Understanding Fossil Butte

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Understanding Fossil Butte

• In the southwest corner of Wyoming, there is a
  flat-topped mountain called Fossil Butte. A
  fossil of a fish was found near the top of Fossil
  Butte in a rock formation that is about 50
  million years old. Fossils of other kinds of
  fishes, as well as turtles, have been found at
  Fossil Butte. The land around Fossil Butte is
  dry, and the Pacific Ocean is more than 1000 km
  away. How could fossils of sea-dwelling animals
  have formed at Fossil Butte?

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• 1. Think of a question that a scientist might ask
  in order to understand why there are fish fossils
  in the desert of Wyoming. Write this question on
  a sheet of paper.
• 2. Discuss your question with your group and
  suggest a possible answer.
• 3. How could a scientist go about finding an
  answer to the question?

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1-1 What is Science?

• A. What Science Is and Is Not
• B. Thinking Like a Scientist
• C. Explaining and Interpreting Evidence
• D. Science as a Way of Knowing
• E. Science and Human Values

BIIE 1f. Distinguish between hypothesis and
theory as scientific terms.
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What is the goal of science?

• To investigate and understand the natural world,
  to explain events in the natural world, and to
  use those explanations to make useful
  predictions.
• Science is the organized way of using evidence to
  learn about the natural world. It also refers to
  the body of knowledge that scientists have built
  up after years of using this process.

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Think like a scientist

• Observation is the process of gathering
  information about events or processes in a
  careful, orderly way involving the senses. The
  info we gather is the data.
• An inference is a logical interpretation based on
  the prior knowledge or experiences we may have.

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Whats the difference?
Statement Observation Inference

• A is a basketball.
• B is a table tennis ball.
• C is a soccer ball.

Object A is round and orange.
Object A is a basketball.
Object C is round and black and white.
Object C is larger than Object B.
Object B is smooth.
Object B is a table-tennis ball.
Each object is used in a different sport.
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Explaining and Interpreting Evidence

• A hypothesis is a proposed scientific explanation
  for a set of observations.
• Scientists use prior knowledge and logical
  inference to create hypotheses.
• Scientific hypotheses must be proposed in a way
  that enables them to be tested.

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Your individual evaluation

• Write an explanation in your own words of what a
  hypothesis is not the books definition.
• Name 3 ways in which a hypothesis may arise.

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Mystery Worms

• I collected some beetles from a rotting log and
  placed them in a container of dry oatmeal in my
  classroom. I kept the box covered with a light
  cloth so that the beetles could not escape. I
  asked one of my students to add potato and apple
  pieces once a week to provide food and moisture
  for the beetles. After several weeks, the student
  reported that there were some strange-looking,
  wormlike organisms in the container.

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• 1. Formulate a hypothesis that might explain the
  presence of the worms in the container.
• 2. How could you test your hypothesis?
• 3. Identify the variables in your proposed
  experiment. Identify the control in your proposed
  experiment.

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1-2 How Scientists Work

• A. Designing an Experiment
• 1. Asking a Question
• 2. Forming a Hypothesis
• 3. Setting Up a Controlled Experiment
• 4. Recording and Analyzing Results
• Drawing a Conclusion
• B. Publishing and Repeating Investigations
• 1. Needhams Test of Redis Findings
• 2. Spallanzanis Test of Redis Findings
• 3. Pasteurs Test of Spontaneous Generation
• 4. The Impact of Pasteurs Work
• C. When Experiments Are Not Possible
• D. How a Theory Develops

BIIE 1n. Know that when an observation does not
agree with an accepted scientific theory, the
observation is sometimes mistaken or fraudulent
and that the theory is sometimes wrong.
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Designing an Experiment

• Asking a question
• Forming a hypothesis
• Setting up a controlled experiment
• Whenever possible, a hypothesis should be tested
  by an experiment in which only one variable is
  changed at a time. All other variables should be
  kept unchanged, or controlled.

