Chapter 1: Scientific Thinking
Your best pathway to understanding the world
Lectures by Mark Manteuffel, St. Louis Community College
Learning Goals
• Describe what science is.
• Describe the scientific method.
• Describe key aspects of well-designed
experiments.
• Describe how the scientific method can be
used to help make wise decisions.
• Describe the major themes in biology.
More than just a
collection of facts,
science is a
process for
understanding the
world.
Scientists
Are
curious
Ask questions about how the world works
Seek answers
• Does the radiation released by cell phones
cause brain tumors?
• Are anti-bacterial hand soaps better than
regular soap?
• Do large doses of vitamin C reduce the
likelihood of getting a cold?
“How do you know that is true?”
The single question that
underlies scientific thinking
Scientific Literacy
how
to think scientifically
how to use the knowledge we gain to
make wise decisions
increasingly important in our lives
literacy in matters of biology is especially
essential
1.2 Biological literacy is
essential in the modern
world.
A brief glance at any newspaper will
reveal
Biological Literacy
The ability to:
1. use the process of scientific inquiry to
think creatively about real-world issues,
2. communicate those thoughts to others,
and
3. integrate them into your decisionmaking.
1.3 The scientific method is
a powerful approach to
understanding the world.
Why and when do people
develop superstitions?
Can animals be superstitious?
The Scientific Method
Observe a phenomenon
Propose an explanation for it
Test the proposed explanation through a
series of experiments
↓
Accurate & valid,
or…
Revised or alternative explanations proposed
Scientific Thinking Is Empirical…
…based on experience and observations
that are rational, testable, and repeatable.
1.4 Thinking like a scientist:
how do you use the scientific
method?
The basic steps in the scientific method are:
Step
1: Make observations.
Step 2: Formulate a hypothesis.
Step 3: Devise a testable prediction.
Step 4: Conduct a critical experiment.
Step 5: Draw conclusions and make
revisions.
1.5 Step 1: Make
observations.
Look for interesting
patterns or cause-andeffect relationships.
Does taking
echinacea reduce
the intensity or
duration of the
common cold?
1.6 Step 2: Formulate a
hypothesis.
A proposed explanation for
observed phenomena
To be most useful, a hypothesis must
accomplish two things:
1. It must clearly establish mutually
exclusive alternative explanations for a
phenomenon.
2. It must generate testable predictions.
Devising Testable Predictions
• We can only evaluate the validity of a
hypothesis by putting it to the test.
• Researchers often pose a hypothesis as a
negative statement, proposing that there
is no relationship between two factors
The Null Hypothesis
A negative statement that proposes that
there is no relationship between two factors
These hypotheses are equally valid but are
easier to disprove.
An alternative hypothesis
It is impossible to prove a hypothesis is
absolutely and permanently true.
Null and Alternative Hypotheses
Echinacea
reduces the duration and
severity of the symptoms of the common
cold.
Or as a null hypothesis:
• Echinacea has no effect on the duration or
severity of the symptoms of the common
cold.
Null and Alternative Hypotheses
Hair
that is shaved grows back coarser
and darker.
Or as a null hypothesis:
• There is no difference in the coarseness or
color of hair that is shaved relative to hair
that is not shaved.
1.7 Step 3: Devise a
testable prediction.
Suggest that, under certain
conditions, we will make
certain observations.
Devising a Testable Prediction
from a Hypothesis
Keep in mind any one of several possible
explanations could be true.
Devising a Testable Prediction
from a Hypothesis
The goal is to:
Propose a situation that will give a particular
outcome if your hypothesis is true…
…but that will give a different outcome if your
hypothesis is not true.
Hypothesis: Eyewitness testimony is
always accurate.
Prediction:
Individuals who have
witnessed a crime will correctly identify
the criminal regardless of whether multiple
suspects are presented one at a time or all
at the same time in a lineup.
Hypothesis: Echinacea reduces the duration and
severity of the symptoms of the common cold.
1.8 Step 4: Conduct a
critical experiment.
an experiment that makes it possible
to decisively determine whether a
particular hypothesis is correct
Hypothesis:
Echinacea reduces the
duration and severity of
the symptoms of the
common cold.
1.9 Step 5: Draw
conclusions, make revisions.
Trial and error
Does echinacea help prevent the common cold?
Hypothesis: Echinacea reduces the duration and
severity of the symptoms of the common cold.
1.10 When do hypotheses
become theories?
Two distinct levels of
understanding that scientists use
in describing our knowledge
about natural phenomena
Hypotheses and Theories
A
hypothesis is a proposed explanation
for a phenomenon.
• a good hypothesis leads to testable
predictions.
Hypotheses and Theories
A
theory is a hypothesis for natural
phenomena that is exceptionally wellsupported by the data.
• a hypothesis that has withstood the test of
time and is unlikely to be altered by any new
evidence
Theories vs. Hypotheses
Repeatedly tested
Broader in scope
Well-designed
experiments
are essential to
testing
hypotheses.
1.11 Controlling variables makes
experiments more powerful.
Elements Common
to Most Experiments
1. Treatment
• any experimental condition applied to individuals
2. Experimental group
• a group of individuals who are exposed to a
particular treatment
3. Control group
• a group of individuals who are treated identically
to the experimental group with the one exception:
they are not exposed to the treatment
4. Variables
• characteristics of your experimental system that
are subject to change
Controlling Variables
the
most important feature of a good
experiment
the
attempt to minimize any differences
between a control group and an
experimental group other than the
treatment itself
Why does this experiment fall
short of qualifying as a good
example of the scientific method?
Experimental
Control
design
group with whom to compare the
treatment group?
The Placebo Effect
The
phenomenon in which people respond
favorably to any treatment
The
placebo effect highlights the need for
comparison of treatment effects with an
appropriate control group.
