the chemistry of life unit iii. what is biochemistry? biochemistry is the study of structure,...
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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 )
Together these substances help form matter!!!
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
http://www.sumanasinc.com/webcontent/animations/content/propertiesofwater/water.html
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
Water-conductingcells
Adhesion
Cohesion
150 µm
Directionof watermovement
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.
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.
Surface Tension
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 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
Water’s High Specific Heat
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.
Hydrogenbond
Liquid waterHydrogen bonds break and re-form
IceHydrogen bonds are stable
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 Shellhttp://www.sumanasinc.com/webcontent/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)
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
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
Neutral solution
Acidic solution
Basic solution
OH–
OH–
OH–
OH–
OH–OH–
OH–
H+
H+
H+
OH–
H+ H+
H+ H+
OH–
OH–
OH–OH–
H+
OH–
H+
H+
H+
H+
H+
H+
H+
OH–
Neutral [H+] = [OH–]
Incr
easi
ng
ly A
cid
ic [
H+]
> [
OH
–]
Incr
easi
ng
ly B
asic
[H
+]
< [
OH
–]
pH Scale0
1
2
3
4
5
6
7
8
Battery acid
Gastric juice,lemon juice
Vinegar, beer,wine, cola
Tomato juice
Black coffee
Rainwater
Urine
SalivaPure water
Human blood, tears
Seawater
9
10
Milk of magnesia
Household ammonia
Householdbleach
Oven cleaner
11
12
13
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 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. Proteins2. Lipids 4. Nucleic Acids
Formation of Macromoleculeshttp://bcs.whfreeman.com/thelifewire/content/chp03/0302002.html
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. 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
Lipidshttp://bcs.whfreeman.com/thelifewire/content/chp03/0302002.html
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
SATURATED
UNSATURATED
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 ACIDShttp://bcs.whfreeman.com/thelifewire/content/chp03/0302002.html
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
Proteinshttp://bcs.whfreeman.com/thelifewire/content/chp03/0302002.html
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
1. 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
are the result of hydrogen bonds at regular intervals along the polypeptide backbone
3. 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
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 ProteinAlpha 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 Structurehttps://mywebspace.wisc.edu/jonovic/web/proteins.html
What determines Protein configuration?
Polypeptide chain of given amino acid sequence can spontaneously arrange into 3-D 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.
Ex. Cellular respiration
Anabolic – consume energy to build complicated molecules from simpler ones.
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:
Reaction proceeds with a net RELEASE of free energy…these reactions occur spontaneously.
Endergonic Reaction:
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
Enzymeshttp://www.sumanasinc.com/webcontent/animations/content/enzymes/enzymes.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!
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/proteinstructure.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
http://bcs.whfreeman.com/thelifewire/content/chp06/0602001.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.