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Lecture Notes
Welcome! Here you will find links to my lecture presentations. These are posted just before or right after the class lecture.
Students: I have linked directly to the Powerpoint files so you can download them and view them at home.
Teachers: I have linked directly to the Powerpoint files so you can download them and use them in your classroom. If you want to edit them you may do that. Attribution is appreciated.

  Introductions
Welcome to AP Biology! An overview of the course and an introduction to the recurring themes that are woven throughout the fabric of this subject.
AP Biology is a rigorous, demanding, stimulating, rewarding course. Here's what to expect & how to succeed.
Biology is an ever-expanding body of knowledge and there are too many details to memorize it all, so we need to create a framework of over-arching themes upon which to organize new knowledge.


  Unit 1 Evolution
A Darwinian view of life! Darwin gave biology its unifying principle -- evolution by natural selection -- explaining both the unity and diveristy of life on Earth. By attributing the diversity of life to natural causes rather than to supernatural creation, Darwin gave biology a strong, scientific, testable foundation.
Our introduction to Darwin the man & the scientist, his ideas, and the inspiration for them.
Let's delve deeper into how natural selection acts on individuals.
What evidence supports this Darwinian view of change over time? What has allowed scientists to elevate Darwin's hypothesis to a biological principle?
Darwin's theory of evolution by natural selection gave scientists the ability to craft testable hypotheses. Here are two extraordinary cases that test the underpinnings of evolution.
Natural selection acts on individuals, but populations evolve. Evolution really means changing how much an allele shows up in a population. What factors alter allele frequencies in populations?
How do you measure/calculate the allele frequencies in a population -- and what does that tell us about the evolutionary forces acting on a population? Watch out, here comes the math!

How do new species arise? What mechanisms divide and isolate populations and send them on separate evolutionary paths.
The history and evolution of life can be documented with evidence already discussed in previous chapters. The of life on Earth is quite another story! Let's see what we hypothesize and what we have experimental evidence to support.


  Unit 2 Classification
Humans have been trying to make sense out of the the diversity of life for a long time. A formal system of classification began wth Carolus Linnaeus and taxonomists have been trying to perfect it ever since. Our current technology of DNA sequencing has allowed us to make better sense of our groupings, but this field is very much in flux.
Life began as one-celled organisms without organelles and this group has continued to be very successful through the ages... and we couldn't live without them! Actually there are more bacteria in YOUR body right now than all the humans that have ever lived! So let's meet our original ancestors. Here is an overview of our present understanding of the evolutionary relationships aomongst the Prokaryotes.
Protists are the "junk drawer" of the Eukaryotic Kingdoms. Taxonomists are actively working on sorting this group out to make better evolutionary sense. Here is an overview of our present understanding of the evolutionary relationships aomongst the Protists.
The Fungi help our world to continue by recycling the nutrients locked up in dead bodies. Here is an overview of our present understanding of the evolutionary relationships aomongst the Fungi.
The Plants have radically changed this planet and animals have them to thank for the world they were able to evolve in. Here is an overview of our present understanding of the evolutionary relationships aomongst the Plants.
The Animals have been able to radiate out and evolve to fill niches in every biome on this planet. Here is an overview of our present understanding of the evolutionary relationships amongst the animals.


  Unit 3 Ecology
No individual is an island unto itself. All organisms exist within an interconnected Web of dependent relationships, extending throughout this small spaceship, we call Earth. This is the study of ecology & human impact on a global-scale.
All organisms exhibit "behavior". They react to to stimuli that comes from others of their kind and from their environment. How much of this behavior is innate and how much is learned? What aspects of this behavior is acted upon by natural selection?
An introduction to the study of ecology and a survey of biomes around the world.
How do populations change over time? What factors affect population density, distribution & age structure? How is the human population faring on this spaceship Earth?
How do populations interact to build communities of interacting and interdependent organisms? How do these communities change over time?
Now, let's put it all together and investigate how communities interact in larger systems ~~ ecosystems. How do ecosystems function and what human activities affect ecosystems on both a local & global scale.
Oh my, what have we done! Let's look at the major environmental issues facing the world today -- all of them unfortunately caused by human action.


  Unit 4 Biochemistry
Biology has chemistry at its foundation, so we need to understand chemical principles to fully understand what drives the evolution & function of living organisms.
Biology has chemistry at its foundation, so we need to understand chemical principles to fully understand what drives the evolution & function of living organisms.
From the oceans to the lakes to our bodily fluids (the internal ocean) to the cytoplasm in a cell, all life occurs in water. So we need to know how water functions to understand what governs life.
So why are we carbon-based life forms anyway? An overview of organic chemistry from simple hydrocarbon (C-H) chains to the full array of biological molecules that are used to build living organisms. The behavior of these larger molecules is driven by small sections of the molecules known as functional groups.
Introduction to macromolecules of life. We learn the value of carbohydrates to living organisms and we learn how to build polysaccharides.
We learn the value of lipids to living organisms and we learn how to build fats.
We learn the value of proteins to living organisms and we learn how to build polypeptides.
We learn the value of nucleic acids to living organisms and we learn how to build RNA & DNA.


