Transcript Chapter 2 of 'Modern Biology' Text-

Chapter 2
of "Modern Biology" Text-
CHEMISTRY (Review)
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CHEMISTRY- The science of the composition, structure, properties,
and reactions of matter
• Structure and function of all living things are governed by the laws of
chemistry
• Understanding the basic principles of chemistry will give you a better
understanding of all living things and how they function!
• QUESTION: What examples can you give of how chemistry is involved in
biology?
CHEM REVIEW
• Matter• Mass• Is MASS the same thing as WEIGHT?
– - The pull of gravity on an object is what gives an object its "weight"
– - A bowling ball having the same mass on Earth and the moon would
weigh less on the moon than it does on Earth due to a gravitational pull
present on the Moon.
– How much do you weigh on other planets??? Find out here:
http://www.exploratorium.edu/ronh/weight/
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Elements
• Pure substances that
cannot be broken
down into simpler
substances
• Periodic Table
• created in 1869 by
Mendeleev
• categorizes elements
and shows trends
• 118 elements, 92
occurring naturally
•Noble or "inert" gases on far right
•Alkali metals on far left (minus H)
•Atomic radii increase from left to right and
decrease from top to bottom
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Biologists love CHONPS most of all!
• 90% of the mass of living things are composed
of combinations of 4 elements: O,C, H, & N
• Throw in P and S and you can make almost
any combination of organic molecules!
– Carbs
– Lipids
– Nucleic acids
– Amino acids, proteins
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Atoms
• Simplest part of an element that retains all properties of that element
• Too small to see so we make up models to help us understand the structure
of atoms and predict how they will act
• Nucleus• Electrons (-) orbit around nucleus; very fast
• Farther an E- is from the nucleus- More ENERGY!
• Atomic Mass• Atomic Number• # of electrons = # of protons
• - Electrons balance out + charge of protons and have very little mass
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Compounds
• Most elements do not exist by themselves in nature
but rather like to combine with other elements
• A molecule is formed when two or more atoms join
together chemically.
• A compound is a molecule that contains at least two
different elements. All compounds are molecules but
not all molecules are compounds.
• 2 H atoms + 1 O atom = 1 H2O molecule
• Chemical properties of compounds are different than
the elements alone (2 gases = liquid)
• “Chemical rxn’s”- chemical bonds can be broken, atoms
can be rearranged, and new chemical bonds are
formed!
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States of Matter
• SOLID: molecules are tightly linked; little movement and
definite shape
• LIQUID: molecules are less tightly linked; moves more freely
than solids; conforms to container
• GAS: molecules are usually not attracted to one another;
move very fast; fills the entire volume of a container
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Bonding
• Most bonding takes place because atoms are
most chemically stable when their outermost
energy levels are filled
Types of Chemical Bonds
• Covalent bonds:
– Strong bonds
– Shared electrons, simulate a full outer orbital
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Polar covalent bond:
• Electrons are shared, but not evenly shared
This creates further potential for hydrogen bonds to form between molecules
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Hydrogen Bonds
• Relatively weak, singly, but rather strong
collectively
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Ionic Bonds
• Strong bonds
• Create ions
• Create electrical charges: when + and – charges
attract, ionic bonds are created
• OXIDATION: Na becomes (Na+) = loses e• REDUCTION: Cl becomes (Cl-)= gains an e-
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Energy
• Definition:
• Amount of energy in the universe remains the same
over time; energy can neither be created or destroyed
• Energy = usable energy + dissipates (ex: heat)
• Many energy forms are important in biology:
–
–
–
–
–
chemical energy
thermal energy
radiant energy
electrical energy
mechanical energy
• Free energy: energy in a system that is available for
work, for example, in a cell, it is the energy available to
fuel cell processes (metabolism, etc)
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Energy and Chemical Reactions
• Exergonic rxn’s = release energy (products have less
chemical energy than reactants)
ex: AB + CD  AC + DB + energy
• Endergonic rxn’s = absorb energy (products have more
chemical energy than reactants)
ex: AB + CD + energy  AC + DB
• Activation energy: energy added to reactants to
"jumpstart" the rxn
• Catalysts: reduce the amount of activation energy that
is needed to start the rxn. See Figure 2-7 in your book.
