the chemistry of life unit iii. what is biochemistry? biochemistry is the study of structure,...

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.