Table of Contents
Overview and Introduction: ................................................................... 8
1: Overview of this course, and the instructional sequence presented. ......................................... 8
2: The AP exam. .................................................................................................................................... 10
A Tour of the Science Practices ....................................................... 15
SP 1: Use Representations and Models to Communicate Scientific Phenomena and Solve
Scientific Problems................................................................................................................................. 15
1. SP 1 discussion ............................................................................................................................ 15
SP 2. Use Mathematics Appropriately. ............................................................................................. 16
1. SP 2 Discussion ............................................................................................................................. 16
2. MATH Skills: Metric system......................................................................................................... 17
3. MATH Skills: Dilutions .................................................................................................................. 19
SP 3. Engage in scientific questioning to extend thinking or to guide investigations within
the course. .............................................................................................................................................. 20
1. SP 3 Discussion ............................................................................................................................. 20
SP 4. Plan and implement data collection strategies appropriate to a particular scientific
question. .................................................................................................................................................. 21
1. SP 4 Discussion ........................................................................................................................... 21
SP 5. Perform Data Analysis and Evaluation of Evidence. .......................................................... 22
1. SP 5 Discussion ........................................................................................................................... 22
2. MATH Skills: Descriptive statistics .............................................................................................. 23
3. MATH Skills: Standard Deviation ................................................................................................ 25
4. MATH Skills: Standard Error ....................................................................................................... 27
SP 6. Work with scientific explanations and theories. ................................................................... 34
1. SP 6 Discussion ............................................................................................................................. 34
SP 7. Connect and relate knowledge across various scales, concepts, and domains. ........... 35
1. SP 7 Discussion ............................................................................................................................. 35
Domain 1:
Evolution ........................................................................... 37
1.1: Natural selection is a major mechanism of evolution. (EK1.A.1) ........................................... 37
1. Natural Selection ........................................................................................................................... 37
2. The Modern Synthesis ................................................................................................................. 38
1.2: Natural selection acts on phenotypic variations in populations. (EK1.A.2) ......................... 40
1. How Natural Selection Works...................................................................................................... 40
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1.3: Evolutionary change is also driven by random processes. (EK1.A.3) ................................. 42
1. Other Evolutionary Forces ........................................................................................................... 42
1.4: Biological evolution is supported by scientific evidence from many disciplines, including
mathematics. (EK1.A.4) ........................................................................................................................ 45
1. Evidence of Evolution .................................................................................................................... 45
2. MATH Skills: HW Theory ............................................................................................................. 47
1.5: Organisms share many conserved core processes and features that evolved and are
widely distributed among organisms today. (EK1.B.1) ................................................................... 50
1. Evidence of Common Ancestry ................................................................................................... 50
1.6: Phylogenetic trees and cladograms are graphical representations (models) of evolutionary
history that can be tested. (EK1.B.2) ................................................................................................ 51
1. Phylogeny ...................................................................................................................................... 51
1.7: Speciation and extinction have occurred throughout the Earth’s history. (EK1.C.1) ...... 54
1. Speciation Concepts ....................................................................................................................... 54
1.8: Speciation may occur when two populations become reproductively isolated from each
other. (EK1.C.2) .................................................................................................................................... 55
1. Speciation process.......................................................................................................................... 56
1.9: Populations of organisms continue to evolve. (EK1.C.3) ....................................................... 57
1. Ongoing evolution of organisms ................................................................................................... 57
1.10: There are several hypotheses about the natural origin of life on Earth, each with
supporting scientific evidence. (EK1.D.1).......................................................................................... 58
1. Origin of life .................................................................................................................................... 58
Domain 2:
Matter ................................................................................ 63
2.1: Organisms must exchange matter with the environment to grow, reproduce and maintain
organization.
(EK2.A.3)....................................................................................................................... 63
1. Matter exchange ............................................................................................................................. 63
2. Properties of Water ........................................................................................................................ 65
3. MATH Skills: pH ........................................................................................................................... 66
4. Constraints on Cell Size ................................................................................................................ 67
5. MATH Skills: Surface Area:Volume Ratio .................................................................................. 69
2.2: The subcomponents of biological molecules and their sequence determine the properties
of that molecule. (EK4.A.1) ................................................................................................................. 70
1. Biological Molecules ..................................................................................................................... 70
2.3: Variation in molecular units provides cells with a wider range of functions. (EK4.C.1) .. 71
1. Variation in Biological Molecules- Carbohydrates and Lipids .................................................. 72
2. Variation in Biological Molecules- Proteins .................................................................................. 72
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3. Variation in Biological Molecules- Nucleic Acids......................................................................... 74
2.4: Cell membranes are selectively permeable due to their structure.
(EK2.B.1) .................. 75
1. Cell Membrane Structure ............................................................................................................... 75
2.5: Growth and dynamic homeostasis are maintained by the constant movement of
molecules across membranes.
(EK2.B.2)........................................................................................ 77
1. Mechanisms of Cellular Transport .............................................................................................. 77
2. Analyzing Transport ........................................................................................................................ 79
3. MATH Skills: Water Potential and Solute Potential .................................................................. 81
2.6: Eukaryotic cells maintain internal membranes that partition the cell into specialized
regions.
(EK2.B.3) ............................................................................................................................... 83
1. Cellular Compartmentalization ....................................................................................................... 84
2. Major Eukaryotic Organelles .......................................................................................................... 85
2.7: The structure and function of subcellular components, and their interactions, provide
essential cellular processes. (EK4.A.2) ............................................................................................. 86
1. Organelle structure and function- information processing .......................................................... 87
2. Organelle structure and function- matter and energy processing............................................ 87
Domain 3:
Energy ............................................................................... 90
3.1: All living systems require constant input of free energy. (EK2.A.1) .................................... 90
1. Bioenergetic Theory ...................................................................................................................... 90
2. MATH Skills: Gibbs Free Energy ................................................................................................ 91
3. Metabolic Strategies ....................................................................................................................... 94
4. MATH Skills: Coefficient Q10 ...................................................................................................... 96
3.2: Interactions between molecules affect their structure and function. (EK4.B.1) .................. 98
1. Enzyme structure and function .................................................................................................... 98
2. Regulation of Enzyme Activity..................................................................................................... 100
3.3: Organisms capture and store free energy for use in biological processes.
(EK2.A.2) . 102
1. Energy Processing ...................................................................................................................... 102
2. Photoautotrophic nutrition- light reactions ................................................................................. 104
3. Photoautotrophic nutrition 2- Carbon fixation ........................................................................... 106
4. Chemoheterotrophic nutrition- anaerobic cellular respiration .................................................. 107
5. Chemoheterotrophic nutrition: Aerobic cellular respiration .................................................... 109
3.4: Cooperative interactions within organisms promote efficiency in the use of energy and
matter. (EK4.B.2) ................................................................................................................................ 111
1. Organizational efficiency in energy processing. ....................................................................... 111
Domain 4:
Information ...................................................................... 114
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4.1: DNA, and in some cases RNA, is the primary source of heritable information. (EK3.A.1)
................................................................................................................................................................ 114
1. DNA Structure ............................................................................................................................. 114
2. DNA Replication............................................................................................................................ 117
3. Protein Synthesis ........................................................................................................................ 119
4. Genetic Information Processing & Expression ......................................................................... 121
5. Genetic Engineering- Techniques ............................................................................................... 123
6. Genetic Engineering- Applications............................................................................................... 125
4.2: In eukaryotes, heritable information is passed to the next generation via processes that
include the cell cycle and mitosis or meiosis plus fertilization. (EK3.A.2) ............................... 128
1. Mitosis .......................................................................................................................................... 132
2. Cell Cycle Control....................................................................................................................... 133
3. Meiosis ........................................................................................................................................... 135
4.3: The chromosomal basis of inheritance provides an understanding of the pattern of
passage (transmission) of genes from parent to offspring. (EK3.A.3) ....................................... 138
1. Mendelian Genetics .................................................................................................................... 138
2. MATH SKILLS: Genetics Probabilities ...................................................................................... 141
3. Chromosomal Disorders ............................................................................................................... 137
4.4: The inheritance pattern of many traits cannot be explained by simple Mendelian genetics.
(EK3.A.4) ................................................................................................................................................ 143
1. Mendelian Extensions ................................................................................................................. 143
2. Non-Mendelian Traits .................................................................................................................. 143
4.5: Gene regulation results in differential gene expression, leading to cell specialization.
(EK3.B.1) ................................................................................................................................................ 146
1. Gene Regulation ......................................................................................................................... 146
2. Prokaryotic Gene Regulation ..................................................................................................... 148
3. Eukaryotic Gene Regulation ...................................................................................................... 150
4. Gene Regulation  Phenotype................................................................................................... 152
4.6: A variety of intercellular and intracellular signal transmissions mediate gene expression.
(EK3.B.2) ................................................................................................................................................ 153
1. Signal Control of Gene Expression .......................................................................................... 153
4.7: Changes in genotype can result in changes in phenotype. (EK3.C.1).............................. 126
1. Mutations...................................................................................................................................... 126
4.8: Biological systems have multiple processes that increase genetic variation. (EK3.C.2) 145
1. Generation of Variation .............................................................................................................. 145
4
4.9: Viral replication results in genetic variation, and viral infection can introduce genetic
variation into the hosts. (EK3.C.3)................................................................................................... 128
1. Viral Genetics................................................................................................................................ 128
4.10: Environmental factors influence the expression of the genotype in an organism.
(EK4.C.2)................................................................................................................................................ 154
1. Environmental Effects on Phenotype. ....................................................................................... 154
Domain 5:
Regulation....................................................................... 155
5.1: Timing and coordination of specific events are necessary for the normal development of
an organism, and these events are regulated by a variety of mechanisms. (EK2.E.1) .......... 155
1. Development ................................................................................................................................ 155
5.2: Interactions between external stimuli and regulated gene expression result in
specialization of cells, tissues and organs. (EK4.A.3) ................................................................. 157
1. Differentiation ............................................................................................................................... 157
5.3: Organisms use feedback mechanisms to maintain their internal environments and
respond to external environmental changes.
(EK2.C.1) ............................................................. 158
1. Feedback Loops.......................................................................................................................... 158
5.4: Homeostatic mechanisms reflect both common ancestry and divergence due to
adaptation in different environments. (EK2.D.2) ............................................................................ 160
Discussion 1: ..................................................................................................................................... 160
Discussion 2: ..................................................................................................................................... 162
5.5: Biological systems are affected by disruptions to their dynamic homeostasis. (EK2.D.3)
................................................................................................................................................................ 162
1. Effects of Disruptions ................................................................................................................. 162
5.6: Plants and animals have a variety of chemical defenses against infections that affect
dynamic homeostasis. (EK2.D.4) ...................................................................................................... 164
1. Immune Systems. ....................................................................................................................... 165
5.7: Timing and coordination of behavior are regulated by various mechanisms and are
important in natural selection. (EK2.E.2) ........................................................................................ 167
Discussion 1: ..................................................................................................................................... 167
Domain 6:
Communication .............................................................. 170
6.1: Cell communication processes share common features that reflect a shared evolutionary
history. (EK3.D.1) ................................................................................................................................ 170
1. Introduction to Communication .................................................................................................. 170
6.2: Cells communicate with each other through direct contact with other cells or from a
distance via chemical signaling. (EK3.D.2) .................................................................................... 171
5
1. Types of Cellular Signals ............................................................................................................ 171
6.3: Signal transduction pathways link signal reception with cellular response. (EK3.D.3) ... 173
1. Signal Transduction Pathways .................................................................................................... 173
6.4: Changes in signal transduction pathways can alter cellular response. (EK3.D.4) .......... 176
1. Alterations to Signaling Pathways............................................................................................... 176
6.5: Individuals can act on information and communicate it to others. (EK3.E.1) .................. 177
1. Communication Between Organisms......................................................................................... 178
6.6: Animals have nervous systems that detect external and internal signals, transmit and
integrate information, and produce responses. (EK3.E.2) ............................................................ 180
1. Neurons ......................................................................................................................................... 180
2. Nervous Systems .......................................................................................................................... 184
Domain 7:
Interactions ..................................................................... 186
7.1: Organisms exhibit complex properties due to interactions between their constituent parts.
(EK4.A.4) ................................................................................................................................................ 186
1. Physiological Interactions ............................................................................................................. 186
7.2: Organisms respond to changes in their external environments. (EK2.C.2) ...................... 188
1. Responses to the Environment ................................................................................................. 188
7.3: Interactions among living systems and with their environment result in the movement of
matter and energy. (EK4.A.6) ........................................................................................................... 189
1. Energy and Matter Acquisition .................................................................................................. 190
2: MATH SKILLS: Productivity Calculations ................................................................................ 193
7.4: All biological systems from cells and organisms to populations, communities and
ecosystems are affected by complex biotic and abiotic interactions involving exchange of
matter and free energy. (EK2.D.1) .................................................................................................. 194
1. Limiting Factors............................................................................................................................. 194
7.5: The level of variation in a population affects population dynamics. (EK4.C.3) ............... 196
1. Population Diversity ...................................................................................................................... 196
7.6: Interactions between and within populations influence patterns of species distribution and
abundance. (EK4.B.3) ........................................................................................................................ 197
1. Community Interactions ................................................................................................................ 198
7.7: Communities are composed of populations of organisms that interact in complex ways.
(EK4.A.5) ................................................................................................................................................ 199
1. Measuring Communities ............................................................................................................... 199
2. MATH SKILLS: Population Growth Equations ......................................................................... 200
7.8: The diversity of species within an ecosystem may influence the stability of the
ecosystem. (EK4.C.4) ......................................................................................................................... 202
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1. Ecosystem Stability ....................................................................................................................... 202
7.9: Distribution of local and global ecosystems changes over time. (EK4.B.4) ..................... 204
1. Ecosystem Changes ..................................................................................................................... 204
7
Overview and Introduction:
1: Overview of this course, and the instructional sequence
presented.
AP Biology is a survey of introductory college-level biology.
Two major parts:
The practice of being a biologist (the Science
Practices), and the knowledge that
biological investigations have generated about the functioning of
living systems.
We can’t spend a lot of time on the first part in video lessons.
But
the skills that you use can and should be applied to the second
part as much as possible.
Given the format, a lot of this application is going to have to
happen by yourself.
in the format.
I’m here to help, but I can only do so much
For you to get the most out of this process, you
will need to take a very active role in your learning.
You can sit
and passively watch the videos and hope the content sticks in
your brain, or you can actively engage with the material that we
will be discussing, writing notes and jotting down the questions
8
that you have as you go through the videos. Then you can
work to get the answers to those questions in a lot of different
places (your teacher, your textbook, and the internet are three
obvious sources).
We will take a brief tour of the seven science practices first to
make sure we are all speaking the same language, and then we
will move in to the content of the course.
I have organized the course content in to seven “domains”, each of
which deal with one major aspect of living systems.
I have a
preferred order to move through them, but they should be able to
be viewed in whatever order works best for you (though within a
domain, it’s best to start at the beginning and move your way
through sequentially).
This organization may be somewhat
different from the order of your class.
That’s okay (it’s actually a
good thing, because you’ll get a different way to look at the
content of this course).
The material that we will discuss is aligned to the AP Biology
Curriculum Framework, which is published by the College Board,
and freely available to anyone with an internet connection.
You
9
can get a copy if you really want, but it’s written for teachers,
and may not be so easy for students to use.
Important note:
The examples that I use are not the only
examples that can be used to address the concepts of this
course.
I’ve marked the examples with the notation “Ex.”, so that
you can easily identify them, and try to supply alternative
examples if you can (that will be really helpful for you).
2: The AP exam.
The AP Biology exam is a 3-hour exam, administered in mid-May.
Depending on your school’s policies
you either have to take it, or will be encouraged to take it (and you
should take it).
You are allowed to bring pencils, pens, and a four-function scientific
calculator (a square root function is
also allowed).
A copy of the formula sheet will be provided for you
(you can not use your own).
The Curriculum Framework contains a list of “learner objectives”.
These are the things that you will be
10
expected to do on the exam.
If you consult the learner objectives,
you will notice that they are written in
such a way as to allow for a wide variety of questions.
Demo Formula Sheet
Sample Learner Objective:
LO 1.1 The student is able to convert
a data set from a table of numbers that reflect a change in the
genetic makeup of a population over time and to apply
mathematical methods and conceptual understandings to
investigate the cause(s) and effect(s) of this change. [See SP 1.5,
2.2]
The exam is broken into two sections:
Section 1:
Multiple Choice and Grid-In Questions:
There are 63
multiple-choice questions and 6 mathematical grid-in questions.
Each multiple choice question has four answer choices.
Many of
these questions will be on the content of the course directly, and
many of the questions will analyze your ability to read and
consider scientific information and apply that information to the
11
understandings of the course. The grid-in questions will require
you to perform a particular mathematical analysis (including BUT
NOT LIMITED to the equations on the formula sheet).
will be administered over a period of 80 minutes.
Section 1
Following
section 1, you will have a 10-minute break period before moving
on to section 2.
Section 2:
Constructed Response Questions:
constructed response questions.
There are 8
2 of these questions will be
multi-part essays, and 6 of them will be smaller, single-part
written responses.
The constructed response questions will also
assess your understanding of the course content and your ability
to consider and apply scientific information to the study of
Biology.
At least one question will require you to graphically
represent information, and your ability to design and analyze
experiments will also be a fundamental feature of this section.
To begin section 2, You will have a 10-minute reading period,
followed by an 80 minute period in which to write your answers.
Part 1 of the exam is graded by machine.
Part 2 of the exam is
graded at a “reading” which takes place in
12
mid-June, during which hundreds of AP Biology teachers and
College Professors meet to read and score
the questions.
Exam grades are on a 1-5 scale.
If you are
planning on attending college, high scores (4 or
5) will often allow you to receive credit for introductory-level Biology
courses, however the specific
policies on college credit vary from institution to institution.
Exam strategies:
Answer every question:
exam.
There is no penalty for guessing on the
You cannot get full credit in question two if you do not
answer all parts of every question.
Time yourself:
For section one, a good rule of thumb is to spend
no more than 1 minute per question.
This will give you 12
minutes at the end to go back and work on any very difficult
questions.
In part 2, you should plan to spend about half of
your time answering the first two, long essays, and then spend
the remaining time addressing the final six.
If you have spent 20
minutes a piece on the first two questions (40 minutes in total),
you have ~6 minutes for each of the shorter questions.
Write succinctly:
make sure to answer the question you are being
asked completely, but only write words that answer the question.
13
There are no points for literary elements in your writing.
Opening and closing paragraphs are useless and waste time.
Answer the question you are being asked:
question.
Do not stray from the
Make sure to address the question and then move on.
Get a good night’s sleep before the exam, and have a positive
attitude:
Both of these have been shown to have a significant
effect on exam performance.
14
A Tour of the Science Practices
SP 1: Use Representations and Models to Communicate Scientific
Phenomena and Solve Scientific Problems.
1. SP 1 discussion
Models are representations of thoughts.
Models can be physical, computational, mathematical, or literally any
other way that a thought can be represented (though in science,
they tend to be one of the first three, or maybe verbal).