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Solutions
• Water is extremely important to all living things, so the chemistry of
living things often involves the study of solutions!
• Solution: mixture in which substances are uniformly distributed in
another substance
– Solutions can be mixtures of liquids, solids, or gases
• Solute:
• Solvent:
• Concentration [ ]: measurement of the amount of solute dissolved in a
fixed amount of solvent
• Saturated?
• Aqueous solutions:
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Acids and Bases
Dissociation: force between H2O molecules is so
H2O
strong that the O- atom from one H2O molecule
can pull off the H+ atom from another molecule
• Water dissociates into H+ and OH- equally
(hydrogen and hydroxide)
• Hydroxide ion formed and H+ ion is released!
• Free H+ ion can react with another H2O molecule
to form a hydronium ion (H3O+)
• Acidity and Alkalinity is a measure of the
relative amount of OH- and H+ ions in a solution!
• pH= measure of how many H+ ions are in a
solution
• Pure water has equal OH- and H+ ions in
solution; pH of 7.0
• Acidic solutions have H+ > OH- ions
– pH is below 7.0
– sour
• Basic solutions have H+ < OH- ions
– pH is above 7.0
– slippery and bitter
H+ + OH-
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Buffers
• Chemical substances that neutralize small
amounts of either an acid or a base added to a
solution
• Most chemical rxn’s in living organisms are
controlled by pH, therefore...
• Buffers are very important for homeostasis.
– If blood pH drops below 7.0 (acidosis), it could be fatal
– If blood pH goes above 7.7 (alkalosis), it could be fatal
• If our blood did not contain a buffering system,
we would not be able to drink and eat
acidic/basic foods!
• Great chem review
• http://scidiv.bcc.ctc.edu/rkr/Biology101/lectures/pdfs/Chemistry
101.pdf
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Chapter 3
of "Modern Biology" Text
BIOCHEMISTRY
WHAT IS BIOCHEMISTRY? - Study of those molecules
used and manufactured by living things!
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WATER
• Living things are 70-80% water by weight
• Most chemical rxns in living things take place
in aqueous environments (either inside or
outside the cells)
• Water is needed to dissolve and transport
nutrients, gases, etc. around us (blood, tissue
fluid, saliva, sweat, etc)
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Water is a covalently bonded
molecule that is also POLAR
(has +, - regions)
• 2 H+ atoms bond with an Oxygen atom at an angle
• Region of the molecule where the O atom is located
has a slightly neg.(-) charge, while the regions of the
molecule where the two H+ atoms are have a slightly
positive charge.
• Oxygen has a greater “custody” of the shared
electrons
• In textbook see pp. 39-42 for water info
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POLAR COVALENT BONDS:
• The polar nature of water makes it the "universal" solvent
• hydrophilic or hydrophobic?
• What types of substances mix well with water?
• Hydrogen Bonds- negative part of the water molecule (O)
forms a bind with the positive charge of the H+ atoms
• H-Bonds = weak when alone, strong when many!
• Cause H2O molecules to cling together & to other substances!
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Water’s polarity is responsible for
some of its unique properties:
Cohesion• Water molecules are attracted
(+/-) to other nearby water
molecules; bonds them
together
• Surface tension = cohesive
forces between water
molecules are strong enough
to act as if their was a "skin" in
the water surface
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Water Properties
Adhesion• Water is attracted (+/-) to other substances.
• meniscus = adhesive forces between water
molecules and glass
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Water Properties
Capillary Action• The climbing ability of water is due to both adhesion and
cohesion
• Enables water to move against the force of gravity and
upward through narrow tubes
• ex) Trees (Sequoias) xylem
CHECK OUT THIS WEBSITE:
http://www.uni.edu/~iowawet/H2OProperties.html
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Water Properties
• Water is very important in temperature
regulation - resists quick temperature changes
and maintains homeostasis!