Clever Hans
Experimental Designs
Blind
experimental design
• The experimental subjects do not know which
treatment (if any) they are receiving.
Double-blind
experimental design
• Neither the experimental subjects nor the
experimenter knows which treatment the
subject is receiving.
Hallmarks of an Extremely
Well-designed Experiment
Blind/double-blind
strategies
Randomized
• The subjects are randomly assigned into
experimental and control groups.
1·12 THIS IS HOW WE DO IT
Is arthroscopic surgery for
arthritis of the knee
beneficial?
How could you determine
whether a particular type
of surgery is effective?
How does general scientific
literacy—particularly among nonscientists such as the volunteers in
this study—help in advancing our
knowledge and understanding
about a particular phenomenon?
The Treatment Groups
1. Arthroscopic surgery with
debridement
2. Arthroscopic surgery with lavage
3. Placebo surgery
What is the take-home
message from these two
graphs?
At two years, the pain
scores were:
Patient Group
Mean Pain Score
1. Debridement
51 ± 23
2. Lavage
54 ± 24
3. Placebo
52 ± 24
What conclusions can you draw from
these results?
1.13 Repeatable experiments
increase our confidence.
Can science be misleading?
How can we know?
Do megadoses of
vitamin C reduce
cancer risk?
An experiment must be
reproducible and repeatable.
1.14 We’ve got to watch
out for biases.
Can scientists be sexist?
How would we know?
Scientific
thinking can
help us make
wise
decisions.
1.15 Visual displays of data can
help us understand and explain
phenomena.
Variables
• Independent Variables
– some measurable entity that is available at
the start of a process and whose value can be
changed as required.
• Dependent Variables
– created by the process being observed and
whose value cannot be controlled.
Take-home message 1.15
• Visual displays of data, which condense
large amounts of information, can aid in
the presentation and exploration of the
data.
Take-home message 1.15
• The effectiveness of such displays is
influenced by the precision and
clarity of the presentation, and it can
be reduced by ambiguity, biases,
hidden assumptions, and other issues
that reduce a viewer’s confidence in
the underlying truth of the presented
phenomenon.
1.16 Statistics can help us
in making decisions
Statistics
A set of analytical and mathematical tools
designed to help researchers gain
understanding from the data they gather.
• Drawing
conclusions based
on limited
observations is
risky.
• Measuring a greater
number of people will
generally help us draw
more accurate
conclusions about
human height.
Making Wise Decisions
About Concrete Things
Does
having access to a textbook help a
student to perform better in a biology
class?
• Students who had access to a textbook scored
an average of 81% ± 8% on their exams…
• …while those who did not scored an average
of 76% ± 7%.
Statistics can also help us to identify
relationships (or the lack of
relationships) between variables.
a
positive correlation
• meaning that when one variable increases, so
does the other
“Correlation
Statistical
is not causation.”
analyses can help us to organize
and summarize.
1.17 Pseudoscience and misleading
anecdotal evidence can obscure the
truth.
1. Pseudoscience: individuals make
scientific-sounding claims that are not
supported by trustworthy, methodical
scientific studies.
2. Anecdotal observations: based on only
one or a few observations, people
conclude that there is (or is not) a link
between two things.
Anecdotal Observations
do
not include a sufficiently large and
representative set of observations of the
world
data
are more reliable than anecdotes
1.18 There are limits to what
science can do.
One of Several Approaches to the
Acquisition of Knowledge
The scientific method is, above all, empirical.
Value judgments and subjective information
Moral statements and ethical problems
On the road to
biological
literacy:
what are the
major themes
in biology?
• 1.19 Important unifying
themes tie together the diverse
topics in biology.
What is Life?
Try to define it
Characteristics shared by all living
organisms and living systems:
• A complex, ordered organization
consisting of one or more cells.
• The use and transformation of energy
to perform work.
• Sensitivity and responsiveness to the
external environment.
Characteristics shared by all living
organisms and living systems:
• Regulation and homeostasis.
• Growth, development, and
reproduction.
• Evolutionary adaptation leading to
descent with modification over time.
Two Unifying Themes
Hierarchical
The
organization
power of evolution
4 Chief Areas of Focus
1. The chemical, cellular, and energetic
foundations of life
2. The genetics, evolution, and behavior of
individuals
3. The staggering diversity of life and the unity
underlying it
4. Ecology, the environment, and the subtle
and important links between organisms and
the world they inhabit
Take-home message 1.19
• The characteristics shared by all
living organisms include:
– complex and ordered organization;
– the use and transformation of energy;
– responsiveness to the external environment.
Take-home message 1.19
• The characteristics shared by all
living organisms include:
– regulation and homeostasis;
– growth, development, and reproduction;
– and evolutionary adaptation leading to
descent with modification.
Chapter 2: Chemistry
Raw materials and fuel for our bodies
Lectures by Mark Manteuffel, St. Louis Community College
Learning Objectives
Describe what atoms are, their structure, and how
they bond.
Understand water’s features that help it support all
life.
Describe carbohydrates—their structure and
function.
Learning Objectives
Describe lipids—their structure and function.
Describe proteins—their structure and function.
Describe nucleic acids—their structure and function.
Atoms form
molecules
through
bonding.
2.1 Everything is made of atoms.
An element is a substance that cannot be broken
down chemically into any other substances.
An atom is a bit of matter that cannot be
subdivided any further without losing its essential
properties.
Atomic Structure:
The nucleus, protons, and neutrons
Atomic Structure: Electrons
Atomic Numbers
Isotopes
Radioactive Atoms
• A few atomic nuclei are not stable and
break down spontaneously
• These atoms are radioactive
• They release, at a constant rate, a tiny,
high-speed particle carrying a lot of energy.
25 Elements Found
in Your Body and
the Big 4
Electron
Shells
The Versatility
of Carbon
Ions
Molecules
Products of bonding!
