Transcript File - Mr. Jacobson`s Site

THE CHEMICAL BASIS
OF LIFE
Chapter 4
4-1 Water
Water
• Needed by all know forms of life
• ~75% of Earth’s surface is covered with water
• Water refers to liquid form. (Solid and gas forms also
seen)
• Total Water on Earth
Structure and Properties of Water
• What are some you can think of?
• Tasteless & odorless
• Transparent…Why is that important?
• Some marine organisms need sunlight to make food
http://www.european-coatings.com/var/ezflow_site/storage/images/european-coatings/home/raw-materialstechnologies/technologies/functional-coatings/relationship-between-surface-wettability-and-transparency-in-four-water-conditions/4481225-1eng-GB/Relationship-between-surface-wettability-and-transparency-in-four-water-conditions.jpg
Chemical Structure of Water
• One atom of O, two Atoms of H
• O attracts negatively charged e- more than the H
• Therefore O has a slightly – charge and the H has a
slightly + charge
• This makes it a polar molecule because it has a different
electrical charge between different parts of the same
molecule
This diagram shows the + and – parts of a water
molecule. It also shows how a charge such as an ion
(Na or Cl) can interact with a water molecule
https://www.ck12.org/flx/show/THUMB_POSTCARD/image/201412291419891717824192_dd7d
db5884cb6b1b7becfbdffca8b557-201412291419895613124263.png
• Opposites attract
• H+ end of one water molecule is attracted to the O- end of
a nearby molecule
• This forms a Hydrogen bond (weak)
• Bonds between molecules are not as strong as inside
molecules
• They are strong enough to hold together nearby
molecules
• Cohesion - between two water molecules
• Adhesion – attraction between two different molecules
Hydrogen bonds form between nearby
water molecules
https://www.ck12.org/flx/show/THUMB_POSTCARD/image/201412291419891717853796_346d
3430d2c73ff668a727c8971858bc-201412291419895613365653.png
Properties of Water
• Water sticks together (cohesion) examples?
https://www.ck12.org/flx/show/THUMB_POSTCARD/image/201412291419891717895411_4e0e
50a24b1bf2b454c2e5736ea4f95d-201412291419895613631251.jpg
• H bonds cause a higher boiling point (100 C, 212 F)
• Higher boiling point causes most water on Earth to be in
liquid state, not gas state
• All living things on Earth need water
• H bonds cause water to expand when frozen
• Causes ice to have lower density than liquid water (ice floats)
http://militaryhuntingandfishing.com/wp-content/uploads/2015/01/Ice-fishing-Canada.jpg
Water and Life
• Human= ~70% water not counting fat (varies)
• Why so much Water?
• Substances the body needs are dissolved in water
• Biochemical reactions occur in water
• 2 Important biochemical reactions:
• 1. photosynthesis: 6CO2 + 6H2O + Energy → C6H12O6 + 6O2
• 2. cellular respiration: C6H12O6 + 6O2 → 6CO2 + 6H2O + Energy.
• Just about all life processes involve water
Water in Biochemical Reactions
http://iws.collin.edu/biopage/faculty/mcculloch/1406/outlines/chapter%205/5-2.JPG
4 - 2 Chemical Compounds in Living
Things
http://www.goldiesroom.org/Multimedia/Bio_Images/04%20Biochemistry/07%20Organic%20Com
pound%20Flowchart.jpg
Carbon is the most important element to life. Without this
element, life as we know it would not exist. Carbon is the central
element in compounds necessary for life.
https://dr282zn36sxxg.cloudfront.net/datastreams/fd%3A834cd68f4940430141b4785fbc583f041a3b02a132b66e75b9266a5f%2BIMAGE%2BIMAG
E.1
The significance of Carbon
• A compound in living things is an Organic Compound
• Organic compounds make up cells/other structures and
carry out life processes
• Carbon is the main element in organic compounds
(important)
http://ww2.coastal.edu/kingw/psyc460/molecules/organic_molecules.jpg
Compounds
• Compound: substance that consists of two or more
elements (always the same)
• The smallest part of a compound is a molecule
• A molecule of water always contains 2 H atoms and 1 O
atom
• Water is not an organic compound
https://dr282zn36sxxg.cloudfront.net/datastreams/fd%3Abf34ad1d559d476bbe62fe8278fc9e8f088e04df8ba2405a6a72a87f%2BIMAGE_THUMB_L
ARGE%2BIMAGE_THUMB_LARGE.1
• Chemical bond: force that holds molecules together (H
bonds in water)
• Chemical reaction: process that changes some chemical
substances into others
• Chemical reactions are needed to form compounds (also
needed to break them apart)
https://dr282zn36sxxg.cloudfront.net/datastreams/fd%3Ad7255fbb9f6b9cd58a848773e0259d611561c237daa1d3de310be325%2BIMAGE_THUMB
_POSTCARD%2BIMAGE_THUMB_POSTCARD.1
Carbon
• Why is carbon needed for life?