You are expected to be able to create, describe, refine, use, and
re-express representations and models in the work that you do in
this course.
Be careful:
Do not make the mistake of confusing a model for the
reality that it represents.
Models are always simplifications of
reality.
3 ways to work on developing your modeling/representation skills:
When you are shown models or representations, take a moment
and acknowledge that is what is happening.
15
Create alternate models and representations of the concepts that
you are investigating from the ones that you are being shown by
your teacher. Develop your own examples of phenomena under
consideration.
Take models and representations that you are using in class, and
identify the simplifications in them.
Refine the model to show
this additional complexity (if possible—things can get very
complicated very quickly).
SP 2. Use Mathematics Appropriately.
1. SP 2 Discussion
Math is the most objective way we have to describe and model
scientific phenomena.
Math is as important to biology as any
other tool.
You are expected to be able to justify the selection of a
mathematical routine, apply a mathematical routine, and estimate
numerical quantities.
Biologists have an unfair reputation for not liking math.
acceptable.
This is not
Math must be embraced, and loved.
16
3 ways to work on developing your math skills:
Practice, practice, practice.
Keep trying to use the math of this
course wherever possible.
Try to come up with estimates of ridiculously big numbers. How
many hairs are on your head?
body?
How many cells are in your
The point is not to get the right answer, but to work
through the process of estimating such things.
When you see math being used in class, try to justify why the
math is appropriate for the task it is being used for.
2. MATH Skills:
Metric system
The metric system is the measurement system of science.
It is
based on powers of 10, which modify a
base quantity (assigned as 100, or as we all know it, 1) of the
major dimensions of matter, energy, and
time in the universe.
Prefixes are used to denote every power of
10 from 10-3 through 103, and then every three powers of ten
larger and smaller.
Biology ranges all over the metric system.
17
Selected prefixes and their quantities are provided on the formula
sheet that you will have during the AP exam.
Factor Prefix Symbol
109
giga
G
106
mega
M
103
kilo
k
10-2
centi
c
10-3
milli
m
10-6
micro
μ
10-9
nano
n
10-12
pico
p
There are a lot of benefits to using the metric system.
The common powers of 10 structure makes arithmetic with widely
different numbers very easy.
It is universal among all scientists on the planet.
A kilogram
always signifies the same mass.
18
You need to use the metric system in all data recording and data
calculations that you engage in during this course.
3. MATH Skills:
Dilutions
The dilution equation is provided on the formula sheet that you will
have during the AP exam.
It is useful in lab.
You may use it or not, but you need to be able
to use it (for the exam, and in your life as a competent
laboratory scientist:
C = concentration
V = Volume
i = initial
f = final
19
You will know (or be able to figure out) three of these variables.
You will use the equation to figure out the fourth.
Sample Problem:
How much of a solution of 2M sucrose must be
diluted to make 3L of a 1M sucrose solution?
ANSWER:
1.5 L
SP 3. Engage in scientific questioning to extend thinking or to
guide investigations within the course.
1. SP 3 Discussion
Not all questions can be addressed scientifically.
There are
inherent limitations on the kinds of questions that science can
answer.
Example:
What happens to us when we die?
Inherently limited in
what science can tell us
Scientific answer:
our bodies are decomposed back in to simpler
compounds, which are reincorporated by the ecosystems of the
planet.
20
You need to be able to pose, refine, and evaluate scientific
questions.
3 ways to work on developing your scientific questioning skills:
Question how the knowledge that you are learning in this course
was determined.
Work on asking scientifically useful/interesting questions…and then
refining them in to even better questions.
Analyze when a question is not going to be appropriate for
scientific investigation.
SP 4. Plan and implement data collection strategies appropriate to
a particular scientific question.
1. SP 4 Discussion
Science relies on data to help answer questions.
Data is generated in many different circumstances, including field
investigations and experimentation.
The circumstances in which data is collected will influence how
useful that data is for answering questions.
21
You need to be able to justify the selection of data, design a plan
to collect data, collect data, and evaluate sources of data.
3 ways to work on developing your data collection skills:
Identify which data sources will be most useful for answering
particular scientific questions.
Determine what sorts of equipment and procedures are used to
collect specific types of data.
Use the data sets generated by other scientists to develop your
answers to scientific questions.
SP 5. Perform Data Analysis and Evaluation of Evidence.
1. SP 5 Discussion
The analysis of data is how science develops explanations.
Analysis and evaluation of data include statistical, graphical, and
computational manipulation of a data source.
22
You need to be able to analyze data, refine observations and
measurements based on the analysis of data, and evaluate the
evidence provided by a data set.
3 ways to work on developing your data analysis skills:
When investigating a particular scientific explanation, evaluate the
data that supports (and refutes) the explanation.
In experimental settings, use the data that is being generated to
determine if the data is appropriate for the experiment.
Based
on this analysis, refine your experimental measurements if
necessary.
Determine the statistical aspects of a particular data set, and
consider how they support or refute a particular explanation for
the data set.
2. MATH Skills:
Descriptive statistics
Descriptive statistics are used to tell us about the characteristics of
a particular data set.
23
Each descriptive statistic tells us something different, and may be
more or less useful depending on the data set, and the concepts
it is supporting or refuting.
Mean, median, mode, range
Sample data set A:
Mean:
5cm, 5 cm, 10 cm, 20 cm
The sum of all of the data points in a data set, divided by
the number of items in the data set.
Explained on the Formula Sheet verbally and also presented in
sigma (sum) notation:
_
x = mean
n = size of the sample (number of
items)
Mean of sample data set A: 10cm
24
Mode:
The most common value among the items in the data set.
Mode of sample data set A: 5 cm
Median:
The middle value of the data set, or the mean of the
middle two values in the data set.
Median of sample data set A:
Range:
7.5 cm
The difference between the highest value and lowest value
in the data set.
Range of sample data set:
3. MATH Skills:
Standard Deviation:
the data set.
15 cm
Standard Deviation
A measurement of the variance of the items in
“How far away from the mean are the items in the
data set?”
25
The higher the standard deviation, the further away most data
points are from the mean of the data set.
The equation is on
the formula sheet in sigma notation.
Almost all data in a data set will lie within +/- 3 standard deviations
of the mean if the data has a normal distribution (“bell curve”).
68% of the data will lie within 1 standard deviation, 95 % will be
within two standard deviations, and 99.7% will be within three
standard deviations (if the data has a normal distribution).
s = standard deviation
Sample data set A:
std. dev:
Sample data set B:
std. dev:
5 cm, 5 cm, 10 cm, 20 cm
Mean:
10 cm
Mean:
10 cm
~7
8 cm, 9 cm, 11 cm, 12 cm
~2
26
These two data sets have the same mean, but their variance is
different.
The meaning of this depends on what the data refers
to.
4. MATH Skills:
Standard Error:
Standard Error
A measurement of the variation in the means of
data sets taken from the same population.
usually have different means.
those means will be.
Different samples will
Standard error tells us how varied
It is the standard deviation of the means
in a sample set.
Useful because if two data sets have means that are more than 2
standard errors away from each other (actually 1.96) have a 95%
confidence that they are statistically significant.
This is typically
the cut-off for being able to reject a null hypothesis (that the
variance between our observation and our expectation is due to
chance)
27
SE = standard error
Standard error of sample data set A:
~3.5
Standard error of sample data set B:
~1
Not a particularly useful statistic for this data set, since the means
of both samples are the same to begin with.
Two different data sets:
Sample set 1:
Mean:
~6.6g
6.2 g, 6.4 g, 6.6 g, 7.0 g
stdev= +/- ~0.34g
st. error:
+/- ~.17
Sample set 2:
Mean = ~12.5g
12.2 g, 12.3 g,
12.6 g, 13.0 g
stdev= +/- ~0.359g
st. error:
+/- ~.18
Here, there is a difference in the means, the standard deviations,
and the standard error of the two data sets.
28
The non-overlap indicates that there is at least a 95% confidence
that the differences between these two means is not due to
chance fluctuations in our data set
5. MATH Skills:
Hypothesis Testing
Our statistical expectation is NOT the same thing as our
experimental expectation.
The hypothesis of the experiment
governs how we frame our statistical expectation, but our
statistical hypothesis is ALWAYS the null hypothesis (that the
variation between expectation and observation is due to chance).
Chi-square:
A way to determine if the variance between what we
observe and what we expect in a set of categorical data is
statistically significant or not.
X2= chi-square value
o = observed values
e = expected values
29
It works best to calculate chi-square data methodically, using a
table approach.
The major areas where categorical data will be encountered in this
course will be in ecology (ex. distribution of organisms in an
environment) and mendelian genetics (ex. Number of progeny
that have certain inherited characteristics).
Sample problem:
An ecologist is habitat preferences of periwinkles on the rocky
coast line of the New England coast.
She hypothesizes that
more periwinkles will be found closer to the tide line.
To test
her hypothesis, she collects data by counting the number of
periwinkles within a .5 m2 quadrat sample that she observes on
a rocky coast line location at low tide:
Distance from low tide:
Number of periwinkles
observed:
At low tide line:
1 meter above low tide:
36
24
30
2 meters above low tide:
10
3 meters above low tide:
3
4 meters above low tide:
2
Total:
75
Determine if the difference in the number of periwinkles observed
in each location is statistically significant:
Step 1:
Frame the null hypothesis- “The difference between the
number of periwinkles that we observe at each location and the
number that we expect is due to chance.”
Fine, but what do we expect?
This step is a bit tricky.
Given the
experimental hypothesis, you might want to state that we expect
more periwinkles closer to the tide line.
But that would make it
impossible to do a chi-square analysis on this data (how many of
the periwinkles should we include for “more”?). So, our statistical
expectation is going to be different from our experimental
expectation.
For this analysis, the statistical expectation is that
periwinkles have no location preference.
This way, if the null
hypothesis is rejected, then we are saying that there is a
31
statistically significant difference in the distribution of periwinkles
on the shoreline, which supports our experimental hypothesis.
Also, by setting up our statistical test like this, we can easily
determine the “expected” values for each of our categories (equal
numbers of the total periwinkles that we have observed).
Chi Square Determination:
Category:
o(observed)
e(expected)
o-e o-e2 (o-e2)/e
At low tide
36
15
21
441 29.4
1 meter above
24
15
9
81
5.4
2 meters above
10
15
-5
25
1.7
3 meters above
3
15
-12 144
4 meters above
2
15
-13 169
X2 =
9.6
11.2
57.3
32
How to use the X2 value:
We compare the chi-square value to a
table of values, according to the number of degrees of freedom
in the data set (the number of categories – 1):
A p value less than or equal to .05 is the typical “cut-off” for
rejecting the null hypothesis (ie. There must be at least a 95%
probability that the variance we observe from what we expect is
NOT due to chance in order for us to reject the null hypothesis).
Our answer from above has 5 degrees of freedom (5 categories of
data).
Comparing our value of 57.3 to the chi-square table, we
can see that our value is above the .05 cutoff of 9.49 (it’s
actually well above the .01 cutoff).
This means that our null
hypothesis is rejected, and an alternative hypothesis (that the
difference between the observed and expected value is not due
to chance) is not rejected.
The results of this statistical
hypothesis test along with the observed data support our
experimental hypothesis.
33
If we don’t reject the null, it DOES NOT mean that the null is
accepted.
It just means that it has failed to be rejected.
SP 6. Work with scientific explanations and theories.
1. SP 6 Discussion
Scientific explanations are always tentative, and supported by
evidence.
The nature of science is not about “proving” anything.
Science works by falsifying possible explanations (“hypotheses”).
A scientific explanation must be testable.
If an explanation cannot
be tested, science can not support or refute it.
Scientific explanations that support a broad range of observable
phenomena are called “theories”.
Theories can be refined over
time to account for additional observations, or they can be
refuted, but they can never be “proven”.
You need to be able to justify claims with evidence, construct
explanations based on evidence, articulate the reasons an
34
explanation or theory is refined or replaced, and evaluate
alternative scientific explanations.
3 ways to develop your scientific explanation skills:
Never make a claim without evidence to support it (remember that
not all evidence is created equal).
Consider the evidence that supports the explanations and theories
that you will be exposed to in this course.
Explain how and why
they have had to be revised over time.
Consider alternative explanations for the phenomena that you
investigate in this course.
Analyze how the available evidence
supports or refutes these alternatives and determine possible
evidence that would support or refute them
SP 7. Connect and relate knowledge across various scales,
concepts, and domains.
1. SP 7 Discussion
Science connects concepts that span several spatial and temporal
scales (in biology, phenomena move from the atomic level to the
entire biosphere, and from fractions of a second to billions of
years).
35
Science also depends on many different kinds of information from a
variety of domains to make explanations.
Biological explanations
use physical, chemical, and mathematical information.
You need to be able to connect phenomena and models across
spatial and temporal scales, and connect concepts across
domains to generalize and extrapolate ideas.
3 ways to develop your “scale-domain” thinking:
Actively consider how the concepts of this course rely on
knowledge from a variety of domains.
Spend time relating temporal scales and spatial scales to the ones
that you are most familiar with.
Consider how biological explanations agree or conflict with
explanations from other sciences.
36
Domain 1: Evolution
1.1: Natural selection is a major mechanism of evolution.
(EK1.A.1)
1. Natural Selection
Darwin/Historical Evolutionary Development
Historical development of evolutionary thought pre-Darwin
Lyell- Geology, Uniformatarianism very old earth.
Malthus- Exponential Population Growth
LaMarck- Evolution.
Inheritance of acquired characteristics (wrong,
but still evolutionary)
Darwin- Uninspired youth.
Ship’s naturalist on board HMS Beagle.
Circumnavigation of the globe. Return to Europe and delay
publication of theory until pressed by Alfred Russell Wallace.
Natural Selection:
Inherent Variation in all organisms.
Overproduction of Offspring (Malthus)
37
Differential success (“fitness”) of different variants in survival and
reproduction (“adaptations”).
Inheritance of adaptations leads to populations becoming better
adapted for the environment over time.
Repeat for millions of years.
Fundamental conclusions:
Ancient age of the Earth (billions of years, not thousands)
Common Ancestry of all organisms on Earth (tree thinking).
Unsettled by Darwin:
Origin of Life
Origin of species
Nature of variation/inheritance
2. The Modern Synthesis
Connection of evolution to change in allele frequencies in
populations/ basic mathematical analysis.
The “Modern Synthesis”- connecting Darwinian evolution to
genetics and modern understanding of inheritance.
38
Traits are the result of genetic instructions in DNA (“genes”)
Variations in traits are the result of changes to genes
(“mutations”)
“alleles”:
different variants in traits
Evolution:
Example:
Changes in allele frequencies over time.
Galapagos Finches/Grant Studies
Studies of finch populations on an isolated island in the Galapagos.
Measurements of the beak dimensions of all birds on the island
every year for decades.
Able to connect changes in beak dimensions to fluctuations in the
environment (precipitation, seed sizes)
Relevant Misconceptions:
Evolution is a “population level” phenomenon.
The evolution of a
population emerges from the individual fitness of members of that
population.
As they survive and reproduce, or not, the
frequencies of alleles in the next generation will change
accordingly.
39
1.2: Natural selection acts on phenotypic variations in populations.
(EK1.A.2)
1. How Natural Selection Works.
Connection of Phenotype to Genotype (Basic Central Dogma)
Genotype:
The alleles that an individual has for a particular trait.
Homozygous:
Heterozygous:
Two copies of the same allele.
Two copies of different alleles for each trait.
Why do we have two alleles for each trait?
Because of sexual
reproduction.
Phenotype:
The trait that an individual shows.
Genotype determines phenotype.
Alleles control the production of proteins and the proteins
determine traits
Dominant vs. recessive alleles-
some alleles (“dominant”) will
control phenotype over other alleles (“recessive”) when both are
present.
Example:
Eye color (simplified)
40
Two alleles: Brown (B) and blue (b).
eyes and blue eyes.
Two phenotypes:
Brown
Individuals who are homozygous will either
have brown (BB) or blue (bb) eyes.
Brown is dominant and blue
is recessive, so heterozygotes will have brown eyes.
Relevant Misconception:
Dominant alleles are “better” than recessive alleles:
Dominant and
recessive have nothing to do with their effect on fitness.
They
only refer to how they contribute to phenotype expression.
Relationship between phenotype and fitness:
Different phenotypes will be more or less fit, depending upon the
requirements of the environment.
“Fitness”:
Ability to contribute genes to the next generation
(reproduction).
The environment determines fitness, and fitness may change as
the environment changes.
Example:
Pesticide Resistance
41
Individuals who are resistant to a pesticide will be more fit than
individuals who are not when the pesticide is present in the
environment.
If there is no pesticide present, resistance will not
contribute to fitness (may detract, depending on the nature of that
resistance).
Human impact on variation:
Humans are able to impact variation in other organisms by
controlling which individuals are able to reproduce.
Artificial selection:
When reproductive success is determined by
human requirements
Examples:
Dogs, monocrop fields
1.3: Evolutionary change is also driven by random processes.
(EK1.A.3)
1. Other Evolutionary Forces
Genetic Drift:
The random, non-selective, changes in allele frequency due to
chance events.
42
Genetic drift has a larger effect on smaller populations, since each
individual is a larger percentage of the total alleles in the
population.
The Founder Effect:
When the descendants of a small, founding population have
different percentages of alleles than the population that the
founders came from.
Example:
The rate of polydactyly in the Amish population is higher
than it is in the European population that the Amish came from.
The Bottleneck Effect:
Following a catastrophic decrease in a population, the survivors of
the “bottleneck” event may have a different percentage of alleles
than the pre-bottleneck population.
Example:
The Cheetah population underwent a major bottleneck
during the last ice age (and subsequent hunting).
Any two
cheetahs are genetically equivalent to identical twins.
43
Gene Flow:
The intermixing of alleles from two overlapping populations.
This
frequently leads to an “equalizing” of differences in allele
frequencies between populations.
Example:
The effect of human migration on population
characteristics since the industrial revolution.
Sexual Selection:
Selection for characteristics that aid an organism’s reproductive
success.
Often these characteristics may seem “maladaptive” for
the individual.
Examples: Peacocks (intersexual), dominance competitions
(intrasexual)
Relevant Misconceptions:
Evolution is a “random” process:
frequencies over time.
Evolution is a change in allele
There are random evolutionary processes
(genetic drift) and non-random, selective processes (natural
selection).
44
1.4: Biological evolution is supported by scientific evidence from
many disciplines, including mathematics. (EK1.A.4)
1. Evidence of Evolution
Geographical/Geological Evidence:
Radiometric dating enables the age of fossils and rock layers to be
determined and establishes the age of the Earth as ~4.5 billion
years.
The appearance of similar fossils on different continents
correlates to the positions of those continents over geologic time,
accounting for continental drift.
The fossil record establishes a history of life on Earth.
are no “anachronisms” in the fossil record.
There
Fish show up millions
of years before mammals.
Living organisms resemble fossilized, extinct forms.
Fossilized organisms showing major evolutionary transitions
between groups are found with regularity.
Example: Tiktallik
45
Anatomical Evidence:
Similarities and differences in the anatomy (morphology) of
organisms provide evidence/clues to how they have evolved.