  Unit 5 Cells
The cell is the building block of all living organisms. Whatever functions a whole organism performs must be performed at the cellular level. So we need to learn, in detail, not only the cast of characters that run the inner workings of a cell by the processes they use to capture energy & fuel life.
 Cell Structure
Introduction to the basic unit of life -- the cell.
From the control center to protein production in the cell.
The coordinated internal membrane system of the cell -- membrane & protein production, the shipping & receiving department of the cell as well as the small membrane bound storage & clean up organelles.
The energy generators of animal & plant cells. The original "Aliens" story!
The cytoplasm doesn't sit in the cell membrane like a bowl of loose Jell-o. It is given structural support by an internal framework of fibers. So let's wrap up this tour of the cell with the internal structures that tie it all together.
It's so much more than a mere boundary holding the cell's contents in like the rubber of a water balloon! It actively controls traffic into & out of the cell. Find out why we use a "Fluid Mosiac model" to describe the cell membrane.
Learn about how traffic is controlled into & out of the cell. Diffusion, osmosis, and semi-permeable membranes! Oh My! How would your world be different if you lived in freshwater vs. salt water vs. on land?
 Metabolism
Life is built on chemical reactions. How do living organisms successfully complete these complex and essential pathways & regulate them to maintain homeostasis.What factors affect the activity & function of enzymes? What mechansims have evolved to increase the efficiency of enzyme pathways what systems have evolved to regulate enzyme function in living organisms.
Remember: The Point is to Make ATP!
Let's take a closer look at this molecule to see why it is the energy currency of life.
Life cannot go on without a constant input of energy. This is an overview of how energy is harvested and moved around living systems.
The work of life must be constantly fueled. This is the beginning of our journey through the elegant process of how cells harvest energy stored in organic molecules and use it to regenerate ATP. We also look at why ATP is the energy currency of living organisms.
The next step on our journey through the step-wise process of how cells harvest energy stored in organic molecules and use it to regenerate ATP. 2 billion years ago a bacteria boldly went where no creature had gone before -- it metabolized oxygen and discovered the energy value of oxidizing sugars!
The final step on our journey through the step-wise process of how cells harvest energy stored in organic molecules and use it to regenerate ATP. So far you've been wondering: Where's the ATP?! Now we find out why eukaryotes have such a metabolic advantage!
The coordination of metabolism -- the balance of energy production vs. building biomolecules -- is critical to cellular survival. If you've got enough ATP what's a cell to do? What feedback mechanisms do cells use to carefully calibrate metabolism to cellular needs?
Our introduction to the light reactions of photosynthesis, Building on principles learned in respiration we can better understand how plants weave light into the energy of life
Continuing on to the Calvin cycle of photosynthesis, Building on principles learned in respiration we can better understand how plants weave air into the stuff of life.
Adaptations to hot, dry climates cause problems for plants. How can you fix carbon if your stomates are closed? Find out how tropical grasses & cacti have solved this metabolic challenge.
 Cell Division
I gotta grow! You started as a cell smaller than a period at the end of a sentence...and now look at you! How did you get from there to here?
How is the cell cycle controlled? What checks and double checks systems exist to ensure cells only reproduce when they are supposed to? And what impact does this have on cancer development and cancer treatment? It will become obvious why is this one of the hottest topics in research today!


  Unit 6: Animal & Plant Systems
An organism is an amazing integrated, coordinated, organized system that is so much greater than the sum of its parts. And the diversity of organisms on this planet is astounding. We will learn about both animal & plant form and function, including the anatomy & physiology of the human body as well as the variation in these systems in other creatures.
 Animals
Animals inhabit almost every part of the biosphere. Despite their amazing diversity of habitat, form, and function, all animals must solve a common set of problems: Animals as different as hydras, halibut, and humans must obtain oxygen, nourish themselves, excrete waste products, and move.
Every mealtime is a reminder that we are heterotrophs dependent on a regular supply of food. All animals eat other organisms -- dead or alive, whole or by the piece.
Every organism must exchange materials and energy with its environment, and this exchange ultimately occurs at the cellular level. For most of the cells making up multicellular organisms, however, direct exchange with the environment is not possible. This constraint is associated with the evolution of physiological systems specialized for material transport and exchange.
Hand-in-hand with the circulatory system, it is only logical to talk about the complementary gas exchange systems that have evolved in animals to support their metabolic demands of needing oxygen for cellular respiration.
How do cell membranes and water conditions (tonicity) and habitat drive the lifestyles of whole organisms? You can amaze your family & friends by explaining to them why bird poop is white & why male birds don't need penises!
Animals are a neatly packaged, vitamin-packed meal to go for any pathogen they bump into. So animals had to evolve rapid-response defense systems to protect themsleves from succumbing to the enemies from within and without.
Animals are mobile and therefore have a world of stimuli that they come in contact with, so they have to be able to react...and react fast. The neuron is exquisitely built for this function
Hormones are offered up as an explanation for the howling of alley cats and the moodiness of teenagers. These powerful substances are also involved in even more dramatic transformations -- the complete change of body form when a caterpillar turns into a butterfly.
In much of our discussion of animals we have assumed mobility. Swimming, crawling, walking, running, hopping, and flying all result from muscles responding to nerves and working against some type of skeleton. What happens when you just got to move?!
Evolution is at a stand still, if you don't reproduce. But the ways in which organisms accomplish that is quite varied and often intriguing. Let's chat about the birds and the bees... and the kangaroos & the koalas, huh?!
An optional presentation illustrating human fetal development...so let's see your true first baby pictures!
The most complex problem in biology is how you go from one cell with all the possibilities to many cells that have specific functions and many limitations.
 Plants
How are plants put together from the ground up.
Plants grow very differently than animals do... and trees never die of old age!
Plants produce organic compounds in their lives and take up water from the ground though their roots. So how do you get food from leaves to everywhere its needed? And how do you get water up to the top of a 50-foot tree? Defying the laws of gravity without breaking a sweat... or maybe not!
Just like animals, plants need a balanced diet... just have to put a serving of manure on the plate. But on a serious note, plant & soil care in agriculture are of significant importance on a global scale.
Yes, plants have sex too!
Being rooted to the ground, plants must respond to whatever environmental change comes their way, but that doesn't mean they are handicapped in how they can respond. You'll be amazed!
We now turn our sights to the evolution of another form of life on Earth -- the plants. Take a deep breath and thank the plants for the air you breathe! This version covers both Plant Diversity 1 & 2.
Continuation of the evolution of plants from above.