Bond Energy
Ions and
Ionic Bonds
Hydrogen
Bonds
Water has
features
that enable it to
support all life.
2.4 Hydrogen bonds make water cohesive.
2.5 Water has unusual properties
that make it critical to life.
Cohesion
Large
Low
heat capacity
density as a solid
Good
solvent
Cohesion
High Heat Capacity
Why do coastal areas have
milder, less variable climates
than inland areas?
Low Density
as a Solid
Why don’t oceans freeze as
easily as fresh water lakes?
2.6 Living systems are highly
sensitive to acidic and basic
conditions.
Hydrogen Ions
and Hydroxide Ions
pH Scale
The
amount of H+ in a solution is a
measure of its acidity and is called pH.
Acids
Bases
H+ Ions and Acids
H+
very reactive
Acids
can donate H+ to other chemicals
Stomach
acids
Bases
Low
H+
High OH
Antacids
Baking
soda, seltzer, milk of magnesia
Blood pH
Buffers
• can quickly absorb
excess H+ ions to
keep a solution from
becoming too acidic,
• and they can quickly
release H+ ions to
counteract any
increases in OH
concentration.
2·7 THIS IS HOW WE DO IT
Do anti-acid drugs impair
digestion and increase the
risk of food allergies?
Carbohydrates
are fuel for
living
machines.
2.8 Carbohydrates include
macromolecules that function as fuel.
Health topics of
the year
Low-carb diet?
Hi-carb diet?
“Carbo-loading”?
Fiber intake?
What are
carbohydrates?
Four Types of Macromolecules
Carbohydrates
Lipids
Proteins
Nucleic
acids
Carbohydrates
C,
H, and O
Primary
fuel for
organisms
Cell
structure
Energy is in the chemical
bonds!
2.9 Glucose provides energy for
the body’s cells
Fuel
for cellular activity
Stored
temporarily as glycogen
Converted
to fat
Glucose
Most
carbohydrates
— ultimately
converted into
glucose
Blood
sugar
What is “carbo-loading”?
2.10 Many complex carbohydrates
are time-released packets of
energy.
More
than 1 sugar (monosaccharide) unit
Disaccharides
•
•
sucrose
lactose
Polysaccharides
•
•
starch
cellulose
Chemical Fuel
Preliminary
Processing
Starch
>
100’s of glucose molecules joined
together
Barley,
wheat, rye, corn, and rice
Glycogen—“animal
starch”
Complex Carbohydrates
“Time-release” fuel pellets
2.11 Not all carbohydrates are
digestible.
Chitin
Cellulose
Fiber
“Roughage”
Colon
cancer prevention/reduction
Termites
ecological role
Lipids store
energy for a
rainy day.
2.12 Lipids are macromolecules with several
functions, including energy storage.
Why does a salad dressing made with
vinegar and oil separate into two layers
shortly after you shake it?
Hydrophobic
Hydrophilic
2.13 Fats are tasty molecules
too plentiful in our diets.
Glycerol:
region
Fatty
“head”
acid “tails”
Triglycerides
Fat molecules contain much more stored
energy than carbohydrate molecules.
Saturated and Unsaturated Fats
#
of bonds in the hydrocarbon chain in a
fatty acid
Health considerations
Chocolate
chip cookie recipes call for
some lipids.
How
will the “chewy-ness” of the
cookies differ depending on whether
you use butter or vegetable oil as the
lipid?
Which
cookies will be healthier?
Many
snack foods contain “partially
hydrogenated” vegetable oils.
Why
might it be desirable to add
hydrogen atoms to a vegetable oil?
What are trans fats?
Olestra
is a recently developed “fake
fat” chemical that gives foods the
taste of fat, without adding the
calories of fats.
What
chemical structure might make
this possible?
2.14 Cholesterol and
phospholipids are used to build
sex hormones and membranes.
Not
all lipids are fats
The
sterols
Cholesterol
Important
component of most cell
membranes.
Can
attach to blood vessel walls and cause
them to thicken.
Cells
in our liver produce almost 90% of
the circulating cholesterol.
Steroid
Hormones
Estrogen
Testosterone
• synthetic variants
of testosterone
Phospholipids and Waxes
Phospholipids
are the major component
of the cell membrane.
Waxes
are strongly hydrophobic.
Proteins are
versatile
macromolecules
that serve as
building blocks.
2.15 Proteins are bodybuilding
macromolecules.
Amino Acids
Twenty
Strung
different amino acids
together to make proteins
2.16 Proteins are an essential
dietary component.
Growth
Repair
Replacement
Food
labels indicate an item’s protein
content.
Why
is this insufficient for you to
determine whether you are protein
deficient, even if your protein intake
exceeds your recommended daily
amount?
Complete Proteins
Have
all essential amino acids
Incomplete
proteins
Complementary
proteins
Study the table to answer the following
2 questions.
What does the blue dot indicate in the
figure below?
1. Presence of an
amino acid in a
food item.
2. Absence of an
amino acid in a
food item.
3. Essential vs.
nonessential
amino acids.
4. Absence of
essential amino
acids in a food
Which combination of foods would
contain all of the essential amino acids?
1. Apples and
white rice
2. Almonds
and lentils
3. White rice
and lentils
4. Almonds
and apples
2.17 A protein’s function is influenced
by its three-dimensional shape.
Peptide
bonds
Primary Structure
The
sequence
of amino acids
Secondary Structure
Hydrogen
bonding
between amino acids
The two most common
patterns:
• twist in a corkscrew-like
shape
• zig-zag folding
Tertiary Structure
Folding
and
bending of the
secondary structure
Due
to bonds such
as hydrogen bonds
or covalent sulfursulfur bonds.
Quaternary Structure
When
two or more
polypeptide chains
are held together by
bonds between the
amino acids on the
different chains.
Hemoglobin
Egg
whites contain much
protein.