• It forms stable bonds with many elements including C
• C forms a variety of complex and simple molecules (10
million C based compounds)
• The millions can be grouped into 4 main types
(macromolecules)
• 1. carbohydrates
• 2. lipids
• 3. proteins
• 4. nucleic acids
• Carbohydrates, proteins and nucleic acids are large
Polymers (large molecules) made up of smaller
monomers (small molecules)
• Built by dehydration (condensation) reactions
• Dehydration reaction: Water is built as two monomers
come together.
http://bio1151b.nicerweb.net/Locked/media/ch05/05_02aPolymers-L.jpg
http://mgh-images.s3.amazonaws.com/9780073227399/612-3-2ICQ1.png
Energy From Carbon
• Is it possible to extract energy from leftover organic
waste?
• From Waste To Watts: Biofuel Bonanza
4-3 Compounds of Life
http://4.bp.blogspot.com/_207DNIaLgc/TBS99jVrLuI/AAAAAAAAAFw/ADLT6H9hPYU/s1600/Carbon+compounds.gif
Carbohydrates
• Carbohydrate: organic compound such as sugar or
starch and is used to store E
• Built of small monomers called monosaccharides
• Contain only Carbon, Hydrogen and Nitrogen
•
https://www.ck12.org/flx/show/image/201412291419891630024152_1d1b9dd1016afe4a756791
605e44e54b-201412291419895625805275.jpg
Monosaccharides and Disaccharides
• Monosaccharide: simple sugar such as fructose (in fruit)
or glucose (digestion of other carbs)
• Glucose (C6H12O6): is used for E in almost all cells and is
a main product of photosynthesis
• Monosaccharide formula = (CH2O)n n is any number
greater than 2
• In glucose what does n equal?
https://upload.wikimedia.org/wikipedia/commons/thumb/8/84/Alpha-Dglucose_Haworth.svg/2000px-Alpha-D-glucose_Haworth.svg.png
• If two monosaccharides come together they form a
disaccharide
• Sucrose is an example, contain glucose and fructose
• Monosaccharides and disaccharides are called simple
sugars
• Major source of E in cells
Sucrose Molecule. This sucrose molecule is a disaccharide. It is
made up of two monosaccharides: glucose on the left and
fructose on the right.
Polysaccharides
• Complex carbohydrate that forms when simples sugars
come together and make a chain
• Two main functions:
• 1. storing E
• 2. forming structures
• What type of polysaccharides to our bodies use to store
E?
• Glycogen
https://www.ck12.org/flx/show/image/201412291419891630086084_d0f36fbefdf81a493c6fedd3c
86c06f1-201412291419895626580615.jpg
Examples of complex carbohydrates and
their functions
Name
Function
Example
Starch
Used by plants to store
energy.
A potato stores starch in
underground tubers.
Glycogen
Used by animals to store
energy.
Cellulose
Used by plants to form
rigid walls around cells.
Chitin
Used by some animals to
A housefly uses chitin for
form an external skeleton.
its exoskeleton.
A human stores glycogen
in liver cells.
Plants use cellulose for
their cell walls.
Biofuels: From sugar to E
• For years there's been buzz, both positive and negative,
about generating ethanol fuel from corn. Is this a good
idea? Is it necessary?
• Biofuels: Beyond Ethanol
Lipids
• An organic compound like fat or oil
• Used by organisms to store E
• Lipids are made of repeating units called fatty acids
• Tow types of fatty acids:
• 1. saturated
• 2. unsaturated
https://www.ck12.org/flx/show/image/201412291419891638863740_b1851c58c1beb264ad82d6
bfad88f967-201412291419895623692225.jpg
Saturated Fatty Acids
• Carbon atoms are bonded to as many hydrogen atoms as
possible in saturated fatty acids
• Molecules have straight chains
• The straight chains can be packed together very tightly,
allowing them to store energy in a compact form
• Solid at room temperature.
• Animals use them to store energy.