  Unit 7: Genetics & Reproduction
We now step beyond organisms to interacting groups. Continuity over time comes from risking close interaction between indivduals within a population. We enter the multi-generational world of genetics, reproduction & evolution. Remember: Nothing in biology makes sense except in the light of evolution.
 Meiosis
We now clearly bridge the connection from cellular processes to the organism. How does one generation beget the next? What cellular processes must occur for organisms to reproduce their own kind. How do meiosis and sexual reproduction then provide the raw materials for evolution?
 Genetics
Out of one man's devotion to breeding & counting garden peas sprouted the whole field of classical genetics. Imagine what you could learn spending your days in the garden!
Out of Mendel's peas were a simple genetic system and a good starting point for the study of genetics, but the relationship between genotype & phenotype is rarely that simple.
What do flipping coins and genetics have in common? It's all in the luck of the draw!
Studying human inheritance reveals Mendelian patterns. A quick survey of some notable recessive diseases in humans.
Sometimes the system just doesn't work right and we get enetic abnormalities caused by large-scale chromosomal errors. Some of these are survivable; most are not.
 Molecular Genetics
We stand on the shoulders of giants! Many people placed a brick in the foundation of our understanding of our genetic material.
So how does DNA make an exact copy of itself? I'm glad you asked! Here are the gory...I mean, molecular details.
The "blueprint" is locked in the nucelar vault, so how do we get the instructions out to the ribosome factory? This is the first step in our stroll through the Central Dogma...
Eukaryotes do not use the "raw" mRNA that is transcribed from DNA. There is a lot of work to be done! This is the second step in our stroll through the Central Dogma...
Now it's time to actually read the mRNA and make the new protein. Meet the machinery that builds life. This is the final step in our stroll through the Central Dogma...
Bacteria may be tiny, but they have a lot to teach us about genetics. They have served as valuable model organisms in biological research.
Earlier, we learned how metabolic systems can be regulated by controlling the action of enzymes, but it is far more efficient to regulate metabolism at the protein production (gene expression) level. Why make proteins when you don't even need them?
Congratulations! The National Institutes of Health have allocated funds and awarded your team the grant to develop a simple, inexpensive DNA test for the sickle cell allele that can be used to efficiently screen large groups of people. Now how do you do it? This presentation is the supportive material to our Sickle Cell Bioinformatics Lab.
It's ALIVE! No, it's NOT! Viruses stand at that threshold between molecules and living organisms. They teach us about the roots of early life on Earth... and they can scare the b'jeez out of us as they cause damage and death in their wake.
We are far more complex than prokaryotes! We are multicellular creatures that pass through developmental stages & have specilaized organs & tissues that perform different functions, yet all our cells still hold the same genes. How does it all work? How are those genes regulated -- how are some turned on & some turned off?
 Biotechnology
Advances in our basic biological understanding of DNA and advances in technology & techniques in recent years have enabled us to make great strides in biotechnology & genomics. Allowing us to now turn our sights to practical applications of DNA technologies. This is very much a story of science & technology working hand & hand. In this lecture, we survey the basic techniques & methods that build the foundation of biotechnology.
Many of the basic techniques can be used in combination or improved upon to develop advanced biotechnology techniques. In this lecture, we survey the various advanced techniques & methods being used in biotechnology today.
We have accrued the basic biological knowledge and we have developed the lab techniques, but then arises the questions of "Should we just because we can?"


  Review
It's time to look back over the course and put it all together -- make sure you see the big picture but can explain it with relevant details.
A review of the 12 AP Biology labs. Sample essay questions are included.
These are the essay questions related to the 12 AP Biology Labs that are included in the PPT above. They are presented in this separate document so it's easier to practice answering them.







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