Why
does beating them
change their texture, making
them stiff?
Egg
whites contain much protein.
Why
does beating them change
their texture, making them stiff?
Why do some people have curly hair
and others have straight hair?
Activation Energy
• Chemical reactions occurring in organisms
can either release energy or consume
energy.
• In either case, the reaction needs a little
“push” in order to initiate the reactioncalled activation energy.
• Enzymes act as catalyst by lowering the
activation energy
An enzyme can reduce the activation
energy in a variety of ways
1) By stressing, bending, or stretching
critical chemical bonds
2) By directly participating in the reaction
3) By creating a microhabitat that is
conducive to the reaction
4) By simply orienting or holding substrate
molecules in place so that they can be
modified.
2.19 Enzymes regulate
reactions in several ways (but
malformed enzymes can cause
problems)
The rate at which an enzyme catalyzes
a reaction is influenced by several
chemical and physical factors
“Misspelled”
Proteins
Incorrect
amino
acid sequence
Active
site
disruptions
Phenylketonuria
Q
Why do some adults get sick
when they drink milk?
Nucleic acids
store
information
on how to
build and run
a body.
2.20
Nucleic
acids are
macromolecules
that store
information.
Two Types of Nucleic Acids
Deoxyribonucleic
acid (DNA)
Ribonucleic acid
(RNA)
Both play central roles
in directing the
production of proteins.
Information Storage
The
information in a molecule of DNA is
determined by its sequence of bases.
Adenine,
guanine, cytosine, and thymine
• CGATTACCCGAT
2.21
DNA holds
the genetic
information
to build an
organism.
Base-Pairing
A
&T
G
&C
What
is the complimentary strand to
this strand: CCCCTTAGGAACC?
2.22
RNA is a
universal
translator,
reading DNA
and directing
protein
production.
RNA differs from DNA in three
important ways.
The
sugar molecule of the sugarphosphate backbone
Single-stranded
Uracil
(U) replaces thymine (T)
Chapter 3: Cells
The smallest part of you
Lectures by Mark Manteuffel, St. Louis Community College
Learning Objectives
Describe what a cell is and the two general types of
cells.
Describe the structure and functions of cell membranes.
Describe several ways in which molecules move across
membranes.
Describe how cells are connected and how they
communicate with each other.
Describe nine important landmarks in eukaryotic cells.
3.1 All organisms are
made of cells.
The cell: the smallest unit of life that can function
independently and perform all the necessary functions of
life, including reproducing itself.
Cells
Robert Hooke, a British scientist, mid-1600s
A cell is a three-dimensional structure, like a
fluid-filled balloon, in which many of the
essential chemical reactions of life take place.
Nearly all cells contain DNA (deoxyribonucleic
acid).
Cell Theory
1. All living organisms are made up of one
or more cells.
2. All cells arise from other pre-existing
cells.
3.2 Prokaryotic cells are structurally simple
but extremely diverse.
Every cell on earth falls into one of two basic categories:
1.
2.
A eukaryotic cell
• has a central control structure called a nucleus which
contains the cell’s DNA.
• eukaryotes
A prokaryotic cell
• does not have a nucleus; its DNA simply resides in the
middle of the cell
• prokaryotes
3.3 Eukaryotic cells have compartments
with specialized functions.
Eukaryotic cells have organelles.
Endosymbiosis Theory
Developed to explain the presence of
two organelles in eukaryotes,
chloroplasts in plants and algae, and
mitochondria in plants and animals.
Humans, deep down, may
be part bacteria.
How can that be?
Cell membranes are gatekeepers.
Why are plasma membranes such
complex structures?
They perform several critical functions.
•
•
•
•
•
take in food and nutrients
dispose of waste products
build and export molecules
regulate heat exchange
regulate flow of materials in and out of
cell
3.5 Molecules embedded within the
plasma membrane help it perform its
functions.
There are four primary types of membrane
proteins, each of which performs a different
function.
The Plasma Membrane
“Fluid Mosaic”
In addition to proteins, two other molecules
are found in the plasma membrane:
1. Short, branched carbohydrate chains
2. Cholesterol
3.6 Faulty membranes can cause
disease.
Why do “beta blockers”
reduce anxiety?
Why is it extremely
unlikely that a
person will catch
HIV from casual
contact—such as
shaking hands—with
an infected
individual?
3.8 Passive transport is the
spontaneous diffusion of molecules
across a membrane.
There are two types of passive transport:
1. Diffusion
2. Osmosis
Diffusion and Concentration Gradients
• Solutes
• Solvents
Simple Diffusion
Facilitated Diffusion
Most
molecules can’t get through plasma
membranes on their own.
Carrier
•
molecules
transport proteins
Defects in Transport Proteins
Can
reduce or even bring facilitated
diffusion to a complete stop
Serious
Many
health consequences
genetic diseases
• Cystinuria and kidney stones
3.9
Osmosis is
the passive
diffusion of
water across
a membrane.
Cells in Solution
Tonicity
• the relative concentration of solutes outside of
the cell relative to inside the cell
Hypertonic
Hypotonic
Isotonic
Q
How do laxatives relieve
constipation?
Milk
of magnesia and magnesium salts
Water
moves via osmosis from the cells
into the intestines.
The Direction of Osmosis
only by a difference in total
concentration of all the molecules
dissolved in the water
Determined
It
does not matter what solutes they are.
3.10 In active transport, cells use
energy to move small molecules
into and out of the cell.
Molecules can’t always move
spontaneously and effortlessly in
and out of cells.
Two distinct types of active transport:
1. Primary
2. Secondary
(differ only in the source of the fuel)
Primary active transport:
uses energy directly from ATP
Secondary Active Transport
An
indirect method many transporter
proteins use for fueling their activities
The
transport protein simultaneously
moves one molecule against its
concentration gradient while letting
another flow down its concentration
gradient.