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Contd

• A deliberately changed variable is the
  manipulated variable, the variable that is
  observed and that changes in response to the
  manipulated variable the responding variable.
• Recording and analyzing results.
• Drawing a conclusion
• Repeating your investigations

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Designing an experiment
State the Problem
Analyze Results
Form a Hypothesis
Draw a Conclusion
Set Up a Controlled Experiment
Publish Results
Record Results
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Redis experiment on spontaneous generation
OBSERVATIONS Flies land on meat that is left
uncovered. Later, maggots appear on the meat.
HYPOTHESIS Flies produce maggots.
PROCEDURE
Uncovered jars
Covered jars
Controlled Variables jars, type of
meat, location, temperature, time
Several days pass
Manipulated Variables gauze covering that keeps
flies away from meat
Responding Variable whether maggots appear
Maggots appear
No maggots appear
CONCLUSION Maggots form only when flies come in
contact with meat. Spontaneous generation of
maggots did not occur.
In a controlled experiment, only one variable is
tested at a time. Redi designed an experiment to
determine what caused the sudden appearance of
maggots. In his experiment, the manipulated
variable was the presence or absence of the gauze
covering. The results of this experiment helped
disprove the hypothesis of spontaneous generation.
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Spallanzanis experiment
Spallanzanis experiment showed that
microorganisms will not grow in boiled gravy that
has been sealed but will grow in boiled gravy
that is left open to the air.
Gravy is teeming with microorganisms.
Flask is open.
Gravy is boiled.
Flask is sealed.
Gravy is free of microorganisms.
Gravy is boiled.
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Pasteurs experiment
Broth is free of microorganisms for a year.
Curved neck is removed.
Broth is teeming with microorganisms.
Broth is boiled.
Pasteurs experiment showed that boiled broth
would remain free of microorganisms even if air
was allowed in, as long as dust and other
particles were kept out.
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When experiments are not possible

• Field studies
• Can you suggest any???

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How does a scientific theory develop?

• In science, the word theory applies to a well
  tested explanation that unifies a broad range of
  observations.
• The theory of plate tectonics and evolution help
  explain why marsupials can be found only in
  Australia and some nearby islands.

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Shells and Snowflakes

• How can we distinguish between living and
  nonliving things, such as a radiolarian (left)
  and a snowflake (right)? A radiolarian is a tiny
  living thing that is covered with a glasslike
  shell and lives in the ocean. A snowflake is a
  crystal made of frozen water.

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• 1. What are some similarities between the
  snowflake and the glass shell of the radiolarian?
• 2. What are some differences between the
  snowflake and the glass shell?
• 3. Would you classify the shell as a living thing
  or a nonliving thing? Explain your answer.

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1-3 Studying Life

• A. Characteristics of Living Things
• 1. Made Up of Cells
• 2. Reproduction
• 3. Based on a Genetic Code
• 4. Growth and Development
• 5. Need for Materials and Energy
• 6. Response to the Environment
• 7. Maintaining Internal Balance
• 8. Evolution
• B. Branches of Biology
• C. Biology in Everyday Life

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Characteristics of living things
Characteristic
Examples
Living things are made up of units called cells.
Many microorganisms consist of only a single
cell. Animals and trees are multicellular.
Living things reproduce.
Maple trees reproduce sexually. A hydra can
reproduce asexually by budding.
Living things are based on a universal genetic
code.
Flies produce flies. Dogs produce dogs. Seeds
from maple trees produce maple trees.
Living things grow and develop.
Flies begin life as eggs, then become maggots,
and then become adult flies.
Living things obtain and use materials and energy.
Plants obtain their energy from sunlight.
Animals obtain their energy from the food they
eat.
Leaves and stems of plants grow toward light.
Living things respond to their environment.
Despite changes in the temperature of the
environment, a robin maintains a constant body
temperature.
Living things maintain a stable internal
environment.
Taken as a group, living things change over time.
Plants that live in the desert survive because
they have become adapted to the conditions of the
desert.
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How can life be studied at different levels?