Vestigial structures:
Structures that have lost their primary
adaptive purpose.
Example:
Whale hind limbs
Homologous structures:
Structures present in a common ancestor,
which have diverged during evolution.
Example:
Vertebrate limbs.
Analogous structures:
Structures that have evolved multiple times
in different lineages to fill similar adaptive needs.
Example:
Wings
Chemical Evidence:
Similarities and differences in DNA and protein sequences. As
lineages diverge, they will accumulate mutations in DNA
sequences, which will alter the sequences of proteins.
46
Mathematical Modeling:
Computational analysis of evolution:
The ability to analyze large
amounts of chemical sequence data to establish evolutionary
relationships among organisms.
Hardy-Weinberg Theory:
The ability to quantify the amount of
evolutionary change from generation to generation to determine
how evolution is affecting the population.
2.
MATH Skills: HW Theory
Hardy-Weinberg equations enable us to determine how much a
population is evolving from generation to
generation.
“Hardy-Weinberg equilibrium”:
population.
Refers to an idealized, non-evolving
Five characteristics:
Large size (no genetic drift)
Random mating (no sexual selection)
Stable environment (no natural selection)
No immigration/emigration (no gene flow)
47
No mutations.
No real population is in HW equilibrium.
Two equations (for a trait controlled by two alleles, where p is the
dominant allele and q is the recessive allele):
Gene pool equation:
p + q = 1
p = frequency of dominant allele, q= frequency of recessive allele
Organism equation:
p2 + 2pq + q2 = 1
p2 = frequency of homozygous dominant individuals, 2pq =
frequency of heterozygotes, and q2 = frequency of homozygous
recessive individuals
To solve HW equations, always determine the frequency of
recessive individuals first, and use that to solve the rest of the
equation.
Sample problem:
In pea plants, the allele for purple flowers is
dominant to the allele for white
48
flowers.
If 99% of the plants in the population have purple
flowers, determine the percentage of heterozygotes in the
population.
Solution:
Given:
99% (.99 frequency) have purple flowers.
Can’t
say how much are p2 and how much are 2pq. But we do know
that p2 + 2pq + q2 = 1, and that in this case p2 + 2pq = .99.
So we can solve for q2, which is .01 (1 percent).
Now we solve
for q, by taking the square root of .01 which is .1 (square root
weirdness in decimal land!).
percent).
If q is .1, than p = 1 - .1, or .9 (90
Now that we know that, we can solve for the
frequency of p2 which is .92 = .81, and the frequency of 2pq,
which is 2*.9*.1 = .18.
So 18% of our population are
heterozygous for flower color.
If the data in a HW problem does not add up to 1, then the
population is NOT in HW equilibrium.
Uses of HW equilibrium:
To determine how a population is evolving from generation to
generation. (Is the population out of HW equilibrium?
Are the p
and q frequencies changing over generations?)
49
To help to determine which evolutionary pressures are affecting a
population more/less.
1.5: Organisms share many conserved core processes and
features that evolved and are widely distributed among
organisms today. (EK1.B.1)
1. Evidence of Common Ancestry
Genetic Code:
All cellular organisms use DNA to store genetic information,
expressing that information through RNA in to protein structure.
The “genetic code” that translates nucleic acid into protein
structure is essentially universal among all lineages of life.
Metabolic Pathways:
All cellular organisms produce usable energy through similar
metabolic pathways.
Example:
glycolysis is the first energy producing metabolic
pathway in essentially every cell on the planet.
Cellular Morphological similarities:
50
All cells on the planet are structured on one of two major
organizational plans.
Prokaryotes:
Cells that lack any internal membrane-enclosed
compartments (“organelles”)
Eukaryotes:
Cells that contain a variety of internal organelles.
Endosymbiosis:
The theory that major eukaryotic organelles (mitochondria and
chloroplasts) evolved from free-living prokaryotic cells that were
engulfed and internalized by eukaryotic ancestors.
Evidence:
DNA sequences, reproduction patterns, double
membrane structure.
1.6: Phylogenetic trees and cladograms are graphical
representations (models) of evolutionary history that can be
tested. (EK1.B.2)
1.
Phylogeny
Phylogenetic tree/cladogram construction:
A cladogram is a diagram that groups items according to the
number of traits that they have in common:
51
The number of characteristics that are shared among the items are
determined.
The items are then arranged in a “tree diagram” to represent these
similarities.
A phylogenetic tree is a cladogram that groups organisms according
to the number of evolutionary traits that they have in common.
Characters/Sequence Data:
To construct a phylogenetic tree, either “shared derived
characters” are used (traits that are representative of the
evolution of the organisms), or the amount of similarity in
DNA/protein sequence information is looked at.
Examples:
vertebrate tree, whole life tree.
Phylogenetic tree construction:
Determine similarities among organisms (character table works well).
Arrange organisms in a tree diagram showing simplest possible
evolution.
52
Maximum parsimony:
All else being equal, a trait is assumed to
only evolve once and be present in all of the descendant
organisms.
SKILL Create A Tree:
Animal
Selected Vertebrates
Opposable
4-chamber Amniotic
Thumb
heart
lungs Spinal
egg
colum
n
Chimpanzee 1
1
1
1
1
Mouse
0
1
1
1
1
Turtle
0
0
1
1
1
Frog
0
0
0
1
1
Fish
0
0
0
0
1
Lamprey
0
0
0
0
0
Continual revision:
As more data is gathered, the phylogenetic relationships among
organisms are continually revised to incorporate that data.
53
Role of computers:
Computer analysis is needed to determine the similarities in
DNA/protein sequence information, as the amount of data is
beyond the human capacity to analyze quickly.
1.7: Speciation and extinction have occurred throughout the
Earth’s history. (EK1.C.1)
1. Speciation Concepts
Species concepts:
Not discussed by Darwin.
“Biological Species”:
A group of organisms that are capable of
successfully reproducing with eachother.
Certain limitations (bacteria?
It’s testable!
Triceratops?):
Have resulted in
other definitions of the term.
Speciation rates:
How quickly do new species evolve?
54
Gradualism:
species are the product of slowly accumulating, small
evolutionary changes.
Punctuated equilibrium:
species undergo long periods of very little
change, followed by rapid, large evolutionary changes.
Evidence for both.
Example:
Major Extinctions- eventually all species go extinct.
There are several periods of greatly increased rates of extinction
through the fossil record.
Following these Mass extinctions, the
species that survive quickly diversify and occupy the vacated
niches left open.
Adaptive radiation:
When one species evolves in to many species that occupy a
variety of available niches.
Common after Mass extinctions
(consider the mammals after the dinosaurs), or when organisms
are isolated on islands (consider the Galapagos finches)
1.8: Speciation may occur when two populations become
reproductively isolated from each other. (EK1.C.2)
55
1. Speciation process
Reproductive Isolation:
If a species is a group of interbreeding organisms, than speciation
occurs when a group of organisms can no longer breed with any
other individuals.
Does the speciation occur when the organisms are physically
separated from their parent population (allopatric), or does it
occur when the organisms are physically in contact with their
parent population (sympatric).
Species Barriers:
Anything that separates one species from another:
Pre-zygotic Barriers:
Prevent gametes from combining into a
fertilized zygote
Physical Barriers- geographical
Temporal Barriers- time of day/seasonal
Behavioral Barriers- mating rituals
Mechanical Barriers- incompatibility of reproductive structures
Chemical Barriers- incompatibility of proteins on gametes
56
Post-zygotic Barriers:
Prevent the hybrid zygote from becoming an
organism capable of reproducing
Reduced viability-
Hybrid is frail
Reduced fertility- hybrid is sterile
Loss of hybrid characters- hybrid loses hybrid traits over
generations.
Examples: Mules, Apples, Fruit Fly Food Preference Study.
1.9: Populations of organisms continue to evolve. (EK1.C.3)
1. Ongoing evolution of organisms
Ongoing evolution of organisms:
Evolution is an ongoing process that can be observed and
studied in currently living populations of organisms.
Examples:
Pesticide resistance:
The application of pesticides to crops drives
the evolution of pesticide resistance among pest organisms, which
requires increased pesticide in subsequent applications.
Rock Pocket Mice:
Coat coloration evolution has been driven by
differences in the rock coloration where the populations live.
57
Different black populations have evolved different mechanisms of
melanin production (“convergent evolution”)
HW eq. applications:
HW Equilibrium can be used to analyze how a population is
evolving from one generation to the next.
1.10: There are several hypotheses about the natural origin of life
on Earth, each with supporting scientific evidence. (EK1.D.1)
1. Origin of life
Nature of science re:
Testable hypotheses for life’s origin.
Two Major hypotheses.
Panspermia:
Life has an extraterrestrial origin, arriving on a meteor
or similar delivery system
Abiogenesis:
The origin of living systems from non-living components.
A
scientific hypothesis because it provides testable predictions.
Four major “milestones” for life to develop from non-life:
Development of the chemicals that living systems are made of.
58
Encapsulation of those chemicals into isolated systems.
Development of an information storage molecule that can be
inherited.
Reproduction of living systems.
RNA world:
The hypothesis that RNA preceded DNA.
Due to RNA’s “double
function” in living systems as an information storage molecule
and a catalytic molecule.
Evolution of metabolic pathways:
The development of the major ways that living systems process
matter and energy.
Glycolysis is thought to have evolved first,
as all modern living systems use it as the first energy production
pathway.
Photosynthesis evolved later, leading to the
oxygenation of the atmosphere.
Aerobic cellular respiration
evolved last, as it requires atmospheric oxygen to be
accomplished.
Endosymbiosis:
The origin of eukaryotic cells from prokaryotic ancestors.
Free-
living ancestors of eukaryotic mitochondria and chloroplasts were
59
engulfed by eukaryotic ancestors, and a symbiotic arrangement
was established.
Supported by a lot of evidence.
Evolution of multicellularity:
Multicellular organisms are able to specialize the structures and
functions of their cells to occupy niches that are unavailable to
unicellular organisms.
Many unicellular organisms have
multicellular life stages, and the systems that multicellular
organisms use to coordinate and communicate among their cells
are evolved from systems that are present in unicellular
organisms.
Deep Time Considerations:
Approximate evolutionary dates (based on current evidence):
Formation of the Earth:
4.5 bya
Origin of life:
Origin of Photosynthesis:
~4
3
Origin of Eukaryotes:
Multicellular life:
Origin of Animals:
bya
bya
2
bya
1
bya
600 mya
60
1.11: Scientific evidence from many different disciplines supports
models of the origin of life. (EK1.D.2)
Discussion 1: Evidence for the Origin of Life
Geological evidence (Dating, Banded Iron, etc.):
Radioisotope dating allows us to establish the approximate age of
fossil evidence.
Different events in life’s history have left geological evidence:
Banded Iron formations:
Deposits of Iron Oxides that coincide with
the hypothesized origin of photosynthesis.
Fossil Fuels:
Massive deposits of fossilized plants and other
producers from the Carboniferous period.
Miller-Urey Experiments:
Starting with simple chemical building blocks, in conditions that
were hypothesized to approximate early earth conditions, simple
organic molecules were produced (step 1 of abiogenesis).
This
finding has been replicated in a variety of experimental conditions.
Commonalities of all organisms:
61
The commonalities among all living systems support evolutionary
descent from a single common ancestor.
It is the simplest
hypothesis to explain the observation.
62
Domain 2: Matter
2.1: Organisms must exchange matter with the environment to
grow, reproduce and maintain organization. (EK2.A.3)
1. Matter exchange
The atoms in living systems are common on this planet.
Living
systems are mostly made of 6 elements
and a handful of other “trace” elements.
Living systems cycle matter from the environment, turning it in to
biologically useful molecules before
returning it back to the environment through life processes.
Carbon:
Carbon is the major structural atom in all organic molecules.
The major non-living source of carbon is the atmosphere (as
CO2).
Carbon is incorporated in to producers through
photosynthesis and from there in to living systems through the
food chain, and returned back to the environment through cellular
respiration, and decomposition.
Oxygen:
63
Oxygen is also found in most organic molecules.
The major
non-living source of oxygen is the atmosphere (as O2) and water
(also the major non-living source of hydrogen).
Oxygen is
incorporated in to cellular respiration and through the food chain.
Oxygen is returned back to the environment through
photosynthesis.
Nitrogen:
Nitrogen is found in all proteins and nucleic acids (present in all
living systems).
The major non-living source of Nitrogen is the
atmosphere (as N2).
Nitrogen is incorporated in to the food
chain through the action of nitrogen-fixing bacteria, which convert
N2 in to molecules that can be used by producers (NO3-), and
from producers through the food chain.
Nitrogen is returned back
to the environment through decomposition and the action of
denitrifying bacteria.
Phosphorous and Sulfur:
Phosphorous is found in all nucleic acids.
Phosphate groups are
used to quickly store and release free energy in cells.
found in all proteins.
elements is rocks.
Sulfur is
The major non-living source of these
Weathering processes release them in to the
64
soil/water, where they are available for producers to incorporate
and then move through the food chain.
Decomposition returns
them back to the environment.
Hydrogen:
Hydrogen is a major component of all organic molecules.
the most common atom in the Universe.
It is
It enters biological
systems largely bonded to oxygen in water, and is returned to
the environment by decomposition and water release.
2. Properties of Water
Water is a major component of all living systems.
Water molecules occupy most of a cell’s volume.
Water has major properties that living systems require.
These properties are due to water’s polarity (unequal sharing of
electrons, leading to a partially positive
and partially negative charge).
65
Hydrogen Bonds:
the polarity of water results in attractive forces
between the oxygen and hydrogen atoms of neighboring water
molecules.
This makes water cohesive (attracted to itself) and
adhesive (attractive to anything else that has positive or negative
charges).
Uses:
Transpiration pull, dissolving of substances.
Temperature buffering:
The presence of hydrogen bonds requires
more energy to be absorbed or released by a given amount of
water to change the temperature of that water.
the specific heat of a substance.
heat.
This is known as
Water has a very high specific
Water can absorb or release a comparatively large amount
of energy before its temperature changes.
Water will keep the
environment warmer when the air cools (because it has a larger
store of energy to release), and keep the environment cooler
when the air warms (because it can absorb a larger amount of
energy without changing temperature).
Uses:
Insulating the ocean. Keeping living systems within
homeostatic temperature ranges.
3. MATH Skills:
pH
66
Water dissociates. A water molecule can be pulled apart into a proton (H+) and a
Hydroxide ion (OH-) by other water molecules. This happens ~ once for every
10,000,000 (107) water molecules.
The products of the H+ and OH- ion concentrations in an aqueous solution is a
physical constant (10-14). As the concentration of one ion increases, the other
must decrease.
In pure water, the concentrations of H+ and OH- are each 10-7 (one in 10 million).
Acids: substances that increase the amount of H+ ions in an aqueous solution.
This will cause the concentration of OH- ions to decrease.
Bases: Substances that decrease the amount of H+ ions in an aqueous solution.
This will cause the concentration of H+ ions to increase.
pH: a measurement of the concentration of H+ ions in a solution.
pH = - log [H+]
This is a complicated way of saying that we can take the exponent of the pH
concentration and negate it (make it positive) to state the pH.
Acids have a pH lower than 7. Bases have a pH higher than 7.
Each whole number on the pH represents a power of 10. A solution with a pH
of 5 has a pH that is 100 times more acidic than a solution with a pH of 7.
4. Constraints on Cell Size
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Living systems are constrained by the need to exchange matter
with the environment.
Cellular life has an upper and lower limit on the size a cell can be:
Lower limit:
Constrained by the need to have a certain amount
of matter inside the cell in order to keep functioning.
Upper limit:
Constrained by efficiency.
Surface area: Volume ratio- as a three-dimensonal object’s volume
increases, so does its surface area.
However, volume increases
as a cubic function of size, while surface area increases as a
squared function.
As volume increases, the efficiency of a cell’s material exchange
with the environment decreases.
Surface Area Increase Adaptations:
A variety of structures have
evolved to maximize surface area in cells and increase material
exchange efficiency
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Examples:
Microvilli:
root hairs:
Plant root cells
Vertebrate intestines
5. MATH Skills:
Surface Area:Volume Ratio
Being able to calculate the surface area and volume of an object, if provided with
its physical dimensions.
Use the formula sheet to find relevant equations.
Sample problem: Determine the relative efficiency of material exchange for a
spherical cell with a radius of 10 μm, and a cubic cell with a side length of
10μm.
Determine the surface area:volume ratio
Surface Area of cube: 6xarea = 6 x 100um2 = 600um2
Volume of cube: l*w*h = 10 x 10 x 10 = 1000um3
SA:V ratio of cube: 600:1000 = .6
Surface Area of sphere: 4 pi r2 = 4 x 3.14 x 100 = ~1257 um2
Volume of a cube: 4/3 pi r3 = 4/3 * 3.14 * 1000 = ~4189 um3
SA:V ratio of sphere: 1257:4189 = ~.3
Divide the surface area by the volume. Smaller numbers mean more volume per
unit of surface area (less efficiency in transport.
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2.2: The subcomponents of biological molecules and their
sequence determine the properties of that molecule. (EK4.A.1)
1. Biological Molecules
Living systems are made of four major types of Macromolecule:
Carbohydrates- Sugars:
function in short-term energy storage
and structural support.
Lipids- Fats, oils, waxes:
function in long-term energy storage, cell
membrane structure, and cell signaling.
Proteins- function in all cellular processes.
Nucleic Acids- DNA and RNA:
function in information storage
and expression of that information by determining protein
sequences.
All macromolecules are synthesized via condensation reactions
(“dehydration synthesis”- the removal of water) and decomposed
via hydrolysis reactions (the addition of water).
Except for lipids, Macromolecules are polymers, made of repeating
subunits (monomers).
Carbohydrates:
Monomer:
Monosaccharide \ Polymer: polysaccharide
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Monosaccharides exist as ring structures.
Lipids:
Steroids, triglycerides, and phospholipids.
Proteins:
Monomer:
Amino acid \ Polymer: polypeptide
There are 20 different types of amino acids used in biological
systems.
They all have the same “Backbone” structure, but differ
based on the composition of the “variable group” that is bonded
to the central carbon.
The bond between two amino acids is referred to as a “peptide”
bond.
Nucleic Acids:
Monomer: nucleotides \ Polymer:
nucleic acid
There are two types of nucleic acids in biological systems (DNA
and RNA).
Each one is made of four types of nucleotides, which
differ from each other based on the type of nitrogenous base that
they contain (DNA:
ACTG / RNA:
ACUG)
2.3: Variation in molecular units provides cells with a wider range
of functions. (EK4.C.1)
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1. Variation in Biological Molecules- Carbohydrates and
Lipids
The structure of carbohydrates and lipids determines their function:
Ex:
Cellulose vs. Amylose (“starch”):
Both are polysaccharide
polymers of glucose monomers, but they vary in the connections
between monomers.
As a result, cellulose is not easily digested,
while amylose is very easily digested.
Ex:
Lipid membrane composition:
Cells will vary the lipid
composition of their membranes in order to respond to changes
in temperature.
One example- changes in cholesterol
concentration to resist increasing and decreasing membrane
fluidity.