Secondary Active Transport
No
At
ATP is used directly.
some other point and in some other
location, energy from ATP was used to
pump one of the types of molecules
involved against their concentration
gradient.
3.11 Endocytosis and
exocytosis are used for bulk
transport of particles.
Many molecules are just too big to get
into a cell by passive or active transport.
Three types of endocytosis:
1. Phagocytosis
2. Pinocytosis
3. Receptor-mediated endocytosis
Pinocytosis: the process of cells taking in
dissolved particles and liquid
3.12 Connections between cells
hold them in place and enable them
to communicate with each other.
Involves
numerous types of protein and
glycoprotein adhesion molecules
Tight Junctions
form
continuous, water-tight seals around
cells and also anchor cells in place
particularly
important in the small intestine
where digestion occurs
Desmosomes
are
like spot welds or rivets that fasten
cells together into strong sheets
function
like Velcro: they hold cells
together but are not water-tight
found
in much of the tissue-lining cavities
of animal bodies
Gap Junctions
pores surrounded by special proteins that form
open channels between two cells
Gap junctions are an important mechanism
for cell-to-cell communication.
Q
Is a breakdown of cell-to-
cell communication related to
cancer?
Contact
inhibition
Tumors
Nine important landmarks distinguish
eukaryotic cells.
3.13 The nucleus is the cell’s genetic
control center.
The nucleus—the largest and
most prominent organelle in
most eukaryotic cells.
The nucleus has two primary
functions:
• genetic control center
• storehouse for hereditary
information
Chromatin
a
mass of long, thin fibers consisting of
DNA with some proteins attached
Nucleolus
an
area near the center of the nucleus
where subunits of the ribosomes are
assembled
Ribosomes
are like little factories.
3.14 Cytoplasm and cytoskeleton
form the cell’s internal environment,
provide its physical support, and can
generate movement.
Cytoskeleton:
Three Chief
Purposes
Cilia and Flagellum
3.15 Mitochondria are the cell’s energy
converters
Bag-within-a-Bag Structure:
the intermembrane space and the matrix
Endosymbiosis
Mitochondria
may have existed as
separate single-celled, bacteria-like
organisms billions of years ago.
Mitochondria
have their own DNA!
We all have more DNA
from one parent than
the other.
Who is the bigger contributor:
mom or dad?
Why?
3.16 THIS IS HOW WE DO IT
Can cells change their
composition to adapt to their
environment?
Why do you think the fat
cells in the cats exposed to
cold shrank so much?
What change in the study would
increase your confidence in the
conclusions?
3.17 Lysosomes are the cell’s
garbage disposals
Lysosomes
round, membrane-enclosed, acid-filled
vesicles that function as garbage disposals
Why is Tay-Sachs disease like a
strike by trash collectors?
50
different enzymes necessary
Malfunctions
Genetic
sometimes occur.
disorder
3.18 In the Endoplasmic reticulum,
cells build proteins and disarm toxins
Rough Endoplasmic Reticulum
The Smooth Endoplasmic Reticulum
Critical Responsibilities of the Smooth ER
3.19 The Golgi apparatus
processes products for delivery
throughout the body
3.19 Golgi apparatus: Where the cell
processes products for delivery
throughout the body
3.20 The cell
wall provides
additional
protection and
support for plant
cells
3.21
Vacuoles are
multipurpose
storage sacs
for cells
The central vacuole can play an important
role in five different areas of plant life:
1.
2.
3.
4.
5.
Nutrient storage
Waste management
Predator deterrence
Sexual reproduction
Physical support
3.22
Chloroplasts
are the plant
cell’s power
plant
The stroma and
interconnected
little flattened
sacs called
thylakoids
Endosymbiosis Theory Revisited
Chloroplasts
bacteria.
Circular
Dual
resemble photosynthetic
DNA
outer membrane
Chapter 4: Energy
From the sun to you in just two steps
Lectures by Mark Manteuffel, St. Louis Community College
Learning Objectives
Understand and be able to explain the following:
How energy flows from the sun and through all life
on earth
How photosynthesis uses energy from sunlight to
make food
Learning Objectives
Understand and be able to explain the following:
How cellular respiration converts food molecules into
ATP, a universal source of energy
Alternative pathways to energy acquisition
4.1 Cars that run on french fry oil?
Organisms and machines need energy to
work.
What are biofuels?
Q
Humans can get energy from
food. Can machines?
Biofuels and Fossil Fuels
Chains
of carbon and hydrogen atoms
• Energy is stored in the bonds
Animal
fats and oils
Energy Conversions
All
life depends on capturing energy from
the sun and converting it into a form that
living organisms can use.
Two
key processes
• Photosynthesis
• Cellular respiration
4.2 Energy has two forms.
Kinetic and Potential
What is energy?
The
capacity to do work
Work
• Moving matter against an opposing
force
Kinetic Energy
The
energy of
moving objects
• Heat energy
• Light energy
Potential Energy
A
capacity to do work that results from the
location or position of an object
Concentration
energy
Food
gradients and potential
has potential energy
Chemical Energy
4.3 As energy is captured and
converted, the amount of energy
available to do work decreases.
Energy Conversions
Only ~1% of the energy released by the sun that
earth receives is captured and converted by plants.
• Converted into chemical bond energy
What happens to the other 99%?
Thermodynamics
The study of the transformation of energy
from one type to another
First Law of Thermodynamics
Energy
It
can never be created or destroyed.
can only change from one form to
another.
Energy Tax!
Every time energy is converted from one form to another the
conversion isn’t perfectly efficient.
Some of the energy is always converted to the least usable
form of kinetic energy: heat.
Second Law of Thermodynamics
Every
conversion of energy includes the
transformation of some energy into heat.
Heat
is almost completely useless to living
organisms
4.4 ATP molecules are like
free-floating rechargeable
batteries in all living cells.