Saturated fatty acids have straight chains, like the three fatty
acids shown in the upper left. Unsaturated fatty acids have bent
chains, like all the other fatty acids in the figure.
https://www.ck12.org/flx/show/THUMB_POSTCARD/image/201412291419891638885315_d771
0104a7a115af8552266dbe2400d0-201412291419895623901534.png
Unsaturated Fatty Acids
• Some carbon atoms are not bonded to as many hydrogen
atoms
• When carbon binds with other groups of atoms, it causes
chains to bend
• Not packed together as tightly
• Liquids at room temperature
• Plants use unsaturated fatty acids to store energy
Wherever carbon binds with these other
groups of atoms, it causes chains to bend
https://www.ck12.org/flx/show/THUMB_POSTCARD/image/201412291419891638885315_d771
0104a7a115af8552266dbe2400d0-201412291419895623901534.png
These plant products all contain
unsaturated fatty acids.
https://www.ck12.org/flx/show/THUMB_POSTCARD/image/201412291419891638908347_eb74
504972aadccdf11183d76a48c1f7-201412291419895624137790.jpg
Types of Lipids
• Triglycerides: the main form of stored energy in animals.
• Phospholipids: the major components of cell
membranes.
• Steroids: serve as chemical messengers and have other
roles.
The left part of this triglyceride molecule represents glycerol. Each of the three long chains
on the right represents a different fatty acid. From top to bottom, the fatty acids are palmitic
acid, oleic acid, and alpha-linolenic acid. The chemical formula for this triglyceride is
C55H98O6. KEY:H=hydrogen, C=carbon, O=oxygen
https://www.ck12.org/flx/show/THUMB_POSTCARD/image/201412291419891638922853_c280f
fdcac7d1ab92620ef3a89a7f1e5-201412291419895624332405.jpg
Lipids and Diet
• Humans need lipids for storing E and forming cell
membranes.
• Lipids also supply cells with E.
• Essential fatty acids must be consumed in food
• These include omega-3 and omega-6 fatty acids.
• Both of these are needed for important biological
processes, not just E.
• Excess dietary lipids can be harmful
• Eating too many may cause weight gain.
• A high-fat diet may also increase lipid levels in the blood.
• Can increase the risk for cardiovascular disease.
• Saturated fatty acids, trans fats, and cholesterol are to
most common
• Cholesterol is mainly responsible for narrowing arteries
and causing the disease atherosclerosis
Proteins
• Organic molecule made up of monomers called amino
acids
• 20 different amino acids found in living things
• Proteins could contain just a few hundred to thousands of
AA
https://www.ck12.org/flx/show/image/201412291419891647531137_9a51ddcf1efd6b4fd4252ba0
84978c25-201412291419895611792531.jpg
This model shows the general structure of all amino acids. Only the side chain, R, varies from one amino acid to another.
For example, in the amino acid glycine, the side chain is simply hydrogen (H). In glutamic acid, in contrast, the side chain is
CH2CH2COOH. Variable side chains give amino acids different chemical properties. The order of amino acids, together
with the properties of the amino acids, determines the shape of the protein, and the shape of the protein determines the
function of the protein. KEY: H = hydrogen, N = nitrogen, C = carbon, O = oxygen, R = variable side chain
https://www.ck12.org/flx/show/THUMB_POSTCARD/image/201412291419891647551687_d528
37d18e923b0b405b65c1f6fe4d14-201412291419895611970234.jpg
Protein Structure
• Amino acids bind together and form a chain called a
polypeptide
• Proteins consist of one or more polypeptide chains
• A protein may have up to four levels of structure.
• A protein’s primary structure is its sequence of amino acids.
• The complex structures of different proteins give them unique
properties, which they need to carry out their various jobs in
living organisms.
• Protein structure animation
The structure of a protein starts with its sequence of amino acids.
What determines the secondary structure of a protein? What are
two types of secondary protein structure?
https://www.ck12.org/flx/show/THUMB_POSTCARD/image/201412291419891647569189_94ef0
6c7910910e7f29005ee3a7cc5c4-201412291419895612215163.png
Functions of proteins
• Help cells keep their shape (structural proteins)
• Make up muscle tissues
• Transport items in and out of cells (transport proteins)
• Act as signals and receive signals
• Enzymes are proteins that speed up chemical reactions in cells
• Others are antibodies which bind to foreign substances such as
bacteria and target them for destruction.
• Carry messages or transport materials (ex. Hemoglobin)
• Protein Functions in the body video
This model represents the protein hemoglobin. The
purple part of the molecule contains iron. The iron
binds with oxygen molecules.
https://www.ck12.org/flx/show/THUMB_POSTCARD/image/201412291419891647589638_be94
1d0d5eebe2cdcc0fa349c8a7c652-201412291419895612474221.jpg
Proteins and Diet
• Proteins are broken down into amino acids when food is
digested
• Cells use the AA to build new proteins
• Essential amino acids must be consumed in foods
• Dietary proteins can be broken down to provide cells with
energy.
Nucleic Acids
• Organic compound such as DNA or RNA that is built of
monomers called nucleotides
• The nucleic acid DNA (deoxyribonucleic acid) consists of
two chains.
