Transcript The Chemistry of Life

The Chemistry of Life
Unit III
What is 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 for life…so biology and chemistry are
closely related!
So what makes up these living things?
 Matter is anything that
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 )
Elements
 When atoms of the same type come together
they make up units called elements.
 An element is a pure substance made of only 1
type of atom (it is usually abbreviated by a
chemical symbol):
Chemical 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

Example: NaCl (salt) or H2O (water)
Chemical 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
Ionic 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
Covalent 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)
Covalent & Ionic Bonds
IONIC BONDS:
electrons are
transferred
between atoms
COVALENT BONDS:
electrons are shared
between atoms
Properties of Water
 Water is the most abundant compound in
living things
 Some of water’s properties that facilitate an
environment for life are:





Cohesive and adhesive behavior
Ability to moderate temperature
Expansion upon freezing
Versatility as a solvent
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The Polarity of 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)
Cohesion & Adhesion
 Collectively, hydrogen bonds hold water molecules
together, a phenomenon called cohesion


the attraction of water molecules to other water molecules as
a result of hydrogen bonding
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
another

adhesion of water to cell walls by hydrogen bonds helps to counter
the downward pull of gravity on the liquids passing through plants
Adhesion
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.
Surface 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.
Moderation 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
stems 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 1°C
Water’s High Specific Heat
 Water’s high specific heat can be traced to hydrogen
bonding


Heat is absorbed when hydrogen bonds break
Heat is released when hydrogen bonds form
 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.


A greater input of energy is required to raise the
temperature of water than the temperature of air!
Minimizes temperature fluctuations to within limits that
permit life
Evaporative 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.
The Density Anomaly
 Ice floats in liquid water because hydrogen bonds in
ice are more “ordered,” making ice less dense
 Water reaches its greatest density at 4°C
 If ice sank, all bodies of water would eventually freeze
solid, making life impossible on Earth
 Due to geometry of water molecule, they must move
slightly apart to maintain the max number of H bonds in
a stable structure.

So at Zero degrees Celsius, an open latticework is
formed, allowing air in – thus ice becomes less dense
than liquid water floats on top of the water.
Hydrogen
bond
Ice
Hydrogen bonds are stable
Liquid water
Hydrogen bonds break and re-form
The 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
Hydration Shell
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• 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)
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Acids 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
pH Scale
0
1
Gastric juice,
2 lemon juice
H+
H+
Battery acid
+
– H
H+ OH
+
OH– H H+
H+ H+
3 Vinegar, beer,
wine, cola
4 Tomato juice
Acidic
solution
5
Black coffee
Rainwater
6 Urine
OH–
H+
OH–
H+
OH–
OH– OH– +
H+ H+ H
Neutral
solution
Neutral
[H+] = [OH–]
Saliva
7 Pure water
Human blood, tears
8 Seawater
9
10
OH–
Milk of magnesia
OH–
OH– H+ OH–
–
OH– OH
OH–
+
H
Basic
solution
11
Household ammonia
12
Household
13 bleach
Oven cleaner
14
Buffers
 The internal pH of most living cells must remain
close to pH 7
 Buffers are substances that minimize changes
in concentrations of H+ and OH– in a solution

They do so by accepting hydrogen ions from the
solution when they are in excess and donating
hydrogen ions when they are depleted
 Most buffers consist of an acid-base pair that
reversibly combines with H+
CO2 + H2O <= H2CO3 => HCO3- + H+
Macromolecules
 Many of the molecules in living cells are so large that
they are known as macromolecules


Formed by a process called polymerization (making large
compounds by joining smaller compounds together)
Smaller unit known as monomer – join together to form
polymers
 Four groups of organic compounds found in living things
are
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

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Carbohydrates
Lipids
Nucleic acids
Proteins
Monomers, Polymers, and Macromolecules
 Monomers: repeating units that serve as
building blocks for polymers
 Polymers: long molecule consisting of many
similar or identical building blocks linked by
COVALENT bonds
 Macromolecules: LARGE groups of polymers
covalently bonded – 4 classes of organic
macromolecules to be studied:
1. Carbohydrates
3. Proteins
2. Lipids
4. Nucleic Acids
Formation of Macromolecules
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 Monomers are connected 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.
The Synthesis and Breakdown of Polymers
As each monomer is
added, a water
molecule is removed –
DEHYDRATION
REACTION.
This is the reverse of
dehydration is
HYDROLYSIS…it
breaks bonds between
monomers by adding
water molecules.
Organic Compounds and Building Blocks
 Carbohydrates – made up of linked monosaccharides
 Lipids -- CATEGORY DOES NOT INCLUDE POLYMERS
(the grouping is based on insolubility)



Triglycerides (glycerol and 3 fatty acids)
Phospholipids (glycerol and 2 fatty acids)
Steroids
 Proteins – made up of amino acids
 Nucleic Acids – made up nucleotides
Carbohydrates – Fuel and Building Material
 Carbs include sugars & their polymers
 Carbs exist as three types:
1. monosaccharides
2. disaccharides
3. polysaccharides (macromolecule stage)
 Made up of C, H, and O in a 1:2:1 ratio (CnH2nOn)
Monosaccharides
 Are major sources of energy for cells!