2. Variation in Biological Molecules- Proteins
The structure of proteins determines their function:
Proteins are functionally responsible for all cellular processes.
They
have a wide and diverse variety of functions, which are
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determined by their structure.
Protein structure is discussed at
four levels of organization:
Primary structure:
the sequence of amino acids in a polypeptide.
This is determined by DNA.
Each amino acid is joined to the
next via a peptide bond.
Secondary structure:
Regular 3D structures that arise in
polypeptide chains due to hydrogen bonding between the oxygen,
nitrogen, and hydrogen of neighboring amino acids.
Since all
polypeptides are made of amino acids, these secondary
structures are found in all proteins.
Tertiary structure:
The unique 3D structure (“conformation”) of a
particular polypeptide chain, due to the variety of interactions
between the variable groups of the amino acids in the
polypeptide and the influence of the environment that the
polypeptide chain is in.
Quarternary structure:
Refers to the overall 3D shape of any
protein that is composed of more than one polypeptide chain.
Not all proteins have this level of structure.
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Ex:
Adult hemoglobin vs. fetal hemoglobin:
Differences in the
polypeptide chains that comprise fetal hemoglobin give the
molecule a higher binding affinity to oxygen, which is necessary
since the fetus needs to get its oxygen from its mothers
hemoglobin.
Ex:
Antibody structure:
Differences in the “variable” regions of the
proteins that comprise antibodies makes it possible to create
millions of different possible antibodies.
Denaturation: The disruption of the structure of a macromolecule
leading to a disruption of its function.
Caused by changes to the
environment of the molecule.
3. Variation in Biological Molecules- Nucleic Acids
Genetic variation leads to molecular variation.
DNA sequence determines protein sequence. Protein sequence
contributes to protein structure.
Protein structure determines
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protein function.
Protein function determines cellular function.
Cellular function determines organism function.
A change in DNA sequence can affect all levels of function in a
living system.
Ex:
Sickle cell anemia- one nucleotide change leads to one amino
acid change. This change alters the function of hemoglobin, and
leads to major disease effects in the organism.
New functions can arise via genetic duplications.
The duplication of
genetic information allows for new variations and adaptations.
Ex.
Antifreeze gene in fish-
temperatures.
allows fish to live in freezing
Evolved from pre-existing genes.
2.4: Cell membranes are selectively permeable due to their
structure. (EK2.B.1)
1. Cell Membrane Structure
Cell membrane structure and function:
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The cell membrane is the boundary between the cell and the
environment.
It also allows the cell to control which substances
pass in to and out of the cell.
The cell membrane is composed of a phospholipid bilayer with
embedded proteins (the “Fluid mosaic” model).
Phospholipid
structure causes them to have a hydrophilic phosphate group
“head”, and hydrophobic fatty acid “tails”.
This leads to
spontaneous arrangements in water with the phosphate heads
pointing toward the water molecules and the fatty acid tails
pointing away.
One such arrangement is the “bi-layer” seen in
cell membranes.
The membrane proteins have a variety of functions:
transport, cell-
cell contact and recognition, anchorage, enzymatic functions, and
others.
Selective Permeability:
Selective permeability is controlled through control of the proteins
present in the cell membrane.
Only small, non-polar molecules
are able to move through the phospholipid bi-layer.
All other
substances must move through proteins
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Cell Wall structure and function:
Many cells have a cell wall external to the cell membrane (animals
and animal-like cells are the only exception).
The cell wall is a
structure made of structural polysaccharides (cellulose in plants
and plant-like cells) that provides structural support, but no
dynamic control of transport.
2.5: Growth and dynamic homeostasis are maintained by the
constant movement of molecules across membranes.
(EK2.B.2)
1. Mechanisms of Cellular Transport
Passive Transport:
Refers to the diffusion of material, moving from an area of high
concentration to an area of low concentration across a membrane.
No energy is required by the cell to enable this process.
Simple/Facilitated Diffusion:
Simple diffusion:
movement through the bi-layer.
Only small non-
polar molecules can do this.
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Facilitated diffusion:
movement through a protein channel. Any
molecule that is not small and nonpolar must diffuse through a
protein pore in the membrane.
Ex: aquaporins.
Active Transport:
Refers to the movement of material from an area of low
concentration to an area of high concentration.
This requires energy, in order to work against the natural tendency
for molecules to diffuse.
Ex:
Na/K pump:
Cells always use
In order to move sodium out of the cell and
potassium in to the cell to establish specific concentrations.
ATP
is used to provide the energy needed to modulate the shape of
the pump proteins.
Bulk Transport:
The movement of large molecules in to or out of the cell.
Requires the use of a vesicle.
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Endocytosis:
Exocytosis:
Movement of large particles in to the cell.
Movement of large particles out of the cell.
2. Analyzing Transport
Tonicity:
A measurement of the relative concentrations of solute and
solvent in two different solutions.
Used to be able to determine how a cell (its internal solution) will
respond when placed in to different aqueous environments (the
external solution).
Three types of tonicity relationships:
Hypertonic:
The solution has more solute (and less solvent)
than the one being compared to.
Hypotonic:
The solution has less solute (and more solvent)
than the one being compared to.
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Isotonic:
The solution has the same amount of solute (and
solvent) as the one being compared to.
Tonicity relationships and effects on cells:
Without the expenditure of energy, material will always diffuse
from high concentration to low concentration, if it is able to move
across the membrane.
Solute will always move from hypertonic solutions to hypotonic
solutions.
Solvent will always move from hypotonic solutions to
hypertonic solutions.
As long as it is able to.
Cells placed in hypertonic solutions will gain solute and lose
solvent (water).
Plasmolysis:
The loss of water
Cells placed in hypotonic solutions will lose solute and gain
solvent (water).
Lysis:
The bursting of the cell membrane.
Animal-like cells are adapted to exist in isotonic solutions.
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Plant-like cells are adapted to exist in hypotonic solutions (the
presence of the cell wall prevents lysis).
3. MATH Skills:
Water Potential:
Water Potential and Solute Potential
A measurement of how likely water is to diffuse
(“osmosis”) in to an area.
Water will move from areas of higher water potential to areas of
lower water potential.
Pure water is assigned a water potential
of 0 (no net diffusion)
Water potential depends on several different factors, but we only
focus on the pressure difference (the “pressure potential”) and the
tonicity (the “solute potential”) as they are the only significant
factors in biological systems.
Water potential equation:
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Ψ – Water Potential
Ψp – pressure potential
Ψs – solute potential
The typical units of water potential are bars aka torr aka mmHg in
a barometer.
In any open air system with no active pressure generation, the
pressure potential will be zero, and the water potential will
depend entirely upon the solute potential.
This is the typical
case when investigating diffusion and osmosis in the lab.
Solute potential calculation
i = ionization constant for the solute (1.0 for sucrose, 2.0 for NaCl,
etc.)
C = molar concentration of the solute
R= pressure constant 0.0831 liter bars/mole K
T= temperature in Kelvin (C + 273)
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Sample Problem:
Determine which of the following solutions will gain the most
water if placed in to a sample of pure water in a piece of
dialysis tubing at the temperature indicated. Assume all
samples are at atmospheric pressure:
Solution:
Solute:
Tonicity:
Temperature
A
Sucrose
2M
298K
B
NaCl
1M
290K
C
Glucose
1M
300K
Water Potential Solution A = -1.0 * 2M * .0831 * 298K =
~ -49.5
bars
Water Potential Solution B = -2.0 * 1M * .0831 * 290K =
~ -
48.2 bars
Water Potential Solution C = -1.0 * 1M * .0831 * 300K =
~ -
24.9 bars
Expect C to gain the most water, since water potential is most
negative.
2.6: Eukaryotic cells maintain internal membranes that partition
the cell into specialized regions. (EK2.B.3)
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1. Cellular Compartmentalization
Compartmentalization:
Increased compartmentalization allows for increased control of life
processes, and increased efficiency of those processes, as
different components of the cell can function in different
environmental conditions.
Different areas of the cell can be specialized to perform different
processes.
Eukaryotes vs. Prokaryotes:
The major difference between the organization of eukaryotes and
prokaryotes is the amount of internal compartmentalization.
Prokaryotes:
The vast majority of life on earth.
internal compartments (“organelles”).
Possess no
Unicellular and smaller than
eukaryotic cells.
Eukaryotes:
Contain many different internal compartments
separated from the rest of the cell by membrane (“organelles”).
Most notably, the nucleus, but many others. Two major types:
“plant-like” and “animal-like”, according to how they process
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energy.
Most eukaryotes are unicellular, too, but all multicellular
organisms (fungi, animals, and plants) are eukaryotes.
Plant-like vs. Animal-like differences:
Plant-like cells contain chloroplasts (for photosynthesis), a large
central vacuole, and an external cell
wall.
Animals do not have any of these organelles.
2. Major Eukaryotic Organelles
Major Eukaryotic Organelles:
Nuclear membrane:
rest of the cell.
Surrounds and separates the DNA from the
Contains pores to allow material to enter and
exit the nucleus and interact with the DNA.
Golgi Apparatus:
A series of flattened membranous disks. Receive
vesicles of membrane and protein from the endoplasmic reticulum
and modify those proteins prior to routing them to their final
destinations.
Also the site of polysaccharide production for the
cell.
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Endoplasmic Reticulum:
throughout the cell.
A series of membranous channels that run
Responsible for producing all membrane
used by the cell and lot of roles in intercellular transport.
Divided in to two parts:
Rough ER:
smooth and rough
Named because it is covered in “bound” ribosomes.
The ribosomes are producing proteins that will be embedded in
membrane or exported from the cell.
Smooth ER:
Not covered in ribosomes.
Involved in toxin
detoxification.
Mitochondria:
The site of aerobic cellular respiration.
A double-
membrane structure, with a highly-folded inner membrane (a
surface area adaptation).
Chloroplasts:
The site of photosynthesis.
A double-membrane
structure with a highly-folded inner membrane (a surface area
adaptation).
2.7: The structure and function of subcellular components, and
their interactions, provide essential cellular processes.
(EK4.A.2)
86
1. Organelle structure and function- information processing
Ribosome structure and function:
All cells contain ribosomes.
Ribosomes are made of two
subunits of RNA and protein. They are able to assemble and
disassemble as required by the cell.
In eukaryotes they are able
to associate and disassociate with the endoplasmic reticulum.
Endomembrane System:
The cellular system by which the information in DNA is
expressed and incorporated in to cellular processes:
Nucleus  ER  Golgi  final destination (membrane or
export).
2. Organelle structure and function- matter and energy
processing
Mitochondria:
Mitochondria have a double membrane which allows for separation
of different processes that take place in the mitochondria.
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The highly folded inner membrane (the “cristae”) contains many
copies of the enzymes needed to produce ATP by the cell, with
maximized surface area.
Chloroplasts:
Chloroplasts have a double outer membrane with inner
membranous stacks called “thylakoids”.
The membrane of the thylakoid contains many copies of the
enzymes and chlorophyll needed to produce chemical energy
from solar radiation during the first part of photosynthesis (the
“light reactions”).
The inside of the thylakoids (the “stroma”) contain the enzymes
needed to produce chemical compounds during the second part
of photosynthesis (Carbon fixation).
Lysosomes:
Lysosomes are membrane-enclosed sacs that contain collections
of digestive, hydrolytic enzymes.
Lysosomes serve roles in
digestion of molecules, recycling a cell’s damaged components,
and programmed cell death.
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Vacuoles:
A vacuole is a membrane-bound sac that stores material.
Plants
have a large central vacuole that increases the cells surface
area: volume ratio by decreasing the active volume of the cell.
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Domain 3: Energy
3.1: All living systems require constant input of free energy.
(EK2.A.1)
1. Bioenergetic Theory
The First law of thermodynamics:
Energy cannot be created or
destroyed, only transformed.
Consequences for living systems:
Living systems need to
continually acquire and transform energy in order to do the work
necessary to remain alive (“metabolism”).
“Free energy”: The energy available in a system to do work.
The Second law of thermodynamics:
Every time energy is
transformed, the entropy (“disorder”) of the universe increases.
Consequences for living systems:
In order to increase their internal
order, or maintain it, living systems must process more ordered
forms of matter in to less ordered forms of matter.
90
Living systems are “open” systems:
Material and energy move in
to living systems from the environment.
Following processing,
living systems return matter and energy back to the environment
in less ordered forms.
In order to increase control of energy processing, living systems
produce free energy in multiple-step pathways, mediated by
enzyme catalysts (which lower the energy required to cause a
chemical reaction to occur).
Decreases in energy processing by living systems results in
disease/death, and an increase in the entropy of the living
system.
2. MATH Skills:
Gibbs Free Energy
Used to determine if a process can occur spontaneously or nonspontaneously.
91
If free energy is released during a process (“exergonic”) it will occur
spontaneously (no energy needed to sustain the reaction following
activation.
If free energy is absorbed during a process (“endergonic”), it will
occur non-spontaneously (energy will be continually needed to
sustain the reaction.
ΔG=
change in free energy (- = exergonic, + = endergonic)
ΔH= change in enthalpy for the reaction (- = exothermic, + =
endothermic)
T = kelvin temperature
ΔS = change in entropy (+ = entropy increase, - = entropy
decrease)
To solve problems, you’ll need to be given values.
Exothermic reactions that increase entropy are always exergonic (Ex.
Cellular Respiration)
92
Endothermic reactions that decrease entropy are always endergonic
(Ex. Photosynthesis).
Other reactions will be spontaneous or not depending on the
temperature at which they occur.
Sample Problem:
Determine which of the following reactions will occur
spontaneously at a temperature of 298K, justify your answer
mathematically:
Reaction 1:
A + B  AB
Delta H:
+245 KJ/mol
Delta S:
-.02 KJ/K
Reaction 2:
BC  B + C
Delta H:
-334 KJ/mol
Delta S:
+.12 KJ/K
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Reaction 1 Delta G= + 245 – (298*-.02) = + 250.96
Reaction 2 Delta G = -334 – (298*.12) = - 369.76
3. Metabolic Strategies
Uses of Biological free energy:
To accomplish cellular work (“metabolism”).
Living systems use
free energy to repair themselves (maintain order), grow (increase
their order), and reproduce (transmit order through time).
Catabolism:
Decomposition
vs. Anabolism:
Synthesis
Metabolic strategies:
The strategy an organism uses to acquire and process free energy
will have consequences for the life cycle of that organism.
Ex.:
endothermy & ectothermy
Ectotherms:
Organisms that conform their internal temperature to
the temperature of the environment.
Requires that an organism
only be metabolically active when the external temperature allows,
but benefits the organism by not requiring any energy expenditure
94
to maintain internal temperature.
Examples:
All organisms
except for birds and mammals.
Endotherms:
Organisms that maintain a metabolically optimal
internal temperature regardless of the external temperature.
Requires that an organism use free energy to maintain internal
temperature, but benefits the organism by allowing a high
metabolism, regardless of the external temperature.
Examples:
birds and mammals.
Effects of Body size on metabolic rate:
Larger organisms require less energy production per unit of mass
than smaller organisms.
This is due mainly to the decreased
surface area:volume ratio in larger organisms, leading to
decreased loss of heat energy to the environment.
Free energy considerations and reproduction:
Reproductive strategies are optimized for particular free energy
considerations.
95
Example:
seasonal reproduction- Organisms reproduce during
particular times of the year to make sure that they have enough
free energy stored to allow for the energy investment involved in
reproduction, and to provide the offspring with the free energy
necessary to grow following birth.
Consequences of insufficient free energy production for individuals,
populations, ecosystems:
All levels of biological systems are affected by the amount of free
energy available.
Individuals will suffer disease/death if they do
not get sufficient free energy as there is less energy to maintain
internal order.
Populations will decrease in reproductive output,
and decline in numbers as there is less energy being used to
maintain the number of individuals through reproduction.
Ecosystems will decrease in complexity and productivity, as there
is less energy moving through them.
4. MATH Skills:
Coefficient Q10
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t2 = higher temperature
t1 = lower temperature
k2= metabolic rate at higher temperature
k1= metabolic rate at lower temperature
Q10 = the factor by which the reaction rate increases when the
temperature is raised by ten degrees.
Q10 tells us how a particular process will be affected by a 10
degree change in temperature.
Most biological processes have a Q10 value between 2 and 3
Sample Problem:
Data taken to determine the effect of temperature on the rate of
respiration in a goldfish is given in the table below. Calculate
the Q10 value for this data.
Temperature (°C)
Heartbeats per minute
97
20
18
25
32
Solution:
Q10 = (32/18)(10/5) = ~1.78
2
= ~3.178
3.2: Interactions between molecules affect their structure and
function. (EK4.B.1)
1. Enzyme structure and function
The relationship between structure and function:
Because the structure of a molecule allows it to accomplish its
functions, changes to the structure of a molecule will also affect
its function.
These changes can have a negative or positive effect on the
function of a molecule.
Molecules can interact with other molecules or their environment in
order to change their structures.
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Enzymes:
Enzymes are reaction catalysts in biological systems.
Most enzymes are proteins, though RNA (“ribozymes”) also have
some catalytic functions.
Catalyst:
any substance that increases the rate of a chemical
reaction by lowering the activation energy of that reaction while
not participating in the reaction.
Enzymes work by physically positioning reactants (“substrate”) in
orientations that increase the likelihood of chemical bonds being
broken or formed.
Enzymes are highly specific for the substrates
that they interact with.
Typically, the name of an enzyme tells you about its substrate in
the first part of its name, and ends in –ase. Ex.
Protease,
lipase, polymerase.
The induced fit model of enzyme function:
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In order to catalyze a reaction, substrate molecules will physically
bind to an area of the enzyme called the “active site”.
The
binding of the substrate to the active site will cause the
conformation of the enzyme to change slightly, catalyzing the
reaction.
co-factors/co-enzymes:
In order to function, many enzymes require organic (co-enzymes:
“vitamins”) or inorganic (co-factors:
“minerals”) groups of atoms
to be complexed with the enzyme.
Ex.
Many enzymes involved
in interacting with DNA require zinc 2+ ions as co-factors.
2. Regulation of Enzyme Activity
Other molecules can affect enzyme structure and function:
Competitive interactions:
Refer to any substance that occupies the active site of an enzyme
that is not the substrate of that enzyme.
These interactions will
inhibit enzyme function.
Non-Competitive (“allosteric”) Interactions:
100
Refer to any substance that binds to an area of an enzyme that is
not the active site and by doing so affects the function of the
enzyme (usually by changing the shape of the active site).
In this way, the end product of a metabolic pathway can influence
the continuation of that pathway by interacting with an enzyme
that catalyzes an earlier step in the pathway (“feedback
inhibition”)
Environmental conditions affect enzyme structure and function:
The local environment of the enzyme can affect the shape of the
enzyme, which will affect the function of the enzyme.
Major
environmental factors include temperature, pH, and salt
concentration.
Other environmental variables can affect the function of the enzyme
by increasing or limiting enzyme-substrate binding.
Major factors
that do this include enzyme concentration, and substrate
concentration.
Enzyme action can be measured in many different ways:
Typical methods include:
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Appearance of a product.
