Title: Chemistry of Life
1Chemistry of Life
2Introduction to Biochemistry
- Biochemistry is the study of structure,
composition (what things are made up of), and
chemical reactions that occur in living things. - Living things (biotic factors) depend on
chemistry to carry out life processes, so biology
and chemistry are closely related!
3AKS Standards 8e - identify the elements that
comprise living cells
4Living things consist of atoms of different
elements.
- Matter is anything that has mass or takes up
space. - Matter is made up of small units called atoms.
- Atoms are made up of 3 subatomic particles
- Protons (which have a charge)
- Electrons (which have a charge)
- Neutrons (which have no charge)
- Together these substances help form matter!
5Elements
- When atoms of the same type come together they
make up units called elements. Elements cannot
be broken down into simpler substance by ordinary
chemical means. - An element is a pure substance made of only 1
type of atom (it is usually abbreviated by a
chemical symbol)
6Chemical Compounds
- Remember that elements are made up of small units
called atoms. When these elements come in close
contact with each other, they often have an
attraction like magnets. - The attraction of these elements often leads to a
bond the joining of atoms to one another. - When two or more elements are put together, they
form a chemical compound. - These compounds are usually represented by a
chemical formula a combination of chemical
symbols that represent the joining of these
elements. - Examples NaCl (salt) H2O (water) CO2
(carbon dioxide)
7Chemical Bonds
- The atoms in compounds are held together by
chemical bonds. - Bond formation involves the electrons that
surround each atomic nucleus. - Electrons that are available to form bonds are
called valence electrons. - The main types of chemical bonds are ionic bonds
and covalent bonds.
8Ionic Bonds
- An ionic bond is formed when one or more
electrons are transferred from one atom to
another - An atom that loses electrons is no longer
neutral, instead it becomes positively charged. - An atom that gains an electron is no longer
neutral, instead it becomes negatively charged. - These positively and negatively charged atoms are
called ions.
9Covalent Bonds
- Sometimes electrons are shared by atoms instead
of being transferred - These electrons are located in a region between
the atoms. - A covalent bond forms when electrons are shared
between atoms. - The structure that results when atoms are joined
together by covalent bonds is called a molecule
(this is the smallest unit of most compounds).
10Review Ionic Covalent Bonds
IONIC BONDS electrons are transferred between
atoms
COVALENT BONDS electrons are shared between atoms
11Interactive review Chemistry of Life
- http//www.classzone.com/cz/books/bio_07/resources
/htmls/interactive_review/bio_intrev.html
Complete this interactive review using your
virtual textbook at home. Concept maps are an
excellent way to organize your thoughts and
review material!
12AKS Standards 8f - explain the impact of water in
life processes (e.g., adhesion, cohesion,
capillarity, density, and osmosis) GPS)
13Life depends on hydrogen bonds in water.
- Water is the most abundant compound in living
things. - Some of waters properties that facilitate an
environment for life are - Cohesive and adhesive behavior
- Ability to moderate temperature (high specific
heat) - Expansion upon freezing
- Versatility as a solvent
- http//www.sumanasinc.com/webcontent/animations/co
ntent/propertiesofwater/water.html
14Polarity Hydrogen Bonding in Water
- The water molecule is a polar molecule the
opposite ends have opposite charges. - Water is polar because the oxygen atom has a
stronger electronegative pull on shared electrons
in the molecule than do the hydrogen atoms. - Polarity allows water molecules to form hydrogen
bonds with each other. These are weak covalent
bonds.
15Cohesion Adhesion
- Collectively, hydrogen bonds hold water molecules
together, a phenomenon called cohesion - Cohesion is the attraction of molecules of like
substance. - Cohesion due to hydrogen bonding contributes to
the transport of water and dissolved nutrients
against gravity in plants. - Adhesion is the clinging of one substance to a
different substance - In other words, water molecules stick to other
things. - Adhesion of water to cell walls by hydrogen bonds
helps to counter the downward pull of gravity on
the liquids passing through plants.
16Adhesion
Water-conducting cells
Direction of water movement
Cohesion
150 µm
- Cohesion and adhesion work together to give
capillarity the ability of water to spread
through fine pores or to move upward through
narrow tubes against the force of gravity.