Ex. Glucose – cellular respiration
 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, 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

 All three have SAME MOLECULAR FORMULA but differ
structurally so they are ISOMERS!
Disaccharides
 Consists 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)
Examples of Disaccharide Synthesis
Polysaccharides
 These are the polymers of sugars – the true macromolecules of the
carbohydrates.
 Serve as storage material that is hydrolyzed as needed in the
body or as structural units that support bodies of organisms.
These are polymers with a
few hundred to a few
thousand
monosaccharides joined
by glycosidic linkages.
Storage & Structural Polysaccharides
 STARCH AND GLYCOGEN are storage polysaccharides.

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Starch: storage for plants
Glycogen: storage for animals
 Cellulose and Chitin are structural polysaccharides:


Cellulose: found in cell wall of PLANTS
Chitin: found in cell wall of FUNGI
Lipids
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 Does not include polymers – only grouped
together based on trait of little or no affinity for
water:

Hydrophobic (water fearing)
 Hydrophobic nature is based on molecular
structure – consist mostly of hydrocarbons!
 Hydrocarbons are insoluble in water b/c of their
non-polar C—H bonds!
Lipids: Highly Varied Group
 Smaller than true polymeric macromolecules
 Insoluble in water, soluble in organic solvents
 Serve as energy storage molecules
 Can act as chemical messengers within and
between cells
 Includes fats, steroids, and waxes
“Fats” -- Triglycerides
 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
 Glycerol is an alcohol with three carbons, each one with a hydroxyl group
 Fatty acid has a long carbon skeleton:


at one end is a carboxyl group (thus the term fatty “acid”)
the rest of the molecule is a long hydrocarbon chain
 The hydrocarbon chain is not susceptible to bonding, so water H-bonds
to another water and excludes the fats
Lipids
The 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
Saturated vs. Unsaturated “Fats”
 Refers to the structure of the hydrocarbon chains of the
fatty acids:

No double bonds between the carbon atoms of the chain
means that the max # 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
 and these tend to kink up and prevent the fats from
packing together
Examples of Saturated and Unsaturated Fats and Fatty Acids
At room temperature, the molecules of
a saturated fat are packed closely
together, forming a solid.
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.
Saturated and Unsaturated Fats and Fatty Acids: Butter and Oil
UNSATURATED
SATURATED
Phospholipids
 Have only two fatty acid tails!
 Third hydroxyl group of glycerol is joined to a
phosphate group (negatively charged)
 Are ambivalent to water – tails are hydrophobic,
heads are hydrophilic.
 At cell surface, get a double layer arrangement –
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.
The Structure of a Phospholipid
NUCLEIC ACIDS
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POLYMERS OF INFORMATION – BUILDING BLOCKS OF DNA & RNA
What Determines the Primary
Structure of a Protein?
 Gene – unit of inheritance that determines
the sequence of amino acids

made of DNA (polymer of nucleic acids)
 Building blocks of nucleic acids are
nucleotides:

phosphate group, pentose sugar, nitrogenous
base (A,T,C,G,U)
Two Categories of Nitrogenous Bases
 Pyrimidines and
Purines:


Pyrimidines:
smaller, have a
six-membered
ring of carbon and
nitrogen atoms
(C , U, T)
Purines: larger,
have a six- and a
five-membered
ring fused
together (A, G)
NUCLEIC ACIDS consist of: phosphate group, pentose sugar, nitrogenous base
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
Nucleic Acids
Proteins
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 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
Hierarchy of Structure in Proteins
 Amino acids – building blocks of proteins

20 different amino acids in nature
 Polypeptides – polymers of amino acids
 Protein – one or more polypeptides folded
and coiled into specific conformations
• 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.
How Amino Acids Join
 Carboxyl group of one is adjacent to amino
group of another, dehydration synthesis
occurs, forms a covalent bond:

PEPTIDE BOND
 When repeated over and over, get a
polypeptide


On one end is an N-terminus (amino end);
On other is a C-terminus (carboxyl end)
Making a Polypeptide Chain
Note: dehydration
synthesis.
Note: carboxyl group
of one end attaches
to amino group of
another.
Note: peptide bond is
formed.
Note: repeating this
process builds a
polypeptide.
Protein’s Function Depends on Its
Conformation
 Functional proteins consist of one or more
polypeptides twisted, folded, and coiled into a
unique shape
 Amino acid sequence determines shape
 Function of a protein depends on its ability to
recognize and bind to some other molecule.
CONFORMATION IS KEY!
Four Levels of Protein Structure
Primary Structure: unique sequence of amino
acids (long chain)
2. Secondary Structure: segments of polypeptide
chain that repeatedly coil or fold in patterns that
contribute to overall configuration
1.