Disappearance of a substrate.
Indirect analogs:
color change, change in temperature, etc.
3.3: Organisms capture and store free energy for use in biological
processes. (EK2.A.2)
1. Energy Processing
Autotrophic nutrition:
Autotrophs (“self-feeders”) are able to use energy from the
environment to convert inorganic molecules in to organic
compounds where free energy is stored.
They are the producers
in all food chains on Earth.
Photosynthetic organisms:
Use visible light energy to convert water
and carbon dioxide in to oxygen gas (waste product) and organic
compounds (sugar precursor molecules).
Examples:
all plants,
and phytoplankton (the major producers on the planet).
Chemosynthetic organisms:
Use high energy inorganic compounds
to convert carbon dioxide and water in to organic compounds.
The specific high energy compounds depend on the organism.
102
Example:
hydrothermal vent producers:
Use H2S as their high
energy compound, which is released from the vents.
Heterotrophic nutrition:
Heterotrophs release free energy from organic compounds (from
the food chain, either autotrophs or other heterotrophs), and
convert those organic compounds in to inorganic compounds.
Anaerobic heterotrophs:
release free energy.
anaerobes:
Do not require oxygen in order to
Examples:
many bacteria, yeast (facultative
can do it if they have to).
Aerobic heterotrophs:
Use oxygen to release free energy.
Release ~20X more free energy from food molecules than
anaerobes do. Examples:
all multicellular fungi and animals.
Electron shuttles:
Biological energy production utilizes reduction/oxidation reactions.
Electrons are taken from some molecules (oxidation) and
transferred to other molecules (oxidation).
directly.
This does not happen
The transfer of electrons occurs via “electron shuttle”
molecules, which can hold electrons when they are taken from
103
molecules and release them to other molecules when needed.
This transfer of electrons also bring protons along for the ride in
Biological systems.
Examples:
NAD+/NADH, FAD/FADH2,
NADP+/NADPH
ATP in Metabolism:
ATP is a short-term free energy storage molecule used in all
biological systems.
When a cell releases free energy from a
food molecule (or incorporates it from sunlight), that free energy
is used to turn a molecule of ADP (2 phosphates) in to a
molecule of ATP (3 phosphates).
The bond between the 2nd and
3rd phosphate is very unstable and easily broken.
When it is
broken, the free energy that is released is used by biological
systems to power cellular work.
2. Photoautotrophic nutrition- light reactions
Photosynthesis is a two-part process:
The light reactions
Carbon Fixation
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Mechanisms of photosynthesis- light reactions
Light is energy:
photons of specific wavelengths are used in the
light reactions.
The light reactions occur in specialized collections of proteins and
chlorophyll called photosystems.
These photosystems are
embedded in the thylakoid membranes of chloroplasts.
During the light reactions, light energy is used to remove electrons
from chlorophyll, and use those electrons to produce ATP and
NADPH.
When excited by photons, chlorophyll sends an electron in to the
excited state.
This excited electron then enters an electron transport chain of
proteins.
Water supplies photosystem II with replacement electrons, and
converts the water in to protons and molecular oxygen.
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Non-cyclic electron flow produces NADPH:
The ETC connects two different photosystems (PS II and PSI).
Electrons produced at PSII move to PSI.
Electrons produced at
PSI either cycle back in to the ETC, and back to PSI, or they
are used by an enzyme to produce NADPH from NAD+
Chemiosmosis produces ATP:
As Electrons move through the ETC, the free energy that is
released is used by the proteins in the chain to actively transport
protons from the stroma into the thylakoid space.
The high
concentration of protons in the thylakoid space provides the free
energy needed to produce ATP.
The only way protons can
diffuse back in to the stroma is through the “motor protein” ATP
synthase.
3. Photoautotrophic nutrition 2- Carbon fixation
Mechanisms of photosynthesis- Carbon fixation
Carbon fixation happens in the stroma of the chloroplasts,
controlled by a collection of enzymes that modulate the “Calvin
cycle”.
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During carbon fixation, the ATP and NADPH produced during the
light reactions will be used to drive the incorporation of carbon
dioxide in to an organic sugar building block called G3P.
Rubisco is the enzyme that incorporates CO2 in to the beginning
of the Calvin cycle.
During the Calvin cycle, the energy in ATP and the electrons in
NADPH are used to reduce 3 5-Carbon molecules of RuBP (plus
3 CO2 from rubisco) in to 6 3-Carbon molecules of G3P.
of these is the product of the cycle.
One
The remaining 5 G3P
molecules are then converted back in to 3 5-Carbon RuBP
molecules to continue the cycle.
G3P can be combined to make sugars, and then used in
respiration to produce ATP to power cellular work or serve as
raw materials (along with other nutrients) to make lipids, amino
acids, or nucleotides.
4. Chemoheterotrophic nutrition- anaerobic cellular
respiration
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Mechanisms of Respiration- glycolysis/fermentation
Glycolysis occurs in the cytoplasm, controlled by a collection of
enzymes.
During glycolysis, 2 ATP are used to convert one 6-Carbon glucose
in to 2 3-carbon pyruvate molecules.
This process also produces
4 ATP molecules (2 net), and 2 molecules of NADH.
Following glycolysis, cells either commit to aerobic cellular
respiration, or use a fermentation pathway to oxidize the NADH
produced in glycolysis back to NAD+ in order to continue
glycolysis.
Fermentation will oxidize NADH by reducing pyruvate in to
another organic molecule (which depends upon the organism
undergoing fermentation).
Ex:
yeast cells- convert pyruvate in to
1 carbon dioxide molecule and 1 2-Carbon ethanol molecule.
Human muscle cells convert pyruvate in to lactic acid.
All fermentation end products are more toxic than pyruvate, but
the conversion is necessary in order to supply glycolysis with
continual NAD+
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5. Chemoheterotrophic nutrition:
respiration
Aerobic cellular
Mechanisms of Respiration- Aerobic Cellular Respiration
In eukaryotes, ACR occurs in the mitochondrion.
Pyruvate must
be transported in to the matrix of the mitochondria.
It is also
converted in to a 2-Carbon acetyl group, which is combined with
a molecule of co-enzyme A.
Citric Acid Cycle.
Acetyl Co-A is the input for the
This conversion produces another molecule of
NADH
The Citric Acid Cycle:
The citric acid cycle occurs in the mitochondrial matrix,
controlled by a collection of enzymes.
During the citric acid cycle, the remaining carbons from glucose (on
the acetyl group) are converted in to carbon dioxide (oxidation).
This process produces 3 NADH and 1 FADH2, along with 1 ATP
per acetyl group.
Chemiosmosis produces ATP:
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Following the citric acid cycle, the NADH and FADH2 that have
been produced during all prior parts of cellular respiration are
oxidized at electron transport chains embedded in the
mitochondrial inner membrane.
As Electrons move through the ETC, the free energy that is
released is used by the proteins in the chain to actively transport
protons from the matrix into the intermembrane space.
The high
concentration of protons in the intermembrane space provides the
free energy needed to produce ATP.
The only way protons can
diffuse back in to the matrix is through the “motor protein” ATP
synthase.
Approximately 3 ATP are produced per NADH oxidized.
Approximately 2 ATP are produced per FADH2 oxidized.
These
numbers vary depending on the particular cellular system.
At the end of the ETC, the electrons combine with oxygen and
protons to produce water.
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All macromolecules are able to enter cellular respiration pathways,
either by being converted in to glucose, or by being converted in
to pathway intermediaries.
3.4: Cooperative interactions within organisms promote efficiency
in the use of energy and matter. (EK4.B.2)
1. Organizational efficiency in energy processing.
Compartmentalization allows for increased efficiency.
Cellular compartmentalization:
By having different metabolic processes occurring in different
cellular compartments, the conditions that those processes occur
under can be varied without interfering with other processes.
Compartmentalization also allows cells to establish specific
locations for specific processes.
Example:
Mitochondrial/Chloroplast compartmentalization allows
for the varied pH/proton sequestration that chemiosmosis will
generate.
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Example:
all of the proteins for required metabolic processes are
isolated and grouped in to different cellular compartments.
This
allows for more efficient progression through a metabolic
sequence, and also increases the likelihood that any feedback
inhibition will be efficient.
Ex.
Gram-negative bacteria have adapted their cell membranes
to compartmentalize processes needed to carry out aerobic
cellular respiration and photosynthesis
Multicellular compartmentalization:
Different systems in a multicellular organism serve different,
cooperative purposes for matter and energy processing:
Digestive system:
Conversion/absorption of complex food
molecules in to metabolic inputs (starch in to glucose)
Respiratory system:
exchange of metabolic gases (oxygen and
carbon dioxide)
Circulatory system:
Delivery of nutrients and removal of waste
products from all cells.
Excretory system:
Removal of waste molecules (water and
nitrogenous wastes).
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All of these systems have different roles in contributing to an
overall metabolic goal.
Microbial cooperation:
Microbial communities diversify in their functions to cooperatively
accomplish metabolic tasks.
Ex:
Animal rumen communities.
Ruminants are herbivorous
mammals (eg cows) who are able to digest cellulose due to the
cooperative actions of microbial communities in their expanded
upper digestive tract (the “rumen”)
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Domain 4: Information
4.1: DNA, and in some cases RNA, is the primary source of
heritable information. (EK3.A.1)
1. DNA Structure
DNA is the hereditary material in all cells.
This understanding is the result of work done by many scientists
over the past 100 years.
Frederick Griffith:
Determined the molecular basis of heredity due
to experiments with different strains of bacteria.
Avery, McCarty and McLeod: Determined that DNA was the
hereditary molecule in cellular systems.
Hershey and Chase:
Conclusively verified the work of Avery,
McCarty, and McLeod.
Erwin Chargaff:
Determined that the amount of adenine = the
amount of thymine, and the amount of guanine = the amount of
cytosine in any DNA sample.
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Watson, Crick, Franklin, and Wilkins:
Determined the structure of
DNA, and related the structure to the role of DNA in heredity.
DNA & RNA Structure and function:
DNA and RNA are both nucleic acids made of nucleotide
monomers.
Nucleotides are comprised of a 5-carbon sugar, a nitrogenous
base, and a phosphate group.
Nucleotides exist in the cytoplasm as “nucleoside tri-phosphates” (ex
ATP, GTP).
The extra phosphates provide the energy necessary
for a nucleotide to be incorporated in to a nucleic acid.
In DNA, the sugar is deoxyribose.
In RNA the sugar is ribose.
The DNA bases are Adenine, Thymine, Guanine and Cytosine.
The RNA bases are Adenine, Uracil, Guanine and Cytosine.
RNA is usually single stranded (nucleotides still H-bond with
eachother due to bending of the RNA molecule), DNA is usually
double stranded.
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Nucleotides in one strand are covalently bonded between the
sugar and phosphate.
Nitrogenous bases hydrogen bond with
nitrogenous bases on opposite strands.
Adenine and
thymine/uracil form 2 Hydrogen bonds, Guanine and cytosine
form 3 hydrogen bonds.
A specific purine (2 rings) always H-
Bonds with a specific pyrimidine (1 ring).
One strand of a nucleic acid has a directionality, referred to as 5’
and 3’, depending on which carbon of the sugar is exposed at
the terminal nucleotide.
The two DNA strands are anti-parallel in orientation.
The organization of nucleic acids differs in prokaryotes, eukaryotes,
and viruses:
Prokaryotes:
Have one circular chromosome, often with at least one small
extra-chromosomal circular plasmid.
Eukaryotes:
Have many linear chromosomes.
Plasmids are rare.
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Viruses:
Have a much smaller amount of genetic material than cells.
The
viral genome can be DNA or RNA, and single stranded or double
stranded.
2. DNA Replication
DNA is the information storage molecule in living systems.
The “Central Dogma” of molecular biology:
Expresses the major
flow of information in biological systems.
DNA molecules are duplicated (“replication”) to convey information
between generations of cells.
DNA information is transcribed in to RNA and then translated in to
proteins in order to participate in cellular activities.
There are other, non-typical paths for information flow seen in viral
systems.
DNA Replication allows for heritability:
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DNA is replicated in a semiconservative process.
One strand of
each molecule serves as the template for the synthesis of the
other strand. Each molecule of DNA is composed of one newly
synthesized strand and one pre-existing strand.
Replication is accomplished through the action of a collection of
enzymes that all function together (the “replisome”).
Helicase:
Opens the DNA helix at the origin sequence for
replication.
Topoisomerase:
Rotates the DNA strand to reduce torsional stress
during replication.
DNA Polymerase:
Responsible for incorporating free nucleotides in
to a new strand of DNA.
end of a molecule.
Can only add nucleotides to the 3’
Makes mistakes.
Nucleic acids can only be synthesized in a 5’ -> 3’ direction,
which requires one new strand to be made continuously, while
the other strand must be synthesized in pieces (“discontinuously”)
called “Okazaki fragments”.
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Ligase:
Enzyme that forms covalent bonds between adjacent
nucleotides in one strand of DNA.
Needed to join the okazaki
fragments together.
3. Protein Synthesis
Transcription converts DNA sequence information in to RNA
sequence Information:
RNA polymerase:
Enzyme that is responsible for making a
strand of RNA (in the 5’ to 3’ direction) from a sequence of DNA.
RNA plays several roles in the expression of genetic information:
mRNA:
RNA sequence of a DNA segment that specifies a
polypeptides amino acid sequence.
tRNA:
Molecules that bring specific amino acids to the ribosome,
as dictated by the mRNA sequence.
rRNA:
Structural components of ribosome subunits.
Regulatory RNA:
Control gene expression by blocking
transcription (RNAi).
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Translation converts mRNA sequence information in to polypeptide
sequences:
Translation occurs at the ribosome.
The genetic code is interpreted as a series of 3-nucleotide
codons (three adjacent nucleotides).
There are 64 possible
codons, which code for all 20 amino acids, along with a START
codon and 3 STOP codons.
The Genetic code is redundant, unambiguous, and punctuated.
The mRNA interacts with the ribosome to begin translation at the
START codon (AUG) closest to the 5’ end of the mRNA.
Following initiation, subsequent amino acids are brought to the
ribosome as specified by subsequent, adjacent codons.
amino acid is transferred to a growing polypeptide chain.
Each
This is
referred to as “elongation”
This process continues until the first STOP codon is reached,
which triggers “termination”; the release of the polypeptide from
the ribosome, and the disassembly of the ribosome.
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4.
Genetic Information Processing & Expression
There are differences in gene processing among viruses,
prokaryotes, and eukaryotes.
Viral gene processing:
Some viruses (“retroviruses”) utilize an enzyme called “reverse
transcriptase” to convert an RNA genome in to a DNA sequence.
This DNA sequence then integrates in to the host cell’s genome
to allow for continuing expression of viral components.
Prokaryotic gene processing:
The lack of a nucleus allows prokaryotes to directly couple
transcription and translation.
Ribosomes can begin translating an
mRNA transcript before RNA polymerase finishes transcribing it
from the DNA.
Eukaryotic gene processing:
Eukaryotes extensively process mRNA transcripts following their
production.
There are three major post-transcriptional
modifications:
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Addition of a poly-A tail to the 3’ end of the transcript:
Aids in
transport of the mRNA from the nucleus and increases the
longevity of the transcript.
Addition of a GTP cap to the 5’ end of the transcript:
similar in
function to the poly A tail.
Removal of introns, and splicing of exons:
Introns are interspersed
sequences of nucleotides that do not code for functional parts of
a polypeptide. They must be removed prior to translation if a
cell is going to make a functional protein.
The remaining,
functional segments (the “exons”) are spliced together to form the
mature mRNA transcript.
Gene expression contributes to phenotypes through the control of
protein activity.
Example:
enzymes.
Enzymes are proteins, and the reactions that
they control will only occur if those enzymes are present.
Example:
Fungal auxotrophs:
Mutant strains of fungi with defective
copies of enzymes that are involved in metabolic pathways.
These strains will only grow if they are provided with intermediary
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nutrients that enter a metabolic pathway after the action of the
defective enzyme.
Example:
Albinos:
The presence or absence of the normal
pigments in an organism are due to the presence or absence of
particular enzymes responsible for pigment production.
5. Genetic Engineering- Techniques
Genetic Engineering allows for direct manipulation of genetic
material.
This differs from selective breeding because it allows for more
targeted control of specific genes.
Genetic Engineering Techniques
Electrophoresis:
separation of DNA molecules based on their size.
Utilizes an electrical field and a gel matrix (typically agarose).
Smaller DNA molecules migrate through the gel faster than larger
molecules.
Used to isolate specific genes from within larger
samples of DNA, or to visualize differences in DNA sequences
among a collection of sequences.
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Transformation:
The direct introduction of DNA sequences in to
prokaryotic cells.
The DNA sequences are delivered on plasmid
vectors which allow for their replication and expression of any
genes on them by the prokaryotic cell.
Used to engineer
prokaryotic cells to produce useful proteins (ex. Human growth
hormone).
The eukaryotic version of transformation is called
“transfection”.
Similar purpose, different methodologies.
Restriction Enzyme Analysis:
Restriction enzymes cut DNA at
specific sequences, producing restriction fragments.
This enables
the isolation of different segments of DNA, for introduction in to
plasmids, sequencing, or a variety of other studies.
Regions of
the human genome associated with identity and diseases will
produce different length restriction fragments depending on the
sequence of DNA present.
Analysis of these Restriction
Fragment Length Polymorphisms allows for establishing identity
and genetic testing for different diseases.
Polymerase Chain Reaction:
In vitro DNA replication, using a
target sequence of DNA, small primers to bracket the target
sequence, a heat-resistant polymerase originally isolated from a
thermophillic bacterium (Thermis aquaticus), and a thermal cycler,
which oscillates between three different temperatures very rapidly.
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Through PCR, billions of copies of a DNA sequence can be
created in a test tube over the span of a few hours.
6. Genetic Engineering- Applications
Many products can be created using genetic engineering:
Genetically modified foods:
genes for desirable characteristics can
be inserted in to the genome of food crops (ex. golden rice)
Transgenic animals:
genes for desirable characteristics can be
inserted in to livestock and other animals (ex. Fluorescent fish)
Pharmaceuticals:
genes for therapeutic proteins can be inserted in
to bacteria to produce large quantities of those proteins (ex.
Insulin).
Cloned animals:
Organisms that do not naturally reproduce
asexually can be made to through genome manipulation in the
laboratory.
There are many ethical considerations associated with genetic
engineering:
Ethical considerations relate to:
Questions of ownership
Questions of consent
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Questions of the definition of life, and what should be legally
permissible.
4.2: Changes in genotype can result in changes in phenotype.
(EK3.C.1)
1. Mutations
Mutations are changes to the genome that can affect phenotypes.
Mutations can be positive, negative, or neutral in terms of their
affect on an organism’s phenotype.
They are caused by
exposure to certain chemicals (‘mutagens’), high energy radiation,
and through DNA replication (in humans the post-error checking
rate of mutations is approximately 1 per 1 billion replicated
bases).
DNA-level mutations:
Substitutions:
Change of one base to another base.
Can affect
the structure of a protein by changing one amino acid, or
changing the placement of a stop codon.