• Some of the levels at which life can be studied
  include molecules, cells, organisms, populations
  of a single kind of organism, communities of
  different organisms in an area, and the
  biosphere. At all these levels, smaller living
  systems are found within larger systems.

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Levels of Organization
Biosphere
The part of Earth that contains all ecosystems
Biosphere
Ecosystem
Community and its nonliving surroundings
Hawk, snake, bison, prairie dog, grass, stream,
rocks, air
Community
Populations that live together in a defined area
Hawk, snake, bison, prairie dog, grass
Population
Group of organisms of one type that live in the
same area
Bison herd
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Levels of Organization cont.
Organism
Individual living thing
Bison
Tissues, organs, and organ systems
Groups of Cells
Nervous system
Brain
Nervous tissue
Smallest functional unit of life
Cells
Nerve cell
Groups of atoms smallest unit of most
chemical compounds
Molecules
DNA
Water
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Putting Size Into Perspective

• Here are some measurements
• A young child is just over 1 m in height. The
  marble in the childs hand has a diameter of
  about 0.01 m. A cell in the palm of the childs
  hand has a diameter of about 0.0001 m.
• You can put these numbers in perspective by using
  a ratio of the larger object to the smaller one.
  This requires dividing the larger number by the
  smaller number. Another way to compare these
  numbers is to look at the place value of the
  number 1. Each time the number shifts one place
  value to the right, it decreases by a factor of
  10. So, 1 is ten times greater than 0.10, and 10
  is one hundred times greater than 0.10.

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• A young child is just over 1 m in height. The
  marble in the childs hand has a diameter of
  about 0.01 m. A cell in the palm of the childs
  hand has a diameter of about 0.0001 m.
• 1. How does the height of the child compare to
  the diameter of the marble?
• 2. How does the marble diameter compare to the
  diameter of the cell?
• 3. How does the height of the child compare to
  the diameter of the cell?

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1-4 Tools and Procedures

• A. A Common Measurement System
• B. Analyzing Biological Data
• C. Microscopes
• 1. Light Microscopes
• 2. Electron Microscopes
• D. Laboratory Techniques
• 1. Cell Cultures
• 2. Cell Fractionation
• E. Working Safely in Biology

BIIE 1a. Select and use appropriate tools and
technology to perform tests, collect data,
analyze relationships, and display data.
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What measurement system do most scientists use?

• Most scientists use the metric system when
  collecting data and performing experiments.
• The metric system is also referred to as SI and
  is based on multiples of 10.
• Help with the metric system available in appendix
  C (pg. 1069).

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Making a Graph from a Data Table
Water Released and Absorbed by Tree
Absorbed by Roots (g/h)
Released by Leaves (g/h)
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Water released by leaves
Time
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8 AM
2
1
10
Relative Rates (g/h)
10 AM
5
1
12
12 PM
4
5
2 PM
6
17
Water absorbed by roots
4 PM
9
16
0
6 PM
14
10
8 AM
10 AM
12 PM
2 PM
4 PM
6 PM
8 PM
8 PM
10
3
Time
Graphs are the simplest way to detect a pattern
of change from a data table. Data can be plotted
to make it easier to interpret.
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How are light microscopes and electron
microscopes similar/different?

• Light microscopes (compound light microscopes)
  produce magnified images by focusing visible
  light rays. Electron microscopes produce
  magnified images by focusing beams of electrons.
• Appendix D (pg. 1070) can help you with this.

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Analyzing Data

• pg. 27

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Laboratory Techniques

• Cell cultures are created from one cell that is
  able to reproduce. They can be used to test
  responses to cells under controlled conditions or
  to study interactions.
• Cell fractionation is a technique used to
  separate the different cell parts.
• The most important part of being in the lab is
  being safe! You will be quizzed on the lab safety
  rules next time in class.

