welcome to biology!

Welcome to Biology!

Unit 1: BiochemistryChapter 1: The Molecules of Life

Chapter 2: The Cell and its Components

Chapter 1: The Molecules of Life

Molecules Interactions between and within moleculesStructure and shape of molecules

MacromoleculesThe 4 major typesRoles in biological organisms

Biochemical reactionsThe 4 major typesThe role of enzymes in reactions

Section 1.1: Chemistry in Living Systems

All matter is composed of elements Cannot be broken down into simpler substances by ordinary

chemical methodsApproximately 92 naturally occurring elementsOnly 6 elements serve as the chemical foundation for life

Carbon Hydrogen Nitrogen Oxygen Phosphorous Sulfur

AtomsAn atom is the smallest

particle of an element that retains the element’s properties

Atomic mass = sum of protons and neutrons

All atoms of an element have the same number of protons, but the number of neutrons can vary

IsotopesIsotopes are atoms of the same element that

have different numbers of neutronsRadioisotopes are unstable and their nucleus

decays over timeThey are valuable diagnostic tools in medicine

Studying the Interactions of Molecules

A molecule is composed of two or more atoms and is the smallest unit of a substance that retains the chemical and physical properties of the substance

Organic molecules are carbon-based Carbon atoms often bind to

each other or hydrogen May also include nitrogen,

oxygen, phosphorous, and/or sulfur

BiochemistryBiochemists study the properties and interactions

of biologically important organic moleculesBiochemistry forms a bridge between

chemistry (the study of the properties and interactions of atoms and molecules) and biology (the study of properties and interactions of cells and organisms).

Understanding the physical and chemical principles that determine the properties of these molecules is essential to understanding their functions in the cell and in other living systems

Interactions within Molecules

Intramolecular forces (“intra” = within) hold the atoms within a molecule togetherThese forces are generally thought of as the

chemical bonds within a moleculeChemical bonds within a molecule are called

covalent bonds.A covalent bond forms when the electrons of two

atoms overlap so that the electrons of each atom are shared between both atoms


Some atoms attract electrons much more strongly than other atoms

This property is referred to as an atom’s electronegativity Oxygen, nitrogen, and chlorine have high electronegativity Hydrogen, carbon, and phosphorus have low electronegativity

When two atoms share electrons, the electrons are more attracted to the atom with the higher electronegativity

Electrons have a negative charge, so that atom would assume a slightly negative charge (∂-)

The atom with lower electronegativity assumes a partial positive charge (∂+)


This unequal sharing of electrons in a covalent bond creates a polar covalent bondEx: A water molecule contains two polar covalent

O-H bonds, where the electrons in each bond are more strongly attracted to the oxygen atom

Molecules that have regions of partial negative and partial positive charge are called polar molecules


When covalent bonds are formed between atoms with similar electronegativities, the electrons are shared equally between the atoms

These bonds are considered non-polarIf these bonds predominate a molecule, the

molecule is considered a non-polar moleculeEx: Carbon and hydrogen

The polarity of biological molecules greatly affects their behaviour and functions in a cell

Interactions between Molecules

Intermolecular forces (“inter” = between) are forces between molecules

They form between different molecules or between different parts of the same molecule (if it is very large)

They are much weaker than intramolecular forces

They determine how molecules interact with each other and with different moleculesThey play a vital role in biological systems

Interactions between Molecules

Intermolecular forces are usually attractive and make molecules associate togetherThey can be broken fairly easily if enough energy

is applied Intermolecular forces are responsible for many of

the physical properties of substancesTwo types of intermolecular interactions are

particularly important for biological systems:Hydrogen bondingHydrophobic interactions

Hydrogen BondingA water molecule has two polar O-H bonds and is a polar

moleculeThe slightly positive hydrogen atoms of one molecule

are attracted to the slightly negative oxygen atoms of other water molecules

This type of intermolecular attraction is called a hydrogen bond. Hydrogen bonds are weaker than ionic and covalent bonds

and are represented by a dotted line Many biological molecules have polar covalent bonds

involving a hydrogen atom and an oxygen or nitrogen atom.

Hydrogen BondingA hydrogen bond is more easily broken than a

covalent bond, but many hydrogen bonds added together can be very strong

The cell is an aqueous environment so hydrogen bonding between biological molecules and water is very importantThey help maintain the proper structure and

function of the molecules

Hydrogen BondingEx: The 3-D shape of DNA,

which stores an organism’s genetic information, is maintained by numerous hydrogen bonds

The breaking and reforming of these bonds plays an important role in how DNA functions in the cell

Hydrophobic InteractionsNon-polar molecules do not form

hydrogen bondsWhen non-polar molecules interact

with polar molecules, they clump together

Non-polar molecules are hydrophobic, literally meaning “water-fearing”

Polar molecules have a natural tendency to form hydrogen bonds with water molecules and are hydrophilic, literally meaning “water-loving”

Hydrophobic InteractionsThe natural clumping

together of non-polar molecules is called the hydrophobic effect

This effect plays a central role in how cell membranes form and helps to determine the 3-D shape of biological molecules as proteins

Ions in Biological SystemsWhen an atom or group of atoms gains or loses

electrons, it acquires an electric charge and becomes an ionWhen it loses electrons, the resulting ion is

positive and is called a canion.When it gains electrons, the resulting ion is

negative and is called an anion.Ions can be composed of only one element,

such as a sodium ion, Na+, or of several elements, such as a bicarbonate ion HCO3

-

Ions in Biological Systems Ions are an important part of living systems

Hydrogen ions, H+, are critical to many biological processes, including cellular respiration (the process by which cells break down nutrients into energy)

Sodium ions, Na+, are part of transport mechanisms that enable specific molecules to enter cells.