Called a “point
mutation” because it affects only one place in the genome.
In/dels:
insertion or deletion of a DNA base.
Can affect the
structure of a protein by changing the amino acid sequence of all
subsequent amino acids following the in/del, or changing the
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placement of a stop codon. Called a “frame shift” mutation
because it affects the “reading frame” of the ribosome.
Chromosomal mutations:
Mistakes that result in large-scale rearrangement of
chromosome sections:
Duplication
Deletion
Inversion
Translocation
Cell division mutations:
Mistakes that occur during cell division resulting in extra/missing
chromosomes (Down’s Syndrome:
Syndrome:
trisomy 21, Turner’s
monosomy X), or entire sets of chromosomes
(polyploidy—really only tolerated in plants)
Evolution requires variation.
Mutations are the ultimate source of
all genetic variation.
The fitness of a mutant is not just a function of it’s genome.
The
environment determines how well
adapted a mutant is.
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Ex.
Heterozygote advantage and sickle cell anemia.
The sickle
cell allele is at a higher frequency in areas where malaria is
endemic.
Heterozygotes for sickle cell are at an advantage over
homozygous non-sickle cell individuals in those areas.
In the
rest of the world, the heterozygote advantage for sickle cell is not
present because malaria is not endemic, and there are other,
limiting effects on heterozygote physiology.
4.3: Viral replication results in genetic variation, and viral infection
can introduce genetic variation into the hosts. (EK3.C.3)
1. Viral Genetics
Viruses are obligate intracellular parasites.
Viruses are sub-cellular,
and as such are generally not considered to be “living”.
They
are only active when infecting and replicating inside a host cell,
and do not have any external metabolism.
Viral anatomy consists of a nucleic acid (DNA or RNA) inside of a
protein coat.
Some eukaryotic viruses also posses an external
lipid envelope.
The “generalized” viral “life” cycle (many variations on this theme):
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Infection:
the virus is able to transfer its genetic information in to a
host cell.
Viruses are specific to particular cell types.
This is
due to the specificity of the receptors they use to attach to host
cells.
Replication:
the viral genome (and viral polymerases if necessary)
utilize host cell materials to manufacture viral proteins and
replicate the viral genome.
Self-assembly:
new viral particles are spontaneously assembled
from their components.
Release:
the new viral particles are released in to the environment
to infect new cells.
Viruses can evolve very rapidly.
Viral polymerases have higher error rates than cellular polymerases.
This produces more spontaneous mutations per replication than
what is seen in cellular systems.
Since more variants are
produced every generation, there is a higher likelihood of variants
being produced who are better adapted for their environment
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(which could include features like evading the host immune
system).
Additionally, when different strains of a virus co-infect the same cell,
they can recombine in to variants that have genetic information
from each strain.
This is the major concern with “bird” and
“swine” flu.
HIV is an interesting viral example:
HIV is a type of retrovirus, a class of viruses that contain an
RNA genome.
When it infects a cell, HIV uses a viral “reverse
transcriptase” to make a DNA copy of its RNA genome.
The
DNA version of the HIV genome is then spliced in to the host
cell genome, where it produces new viruses through the host
cell’s normal protein synthesis machinery (RNA polymerase and
ribosomes).
HIV infects one type of immune system cell (the “Helper T-Cell”),
which leads to an eventual collapse of the infected person’s
immune system, and the development of AIDS.
The body is
then susceptible to a series of “opportunistic infections”, which
are invariably fatal if not treated.
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Modern treatments for AIDS include a variety of antiviral drugs
that interfere with the HIV life cycle.
Viruses are effective at transferring genetic information.
Viruses serve as “vectors” for delivering genetic information.
Usually this is the viruses own genetic information, but sometimes
viruses can be packaged with DNA from the host cell genome
(“transduction”).
An active avenue of research is looking at using
customized viruses to deliver functional genes to populations of
cells with genetic defects.
There is no “cure” for a viral infection
The ability of a virus to remain dormant in a host cell’s genome
enables a viral infection to remain latent for long periods of time,
before signals trigger the re-emergence of the active virus.
In
mammals, the immune system recognizes and rapidly responds to
recurring viral infections, as long as the virus hasn’t mutated to
the point that the immune system can no longer recognize it.
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4.4: In eukaryotes, heritable information is passed to the next
generation via processes that include the cell cycle and mitosis
or meiosis plus fertilization. (EK3.A.2)
1. Mitosis
All cells reproduce through division (binary fission in bacteria)
The Cell Cycle describes the major events of the life of a cell.
Interphase vs. M-phase:
Interphase is ~95% of the cell cycle:
G1:
The cell is growing and (if it is going to divide), preparing
for DNA replication.
S:
The cell replicates its DNA.
G2:
The cell repairs replication errors and prepares for
division
M-phase:
G0:
Cell division.
permanent interphase that non-dividing cells exist in until
death.
Through the cell cycle, cells are able to serve the life functions of
growth (making more cells), repair (replacing damaged cells), and
reproduction (making new generations of cells)
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The behavior of chromosomes during the cell cycle allows for
heritability.
Mitosis produces two genetically identical “daughter cells”:
The events of mitosis are structured to transmit a complete
genome to both daughter cells.
The stages of mitosis occur as
a continual process.
Prophase:
the replicated chromosomes condense.
Chromosomes
are tightly wound DNA molecules, wrapped around histone
proteins.
Packing makes moving easier.
Prometaphase:
Metaphase:
The nuclear envelope breaks down.
The chromosomes align at the middle of the cell,
attached to the mitotic spindle
Anaphase:
The chromosomes are separated at the centromere
and migrate to opposite poles of the cell.
Telophase:
the chromosomes decondense, a nuclear envelope
reforms around each set.
Cytokinesis:
the cell membrane is cleaved, producing two cells.
2. Cell Cycle Control
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Mitosis is under strict cellular control.
In order to move through the
stages of the cell cycle, a cell needs to pass through a series of
“checkpoints” (internal conditions must be appropriate).
Cancer:
the result of loss of the cell-cycle controls in a cell.
Will
inevitably result in the death of the organism.
Cells are able to stop dividing, start dividing again if given proper
signals from other cells, and remain at particular stages of the
cell cycle for long periods of time.
The control of the cell cycle is accomplished through the action of
proteins:
Example:
Mitosis Promoting Factor (MPF)- controls the “Mitosis
checkpoint” of the cell.
enter mitosis.
proteins.
If MPF is not present, a cell will not
MPF is the result of the combination of two other
One (Cdk- cyclin dependent kinase) is always present
in the cell.
The other one (cyclin) is only made once a cell has
met the criteria needed to enter mitosis.
External signals also control the cell cycle:
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Example:
Platelet Derived Growth Factor (PDGF)- Released at the
site of tissue injury by platelets.
Causes non-dividing cells to
begin dividing to repair damaged tissue.
3. Meiosis
Meiosis produces cells with half of the normal amount of genetic
material.
Sexual reproduction requires that two “haploid” cells combine to
produce one “diploid” cell during fertilization.
Meiosis is the
process that produces these haploid “gametes”.
The events of meiosis are similar to those of mitosis with a few
key differences:
There are two sequential rounds of cell division:
Cells progress
through meiosis 1 (PMAT1) and then through meiosis 2 (PMAT2)
without replicating DNA in-between.
become two cells.
After meiosis 1, one cell has
After meiosis 2, each of the two cells
produced in meiosis 1 have become two cells.
At the end of
meiosis, one diploid cell has become four haploid cells.
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Crossing over:
During prophase 1, the homologous pairs of
chromosomes physically associate with each other and exchange
genetic material.
This results in every chromosome being a
unique combination of the genetic material from both members of
the homologous pair.
Independent Assortment:
During metaphase 1, chromosomes line
up in the middle of the cell still attached to their homologs.
The
orientation of one pair of chromosomes has no effect on the
orientation of any other pair.
Meiosis and the sexual life cycle generate tremendous variation.
Variation due to independent assortment:
expressed as 2^n.
In
humans = ~8,000,000 possible orientations of our 23
chromosomes.
Variation due to fertilization:
expressed as (2^n)(2^n). In
humans = ~70,000,000,000,000 possible combinations.
Variation due to Crossing Over:
“functionally infinite”
combinations of genetic information.
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3. Chromosomal Disorders
Many Genetic Disorders are explained by mistakes during the cell
cycle.
Non-disjunction:
Due to problems with the separation of chromosomes during
meiosis, cells can be produced with extra chromosomes or
missing chromosomes.
The majority of these errors are fatal to
the developing organism, but some are tolerated, leading to
diseases.
Ex.
Down’s Syndrome:
chromosome 21.
Results from having three copies of
Has wide-ranging effects on the physiology of
the person.
Ex.
Klinefelter’s Syndrome: Results from having two X
chromosomes and one Y chromosome.
Individuals are
phenotypically “male” but have some female secondary sexual
characteristics, and are sterile.
Genetic tests are available, but pose ethical questions.
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Karyotype analysis:
chromosomes.
isolation and visualization of an individual’s
Can be used to diagnose non-disjunction related
genetic conditions.
Modern genetic tests can also determine a host of other genetic
diseases that are not able to be visualized on a karyotype (Ex.
Huntington’s Chorea)
This information can be used by parents to determine if they
would like to continue a pregnancy, or prepare for a baby with a
medical condition.
There are major ethical considerations that accompany these
decisions.
Questions of reproductive rights, and issues of
ownership of genetic information, privacy, and historical contexts
(e.g. eugenics).
4.5: The chromosomal basis of inheritance provides an
understanding of the pattern of passage (transmission) of genes
from parent to offspring. (EK3.A.3)
1. Mendelian Genetics
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The behavior of chromosomes explains the inheritance of traits.
Since genes are on chromosomes, the movements of
chromosomes during meiosis will determine the inheritance of the
genes they contain.
The mathematical analysis of heredity was originally developed by
Gregor Mendel, who analyzed the inheritance of traits in pea
plants.
Mendel developed several major concepts to explain his
observations, which have since been related to the behavior of
chromosomes, and the relationship between genes and
phenotypes:
Reminder- Genotype vs. Phenotype
Genotype:
the alleles that an organism has for a particular trait.
Homozygous vs. Heterozygous
Phenotype:
the trait that an organism shows.
Sexually reproducing organisms have two alleles for any trait:
One allele is inherited from each parent.
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“Dominant” vs. “recessive” alleles:
the disappearance and then reappearance of certain traits is
explained by the fact that these traits are “recessive”.
When an
allele for a recessive trait is present along with an allele for a
dominant trait, the dominant trait will be expressed.
In order for
a recessive trait to be expressed, both alleles have to be for the
recessive trait.
Segregation of alleles:
During meiosis, each gamete will receive one of the organism’s
two alleles.
Each organism will produce an equal number of
gametes with each allele.
Independent Assortment:
During meiosis, the segregation of one allele has no effect on
the segregation of any other allele, as long as the alleles are on
separate chromosomes (“unlinked”).
Using these concepts, the inheritance of different characteristics can
be predicted based on the
140
proportions of offspring who show different phenotypes for those
characteristics.
2. MATH SKILLS:
Genetics Probabilities
The inheritance of unlinked genes are independent events (similar
to multiple flips of a coin).
The probability of multiple independent events occurring together is
equal to the product of the probabilities of each individual event.
Using this, we can determine the probability of a particular group of
offspring being produced from a particular cross by determining
the individual probabilities for each trait and then multiplying them
together.
This only works for unlinked genes.
Sample Problem:
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In pea plants the gene for wrinkled seed pods (R) is dominant to
the gene for smooth pods (r), and the gene for yellow seeds
(Y) is dominant to the gene for green seeds (y).
A heterozygous wrinkled, yellow pea plant is crossed with a
homozygous smooth, green pea plant.
What fraction of its
offspring will be smooth and yellow?
Cross:
RrYy x rryy
Offspring:
rrY_
½ * ½ = 1/4
Also, given the limited genotypes for organisms, each type of cross
produces characteristic genotypic and phenotypic ratios of
offspring.
Sample Problem:
In a cross between two organisms with the following genotypes:
AaBBCcddEe
x aaBbCcDdEe
What is the probability of getting offspring with the genotype
aaBbccDdEE?
½ x ½ x ¼ x ½ x ¼ = 1/128
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4.6: The inheritance pattern of many traits cannot be explained by
simple Mendelian genetics. (EK3.A.4)
1. Mendelian Extensions
Many traits are not inherited in simple Mendelian ratios.
These
traits can involve a lot of different
aspects of genetics and physiology, but will always affect the ratios
of offspring that are shown.
Incomplete Dominance/Codominance:
The heterozygote has a
different phenotype than either homozygote (ex. Snapdragon color,
human blood type)
Multiple alleles:
Traits have more than two alleles (ex. Human
ABO blood types)
2. Non-Mendelian Traits
Certain modes of inheritance are non-mendelian.
Many traits are linked to certain chromosomes.
Mendelian ratios
only refer to situations where each gene is inherited
independently of each other.
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The inheritance of these traits depends on the inheritance of these
chromosomes.
Much of this work was done by TH Morgan’s lab at Columbia in
the early 1900’s.
Sex linkage:
Traits are on the X chromosome.
Males will show
the recessive characteristic much more often than females. (Ex.
white eyes, color blindness)
Sex-limited traits:
Traits that are only expressed in one sex. (ex.
milk production, pattern baldness)
Linked genes: Genes that are on the same chromosome will be
inherited together, except when crossing over results in
recombination.
Can be identified by their divergence from
Mendelian expected ratios of offspring.
Linkage analysis:
Can be used to investigate the distance between
linked genes on the same chromosome.
The greater the
distance between two genes on a chromosome, the more often
crossing over will occur between them (the greater the frequency
of recombinants).
Some genes are not inherited through the nuclear genome of a cell.
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Non-nuclear inheritance refers to the inheritance of genes in the
chloroplast and mitochondrial genomes.
The chloroplasts and mitochondria of cells are randomly assorted
when daughter cells and gametes are being produced, so the
traits they carry are not inherited via Mendelian mechanisms.
Ex.
All mammals inherit their mitochondria from their mother’s egg
cell (“matrilineal inheritance”).
This can be used to track human
ancestry and historical migration.
4.7: Biological systems have multiple processes that increase
genetic variation. (EK3.C.2)
1. Generation of Variation
All lineages of life have modes of generating genetic variation.
Mistakes during DNA replication:
Error proofing of DNA is not 100% accurate (thermodynamically
impossible).
So all DNA will contain some number of mutations
due to replication.
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Horizontal transfer of genetic material in bacteria:
Refers to the transmission of genes between members of the
same generation of bacteria.
Transformation:
the uptake of DNA directly from the
environment.
Transduction:
Conjugation:
Transposition:
The transfer of DNA via viral infection.
The transfer of DNA through cell-cell contact
The replication and movement of DNA segments
separate from replication of the genome.
Sexual reproduction:
Meiosis and the random nature of fertilization produce functionally
infinite combinations of genetic material in sexual reproducing
organisms.
Sexual reproduction has evolved independently in all
major eukaryotic lineages (protists, fungi, animals, and plants).
The unifying characteristic is that haploid cells are produced,
which unite during fertilization to form a diploid zygote.
4.8: Gene regulation results in differential gene expression,
leading to cell specialization. (EK3.B.1)
1. Gene Regulation
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Regulatory DNA sequences control transcription rates by interacting
with regulatory proteins (“transcription factors”):
Promoter:
sequences of DNA that precede the start of a
transcribed gene.
polymerase.
Recognized by transcription factors and RNA
The presence of transcription factors on the
promoter make transcription possible.
Enhancers:
sequences of DNA further upstream than the promoter.
The presence of transcription factors on these regions increase
the rate of transcription (“up regulation”)
Regulatory RNA elements and regulatory proteins.
Produced by
regulatory genes, and associate with
regulatory DNA sequences to allow for transcription.
Regulatory DNA sequences serve as molecular “switches”.
When
the required transcription factors are
present, the switch is “on”, and transcription occurs.
When the
required factors are not present, the switch is “off”, and no
transcription occurs.
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2. Prokaryotic Gene Regulation
Prokaryotes control gene expression almost entirely by controlling
transcription.
The lack of a nucleus makes this efficient.
Operons:
Groups of genes (“structural genes”) that all contribute to a
specific metabolic processes (e.g. digestion of lactose, synthesis
of tryptophan).
Transcription of all of the genes is regulated by a single promoter.
Repressor protein:
a regulatory protein that allows/blocks
transcription by physically associating/disassociating with a region
of the promoter called the “operator”.
The modulation between the active and inactive forms of the
repressor protein is accomplished through an allosteric interaction
with the molecules that are acted upon by the particular
metabolic pathway.
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The operational “logic” of the operon will depend on how
necessary the product of the metabolic pathway it controls is for
the cell.
Ex.
The Lac Operon:
Involved in the digestion of lactose.
“inducible”:
usually “off”, only “on” when lactose is present in the
cell.
The binding of lactose to the repressor protein causes its
conformation to change and it to dissociate from the operator.
Ex.
The Trp Operon:
Involved in the synthesis of tryptophan
“repressible”:
Usually “on”, only “off” when there is an excess of
tryptophan present in the cell.
The binding of tryptophan to the repressor protein causes its
conformation to change and it to associate with the operator.
Upregulation:
The binding of other regulatory proteins to the
operator can increase the rate of transcription of the structural
genes to many times above the baseline level.
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Ex.
The Catabolite Activator Protein:
When particular energy-
producing molecules are low, the cAMP molecular signal
associates with the CAP protein.
This CAP/cAMP complex
associates with the promoter of operons involved in energy
production (e.g. the lac operon) and increases the amount of
transcription by directly recruiting RNA polymerase to the
promoter.
Constitutive genes:
Genes that are constantly transcribed and are
not under major regulatory control.
Ex.
Ribosomal RNA genes.
3. Eukaryotic Gene Regulation
Eukaryotes control gene expression at steps in the process
Pre-Transcriptional controls:
Access to genes:
winding and unwinding of DNA around histone
proteins is controlled by enzymatic acetylation and de-acetylation
of “tail” regions of the histones.
Different types of cells will have
different regions of the genome accessible for transcription.
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Regulation of transcription:
Eukaryotes have a wide variety of
transcription factors that control transcription (activators and
repressors).
Different types of cells will have different collections
of transcription factors present, to allow the transcription of
certain accessible genes and block transcription of others.
Post-Transcriptional/Pre-Translational controls:
Post-Transcriptional processing:
Poly-Adenylation, 5’ capping, and
intron splicing all must occur to produce a functional transcript.
“alternate splicing”:
combining different exons from the same
transcript to produce multiple gene products from one transcript.
RNA interference (RNAi):
the blocking of transcription by small
interfering RNA molecules, which bind to specific transcripts and
keep the ribosome from being able to translate them.
Post-Translational controls:
Targeting of polypeptides:
signals on the polypeptide determine if
the polypeptide will be made in the cytoplasm, or if the ribosome
will associate with the ER.
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Ubiquinone/Proteosome degradation:
Tagging of a protein by a
ubiquinone molecule will cause the protein to be degraded by a
“proteasome” complex.
4. Gene Regulation  Phenotype
The control of gene expression leads to the control of phenotypes.