• H2O has a very high specific heat- which
means it can absorb or lose a large amount of
heat energy before its temperature changes
• Thus, water has a moderating effect on
temperatures
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Organic Compounds
• All compounds discovered can be classified
into two broad categories: inorganic and
organic
• "Organic" =
• The compounds of life consist of primarily 6
elements: "CHONPS"
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Chemistry of CARBON is the
chemistry of LIFE!
• Carbon forms the “backbone” (framework) of
all organic molecules
• C has four e- in its outermost energy level, but
needs 8 to fill it, so it readily forms covalent
bonds!
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• A description of carbon: "It is shamelessly
promiscuous. It is the party animal of the
atomic world, latching on to many other
atoms (including itself) and holding tight,
forming molecular conga lines of hearty
robustness.“ – Bill Bryson, from “A Short History Of Nearly Everything”
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Carbon, the basis for life
• Carbon likes to bond, with other atoms and
with itself
• single bonds• double bonds• triple bonds28
Carbon videos
NPR: It’s All About Carbon
http://www.npr.org/news/specials/climate/video/
Making Carbon Bonds
Breaking Carbon Bonds
Carbon In Love
What Do We Do?
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Functional Groups
• Clusters of atoms that influence the properties
of the molecules they compose
"R" stands for any group of atoms that is
attached by a covalent bond to a
chemical functional group
-OH (hydroxyl group) is the functional
group for chemicals referred to as
"alcohols“
-NH4 (amino group) gives molecules
slightly basic properties
-COOH (carboxyl group) gives slightly
acidic properties
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Simple & Complex Molecules
• Molecules are often built up from smaller, simpler molecules:
MONOMERS
• Monomers bond together to produce: POLYMERS
• Large polymers are called: MACROMOLECULES
• Monomers are bonded by condensation rxn’s (aka:
dehydration synthesis): release of H2O molecules
• Polymers are broken down by hydrolysis: addition of water
that breaks bonds between polymers
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There are Four Major Classes of Organic
Compounds:
CARBOHYDRATES (= ENERGY)
• - The most abundant organic compounds
in nature
Monosaccharides - simple sugars; "building
blocks of all carbs"
• C:H:O = approx. 1:2:1
• Example: C6H12O6
• Three main monosaccharides:
• glucose- main source of energy for cells
• fructose- sugar in fruits and honey (the
sweetest monosaccharide)
• galactose- sugar in milk and yogurt
–
•
glucose, fructose, & galactose have the same
chemical formula: C6H12O6 ?!
“isomers”- same chemical formula but
different forms = two substances with
different properties
Disaccharides - two
monosaccharides bonded together
by condensation rxn’s ~ glycosidic
bonds
glucose + fructose = sucrose
(common table sugar)
glucose + galactose = lactose
(major sugar in milk)
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Carbs, continued
Polysaccharides - several monosaccharides bonded together by
condensation rxn’s; GIANT, storage molecules
• Examples: glycogen (animals), starch (plant), cellulose (plant
fiber), chitin (insect)
• Cell stores energy it doesn’t use by converting
monosaccharides into disaccharides/polysaccharides
• Glycogen- stored in liver and muscles- once storage is full,
glycogen turns to fat!
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The Role of Enzymes in Starch Digestion
• Monosaccharides- soluble in water & CAN pass
through cell membrane by diffusion
• Disaccharides- are soluble in water and CANNOT
pass through the cell membrane (too BIG!)
– when a cell needs energy, disaccharides are broken down
into its monomers by hydrolysis!
• Polysaccharides- are NOT soluble in water and
CANNOT pass through the cell membrane without a
series of hydrolysis rxn’s!
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Proteins
• Large and often complicated molecules
• Mostly C,H,O, & N
• Hundreds of thousands of different kinds in
each cell
• Make up skin, muscles, pigments, antibodies,
hormones & enzymes
• Proteins are polymers composed of amino
acid monomers (20 AA groups in total)
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Amino Acids
• Central carbon atom covalently bonded to 4 other atoms
• Amino Acid (general structure):
• R groups give each amino acid its unique
properties (acidic, basic, polar, nonpolar, etc.)