How do cells directly fuel their
chemical reactions?
None
of the light energy from the sun can
be used directly to fuel cellular work.
First
it must be captured in the bonds of a
molecule called adenosine triphosphate
(ATP).
Structure of ATP
ATP Molecules
Cells
cannot use light energy directly to do
work.
First,
the energy has to be converted into
chemical energy in ATP molecules.
Adenosine Triphosphate
Pop off the third phosphate group
• ATP ADP + Phosphate group + energy release
Release
a little burst of energy!
Use
this energy to drive chemical
reactions necessary for cellular
functioning.
• Building muscle tissue
• Repairing a wound
• Growing roots
Recycling in the Cell
ADP + phosphate group + energy = ATP
4.5 Where does plant matter come from?
Photosynthesis: the big picture.
From a seed
to a tree:
Where does
the mass
come from?
Photosynthetic Organisms
Photosynthesis: The Big Picture
3
inputs
2
products
4.6 Photosynthesis take place in
the chloroplasts
Organelles found in plant cells
A Closer Look at Chloroplasts
4.7 Light energy travels in waves:
plant pigments absorb specific
wavelengths
Light Energy
A type of kinetic energy
Made up of little energy packets called photons
Light Energy
Different photons carry different amounts of
energy, carried as waves.
Length of the wave = amount of energy the
photon contains.
Electromagnetic Spectrum
Range of
energy that is
organized into
waves of
different
lengths.
Shorter the
wavelength,
higher the
energy.
Visible Spectrum
Range
of energy humans see as light
ROYGBIV
Pigments
= molecules that absorb light
Chlorophyll
Plant
pigment
Absorbs
certain wavelengths of energy
(photons) from the sun
Absorbed
energy excites electrons
Plant Pigments
Plant
pigments can only absorb specific
wavelengths of energy
Therefore,
plants produce several
different types of pigments
Plant Pigments
Chlorophyll
a
Chlorophyll
b
Carotenoids
4.8 Photons cause electrons in
chlorophyll to enter an excited state.
Electron Excitation
Conversion
of electromagnetic energy into
chemical energy of bonds between atoms
Photons
of specific wavelengths bump
electrons up a quantum level into an
excited state
Two Potential Fates of Excited
Electrons
(1) Electrons return to their resting,
unexcited state.
(2) Excited electrons are passed to other
atoms.
The Passing of Electrons
in Their Excited State
Chief
way energy moves through cells
Molecules
that gain electrons always carry
greater energy than before receiving them
• Can view this as passing of potential energy from
molecule to molecule
4.9 Photosynthesis in detail:
the energy of sunlight is
captured as chemical energy.
FOLLOW THE ELECTRONS!
The “Photo” Part
Sunlight
ATP
A high-energy electron carrier
Electrons That Leave the
Photosystem Are Replenished
Where does oxygen come from?
An Electron Transport Chain
Connects the two photosystems
Product #1 of the “Photo” Portion
of Photosynthesis:
ATP
The Second Photosystem
Follow
the electrons
Product #2 of the “Photo” Portion
of Photosynthesis:
NADPH
Products from the “Photo”
Portion
ATP
and NADPH
Time
for the “synthesis” part!
“SYNTHESIS”
4.10 Photosynthesis in detail:
the captured energy of
sunlight is used to make food.
The Calvin Cycle
Series of
chemical
reactions
Occurs in
stroma
Enzymes are
recycled
The Processes in the Calvin Cycle
Occur in Three Steps:
4.11 The battle against world
hunger can use plants adapted to
water scarcity.
Evolutionary Adaptations
Some
plants thrive in hot, dry conditions
Adaptations
that reduce evaporative water
loss
• How do plants use water?
Stomata
Pores for gas exchange
How to get CO2 when stomata are shut?
C4 Photosynthesis
• C4 plants produce ultimate “CO2-sticky
tape” enzyme.
• C4 photosynthesis adds an extra set of
steps.
CAM Photosynthesis
Close
stomata during hot dry days
At
night, stomata open, CO2 let in and
temporarily bound to a holding molecule
During
day, CO2 gradually released and
used while stomata are closed
All Three Photosynthetic Pathways
Cellular respiration
converts food
molecules into
ATP,
a universal source
of energy for living
organisms.
4.12 How do living organisms
fuel their actions?
Cellular respiration: the big
picture.
Cellular
Respiration
The big picture
A Human Example
Eat food
Digest it
Absorb nutrient molecules into bloodstream
Deliver nutrient molecules to the cells
At this point, our cells can begin to extract
some of the energy
• stored in the bonds of the food molecules
4.13 The first step of cellular
respiration: glycolysis is the universal
energy-releasing pathway.
Glycolysis: the universal energy-releasing
pathway
Glycolysis
Three of the ten steps yield energy
– quickly harnessed to make ATP.
High-energy electrons are transferred to NADH.
Net result:
each
glucose molecule broken down into two
molecules of pyruvate
ATP molecules produced
NADH molecules store high-energy electrons
4.14 The second step of
cellular respiration: the Krebs
cycle extracts energy from
sugar.
The
Preparatory
Phase to the
Krebs Cycle
Payoff from the Krebs cycle:
ATP
NADH
FADH2
4.15 The third step
in cellular respiration:
ATP is built in the electron
transport chain.
Mitochondria
Two
key features of mitochondria are
essential to their ability to harness energy
from molecules:
• Feature 1: mitochondrial “bag-within-a-bag”
structure
• Feature 2: electron carriers organized within the
inner “bag”
The
“bag-withina-bag”
Follow the Electrons… (just as we did
in photosynthesis)
#2) This proton concentration
gradient represents a significant
source of potential energy!
Proton Gradients
and Potential Energy
The force of the flow of H+ ions fuels the
attachment of free-floating phosphate
groups to ADP to produce ATP.