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Whats the matter?

• All of the materials around you are made up of
  matter. You are made up of matter, as are the
  chair you sit on and the air you breathe. With
  your group
• 1. Give an example of solid matter.
• 2. Give an example of liquid matter.
• 3. Give an example of gaseous matter.
• 4. Is all matter visible?
• 5. Does all matter take up space?

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2-1 The Nature of Matter

• A. Atoms
• B. Elements and Isotopes
• 1. Isotopes
• 2. Radioactive Isotopes
• C. Chemical Compounds
• D. Chemical Bonds
• 1. Ionic Bonds
• 2. Covalent Bonds
• 3. Van der Waals Forces

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What three subatomic particles make up atoms?

• The subatomic particles that make up atoms are
  protons, neutrons, and electrons.
• Atoms are the basic units of matter.
• Protons are positively charged.
• Electrons are negatively charged.
• Neutrons have no charge.

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An Element in the Periodic Table
Atomic number
6
C
Element symbol
Carbon
Element name
12.011
Atomic mass
An element is a pure substance that consists
entirely of one type of atom.
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Isotopes of Carbon
Nonradioactive carbon-12
Nonradioactive carbon-13
Radioactive carbon-14
6 electrons 6 protons 6 neutrons
6 electrons 6 protons 8 neutrons
6 electrons 6 protons 7 neutrons
Atoms of the same element that differ in the
number of neutrons they contain are isotopes.
Isotopes are identified by their mass number
(pn). Because they have the same number of
electrons, all isotopes of an element have the
same chemical properties.
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What are the two main types of chemical bonds?

• The main types of chemical bonds are ionic bonds
  and covalent bonds.
• Ionic bonds are formed when one or more electrons
  are transferred from one atom to another.
  Positively and negatively charged atoms are ions.
• Covalent bonds form when electrons are shared
  between atoms. The structure that results when
  atoms are joined together by these bonds are
  called molecules.

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Ionic Bonding
Sodium atom (Na)
Chlorine atom (Cl)
Sodium ion (Na)
Chloride ion (Cl-)
Transfer of electron
Protons 11 Electrons -11 Charge 0
Protons 17 Electrons -17 Charge 0
Protons 11 Electrons -10 Charge 1
Protons 17 Electrons -18 Charge -1
The chemical bond in which electrons are
transferred from one atom to another is called an
ionic bond. The compound sodium chloride forms
when sodium loses its valence electron to
chlorine.
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Van der Waals forces

• The slight attraction that develops between the
  oppositely charged regions of nearby molecules.
• Help geckos grip smooth, vertical surfaces.

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BioDetectives

• Historys Mystery An Introduction to Forensic
  Science

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Water, Water Everywhere

• If you have ever seen a photograph of Earth from
  space, you know that much of the planet is
  covered by water. Water makes life on Earth
  possible. If life as we know it exists on some
  other planet, water must be present to support
  that life.

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With your group

• 1. Make a list of five things that have water in
  them. (Do not list water!)
• 2. Discuss your list with the list of another
  group of students across from your group. Did
  your lists contain some of the same things? Did
  anything on the other list surprise you?
• 3. Did either list contain any living things?

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2-2 Properties of Water

• A. The Water Molecule
• 1. Polarity
• 2. Hydrogen Bonds
• B. Solutions and Suspensions
• 1. Solutions
• 2. Suspensions
• C. Acids, Bases, and pH
• 1. The pH Scale
• 2. Acids
• 3. Bases
• 4. Buffers

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Why are water molecules polar?

• A water molecule is polar because there is an en
  even distribution of electrons between the oxygen
  and hydrogen atoms.
• The negative pole is near the oxygen atom and the
  positive pole is near the hydrogen atoms.

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Hydrogen bonds

• Not as strong as ionic or covalent bonds.
• Cohesion is an attraction between molecules of
  the same substance. Because of hydrogen bonding,
  water is very cohesive.
• Adhesion is an attraction between molecules of
  different substances.