17Surface Tension
- The high surface tension of water, resulting from
the collective strength of its hydrogen bonds,
allows the water strider to walk on the surface
of the pond. - Surface tension is directly related to the
cohesive property of water it is a measurement
of how difficult it is to stretch or break the
surface of a liquid.
18Moderation of Temperature
- Water can absorb or release a large amount of
heat with only a slight change in its own
temperature. The ability of water to stabilize
temperature results from its relatively high
specific heat - This is the amount of heat that must be absorbed
or lost for 1g of a substance to change its
temperature by 1C. - Hydrogen bonds give water an abnormally high
specific heat, and water therefore resists
changes in temperature. - Waters high specific heat can be traced to
hydrogen bonding. Heat is absorbed when hydrogen
bonds break, and heat is released when hydrogen
bonds form. - The high specific heat of water is due to
hydrogen bonding. H-bonds tend to restrict
molecular movement, so when we add heat energy to
water, it must break bonds first rather than
increase molecular motion.
19Evaporative Cooling
- Evaporation is transformation of a substance from
liquid to gas. Heat of vaporization is the heat
a liquid must absorb for 1 g to be converted to
gas. As a liquid evaporates, its remaining
surface cools, a process called evaporative
cooling. - The high amount of energy required to vaporize
water has a wide range of effects - Helps stabilize temperatures in organisms and
bodies of water. - Evaporation of sweat from human skin dissipates
body heat and helps prevent overheating on a hot
day or when excess heat is generated by strenuous
activity.
20The Density Anomaly
- Ice floats in liquid water because hydrogen bonds
in ice are more ordered, making ice less dense. - If ice sank, all bodies of water would eventually
freeze solid, making life impossible on Earth.
21The Solvent of Life
- Water provides living systems with excellent
dissolving capabilities. - A solution is a liquid that is a homogeneous
mixture of substances - Solvent (dissolving agent)
- Solute (substance that is dissolved)
- An aqueous solution is one in which water is the
solvent.
22Hydration Shellhttp//www.sumanasinc.com/webconte
nt/animations/content/propertiesofwater/water.html
- A hydration shell refers to the sphere of water
molecules around each dissolved ion in an aqueous
solution. Water will work inward from the
surface of the solute until it dissolves all of
it (provided that the solute is soluble in water).
If a spoonful of salt (or other ionic substance)
is placed in water, the ions in the salt and the
water molecules have a mutual affinity owing to
the attraction between opposite charges. O is
negative and attracts to positive sodium. H is
positive and attracts to negative chlorine. As a
result, water will surround the individual sodium
and chloride ions, separating and shielding them
from one another (called a hydration
shell). WATER IS THE SOLVENT OF LIFE molecules
within a living system must be broken down in
order to be used by the system!
23Acids and Bases
- An acid is any substance that increases the H
concentration of a solution. - A base is any substance that reduces the H
concentration of a solution. - A solutions acidity, or H ion concentration, is
measured by the pH scale.
24pH Scale
0
1
Battery acid
Gastric juice, lemon juice
2
H
H
H
Vinegar, beer, wine, cola
OH
H
3
H
OH
Increasingly Acidic H gt OH
H
H
H
4
Tomato juice
Acidic solution
Black coffee
5
Rainwater
6
Urine
OH
Saliva
OH
Neutral H OH
7
Pure water
OH
H
H
OH
OH
Human blood, tears
H
H
H
8
Seawater
Neutral solution
9
10
Increasingly Basic H lt OH
Milk of magnesia
OH
OH
11
OH
OH
H
Household ammonia
OH
OH
OH
H
12
Basic solution
Household bleach
13
Oven cleaner
14
25Buffers
- One way pH is regulated in organisms is by
substances called buffers. - A buffer is a compound that can bind to an H ion
when the H concentration increases, and can
release H ion when the H concentration
decreases. - In other words, buffers lock up H ions and
help to maintain homeostasis. - Most buffers consist of an acid-base pair that
reversibly combines with H - CO2 H2O ? H2CO3 ? HCO3- H
26Critical Thinking Activities Compare
ContrastConnecting Concepts
- How do polar molecules differ from non-polar
molecules? How does this difference affect their
interactions? - When sugars are broken down to produce usable
energy for cells during cellular respiration, a
large amount of heat is released. Explain how
the water inside a cell helps to keep the cells
temperature constant. - Polar molecules have charged regions due to
unequal sharing of electrons. Nonpolar molecules
do not have charged regions because electrons
are shared more equally. The charge differences
tend to keep the molecules separate. - Water has a high specific heat water in a cell
can absorb a large amount of energy before its
temperature changes.