4.16 THIS IS HOW WE DO IT
Can we combat the fatigue
and reduced cognitive
functioning of jet lag with
NADH pills?
Pure or Basic Science
and Applied Science
• What is jet lag and why is it of
scientific interest?
• How is jet lag related to cellular
respiration?
Why should NADH alleviate
symptoms of jet lag?
• If levels of NADH could be increased by
taking the molecule in pill form, this might
lead to increased production of usable
energy through the electron transport
chain.
• Testable prediction:
– “Supplementing NADH should counteract
some of the effects of jet lag, including
reduced cognitive functioning and fatigue.”
Experimental Setup
• The researchers used a randomized,
controlled, double-blind experimental
design.
• 2 groups: Placebo or NADH
• Battery of tests
• Overnight “red-eye” flight
• Retesting
Did NADH reduce the
symptoms of jet lag?
1. Vigilance
Placebo: 37% of subjects made
omission errors.
NADH: 14% of subjects made omission
errors.
Did NADH reduce the
symptoms of jet lag?
2. Working memory
Placebo: Subjects answered 6.8 more
problems per minute than in the
baseline test.
NADH: Subjects answered 13.2 more
problems per minute than in the
baseline test.
Did NADH reduce the
symptoms of jet lag?
3. Multi-tasking
Placebo: Subjects increased performance by
19.2 points over baseline.
Subjects’ reaction time was slower than
baseline by 0.44 seconds.
NADH: Subjects increased performance by
77.5 points over baseline.
Subjects’ reaction time was faster than
baseline by 0.15 seconds.
Did NADH reduce the
symptoms of jet lag?
4. Visual perception
Placebo: Subjects completed 1.4 more
items per minute than at baseline.
NADH: Subjects completed 5.4 more
items per minute than at baseline.
Did NADH reduce the
symptoms of jet lag?
5. Sleepiness
Placebo: 75% of subjects reported
increased sleepiness.
NADH: 25% of subjects reported
increased sleepiness
What conclusions can we draw
from these results?
• The researchers’ conclusion, supported by
the evidence, was that “NADH appears to
be a suitable short-term countermeasure
for the effects of jet lag on cognition and
sleepiness.”
There are
alternative
pathways to
energy
acquisition.
4.17
Beer, wine, and
spirits are byproducts of
cellular
metabolism in
the absence of
oxygen.
4.18
Eating a
complete diet:
cells can run
on protein and
fat as well as
on glucose.
Learning Objectives
Understand and be able to explain the following:
How energy flows from the sun and through all life
on earth
How photosynthesis uses energy from sunlight to
make food
How cellular respiration converts food molecules into
ATP, a universal source of energy
Alternative pathways to energy acquisition
Chapter 5: DNA, Gene
Expression, and Biotechnology
What is the genetic code,
and how is it harnessed?
Lectures by Mark Manteuffel, St. Louis Community College
Learning Objectives
Describe what DNA is and what it does.
Explain the process of gene expression
involving transcription and translation.
Explain the causes and effects of damage to
the genetic code.
Discuss biotechnology in agriculture.
Describe biotechnology and its implications
for human health.
DNA: what is
it, and what
does it do?
5.1 Knowledge about DNA is
increasing justice in the world.
Q
What is the most common reason why
DNA analyses overturn incorrect
criminal convictions?
Selfish dictators may owe their behaviour
partly to their genes, according to a study
that claims to have found a genetic link to
ruthlessness.
–Nature, April 2008
Too Many One-Night Stands? Blame Your
Genes . . .according to a new study, it may
be fair to say that while you jolly well could
help cheating, your particular genes did make
things more difficult.
— Time magazine, December 2010
5.2 The DNA molecule contains
instructions for the development
and functioning of all living
organisms.
DNA “Double Helix”
Nucleic acids and nucleotides
Sugars, Phosphates,
and Bases
A, T, C, and G
The Base pairs
Base-pairing rules
5.3 Genes are sections of DNA that
contain instructions for making
proteins.
Why is DNA considered the
universal code for all life on
earth?
Genes
A
sequence of bases in a DNA molecule
that carries the information necessary for
producing a functional product, usually a
protein molecule or RNA.
Locus:
the location or position of a gene
on a chromosome.
Genetic Information
• The sequence of bases in DNA carries
information.
• “AAAGGCTAGGCC…” continuing on for
another 3,000 or so bases.
5.4 Not all DNA contains instructions
for making proteins.
An onion has five times as
much DNA as a human.
Why doesn’t that make them
more complex than us?
The
Proportion
of the DNA
That Codes
for Genes
Introns
Non-coding
regions of DNA
May
take the form of short (or long)
sequences that are repeated thousands of
times
May
also consist of gene fragments, duplicate
versions of genes, and pseudogenes
5.5 How do genes work?
An overview
Genotype
• all of the genes contained in an
organism
Phenotype
• the physical manifestations of the
instructions
Building
organisms:
information in
DNA directs the
production of
the molecules
that make up
an organism.
5.6 In transcription, the information
coded in DNA is copied into mRNA.
5.7 In translation, the mRNA copy
of the information from DNA is
used to build functional molecules.
Several ingredients must be present in
the cytoplasm for translation to occur.
Free
amino acids
Ribosomal
Transfer
units
RNA
The Genetic Code
5.8 Genes are regulated in
several ways
Gene Expression & Gene Regulation
Microarrays
• A powerful tool used to monitor the
expression levels of thousands of genes
simultaneously
• Particularly useful in exploring how gene
expression differs in response to an
illness, or the treatment of an illness, or in
response to aging
Controlling Gene Expression
• Transcription factors
– proteins that bind to specific regulatory sites
on the DNA
• “positive control”
&
• “negative control”
Prokaryotic Gene Control
and the lac operon
Elements of Gene Control
• Promoter
• Operator
• Regulatory Gene
Eukaryotic Gene Control
• There are many other
ways that genes can be
regulated, besides
operons.