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Solutions and suspensions

• Mixtures are materials composed of two or more
  elements or compounds that are physically mixed
  together but not chemically combined (salt and
  pepper).
• Solutions occur when all components are
  distributed throughout the solution.
• Suspensions are mixtures of water and
  nondissolved materials.

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NaCl Solution
Cl-
Cl-
Na
Na
Water
Water
When an ionic compound such as sodium chloride is
placed in water, water molecules surround and
separate the positive and negative ions.
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pH Scale
Oven cleaner
The pH scale is used to indicate the
concentration of H ions in a solution.
Bleach
Ammonia solution
Increasingly Basic
Soap
Sea water
Human blood
Neutral
Pure water
Milk
Normal rainfall
Acid rain
Increasingly Acidic
Tomato juice
Lemon juice
Stomach acid
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What are acidic and basic solutions?

• Acidic solutions contain higher concentrations of
  H ions than pure water and have pH values below
  7.
• Basic, or alkaline, solutions contain lower
  concentrations of OH- ions than pure water and
  have pH values above 7.

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Lifes Backbone

• Most of the compounds that make up living things
  contain carbon. In fact, carbon makes up the
  basic structure, or backbone, of these
  compounds. Each atom of carbon has four electrons
  in its outer energy level, which makes it
  possible for each carbon atom to form four bonds
  with other atoms.
• As a result, carbon atoms can form long chains. A
  huge number of different carbon compounds exist.
  Each compound has a different structure. For
  example, carbon chains can be straight or
  branching. Also, other kinds of atoms can be
  attached to the carbon chain.

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• 1. On a sheet of paper, make a list of at least
  five things that contain carbon.
• 2. Review your list. If you think some things on
  your list contain only carbon, write only
  carbon next to them.
• 3. If you know other elements that are in any
  items on your list, write those elements next to
  them.

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2-3 Carbon Compounds

• A. The Chemistry of Carbon
• B. Macromolecules
• C. Carbohydrates
• D. Lipids
• E. Nucleic Acids
• F. Proteins

BI 1h. Students know most macromolecules in cells
and organisms are synthesized from a small
collection of simple precursors. BI 4e. Students
know proteins can differ from one another in the
number and sequence of amino acids. BI 4f.
Students know why proteins having different amino
acid sequences typically have different shapes
and chemical properties.
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Carbon Compounds
Acetylene
Butadiene
Benzene
Isooctane
Methane
Carbon compounds have four valence electrons to
bond with other elements. It can form single,
double, or triple bonds with other carbon atoms.
Each line here represents one covalent bond.
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Macromolecules

• Formed by polymerization.
• Molecules in living cells that are large.
• Smaller units are monomers.
• Join together to form polymers.

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What are the functions of each group of organic
compounds?

• Four groups of organic compounds found in living
  things are carbohydrates, lipids, nucleic acids,
  and proteins.

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Carbohydrates

• Living things use carbohydrates (like starches
  and sugars) as their main source of energy.
  Plants and some animals also use carbohydrates
  for structural purposes.

Starch
Glucose
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Contd

• Monomers in starch polymers are sugar molecules.
• Single sugarsmonosaccharides
• Many monosaccharidespolysaccharides

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Lipids

• Lipids can be used to store energy. Some lipids
  are important parts of biological membranes and
  waterproof coverings.
• Contains a glycerol backbone with three fatty
  acid chains attached.
• Saturated fats contain only single bonds.
• Unsaturated fats contain both single and double
  bonds.

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Nucleic Acids

• Nucleic acids store and transmit hereditary, or
  genetic, information.
• The monomers that make up a nucleic acid are
  nucleotides that consists of a 5-carbon sugar, a
  phosphate group, and a nitrogenous base.
• Two kinds DNA (sugar deoxyribose) and RNA (sugar
  ribose).