Phenotypes are the result of protein interactions within the cell.
By
controlling the production of proteins, cells influence the
manifestation of particular phenotypes.
Multicellular organisms control cellular differentiation through
differential gene expression.
The reason that different types of cells are present in a multicellular
organism are because different cell types are expressing different
genes, which leads to their differing phenotypes.
Even genetically identical organisms can have different phenotypes
due to differences in gene expression.
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Ex.
Cloned mammals have noticeable phenotypic differences…so do
identical twins.
4.9: A variety of intercellular and intracellular signal transmissions
mediate gene expression. (EK3.B.2)
1. Signal Control of Gene Expression
Signals that are transmitted between and within cells affect gene
expression:
Example:
yeast mating- two mating types:
Alpha and a. Each
mating type produces a pheromone that interacts with receptors
on the cell membrane of the opposite mating type.
When this
interaction occurs, the genes that control the development of the
mating structure (the “shmoo”) in the yeast are activated, and the
two mating types fuse together in a fertilization event.
Signals that are transmitted between and within cells affect cell
function:
Example:
Hox Genes:
present in all animals.
Control the
development of specific sections of an animal’s body.
The
presence of Hox transcription factors activate the genes needed
to begin the development of a particular segment of an animal’s
body (“morphogenesis” and “differentiation”).
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4.10: Environmental factors influence the expression of the
genotype in an organism. (EK4.C.2)
1. Environmental Effects on Phenotype.
Phenotype is a product of genotype AND environment:
The genome is not a blueprint.
It is more like a recipe.
An organism’s environment has a major role in determining the
organism’s phenotype.
The environment can determine phenotype directly:
Examples:
Hydrangea flower color and soil pH, sex determination
in reptiles,
The genome can respond to the environment:
Example:
Seasonal changes in fur color, height and weight in
humans, tanning response.
“Plasticity”:
The interactions between environment and genome can
be very complex.
It becomes difficult to draw the nature vs.
nurture line in many cases.
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Domain 5: Regulation
5.1: Timing and coordination of specific events are necessary for
the normal development of an organism, and these events are
regulated by a variety of mechanisms. (EK2.E.1)
1. Development
The development of an organism is coordinated by sequential
changes in gene expression.
Starting as an undifferentiated cell, a multi-cellular organism
possessing many different types of cells is produced.
Differentiation requires the expression of cell type-specific proteins.
Several major processes accomplish differentiation:
Pattern formation:
Established by positional cues, usually protein
gradients (ex. Bicoid, Hox genes).
Once body plan axes are
established, morphogenesis can begin.
Induction:
local signals communicated among populations of cells
to control their specific development.
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Environmental cues:
Particular molecules and conditions must be
present in the local environment for development to proceed
properly (ex. The conditions of the uterus, or the role of
temperature and moisture in triggering seed development).
Evidence from experiments and nature have informed thinking about
development:
Developmental mutants:
mutations in normal developmental
pathways lead to malformations in embryonic development.
Genetic transplantation experiments:
removing/moving regions of
the developing embryo to other areas affect pattern formation.
The use of reporter genes help to determine which genes are
active when and where during organism development.
Silencing of specific genes is also important for normal development.
It’s not just what you turn on, it’s also what you turn off.
The presence of specific microRNA’s during development will
prevent certain genes from being expressed.
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Programmed cell death is required for normal development:
Apoptosis:
programmed cell death.
The cell breaks itself down
in to small “blebs”, which are absorbed by surrounding cells.
Required for many different aspects of development.
example:
One
digit formation in vertebrates.
5.2: Interactions between external stimuli and regulated gene
expression result in specialization of cells, tissues and organs.
(EK4.A.3)
1. Differentiation
Differentiation is controlled by internal cues (ex. Hox gene products)
and external cues (ex. Temperature,
or the presence/absence of specific signaling molecules).
These all
work to regulate protein expression
by turning on/off genetic “switches” through controlling the
presence/absence of regulatory genes that
allow or block transcription.
Differentiation of the gene products present in cells leads to
structural and functional divergence in the
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roles that those cells play in the organism (ex. Neuron vs. blood
cell)
The environment plays a major role in controlling gene expression
in mature cells (ex. Changes in UV radiation leading to melanin
production, presence of insulin leading to increased glucose
intake).
5.3: Organisms use feedback mechanisms to maintain their
internal environments and respond to external environmental
changes. (EK2.C.1)
1. Feedback Loops
Feedback is a universal characteristic of open systems.
Feedback loops are seen at all levels of organization in living
systems.
Negative feedback loops are regulatory in nature.
Negative feedback:
any situation where the output of a process
decreases the occurrence of that process.
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Example:
lac operon- the presence of lactose activates a metabolic
pathway that results in the digestion of lactose.
Example:
Temperature regulation in animals- if animals get too
cold, they shiver and increase metabolic rate to generate heat.
If
animals get too hot, they sweat to cool down.
Example:
Population growth- As a population grows, resource are
depleted to the point where the population can no longer
continue to grow.
Negative feedback maintains homeostasis.
Positive feedback loops are amplifying in nature
Positive feedback:
any situation where the output of a process
increases the occurrence of that process.
Example:
labor- contractions of the uterus increase pressure on
the cervix, which triggers the release of oxytocin by the pituitary
gland, which increases the rate of contractions of the uterus.
159
Example:
fruit ripening- controlled by the hormone ethylene.
As a
fruit ripens, it produces more ethylene, which causes the fruit to
ripen more rapidly
Positive feedback causes transformation in the system.
5.4: Homeostatic mechanisms reflect both common ancestry and
divergence due to adaptation in different environments.
(EK2.D.2)
Discussion 1:
Divergence in homeostatic mechanisms is due to the requirements
of different environments
Examples:
Respiratory systems of aquatic and terrestrial animals-
external vs.
internal respiratory surfaces.
Respiration (the exchange of gases) must occur over a thin, moist
membrane.
Animals that live in aquatic environments can use external
structures to respire (gills in fish, or
skin in frogs).
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Animals that live on land must use internal structures to respire
(lungs/alveoli in terrestrial
tetrapods, spiracles in insects)
Nitrogenous waste production in aquatic and terrestrial animalsThe waste products from digesting proteins/nucleic acids must be
excreted from the body of the organism.
Animals that live in water convert nitrogenous waste directly in to
ammonia, which is highly toxic but can be heavily diluted and
easily excreted in to the watery environment along.
Animals that live on land can not afford to lose as much water
when excreting nitrogenous waste.
Mammals are able to convert nitrogenous waste into urea which is
less toxic than ammonia, so
it does not need to be as diluted with water, and can be stored for
periodic elimination from the body.
Birds, reptiles, and many insects convert nitrogenous waste to uric
acid, which is the least toxic, and requires the least dilution with
water.
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Discussion 2:
Similarities in homeostatic control systems are due to common
ancestry and convergent evolution.
Example:
Excretory systems in animals.
Differences are due
All excretory systems in animals involve filtration, reabsorption,
secretion, and elimination
Examples:
Example:
Flame bulb/nephridium/kidney(nephron)
Circulatory systems in vertebrates-
All vertebrate circulatory systems are closed, and use a single heart
to pump blood from the body to the respiratory surface and back.
Examples:
Fish/Reptile/Mammal/Bird- Mammal and Bird 4 chamber
heart is an example of convergent evolution.
5.5: Biological systems are affected by disruptions to their
dynamic homeostasis. (EK2.D.3)
1. Effects of Disruptions
The effects of disruptions to biological systems can be seen at all
levels of organization.
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Disruptions to molecular pathways and cellular structure can
adversely affect the homeostasis of the
organism:
Example:
Response to toxins
Toxins usually interfere with specific metabolic pathways (ex.
Cyanide, Carbon Monoxide), or cause major damage to cells (ex.
Snake venom cytotoxins, Concentrated acids).
This interference
can lead to major injury or death.
Example:
Dehydration
The loss of water causes the tonic environment of cells to become
less than optimal for continuing cellular work.
The changes in
concentrations of molecules can lead to organ failure or death.
Disruptions to ecosystems can adversely affect the balance of the
ecosystem.
Example:
Invasive species-
If an invasive species is able to outcompete a native species, or
place a rapid stress on a native species (e.g. predation), the
trophic structure of the ecosystem can be degraded (e.g.
163
decrease in the diversity and abundance of native species) or
collapse.
Example:
Disturbance-
Natural disturbances include disasters like fires, earthquakes, etc.
These massive, rapid changes to the environment can eliminate
major populations from the ecosystem, leading to degradation or
collapse of the ecosystem.
In all cases, biological systems are able to adjust to the disruptions
and rebound (your immune system might be able to produce
venom antibodies—Bill Haast, you can drink more water, the
populations in an ecosystem can adapt to the presence of an
invasive, or an ecosystem can gradually undergo successional
changes to return to the pre-disturbance state), IF the disruptions
are not too large and too rapid for the homeostatic feedback
loops to function.
If the disruptions are too large scale, and too
rapid, disease, degradation, and death are unavoidable.
5.6: Plants and animals have a variety of chemical defenses
against infections that affect dynamic homeostasis. (EK2.D.4)
164
1. Immune Systems.
Nonspecific immune responses are found in all multicellular
organisms.
Plants:
Have the ability to recognize pathogens by their effects,
and trigger responses that destroy infected tissue and protect
uninfected tissue.
Invertebrates:
Toll-receptor systems that recognize specific
molecules usually associated with pathogens (ex. Lipid Acomponent of bacterial cell walls) and trigger immune responses.
Vertebrates:
External:
Internal:
Multiple external and internal nonspecific defenses
skin, mucous, tears, sweat (lysozyme)
Inflammatory response:
When pathogens are present
inside the body, nearby cells recruit non-specific phagocytic white
blood cells to the area of infection.
These phagocytes engulf
and destroy the pathogens, and present molecules from them
(“antigens”) to the specific immune system.
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Mammals have a highly developed specific immune response:
There are two major divisions of the specific immune system.
They
both involve the lymphocytes (B-cells
and T-cells):
Cell-mediated response:
specific T-cells are developed to target
specific antigens on the surface of specific pathogens.
These T-
cells trigger the destruction of those pathogens, and infected cells
through cell-cell interactions.
Humoral response:
specific B-cells are developed that produce
and secrete antibodies that bind to specific antigens on the
surface of specific pathogens.
These antibodies bind to the
antigens on pathogens and target them for destruction by the
non-specific immune system, or prevent them from continuing
their life cycle.
Clonal selection:
The process by which specific lymphocytes are
produced by the immune system.
When presented with a
particular antigen, a large variety of lymphocytes are produced,
each with a different variation of receptor.
Only the cells who
react with the specific antigen are allowed to reproduce (the other
166
cells undergo apoptosis).
The next generation of lymphocytes
undergoes another round.
This process continues until a
population of lymphocytes with a very specific receptor for a
particular antigen is produced.
Immunological Memory:
Once a specific immune response is
generated, a small population of lymphocytes that react to the
triggering antigen remain in the lymphatic system for the
remainder of the life of the individual.
When the same antigen is
presented in a subsequent infection, the immune response is
much faster and larger, which controls the infection more rapidly.
This assumes that the pathogen has not evolved so that its
antigens are no longer recognized by the immune system.
Memory is also the basis of vaccination, which presents antigens
to the immune system without the pathogen present, so that the
immune system can develop its response prior to infection.
5.7: Timing and coordination of behavior are regulated by various
mechanisms and are important in natural selection. (EK2.E.2)
Discussion 1:
Changes in the environment are able to cause changes in behavior.
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The interaction between the environment and internal signals
regulate plant responses.
Example:
Phototropism- Growth in response to light.
Controlled
by the production and unequal distribution of the hormone auxin.
Auxin production is highest in dark cells, which causes them to
lengthen.
Unequal lengthening results in movement toward light
sources.
Example:
Photoperiodism-
Flowering in response to periods of
light and dark of specific length.
Controlled by phytochrome
molecules, which alternate between active and inactive forms as
a result of exposure to light for periods of “critical” length.
The interaction between the environment and internal signals
regulate and synchronize animal
responses with the cycles of the environment.
Example:
circadian rhythms-
internal physiological cycles
present in all eukaryotes, which last for 24 hours (ex. Sleep/wake
cycle).
These cycles are present even when environmental cues
are removed, but in their absence the cycles lose their calibration
to the day/night cycle of the environment (ex. Jet lag).
168
Example:
Hibernation/estivation/migration- periods of dormancy,
or relocation in response to seasonal variations in productivity of
an environment.
The interaction between the environment and internal signals
regulate and synchronize fungal, bacterial, and protist responses
with the cycles of the environment.
Example:
Fruiting Body Formation- the development of reproductive
structures in fungi, some protists, and some bacteria.
Controlled
by the sensing of appropriate external conditions, and subsequent
gene expression.
Example:
Quorum Sensing- changes in bacterial behavior once a
specific population density is reached. (ex. Bioluminescence in V.
fisherii)
In all cases, interactions between environmental signals and internal
signals are required to evoke a particular behavior.
In as much as any behavior can be inherited, it can be adapted by
natural selection.
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Domain 6: Communication
6.1: Cell communication processes share common features that
reflect a shared evolutionary history. (EK3.D.1)
1. Introduction to Communication
Communication requires the generation, transmission, and reception
of a signal.
In cellular systems, these signals are generally chemical molecules,
but can also include direct detection of environmental conditions
(eg. Light, sound, temperature).
These pathways are referred to
as “signal transduction” pathways.
All organisms engage have signal transduction pathways:
Signal transduction pathways are very important for the continued
life of an organism, and are heavily adapted by natural selection.
Unicellular signaling pathways:
In unicellular organisms, signaling
pathways affect the responses of cells to their environment.
170
example- quorum sensing.
Involves the generation of chemical
signals in response to environmental variables, and they both
operate by changing cell activity via regulating gene expression.
Multicellular signaling pathways:
In multicellular organisms,
signaling pathways affect responses that coordinate multiple
populations of cells and support the functioning of the organism.
Example:
glands.
epinephrine- a hormone signal produced by the adrenal
Triggers different responses in different tissues.
In the
liver, the reception of the epinephrine molecule causes the
breakdown of glycogen in to glucose and the release of that
glucose in to the bloodstream.
6.2: Cells communicate with each other through direct contact
with other cells or from a distance via chemical signaling.
(EK3.D.2)
1. Types of Cellular Signals
Cell communication always involves the production, exchange, and
receipt of chemical messages.
Cell communication through cell-cell contact:
171
Ex.
Immune System:
Direct contact is needed for activation of the
specific immune response (antigen presentation).
Ex.
Plasmodesmata:
Channels in the cell walls of plant-like cells
which allow for direct passage of materials and signaling
molecules from cell to cell.
Cell communication through local signaling:
Messages are produced by cells and diffuse to local cell
populations
Ex.
Neurotransmitters:
chemicals released by one neuron are
received by another neuron over the synaptic space, resulting in
the propagation of the signal.
Ex.
Plant Immune Response:
chemicals produced by infected
cells are received by nearby cells and result in activation of
defense mechanisms in those cells.
Cell communication through distance signaling:
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Endocrine system:
the production of endocrine signaling
molecules (“hormones”) by glands are then transported through
the circulatory system to all other parts of the body.
Ex.
Insulin:
produced by the pancreas, affects all cells in the
body (specific liver effects).
Ex.
Human growth hormone:
produced by the pituitary gland in
the brain, affects all cells in the body.
Ex.
Sex hormones:
FSH and LH- produced by the pituitary
gland, affect the gonads (testes and ovaries). Estrogen,
Testosterone- produced by the gonads, affect all cells of the body.
6.3: Signal transduction pathways link signal reception with
cellular response. (EK3.D.3)
1. Signal Transduction Pathways
Signal transduction begins with reception.
Signal reception is accomplished through receptor proteins.
Depending on the chemistry of the ligand, receptor proteins will be
located at the cell membrane, or
173
in the cytoplasm.
Receptor proteins have a diversity of structures, depending on the
signal they receive, but there are some general features:
An area of the protein that interacts with the signaling molecule
(the “ligand”)
An area of the protein that transmits (“transduces”) the signal to
another protein.
When the ligand interacts with the receptor protein, it causes a
conformational change in the receptor, which results in the
activation of the transduction pathway in the cell.
Example:
G-protein linked receptor- a membrane receptor.
When
the ligand binds to the GPL-receptor, the conformational change
causes phosphorylation (activation) of a g-protein, which then
phosphorylates the next protein in the response pathway, etc.
Example:
Ligand-gated ion channels-
another membrane receptor.
When the ligand binds to the channel, the conformational change
causes the channel to open, and ions to move freely in to the
cell.
This change in ion concentration will then trigger cellular
responses by changing the shape of various proteins.
174
Transduction of a chemical signal results in the conversion of signal
reception in to cellular response.
Transduction is accomplished via activation of a protein through
phosphorylation, or a change in intracellular conditions (a change
in ion concentration).
Signal transduction activates a cascading response, which can
result in the amplification of the original signal (one ligand - >
exponentially increasing activated proteins).
The complexities of cellular responses that result from signal
reception are due to the interconnected structure of transduction
pathways inside a cell.
Most signaling pathways involve the activation of “second
messenger” response pathways inside a cell.
Second messengers are internal signaling molecules, often
activated by multiple external signals:
Ex.
Cyclic AMP -> when present in a cell, activates various
catabolic metabolic pathways.
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The modification of proteins in a signal transduction pathway is akin
to turning them “on” and “off”.
This is often accomplished by the
addition of phosphates to activate proteins (by “kinase” enzymes)
and the removal of phosphates to deactivate proteins (by
“phosphatases”).
Cellular responses involve changes in gene expression, and the
activation of already present, inactive
proteins.
6.4: Changes in signal transduction pathways can alter cellular
response. (EK3.D.4)
1. Alterations to Signaling Pathways
Alterations in signal transduction pathways will affect the functioning
of cells, and the homeostasis of the organism.
Many diseases result from alterations to signal transduction
pathways:
Ex.
Diabetes:
Type 1- failure to produce the insulin hormone.
Type 2- failure to activate the insulin response in target cells.
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Immediate effects- inability of the body to effectively regulate
blood-glucose concentration.
Long-term effects:
vascular system
problems, poor wound healing, blindness, neurological
degeneration, death.
Ex.
Neurological disease:
Parkinson’s Syndrome- death of
neurons in the brain that produce the dopamine neurotransmitter.
Results in degeneration of the muscular system.
Ex.
Cancer- failure of cells to respond to the normal apoptosis
pathway that should be triggered when cell cycle mutations
accumulate.
Results in uncontrolled cell growth.
Many drugs work by altering signal transduction pathways:
Ex.
Antihistamines:
block the release of histamine signaling
molecules by mast cells.
Results in decreased inflammatory
response.
Ex.
Birth Control:
Provide hormones that prevent ovulation and
normal menstrual cycle progression.
6.5: Individuals can act on information and communicate it to
others. (EK3.E.1)
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1. Communication Between Organisms
Organisms are able to acquire information about their environment
and exchange that information with others.
Stimuli: Anything that triggers a response. Stimuli are external to
the organism.