• Transcription Regulation
– Activators & Repressors
– Enhancer Sequences
– Chemical interference
• Post-Transcription
Regulation
Damage to the
genetic code
has a variety of
causes and
effects.
5.9 What causes a mutation,
and what are its effects?
Alteration
DNA
of the sequence of bases in
• can lead to changes in the structure and
function of the proteins produced
• can have a range of effects
Breast Cancer in Humans
Two
human genes, called BRCA1 and
BRCA2
More
than 200 different changes in the
DNA sequences of these genes have been
detected,
each
of which results in an increased risk
of developing breast cancer.
Mutations in Sex Cells
& Non-Sex Cells
• Differences?
• Which may get passed on to offspring?
Q
Why do dentists put a heavy
apron over you when they
X-ray your teeth?
Ionizing Radiation
Q
Why is it dangerous to be
near the core of a nuclear
power plant?
5.10 THIS IS HOW WE DO IT
Does sunscreen use reduce
skin cancer risk?
What happens when our skin
cells are exposed to the sun?
• UVB radiation
• Inflammation
• Skin cancer?
– melanoma
Why would anyone question
whether sunscreen has a
positive effect?
• 1960s and 1970s: sunscreens widely
available
• Increase in incidence of melanoma
• Swedish study
Sunscreen users were at
greater risk for cancer!
How can that be?
• False sense of security
• UVA & UVB
How can you figure out whether
sunscreen users are actually
protected from cancer?
• Case-controlled studies
• Assumptions and confounding variables
“Randomized controlled trials.”
Why are they better than casecontrolled studies?
• Randomly assigned 1,621 adults to one of
two groups:
1) regular sunscreen use and
2) discretionary sunscreen use.
Results?
• Sunscreen-use group
• 11 melanoma detects
• Discretionary-use group
• Twice as many new melanomas detected!
• Invasive melanomas 4x more frequent!
If randomized controlled
studies are so much better,
why would anyone bother
doing case-controlled studies?
• Difficult to conduct
• Relatively expensive
• Compliance issues
5.11 Faulty genes, coding for faulty
enzymes, can lead to sickness.
How
can people respond so differently to
alcohol?
A
single difference in a single pair of bases
in their DNA.
A “fast-flush” response
Q
Why do many Asians have
unpleasant experiences
associated with alcohol
consumption?
From mutation to illness in
just four steps:
(1) A mutated gene codes for a nonfunctioning protein, usually an enzyme.
(2) The non-functioning enzyme can’t
catalyze the reaction as it normally
would, bringing it to a halt.
From mutation to illness in
just four steps:
(3) The molecule with which the enzyme
would have reacted accumulates, like a
blocked assembly line.
(4) The accumulating chemical causes
sickness and/or death.
Biotechnology
is producing
improvements
in agriculture.
5.12 What is biotechnology?
And What Is Genetic Engineering?
Adding,
deleting, or transplanting genes
from one organism to another, to alter the
organisms in useful ways
5.13
Biotechnology
can improve food
nutrition and
make farming
more efficient
and eco-friendly
Q
How might a genetically
modified plant help 500
million malnourished people?
Nutrient-rich “golden rice”
Almost everyone in the U.S. uses
genetically modified crops regularly
without knowing it.
What crops are responsible for this?
Insect Resistance
Q
How can genetically modified
plants lead to reduced pesticide
use by farmers?
Herbicide Resistance
Faster Growth and Bigger Bodies
5.14
Fears and
risks: are
genetically
modified foods
safe?
Concern#1. Organisms that we want to kill may
become invincible.
Concern#2. Organisms that we don’t want to kill
may be killed inadvertently.
Concern#3. Genetically modified crops are not
tested or regulated adequately.
Concern#4. Eating genetically modified foods is
dangerous.
Concern#5. Loss of genetic diversity among crop
plants is risky.
Concern#6. Hidden costs may reduce the financial
advantages of genetically modified crops.
Biotechnology
has the
potential for
improving
human health
(and criminal
justice).
5.15 The treatment of diseases and
production of medicines are improved
with biotechnology
Prevent
Cure
diseases
diseases
Treating
diseases
• The treatment of diabetes
Q
Why do some bacteria
produce human insulin?
Recombinant DNA technology
Several important achievements followed
the development of insulin-producing
bacteria, including:
(1) Human growth
hormone (HGH)
(2) Erythropoietin
What is “blood doping”?
How does it improve some
athletes’ performance?
5.16 Gene Therapy:
biotechnology can help
diagnose and prevent
diseases
But has had a limited success
in curing them
1) Is a given set of parents likely to
produce a baby with a genetic
disease?
2) Will a baby be born with a genetic
disease?
cystic fibrosis
sickle-cell anemia
Down syndrome
others
3) Is an individual likely to develop a
genetic disease later in life?
breast
cancer
prostate
skin
cancer
cancer
Ethical Dilemmas
Discrimination
Health
How
insurance
to proceed with the information?
Q
Why has gene therapy had
such a poor record of success
in curing diseases?
Gene Therapy Difficulties
(1) Difficulty getting the working gene into
the specific cells where it is needed.
(2) Difficulty getting the working gene into
enough cells and at the right rate to have a
physiological effect.
Gene Therapy Difficulties
(3) Difficulty arising from the transfer
organism getting into unintended cells.
(4) Difficulty regulating gene expression.
5.17 Cloning—ranging from
genes to organs to
individuals—offers both
promise and perils
Are there any medical
justifications for cloning?
Can a human be cloned (and
should they be)?
5.18 DNA as an individual identifier: the
uses and abuses of DNA fingerprinting
DNA From Different Humans
• 99.9% identical
• So what differs?
• Highly variable regions
• STRs
What is a DNA
fingerprint?
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