27Interactive review Properties of Water
- http//www.classzone.com/cz/books/bio_07/resources
/htmls/interactive_review/bio_intrev.html
Complete this interactive review using your
virtual textbook at home. Concept maps are an
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review material!
28AKS Standards 8k - describe the four basic types
of organic macromolecules (carbohydrates, lipids,
proteins, and nucleic acids) and their function
in the cell (GPS)
29Carbon atoms have unique bonding properties.
- Carbon is often called the building block of life
because carbon atoms are the basis of most
molecules that make up living things. - Carbon is so important because its atomic
structure gives it bonding properties that are
unique among elements. - Each carbon atom has four unpaired electrons in
its outer energy level. - Therefore, carbon atoms can form covalent bonds
with up to four other atoms.
30Four main types of carbon-based molecules are
found in living things.
- Many of the molecules in living cells are so
large that they are known as macromolecules. - They are formed by a process called
polymerization (making large compounds by joining
smaller compounds together). - The smaller unit (building block) is known as
monomer these join together to form polymers
(the macromolecule). - The four groups of organic compounds found in
living things are - Carbohydrates
- Lipids
- Nucleic acids
- Proteins
- http//bcs.whfreeman.com/thelifewire/content/chp03
/0302002.html
31Formation of Macromoleculeshttp//bcs.whfreeman.c
om/thelifewire/content/chp03/0302002.html
- Monomers are connected into polymers by a
reaction in which 2 molecules are bonded to each
other through a loss of a water molecule - (Called a condensation reaction or dehydration
reaction) because a water molecule is lost. - Polymers are disassembled into monomers by
hydrolysis, a process that is essentially the
reverse of the dehydration reaction. - Hydrolysis means to break with water. Bonds
between monomers are broken by the addition of
water molecules.
32The Synthesis and Breakdown of Polymers
As each monomer is added, a water molecule is
removed DEHYDRATION REACTION.
This is the reverse of dehydration is
HYDROLYSISit breaks bonds between monomers by
adding water molecules.
33Carbohydrates
- Carbohydrates are molecules composed of carbon,
hydrogen, and oxygen in a 121 ratio (CnH2nOn). - They include simple sugars and their polymers.
- They can be broken down to provide a source of
usable chemical energy for cells and they are
also a major part of plant cell structure. - Carbs exist as three types
- 1. monosaccharides
- 2. disaccharides
- 3. polysaccharides (macromolecule stage)
34Monosaccharides
- Monosaccharides are major sources of energy for
cells! - Ex. Glucose cellular respiration.
- Monosaccharides are simple enough to serve as raw
materials for synthesis of other small organic
molecules such as amino and fatty acids. - Most common glucose, fructose, galactose.
- Glucose
- made during photosynthesis
- main source of energy for plants and animals
- Fructose
- found naturally in fruits
- is the sweetest of monosaccarides
- Galactose
- found in milk
- is usually in association with glucose or
fructose
35Disaccharides
- Disaccharides consist of two monosaccharides
joined by a glycosidic linkage a covalent bond
resulting from dehydration synthesis. - Examples
- Maltose 2 glucoses joined (C12H22O11)
- Sucrose glucose and fructose joined (C12H22O11)
- Lactose glucose and galactose joined (C12H22O11)
36Examples of Disaccharide Synthesis
37Polysaccharides
- These are the polymers of sugars the true
macromolecules of the carbohydrates. - They serve as storage material that is hydrolyzed
as needed in the body or as structural units that
support bodies of organisms. - Starches, glycogen, and cellulose are examples of
polysaccharides.