The ability of organisms to respond to signals from the environment
and other organisms (“behavior”) will lead to greater or lesser
reproductive success.
Ex.
Predator warnings-
when the presence of a predator in the
environment is detected, members of a population will often
signal that presence to other members.
Ex.
Herbivory responses- The detection of chemicals associated
with hebivores by plants results in a variety of defenses including
the production of toxic chemicals, and the recruitment of
herbivore parasites/predators.
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Animals have highly developed sensory systems, which can detect
and communicate via visual, auditory, tactile, chemical, and
electrical signals.
Ex.
Bee Dances:
A tactile signal to other bees that relates the
position of food sources to the location of the hive.
Ex.
Swarming Behavior:
The result of positive feedback in
chemical signaling pathways (“pheromones”).
Ex.
Prey detection by electrical signals in snakes and fish.
As long as behaviors have a genetic component, and
increase/decrease survival and reproductive success of organisms,
natural selection can adapt them for an organism’s particular
environment.
Natural selection will favor any behavior that increases survival and
reproductive success.
Ex.
Courtship and mating rituals.
Ex.
Foraging behaviors in animals.
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Natural selection will allow for the evolution of cooperative behavior
if it increases the fitness of the individual OR genetically related
individuals:
Ex.
Schooling in fish
Ex.
Colonial insects
6.6: Animals have nervous systems that detect external and
internal signals, transmit and integrate information, and produce
responses. (EK3.E.2)
1. Neurons
The neuron is the structural unit of the nervous system:
A neuron is a highly-specialized cell used by the nervous system
to detect signals and transmit them to other neurons/response
effectors (muscles or glands).
Neuron structure allows for neuron function:
Dendrites:
connect to other neurons or sensory receptors at
synapses.
Cell Body:
Detect signals across the synapse.
Contains the majority of the neuron’s organelles.
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Axon:
Conducts an electrochemical signal to the next
neuron/effector in the neural pathway.
Most axons are surrounded by a layer of highly myelinated
Schwann cells that insulate the neuron and increase the rate of
signal transmission.
Neuron signals move from dendrites to the axon to the nerve
terminals.
The structure of particular neurons depends on the role of the
neuron in the nervous system.
Neurons allow for signals to be generated, detected, transmitted,
and integrated by animals.
Neuron signals are electrochemical “action potentials.”
The membrane of a neuron is polarized, with active maintenance of
different concentrations of ions inside and outside of the cell (the
“resting potential”).
cell.
Na+ is at a higher concentration outside the
K+ is at a higher concentration inside the cell
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An action potential results from the depolarization of a neuronal
membrane’s resting potential.
When the membrane is depolarized to a “threshold” potential,
voltage gated channels in the axon open, and a rapid exchange
of ions occurs:
Na+ moves in to the cell, triggering a massive depolarization (inside
the cell becomes more positive relative to outside the cell).
At the peak of the depolarization, K+ ion channels also open,
allowing K+ ions to move out of the cell.
Peak depolarization triggers the closing of the Na+ channels, K+ ion
channels remain open.
As K+ continues to move out of the cell,
the membrane becomes hyperpolarized.
The action of Na+/K+ pump proteins restores the polarization of the
membrane back to the resting potential.
Once the resting potential is restored, the neuron can send another
action potential.
Action potentials are binary (“all or nothing”), self-propagating, and
unidirectional.
The initial depolarization of the membrane triggers
the depolarization of the next area of the membrane.
The
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hyperpolarization following an action potential prevents the action
potential from moving backwards along the axon.
Myelination greatly increases the speed of action potential
transmission, as the signal moves along nodes (“saltatory
conduction”).
Neurons transmit signals to other neurons across synapses.
The arrival of an action potential at the terminal of an axon triggers
the release of neurotransmitter molecules in to the synaptic space.
Different neurotransmitters will have different effects on different
types of neurons.
Ex.
Acteylcholine:
Released by motor neurons at the
“neuromuscular junction” (the synapse between them and muscle
cells.
Ex.
Triggers contraction of the muscle
Serotonin:
Released by neurons in the brain involved in
emotional responses.
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These effects can be excitatory (make the next neuron more likely
to send an action potential), or inhibitory (make the next neuron
less likely to send an action potential).
Transmission of information along neurons will ultimately result in
a response (the operation of muscles, or the secretion of
signaling molecules by a gland).
2. Nervous Systems
Animal Nervous Systems have varying levels of complexity.
Evolutionary trends towards centralization and “cephalization” are
demonstrated.
In vertebrates, the brain is the central unit for integrating nervous
system information and coordinating
responses.
Different regions of the brain serve different functions:
Ex.
Ex.
Medulla/Cerebellum/Cerebrum
Right/left hemisphere separation.
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Ex.
Vision and Hearing centers.
Ex.
Motor movement.
Ex.
Abstract thought and emotion.
Ex.
Right/left hemisphere separation.
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Domain 7: Interactions
7.1: Organisms exhibit complex properties due to interactions
between their constituent parts. (EK4.A.4)
1. Physiological Interactions
Multicellular organisms are organized into organ systems, which
contain organs that work together to accomplish life processes:
Ex.
Stomach and Small Intestine:
Salivary amylase begins the
digestion of polysaccharides in to monosaccharides.
The
stomach combines food with gastric juice, which breaks down
food via exposure to hydrochloric acid, and digests proteins
through the action of pepsin.
of the stomach.
Pepsin is only active in the low pH
When food is transported to the small intestine
the initial section of the small intestine adds pancreatic fluid and
bile to the food mixture, the enzymes present in pancreatic fluid
continue the digestion of food molecules, and bile emulsifies fat
globules.
Pancreatic enzymes are only active in the high pH of
the small intestine.
The later section of the small intestine
provides a lengthy surface area over which the end products of
digestion are absorbed in to the body.
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Ex.
Plant organs:
soil.
The roots absorb nutrients and water from the
The leaves produce sugars through photosynthesis, the
stem allows for exchange of materials between roots and leaves.
Organ systems also interact to accomplish life processes:
Ex.
Respiratory and Circulatory system:
The respiratory system
allows for oxygen to be absorbed in to the circulatory system.
The circulatory system transports oxygen to cells (via hemoglobin
in red blood cells) and transports carbon dioxide waste products
(as bicarbonate ions) from cells back to the lungs for excretion
from the body.
If the body is not producing enough energy, the
increase in carbon dioxide in the circulatory system causes a
drop in pH of the blood which is detected by the nervous system
and triggers an increase in respiratory rate.
Ex.
Nervous and Muscular Systems:
The nervous system
allows for stimuli to be integrated and a response to be
coordinated.
The muscular system responds to signals from the
nervous system (action potentials), and contracts muscle groups
to accomplish motility.
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Ex.
Shoot System & Root System.
The vascular bundles
provide the leaves with the water necessary to continue
photosynthesis via xylem tissue, and provides the nonphotosynthetic cells of the plant with sugars via phloem tissue.
The transport of these materials is regulated by the rate of their
absorption by other areas of the plant.
In leaves, as water
evaporates, cohesive attractions move water from the xylem in to
the leaf, which “pulls” water through the xylem.
As sugar is
produced at the leaf (the source), it is transported into phloem.
Sugar moves through the phloem until being offloaded at a
destination (the sink)
7.2: Organisms respond to changes in their external environments.
(EK2.C.2)
1. Responses to the Environment
Organisms can respond to changes in their environment by
changing behavior:
Ex.
Fixed action patterns in sticklebacks.
Ex.
Taxis
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Organisms can respond to changes in their environment by
changing their physiology:
Ex.
Phototropism
Ex.
Shivering/Sweating.
There is not a clear line between physiology and behavior.
Proximate vs. Ultimate explanations:
Proximate:
Ultimate:
How an organism accomplishes a response.
Address the evolutionary reasoning for the response.
Ex. Imprinting:
Proximate Explanation:
Immediately after birth, the organism has a
“critical period” wherein it will imprint on any moving object near
it.
Ultimate Explanation:
Organisms who imprint are more likely to
survive, since the object they are most likely to see is a parent.
7.3: Interactions among living systems and with their environment
result in the movement of matter and energy. (EK4.A.6)
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1. Energy and Matter Acquisition
Organisms are adapted to acquire and use matter and energy in
their particular environments.
These adaptations can be
physiological (eg. Gills) or behavioral (eg. Hunting behavior).
A
well adapted organism for a particular environment may be poorly
adapted for another environment (the polar bear in the desert).
Energy flows through an ecosystem, matter cycles.
Energy is incorporated in to a community by the producers in
that community.
Producers will usually occupy the greatest
biomass in the ecosystem.
Primary productivity:
the total amount of energy converted into
biologically useful forms by producers.
GPP (total) vs. NPP (total
available to consumers= GPP- metabolism and lost energy).
Not all ecosystems are equally productive.
The highest
productivity is found in locations where there is the most direct
sunlight (tropics) and enough nutrients (temperate and cooler
bodies of water).
Productivity also fluctuates seasonally, and with
changes to climate.
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Within a food chain, only ~10% of energy at any trophic level will
be passed on to the next trophic level.
Trophic interactions are represented as food chains and foodwebs.
Trophic structure can also be represented as pyramids (of
biomass, numbers, etc.)
Matter cycles between living and non-living components of an
ecosystem.
All matter cycles involve the movement of matter between abiotic
and biotic reservoirs in an ecosystem.
Producers are the major pathway for matter to move from the
environment to the community.
Decomposition is the major way
for matter to move from the community back to the environment.
Within a community, matter moves through the food chain.
Community interactions influence the movement of matter and
energy.
These influences can be modeled.
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Competition for resources limits the growth a population.
As
competition increases, population growth approaches zero (the
“logistic model”)
The effects of many limiting factors increases as the population
density increases (“density-dependent interactions”).
Ex.
Space,
predation, accumulation of waste, etc.
Human activity can impact ecosystems locally, regionally, and
globally:
The exponential growth of the human population has lead to
increasing resource consumption in all ecosystems in which the
human population lives.
Humans now have a major impact on all ecosystems on the
planet.
This impact is largely detrimental to other organisms in
these ecosystems (though not wholly).
Human activities have reduced the population sizes of many other
organisms through direct consumption and habitat destruction.
Many species have gone extinct in part, or in whole due to
human impact on the ecosystems in which they live.
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2: MATH SKILLS:
Productivity Calculations
It’s mostly accounting.
Total energy and matter in to a system has
to equal total energy and matter out of the system.
Sample problem:
A caterpillar consumes 100 kilocalories of energy.
It uses 35
kilocalories for cellular respiration, and loses 50 kilocalories as
waste (heat and in waste products).
Determine the trophic
efficiency for its creation of new biomass.
Total Energy: 100 Kcal
Lost and Respired:
35 + 50 = 85 kcal
Total for growth: 15 kcal
Efficiency:
part/total = 15/100 = .15 (as decimal, 15 as
percentage, 3/20 as a fraction, etc.)
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The formula sheet also provides two conversion factors to use the
amount of oxygen gas produced in photosynthesis as an indicator
of gross primary productivity:
mg O2/L x 0.698 = mL O2 /L
mL O2/L x 0.536 = mg carbon fixed/L
You are more likely to need to understand that ecosystems with
greater productivity are more stable and diverse than ecosystems
with less productivity than you will need to do any particularly
complicated math in this area of the course.
7.4: All biological systems from cells and organisms to populations,
communities and ecosystems are affected by complex biotic and
abiotic interactions involving exchange of matter and free
energy. (EK2.D.1)
1. Limiting Factors
Biotic and abiotic interactions affect all levels of biological systems.
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Cellular activities are affected by abiotic and biotic interactions:
Ex.
Cellular proliferation is controlled by the density of cells in
the environment, and the amount of resources available.
Ex.
Biofilms- complex microbial communities that are established
and maintained by the actions of all species present in the
biofilm.
Organism activities are affected by abiotic and biotic interactions:
Ex.
Predator-prey relationships.
The cyclical nature of
population changes demonstrates their interdependence.
Ex.
Resource availability in the environment determines an
organism’s behavior (foraging, hibernation, etc.)
The stability of populations, communities, and ecosystems are
affected by abiotic and biotic interactions:
Ex.
Resource availability and productivity influence the
complexity and diversity of the community, and the size of the
populations that comprise the community.
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Ex.
Algal Blooms-
Sudden changes in nutrient availability in
aquatic environments can lead to a rapid increase in producers,
and can trigger the death of other populations in the ecosystem
(due to loss of nutrients, or toxins produced by the algae).
In all cases:
Biotic and abiotic interactions both play roles in
affecting biological systems at all levels of organization.
These
affects can be beneficial, detrimental, or variable in their effects
on the system and its state at the time of the interaction.
7.5: The level of variation in a population affects population
dynamics. (EK4.C.3)
1. Population Diversity
The ability of a population to respond to changes in its environment
(“resilience”) is directly related to its genetic diversity.
Populations with the least genetic diversity are most at risk for
extinction in an ecosystem.
Ex.
Potato Blight- a major cause of the Great Famine in Ireland.
Irish potatoes were all the same
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strain, greatly decreasing their genetic diversity.
all susceptible to the blight fungus.
This made them
Eventually, resistant strains
were developed by incorporating genetic diversity from South
American strains.
Genetic diversity leads to a diversity of responses among individuals
in a population to the same environmental changes.
This
diversity can be physiological or behavioral.
Ex.
Black Plague- Already present variations in the gene for the
receptor used to infect cells lead to the increased survival of
resistant individuals.
Ex.
Not all animals in a herd stampede when exposed to a panic
stimulus.
HW eq. can be used to model allele variation in a population, and
inform hypotheses about how environmental changes might affect
populations.
Genetic variation can also be estimated through
direct population sampling.
Other modes of estimating diversity
include phenotype sampling, and fossil record analysis.
7.6: Interactions between and within populations influence
patterns of species distribution and abundance. (EK4.B.3)
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1. Community Interactions
Interactions between populations affects the distribution and
abundance of organisms.
Niche:
the total interactions of an organism with its environment.
Competition, and predation can limit the distribution and
abundance of a population.
Competitive exclusion principle:
When two species have
overlapping requirements in the same ecosystem, one species will
outcompete the other for those overlapping resources.
Symbiosis can limit or expand the distribution of a population:
Mutualism and commensalism are expansive.
Parasitism is limiting.
A population has properties unique to its level of organization.
These properties emerge from the
interactions among the individuals who comprise the population with
each other and the ecosystem.
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The distribution and abundance of a population can be disrupted by
a variety of environmental changes:
Ex.
Catastrophes (mount st. Helens).
Changes in resource
availability (algal blooms, role of iron in aquatic ecosystems).
Human activities (introduction of invasive species).
Interactions among populations can be modeled, and modeling can
inform predictions about the effects of those interactions.
It is not possible to accurately model the entirety of interactions
between populations and their environment.
This makes
prediction about the effects of changes on a population inherently
uncertain (Hardin’s Law).
7.7: Communities are composed of populations of organisms that
interact in complex ways. (EK4.A.5)
1. Measuring Communities
Community structure can be measured in different ways:
Species composition:
the number, distribution, and abundance of
the species in the community.
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Species diversity:
the variation within the species and
populations in the community.
Mathematical models can be used to investigate population growth
patterns:
Exponential model:
Logistic equation:
assumes unlimited resources.
accounts for the effect of carrying capacity on
population growth.
Demographic Representations:
Age structure of populations
Mathematical models can be used to illustrate and investigate
population interactions:
2. MATH SKILLS:
Population Growth Equations
Four Given Equations:
Rate of change over time:
Population Growth Rate
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Exponential Model:
Logistic Model
Using the right equation is half of the battle.
Sample Problem:
Over the span of one year, there are 20 deaths and 35 births in
a population of 200 African elephants.
Determine the maximum per capita growth rate of the population.
If the carrying capacity for the population in the environment
is 300 elephants, determine the number of elephants that can
be predicted in the population at the end of the next year, if
the intrinsic per capita growth rate does not change.
Solution:
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What is the maximum per capita growth rate for the population?
dN/dt = B – D
dN/dt = 35 -20
dN/dt = rmaxN 15 = rmax 200
dN/dt = 15 elephants per year.
rmax = 15/200 rmax = .075
What will next year’s population be if the carrying capacity is 300
elephants?
dN/dt = rmax N (K-N/K) = .075 215 (85/300) = ~4.6 elephants =
4 elephants + 215 = 219 elephants
7.8: The diversity of species within an ecosystem may influence
the stability of the ecosystem. (EK4.C.4)
1. Ecosystem Stability
Different ecosystems have differing amounts of biodiversity.
The more biodiversity present in an ecosystem, the more stable the
ecosystem will be, and the more resilient it will be when exposed
to changes.
3 levels of biodiversity:
The genetic diversity in a population.
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The number of populations in a community.
The diversity of ecosystems in a Biome.
Ecosystems are interaction networks (they depend on interactions
among the components).
possible interactions.
The more components, the more
The less important any one interaction is
to the functioning of the ecosystem.
Decreasing biodiversity decreases the number of components in the
ecosystem, and increases the reliance on any remaining
interactions to keep the ecosystem functional.
If something then
happens to the relied-upon species, the ecosystem may collapse.
Keystone species- species that have a large role in maintaining the
structure of the ecosystem.
The removal of keystone species
from an ecosystem will often result in the collapse of the
ecosystem.
Ex.
Sea otters in kelp forests, sea stars in intertidal
systems.
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Facilitation:
When one species makes it possible for other
species to occupy an area.
Ex.
Beavers
Producers are required for the continuing functioning of an
ecosystem.
Changes in the amount of producers affects the total
amount of matter and energy moving through the community,
which will affect the structure of the community.
Limiting Factors:
The abiotic and biotic factors present in the
environment that are most scarce.
Limiting factors limit the
growth of populations and the complexity of the environment.
Changes in the availability of limiting factors leads to changes in
the structure of the community.
7.9: Distribution of local and global ecosystems changes over time.
(EK4.B.4)
1. Ecosystem Changes
Geological and meteorological events can have large effects on
ecosystems (“disturbances”). The effect a
disturbance has on an ecosystem is directly proportional to the rate
and scale of the disturbance (a forest fire will have a major
effect, but not as major as a meteorite impact.
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Biogeographical data can illustrate the historical effects of
disturbances on the history of life on Earth.
Ex.
Contental drift, meteor impacts
Ecosystems have ways to recover from disturbances (ex.
Succession).
“Nature Abhors a vacuum”.
Human impacts have a disproportionate effect on the rate of
change in ecosystems.
The effects of human impacts are difficult
to predict, and far-ranging across all ecological scales (from
populations to ecosystems to the biosphere).
Ecosystem services:
The processes that are accomplished by
ecosystems that enable life on Earth to persist (food sources,
nutrient recycling, air and water purification).
Human activities
disrupt the functioning of these ecosystem services, and are
contributing to an accelerated extinction rate.
Ex. Climate change (and associated ecosystem degradation related
to fossil fuel consumption), overexploitation of resources (slash
and burn techniques in the rainforest), transmission of emerging
diseases (ex. MERS-CoV).
The effect of warfare.
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Human Impacts are accelerating as the population increases.
How will human impact affect the long term viability of the
biosphere, and our place in it?
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