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Proteins

• Some proteins control the rate of reactions and
  regulate cell processes. Some are used to form
  bones and muscles. Others transport substances
  into or out of cells or help to fight disease.
• Are polymers of amino acids.

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Amino Acid
Carboxyl group
Amino group
General structure
Alanine
Serine
Amino acids are monomers of proteins. All amino
acids have an amino group at one end and a
carboxyl group at the other end. What
distinguishes one amino acid from another is the
R-group section of the molecule.
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Protein
Amino acids
Proteins help to carry out chemical reactions,
transport small molecules in and out of cells,
and fight disease. Proteins are made up of chains
of amino acids folded into complex structures.
Each protein has a specific role
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Carbon Compounds
include
that consist of
that consist of
that consist of
that consist of
which contain
which contain
which contain
which contain
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Matter and Energy

• Imagine sitting around a campfire and watching
  the flames flicker? The burning of wood is a
  chemical reactiona process that changes one set
  of chemicals into another set of chemicals. A
  chemical reaction always involves changes in
  chemical bonds that join atoms in compounds. The
  elements or compounds that enter into a chemical
  reaction are called reactants. The elements or
  compounds produced by a chemical reaction are
  called products. As wood burns, molecules of
  cellulose are broken down and combine with oxygen
  to form carbon dioxide and water vapor, and
  energy is released.

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• 1. What are the reactants when wood burns?
• 2. What are the products when wood burns?
• 3. What kinds of energy are given off when wood
  burns?
• 4. Wood doesnt burn all by itself. What must you
  do to start a fire? What does this mean in terms
  of energy?
• 5. Once the fire gets started, it keeps burning.
  Why dont you need to keep restarting the fire?

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2-4 Chemical Reactions and Enzymes

• A. Chemical Reactions
• B. Energy in Reactions
• 1. Energy Changes
• 2. Activation Energy
• C. Enzymes
• D. Enzyme Action
• 1. The Enzyme-Substrate Complex
• 2. Regulation of Enzyme Activity

BI 1b. Students know how enzymes are proteins
that catalyze biochemical reactions without
altering the reaction equilibrium and the
activities of enzymes depend on the temperature,
ionic conditions, and the pH of the surroundings.
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Chemical reactions

• Processes that change or transform one set of
  chemicals into another.
• The elements of compounds that enter into the
  reaction are the reactants.
• The elements of compounds that are produced by
  the reaction are the products.
• Chemical reactions always involve changes in the
  chemical bonds that join atoms in compounds.

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How do energy changes affect whether a chemical
reaction will occur?

• Chemical reactions that release energy often
  occur spontaneously. Chemical reactions that
  absorb energy will not occur without a source of
  energy.
• Activation energy is the energy that is needed to
  get the reaction started.

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Chemical Reactions
Energy-Releasing Reaction
Energy-Absorbing Reaction
Activation energy
Products
Activation energy
Reactants
Reactants
Products
Chemical reactions that release energy often
occur spontaneously. Chemical reactions that
absorb energy will occur only with a source of
energy. The peak of each graph represents the
energy needed for the reaction to go forward. The
difference between this required energy and the
energy of the reactants is the activation energy.
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Analyzing Data

• How does pH affect an enzyme? pg. 51

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Enzymes

• Enzymes are proteins that speed up chemical
  reactions that take place in cells .
• A catalyst is a substance that speeds up the rate
  of a chemical reaction.

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Effect of Enzymes
Notice how the addition of an enzyme lowers the
activation energy in this reaction. This action
speeds up the reaction.
Reaction pathway without enzyme
Activation energy without enzyme
Activation energy with enzyme
Reactants
Reaction pathway with enzyme
Products
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Enzyme Action
Enzyme (hexokinase)
Glucose
Substrates
Products
ADP
The reactants of enzyme catalyzed reactions are
known as substrates.
Glucose-6- phosphate
ATP
Products are released
Active site
Substrates bind to enzyme
Enzyme-substrate complex
Substrates are converted into products
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