These are polymers with a few hundred to a few
thousand monosaccharides joined by glycosidic
linkages.
38Storage Structural Polysaccharides
- Starch and Glycogen are storage polysaccharides.
- Starch sugar/energy storage for plants
- Glycogen sugar/energy storage for animals
- Cellulose and Chitin are structural
polysaccharides - Cellulose found in cell wall of PLANTS
- Chitin found in cell wall of FUNGI
39Lipids
- Lipids are a group of macromolecules that does
not include polymers they are only grouped
together based on trait of little or no affinity
for water all lipids are hydrophobic (water
fearing). - The hydrophobic nature of lipids is based on
molecular structure they consist mostly of
hydrocarbons! Hydrocarbons are insoluble in
water because of their non-polar CH bonds! - Lipids are composed of carbon, hydrogen, and
oxygen (like carbohydrates), but not in a 121
ratio. - Lipids serve as energy storage molecules. The
can also act as chemical messengers within and
between cells and are major components of
biological membranes. - Groups of lipids include
- Fats
- Steroids
- Waxes
- Phospholipids
40Fats -- Triglycerides
- Triglycerides are made of two kinds of smaller
molecules glycerol and fatty acids (one
glycerol to three fatty acids). - Dehydration synthesis hooks these up 3 waters
produced for every one triglyceride - ESTER linkages bond glycerol to the fatty acid
tails bond is between a hydroxyl group and a
carboxyl group. - Fats are used for protection, cushion, and energy
backup.
41The Synthesis and Structure of a Fat, or
Triglycerol
- One glycerol 3 fatty acid molecules
- One H2O is removed for each fatty acid joined to
glycerol - Result is a fat
42Saturated v. Unsaturated Fats
- The terms saturated and unsaturated refer to
the structure of the hydrocarbon chains of the
fatty acids. - No double bonds between the carbon atoms of the
chain means that the maximum of hydrogen atoms
is bonded to the carbon skeleton (SATURATED). - THESE ARE THE BAD ONES!!! they can cause
atherosclerosis (plaque develop, get less flow of
blood, hardening of arteries)! - If one or more double bonds is present, then it
is UNSATURATED. - These tend to kink up and prevent the fats from
packing together
43Examples of Saturated and Unsaturated Fats and
Fatty Acids
At room temperature, the molecules of an
unsaturated fat cannot pack together closely
enough to solidify because of the kinks in their
fatty acid tails.
At room temperature, the molecules of a saturated
fat are packed closely together, forming a solid.
44Phospholipids
- Phospholipids are a special kind of lipid that
have only two fatty acid tails! - The third hydroxyl group of glycerol is joined to
a phosphate group (negatively charged) - Phospholipids are ambivalent to water tails are
hydrophobic, heads are hydrophilic. - At the cell surface, phospholipids have a double
layer arrangement called a phospholipid bilayer. - Hydrophilic head of molecules are on outside of
the bilayer, in contact with aqueous solutions
inside outside cell. - Hydrophobic tails point toward interior of
membrane, away from water.
45The Structure of a Phospholipid
46Proteins
- Proteins account for over 50 of dry weight of
cells - Used for structural support
- storage
- transport
- signaling
- movement
- defense
- metabolism regulation (enzymes)
- Are the most structurally sophisticated molecules
known - Are polymers constructed from 20 different amino
acids -
47(No Transcript)
48Hierarchy of Structure in Proteins
- Amino acids building blocks of proteins there
are 20 different amino acids in nature. - Polypeptides polymers of amino acids.
- Protein one or more polypeptides folded and
coiled into specific conformations.
49- All differ in the R-group (also called side
chain). - The physical and chemical properties of the
R-group determine the characteristics of the
amino acid. - Amino acids possess both a carboxyl and amino
group.
50How Amino Acids Join
- The carboxyl group of one amino acid is joined to
the amino group of another, dehydration synthesis
occurs, and a special type of covalent bond
called a peptide bond forms. - When repeated over and over, a polypeptide is
built.
Note this is dehydration synthesis. Note
carboxyl group of one amino acid end attaches to
amino group of another amino acid end. Note
peptide bond is formed. Note repeating this
process builds a polypeptide.