• The nucleic acid RNA (ribonucleic acid) consists of just
one chain.
https://www.ck12.org/flx/show/image/201412291419891657593749_a7dca734fd0631b79caf57a
9bd55e12a-201412291419895618456881.jpg
Structure of Nucleic Acids
• Each nucleotide consists of three molecules:
• 1.sugar
• 2.phosphate group
• 3.nitrogen base
• The sugar of one nucleotide binds to the phosphate group
of the next nucleotide.
• This is known as the sugar-phosphate backbone.
Sugars and phosphate groups form the backbone of a
polynucleotide chain. Hydrogen bonds between complementary
bases hold two polynucleotide chains together.
https://www.ck12.org/flx/show/THUMB_POSTCARD/image/201412291419891657648644_7c87
315afd616680c5bc3005a4272da3-201412291419895618627111.png
Roles of Nucleic Acids
• DNA contains the genetic instructions for the correct
sequence of amino acids in proteins
• RNA uses the information in DNA to assemble the correct
amino acids and help make the protein.
• DNA is passed from parents to offspring when organisms
reproduce.
• This is how inherited characteristics are passed from one
generation to the next.
The letters G, U, C, and A stand for the bases in RNA. Each group of three
bases makes up a code word, and each code word represents one amino acid
(represented here by a single letter, such as V, H, or L). A string of code words
specifies the sequence of amino acids in a protein.
https://www.ck12.org/flx/show/default/image/201412291419891657734922_62591ee5945d4c53
aafd63c3d40c8308-201412291419895618946619.png
Enzymes and Biochemical Reactions
• Most chemical reactions within organisms would be
impossible under the conditions in cells (ex. Temp to low)
• The rate of reactions must be increased by a catalyst
• Catalyst: a chemical that speeds up chemical reactions
called enzymes (biological catalysts)
http://upload.wikimedia.org/wikipedia/commons/d/d9/S,S-Jacobsen's-catalyst-from-xtal-3Dballs.png
• Enzymes are not reactants
• They help the reactants but are not used up in the
reactions
• They may be used many times
• Enzymes are highly specific for particular chemical
reactions
• Catalyze only one or a few types of reactions.
• Efficient in speeding up reactions
• Can catalyze up to several million reactions per second
• A typical biochemical reaction might take hours or even
days to occur under normal cellular conditions without
an enzyme but less than a second with an enzyme
• Enzymes video
Importance of Enzymes
• Enzymes are involved in most of the biochemical reactions
• Enzymes allow reactions to occur at the rate necessary for life.
• In animals, an important function of enzymes is to help digest
food.
• Digestive enzymes speed up reactions that break down large
molecules of carbohydrates, proteins, and fats into smaller
molecules the body can use.
• Without digestive enzymes, animals would not be able to break
down food molecules quickly enough to provide the energy and
nutrients they need to survive.
Enzyme Function
• Enzymes lower the activation energy of chemical
reactions.
• Activation energy: the energy needed to start a chemical
reaction.
• Enzyme animation
The reaction represented by this graph is a combustion reaction involving the reactants glucose
(C6H12O6) and oxygen (O2). The products of the reaction are carbon dioxide (CO2) and water (H2O).
Energy is also released during the reaction. The enzyme speeds up the reaction by lowering the
activation energy needed for the reaction to start. Compare the activation energy with and without the
enzyme.
https://www.ck12.org/flx/show/THUMB_POSTCARD/image/201412291419891707633029_f9370
a04b35e3f7b1a41b2f1fdd6b5be-201412291419895624795172.png
• Enzymes bring reactants together, don’t have to expend
energy moving until they collide at random.
• Enzymes bind reactant molecules (called the substrate),
tightly and specifically, at a site on the enzyme molecule
called the active site
• Active site is specific for the reactants of the biochemical
reaction the enzyme catalyzes. (puzzle pieces)
• Enzymes also position reactants correctly which allows
the molecules to interact with less energy.
• Enzymes also allow reactions to occur by different
pathways that have lower activation energy.
This enzyme molecule binds reactant molecules—called substrate—at its active site,
forming an enzyme-substrate complex. This brings the reactants together and positions
them correctly so the reaction can occur. After the reaction, the products are released from
the enzyme’s active site. This frees up the enzyme so it can catalyze additional reactions.
https://www.ck12.org/flx/show/THUMB_POSTCARD/image/201412291419891707681181_e7a5
9293e694eec9e09a0b865129bb23-201412291419895625036943.jpg
• The activities of enzymes also depend on
the temperature, ionic conditions, and the pH of the
surroundings.
• Many enzymes lose function at lower and higher
temperatures.
• At higher temperatures, an enzyme’s shape deteriorates.
• Only when the temperature comes back to normal does
the enzyme regain its shape and normal activity.