• Peptide: two or more AAs bonded together
by covalent bonds called peptide bonds
• Polypeptide: exceptionally large chain of
amino acids
• Proteins are composed of one or more
polypeptides
• Proteins are usually bent and folded upon
themselves (hydrogen bonds among individual
AAs)
• Protein shape is affected by temperature, pHcan be denatured! (ex: cooked egg white vs.
uncooked egg white)
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ENZYMES are important proteins
• Many chemical reactions in living cells (and organisms) are
regulated by ENZYMES
• Enzymes are globular proteins in living systems that mediate
metabolic reactions
• Metabolism: the series of energy exchanges and chemical
reactions that occur in living systems (cells, organisms)
• catabolic activities = breakdown of larger molecules into
smaller;
AB ==> A + B
• anabolic activities = synthesis of larger molecules from
smaller ones;
A + B ==> AB
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• Enzymes act as catalysts (push, or speed up, chemical
reactions)
• Enzymes lower the ACTIVATION ENERGY of reactions (ex: heat
required) to enable chemical bonds to form or break more
easily:
A + B ==> AB or AB==> A + B
• Enzymes mediate the reaction in the substrate but do not
take part in the reaction themselves, so enzymes can be reused again and again
• Some classes of enzymes:
– Proteases
– Lipases
– Amylases (sucrase, lactase, etc.)
• most enzyme names end in -ane or -ase suffix, and
most are named after the substrate upon which they act
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• Each Enzyme acts upon a specific substrate (there are thousands of
different enzymes in the body to mediate thousands of different
reactions)
• Enzymes have an active site, to fit with their substrate in a "lock-and-key"
fashion
• Sometimes, to get a good "fit", enzymes require a vitamin or mineral to fit
into the active site: COENZYME
• "Induced Fit Hypothesis" a change in the shape of an enzyme’s active site
may occur, which allows it to bind more effectively to its substrate
• Enzymes can be deactivated (DENATURED) when their 3-D active site is
warped by heat or drastic pH changes (acid)
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LIPIDS
• Large, nonpolar molecules that are insoluble in H2O
(hydrophobic)
• Fats, waxes, oils store energy very efficiently (concentrated
energy)
• Ratio of C:H:O is > than in carbs; LARGE # of C-H bonds
• Most lipids have "fatty acids"- long, straight carbon chains
with a carboxyl group (-COOH) attached at one end
Saturated: each C atom is covalently
bonded to four atoms; solid at RT
Unsaturated: not bonded to the
maximum # of atoms that it can; usually
liquid at RT
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Lipids are divided into three categories
based on their structure:
1) TRIGLYCERIDES: fats and oils - glycerol plus three fatty acids (mostly 16-18C)
- Saturated- shortening, animal fat
- Unsaturated: most plant oils
2) PHOSPHOLIPIDS - like fats, but with two fatty acids and a phosphate group
(PO4)
3) WAXES – long fatty acid and an alcohol group
4) STEROIDS- different structure from other lipids
- composed of 4 fused carbon rings
- Important steroids:
Cholesterol, testosterone, estrogen, progesterone, cortisol
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NUCLEIC ACIDS
• Nucleic acids are long chains (polymers)of
nucleotides
• Nucleotides are the monomers of nucleic
acids
• Each nucleotide includes a nitrogenous base
(R group), a 5-carbon sugar, and a phosphate
group
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DNA: Deoxyribonucleic acid
• Contains genetic
information
• Composed of:
1) deoxyribose sugar
2) phosphate group
3) 4 different nitrogen bases:
adenine, guanine, cytosine,
and thymine
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RNA: Ribonucleic acid
• Stores and transfers genetic information for
making proteins from nucleus to ribosomes
• Like DNA, RNA is composed of nucleotides:
1) ribose sugar
2) phosphate group
3) 4 different nitrogen bases: adenine, guanine,
cytosine, and uracil
• DNA IS DOUBLE STRANDED AND RNA IS
SINGLE STRANDED!
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