51A Proteins Function Depends on Its Conformation
- All proteins in nature differ in the number and
order of amino acids in the polypeptide chains.
The amino acid sequence determines a proteins
structure and function. - Proteins are very sophisticated molecules that
have four layers of structure - Primary Structure unique sequence of amino
acids (long chain) - Secondary Structure segments of polypeptide
chain that repeatedly coil or fold in patterns
that contribute to overall configuration. These
are the result of hydrogen bonds at regular
intervals along the polypeptide backbone. - Tertiary Structure superimposed on secondary
structure irregular contortions from
interactions between side chains. - Quaternary Structure the overall protein
structure that results from the aggregation of
the polypeptide subunits.
52The Four Levels of Protein Structurehttps//myweb
space.wisc.edu/jonovic/web/proteins.html
53The External Environment Can Affect Protein
Structure
- The polypeptide chain of given amino acid
sequence can spontaneously arrange into 3-D
shape. - This configuration also depends on physical and
chemical conditions of proteins environment. - If pH, salt , temp, etc. are altered, protein
may unravel and lose native conformation this
process is called denaturation. - Denatured proteins are biologically inactive.
- Anything that disrupts bonding can denature a
protein. -
54NUCLEIC ACIDS
- Nucleic acids are polymers of information, they
are the building blocks of DNA and RNA. - Nucleic acids are units of heredity. They store
and transmit genetic information. - The building blocks of nucleic acids are
nucleotides each nucleotide contains a phosphate
group, a pentose sugar, and a nitrogenous base
(A,T,C,G,U).
55NUCLEIC ACIDS consist of phosphate group,
pentose sugar, nitrogenous base
56Types of Nucleic Acids
- Exist as 2 types DNA and RNA
- DNA -- double stranded (entire code)
- sugar is deoxyribose
- never leaves nucleus
- bases are A,T,C,G
- involved in replication and protein
synthesis - RNA -- single stranded (partial code)
- sugar is ribose
- mobile nucleus and cytoplasm
- bases are A,U,C,G
- involved in Protein Synthesis
-
-
57Interactive review Macromolecules
- http//www.classzone.com/cz/books/bio_07/resources
/htmls/interactive_review/bio_intrev.html
Complete this interactive review using your
virtual textbook at home. Concept maps are an
excellent way to organize your thoughts and
review material!
58(No Transcript)
59Bonds break and form during chemical reactions.
- Everything that happens in an organism its
growth, its interaction with the environment, its
reproduction, and even its movement is based on
chemical reactions. - A chemical reaction is a process that changes one
set of chemicals into another set of chemicals - Chemical reactions can occur slowly or very
quickly. - The elements that enter into a chemical reaction
are known as reactants. - The elements or compounds produced by a chemical
reaction are known as products. - Chemical reactions always involve the breaking of
bonds in reactants and the formation of new bonds
in products. - Energy is released or absorbed whenever chemical
bonds form or are broken.
60Metabolic Processes
- Metabolism is the totality of an organisms
chemical reactions (all processes that involve
building materials or breaking down materials) - Catabolic degradative processes, where complex
molecules are broken down into simpler compounds
and energy is released. - Ex. Cellular respiration
- Anabolic consume energy to build complicated
molecules from simpler ones. - Ex. Photosynthesis
- These pathways intersect in such a way that the
energy released from Catabolic processes can be
used to drive Anabolic processes. - This transfer of energy is called Energy Coupling
61Energy Changes in Exergonic and Endergonic
Reactions
Exergonic Reaction Reaction proceeds with a net
RELEASE of free energythese reactions occur
spontaneously.
Endergonic Reaction Reaction proceeds with an
ABSORPTION of free energythese reactions are not
spontaneous.
62WebQuest Prions Public Healthhttp//www.classz
one.com/cz/ot/bio_webquest/02/intro.jsp
- Prions are misfolded proteins that cause mad cow
disease and, in humans, Creutzfeldt-Jakob
disease. In this webquest, you will learn about
prions and how they infect people and other
animals. Determine if the drastic steps taken to
prevent the spread of prions actually keeps
people safe.
