on egg contact and cut through egg wall

2. penetration of 1st sperm causes chemical cascade (very rapid) to block other sperm.

i. Designed to prevent polyspermy

ii. Utilizes Ca2+ - release causes multi-step activity to permanently block other sperm

3. nuclear fusion as part of a “flash” that starts the whole development process

Development of the fertilized egg = 3 stages

1. cleavage = special mitosis one cell to multicell embryo (blastula)

2. gastrulation = blastula to ___________________

3. organogenesis = cell differentiation into ____________________

** all activity through stage 1, 2 nd most of 3 involves STEM CELLS which are totipotent

Early embryo differentiation is cued by major gene types:

(Ch. 21)Pole (animal and vegetal) determined by __________________________ genes

Axes of embryo (left/right, front/back) determined by _______________________genes

Structures (tissues and organs) and their orientation determined by _________________ genes

Cleavage

Cell

to

morula

to

blastula

Gastrulation

Blastula

With poles

to gastrula

with layers

Organogenesis

Determination

of 3 layers to

specific tissues

Basis of development/determination beyond gastrulation is:

GENETIC!! – gene induction gene expression protein signal production cell activity change

Positional – where are the cells as they relate to each other

Keys to success:

- cell can shift/move slightly =

- cells react to signals based on position = Figures 21.4 and 47.20

- inductions follow positional pattern formation guidelines =

Limb example from text – Figures 47.23 and 47.24

· precise folds create zones (AER & ZPA) that further direct and induce limb bud in limb development by way of protein growth factors (results of gene expression) chemical cues

remember plants and chemical cues/signals

(evolutionary link and commonality)

AP BIOLOGY – Animal Kingdom Project

Items to include in each family/group profile page:

a. Family/group name – scientific and common

b. Number of species in the group

c. General physical characteristics along with defining characteristics of the group

d. Habitat information for group – general

e. Reproductive strategy – may be included in general characteristics is it is defining for the group

f. Important interactions with other members of kingdom Animalia

g. Representative picture of member of the group

4 pts. per group, with grade based on a 4-point scale of criteria completion (see above) and attention to detail total grade of 212 points

**An animal kingdom assessment will be given upon completion of this sizeable project, so it is important that you pay attention to what you are writing about each group. You do not need to know every detail, just general characteristics of each.

Questions? ASK!

GOOD LUCK

KINGDOM ANIMALIA FAMILY / GROUP LIST

*PSEUDOCOELEMATA

Gastrotricha

Nematomorpha

Rotifera

Nematoda

*ACOELOMATA

Nemertina (nemertea)

Platyhelminthes

Ctenophora

Cnidaria

Porifera

Placozoa

*COELOMATA

Onychophora

Targdigrada

Pentastoma

Priapulida

Pogonophora

Echiura

Sipuncula

Arthropoda

arachnida

crustacea

chilopoda

insecta

Annelida

polychaeta

(*PROTOSTOMES)oligochaeta

hirudinea

Molluska

bivalvia

gastropoda

cephalopoda

Echinodermata

Chaetognatha

Hemichordata

(*DEUTEROSTOMES)Chordata

tunicata

cephalochordata

*vertebrata

agnatha

chondrichthytes

osteichthytes

amphibiana

reptilia

aves

mammalia

*prototherian

monotremata

*metatherian

marsupial

*eutherian

chiroptera

insectivora

lagomorpha

primate

rodentia

carnivora

edentata

artiodactyla

perissodactyla

proboscidea

sirenia

cetacean

Terms with and asterisk and in italics are used for orientation only; there is no page requirement for these 7 groupings

AP BIOLOGY – Animal Kingdom Project Form

h. Family/group name(s) = Scientific:

Common:

i. Number of species in the group =

j. General physical characteristics of group =