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
4. Quaternary Structure: the overall protein structure
that results from the aggregation of the polypeptide
subunits
3.
The Primary Structure of a Protein
This is the unique amino acid
sequence…notice carboxyl
end and amino end!
These are held together by
PEPTIDE bonds!!!
The Secondary Structure of a Protein
Alpha Helix & Beta Pleated Sheet
BOTH PATTERNS HERE
DEPEND ON HYDROGEN
BONDING BETWEEN C=O
and N-H groups along the
polypeptide backbone.
Alpha Helix – delicate coil
held together by H-bonding
between every fourth amino
acid
Beta pleated sheet – two or
more regions of the
polypeptide chain lie parallel
to one another. H-bonds
form here, and keep the
structure together.
NOTE – only atoms of
backbone are involved,
not the amino acid side
chains!
Tertiary Structure of a Protein
 Tertiary structure: superimposed on secondary
structure; irregular contortions from interactions
between side chains (R-groups) of amino acids:


nonpolar side chains end up in clusters at the core of
a protein – caused by the action of water molecules
which exclude nonpolar substances
“hydrophobic interaction”
 van der Waals interactions, H-bonds, and ionic bonds all add
together to stabilize tertiary structure
 may also have disulfide bridges form …when amino acids with 2
sulfhydryl groups are brought together – these bonds are much
stronger than the weaker interactions mentioned above
Examples of Interactions Contributing
to the Tertiary Structure of a Protein
Quaternary Structure
 Quaternary Structure: the overall protein
structure that results from the aggregation of
the polypeptide subunits


Ex. collagen – structural
Ex. hemoglobin – globular
The Quaternary Structure of Proteins
Review: The Four Levels of Protein Structure
https://mywebspace.wisc.edu/jonovic/web/proteins.html
What determines Protein configuration?
 Polypeptide chain of given amino acid
sequence can spontaneously arrange into 3D shape


Configuration also depends on physical and
chemical conditions of protein’s environment
if pH, salt [ ], temp, etc. are altered, protein
may unravel and lose native conformation –
DENATURATION
•Denatured proteins are biologically inactive!
•Anything that disrupts protein bonding can denature a protein!
Denaturation and Renaturation of a Protein
Denatured proteins can often renature when environmental
conditions improve!
Metabolic Pathways
 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.


Anabolic – consume energy to build complicated molecules
from simpler ones.




Ex. Cellular respiration
Ex. Protein synthesis
These pathways intersect in such a way that the energy
released from Catabolic can be used to drive Anabolic
This transfer of energy is called Energy Coupling
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



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
Energy Changes in Exergonic and Endergonic Reactions
Exergonic Reaction:
Endergonic Reaction:
Reaction proceeds with a net
RELEASE of free energy…these
reactions occur spontaneously.
Reaction proceeds with an
ABSORPTION of free energy…these
reactions are not spontaneous.
Activation 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 catalysts 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
Enzymes
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 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!
Chemical Reactions and Enzymes
 Activation energy- energy needed to get a reaction
started
 Enzymes are proteins that act as biological catalysts
(speed up a reaction)
Enzyme 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
Enzymes
 The reactant an enzyme acts on is its
substrate.
 Enzymes are substrate specific, and can
distinguish its substrate from even closely
related isomers!
 Each enzyme has an active site – the
catalytic center of the enzyme!
Chemical Reactions and Enzymes
Enzymes – VERY IMPORTANT!
 Changes the rate of a chemical reaction
 Enable specific molecules, called
substrates, to undergo chemical change
 See “Inside Story” – page 166
Physical and Chemical Environment
Affects Enzyme Activity
 Temperature – too high, denatures protein
 pH – too high or too low, denatures 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/content/proteinstruct
ure.html
Inhibitors
 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 can’t work on
substrate
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06/0602001.html
Figure 6.17 Inhibition of Enzyme Activity
Mimics the substrate and
competes for the active site.
Binds 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.
Feedback inhibition
Feedback Inhibition:
Switching off of a metabolic
pathway by its end product,
which acts an inhibitor of an
enzyme within the pathway.