63AKS Standards 8j - explain how enzymes function
as catalysts (GPS)
64Activation Energy
- Chemists call the energy that is needed to get a
reaction started the activation energy. - Some chemical reactions that make life possible
are too slow or have activation energies that are
too high to make them practical for living
tissue. - These chemical reactions are made possible by
catalysts. - A catalyst is a substance that speeds up the rate
of a chemical reaction - Catalysts work by lowering the activation energy
needed to make the reaction occur.
65Enzymes allow chemical reactions to occur under
tightly controlled conditions.http//www.sumanasi
nc.com/webcontent/animations/content/enzymes/enzym
es.html
- Enzymes are proteins that act as biological
catalysts. - Cells use enzymes to speed up chemical reactions.
- Enzymes act by lowering the activation energies
required to start these chemical reactions. - Enzymes are very specific, generally catalyzing
only one chemical reaction. - Enzymes are not changed or used up during
chemical reactions. - Enzymes cannot cause chemical reactions these
reactions would all occur naturally, just at a
slower rate!
66Chemical Reactions and Enzymes
- Activation energy- energy needed to get a
reaction started - Enzymes are proteins that act as biological
catalysts (speed up a reaction) by lowering the
activation energy required to start the reaction.
67Enzymes in Action
- For a chemical reaction to take place, the
reactants must collide with enough energy so that
existing bonds will be broken and new bonds will
be formed. - Enzymes speed up chemical reactions by providing
a site where reactants can be brought together to
react. - Such a site reduces the energy needed for the
reaction by placing the reactants in a position
favorable for the reaction to occur. - The reactants of enzyme-catalyzed reactions are
known as substrates. - Enzymes can be affected by changes in pH, changes
in temperature and can be turned on or off at
critical stages in the life of a cell.
68The Active Site of Enzymes
- The reactant an enzyme acts on is its substrate.
- Enzymes are substrate specific, and can
distinguish its substrate from even closely
related molecules! - Each enzyme has an active site the catalytic
center of the enzyme! This is the area where the
enzyme attaches to or reacts with the substrate.
69Chemical Reactions and Enzymes
70Physical and Chemical Environments Affects Enzyme
Activity
- Because they are PROTEINS, the shape of an enzyme
is very important in determining its function.
Anything that changes the shape of an enzyme
will interfere with its ability to react with its
substrate. - Temperature too high, denatures protein too
low, freezes protein in such a way that it cannot
alter its shape to react - pH too high or too low, denatures protein
- Salinity ions of salt can compete with an
enzymes bonds and denature the protein - Cofactors inorganic nonprotein helper bound to
active site must be present for some enzymes to
function (zinc, iron, copper) - Coenzymes organic nonprotein helper bound to
active site again, must be present (vitamins) - http//www.sumanasinc.com/webcontent/animations/co
ntent/proteinstructure.html
71Inhibitors
- Enzyme Inhibitors stop enzyme from working!
- 2 types competitive and noncompetitive
- Competitive blocks active site, mimics substrate
- Noncompetitive bind to another part of enzyme and
change shape of enzyme so cant work on
substrate - http//bcs.whfreeman.com/thelifewire/content/chp06
/0602001.html
72Inhibition of Enzyme Activityhttp//bcs.whfreeman
.com/thelifewire/content/chp06/0602001.htm
Enzyme Inhibitors stop enzyme from working.
There are 2 types of enzyme inhibitors
competitive and noncompetitive.
Competitive inhibitors mimic the substrate and
competes for the active site. This effectively
blocks the enzyme from working.
Noncompetitive inhibitors bind to the enzyme at a
location away from the active site, but alters
the shape of the enzyme so that the active site
is no longer fully functional.
73Critical Thinking Activities Inferring
Connecting Concepts
- Some organisms live in very hot or very acidic
environments. Would their enzymes function in a
humans cells? Why or why not? - Organisms need to maintain homeostasis, or stable
internal conditions. Why is homeostasis
important for the function of enzymes? - No, those enzymes function under different
conditions than are found in humans. - If homeostatic conditions, such as temperature or
pH, are not maintained, then the hydrogen bonds
that keep an enzyme in its correct shape will
weaken or break and the enzymes structure will
change this will affect its function.