Since the cell is an aqueous environment, almost all ions are considered free or disassociated ions (Na+

(aq)) since they dissolve in water, rather than as ionic compounds such as sodium chloride (NaCl(s)).

Functional GroupsOrganic molecules that are made up of only carbon and

hydrogen atoms are called hydrocarbonsHydrocarbons share similar properties including:

Non-polar Do not dissolve in water Relatively low boiling points (depending on size) Flammable

The covalent bonds between carbon and carbon and between carbon and hydrogen are “energy-rich” Breaking them releases a great deal of energy Most of the hydrocarbons you encounter in everyday life, such

as acetylene, propane, butane, and octane, are fuels

Functional GroupsThough hydrocarbons share similar properties, other

organic molecules have a wide variety of properties Most organic molecules have other atoms or groups of

other atoms attached to their central carbon-based structure.

A cluster of atoms that always behaves in a certain way is called a functional group Functional groups contain atoms such as oxygen (O),

nitrogen (N), phosphorus (P), or sulfur (S).Certain chemical properties are always associated

with certain functional groups

Table 1.1

Structures and Shapes of Molecules

A molecular formula shows the number of each type of atom in an element or compoundEx: H2O, C3H7NO2, and C6H12O6

Structural formulas show how the different atoms of a molecule are bonded together

When representing molecules using a structural formula, a line is drawn between atoms to indicate a covalent bondA single line indicates a single covalent bond, double

lines indicate a double bond, and triple lines indicate a triple bond

Structural Formulas

Structural FormulasStructural formulas can

also be presented in a simplified form, particularly for biological molecules

Carbon atoms are indicated by a bend in the line Their symbol, C, is omitted Hydrogen atoms attached to

these carbon atoms are omitted but are assumed to be present

Shapes of MoleculesStructural formulas are 2-D representations, but

molecules take up space in 3 dimensionsIn fact, the 3-D shape of a molecule influences

its behaviour

Ball-and-stick Model Space-filling Model

Section 1.2: Biologically Important Molecules

Many of the molecules of living organisms are composed of thousands of atomsThese are called macromolecules, which are large

molecules that often have complex structuresMany macromolecules are polymers

Long chain-like substances composed of many smaller molecules linked together by covalent bonds

These smaller molecules are called monomers, which can exist individually or as units of a polymerThe monomers in a polymer determine the properties of

that polymer.

Protein

Nucleic Acid

Carbohydrate

Lipid

CarbohydratesCarbohydrates contain carbon, hydrogen, and oxygen

in the ratio of 2 hydrogen and 1 oxygen for every carbonThe general formula for carbohydrates is (CH2O)n where

“n” is the number of carbon atomsSugar and starches are examples of carbohydrates

They store energy in a way that is easily accessible by the body

Most carbohydrates are polar and dissolve in waterDue to high proportion of hydroxyl functional groups,

and often carbonyl groups

Monosaccharides and Disaccharides

Monosaccharides are simple sugars that consist of 3 to 7 carbon atoms“Mono” = one and “saccharide” = sugar

Common examples include:Glucose is the sugar the cells in the body use first for

energy (i.e. blood sugar)Fructose is a principal sugar in fruitsGalactose is a sugar found in milk

Glucose Fructose Galactose


These 3 simple sugars have the same molecular formula (C6H12O6) but the 3-D shapes of their structures and the relative arrangement of their hydrogen atoms and hydroxyl groups differMolecules that have the same molecular formula

but have different structures are called isomers

Due to their different 3-D shapes, they’re treated very differently by your body and in the cellEx: Your taste buds detect fructose as being much

sweeter than glucose

Two monosaccharides can join to form a disaccharide. The covalent bond between

them is called a glycosidic linkage

It forms between specific hydroxyl groups on each monosaccharide.

Common table sugar is the disaccharide sucrose (glucose and fructose)

Lactose (galactose and glucose) is found in dairy products


Glycosidic linkage

Sucrose

PolysaccharidesMany monosaccharides can join together by

glycosidic linkages to form a polysaccharide (“poly” = many)

Three common polysaccharides are starch, glycogen, and cellulose

All three are composed of monomers of glucose, but they differ in the ways the glucose units are linked togetherThis results in them having different 3-D shapes

Starch and GlycogenThe differences in their 3-D shapes also leads to

them having different functionsPlants store glucose in the form of starch and

animals store glucose in the form of glycogenThey provide short-term energy storage, whereby

glucose can be easily accessed from their breakdown within the cell

Starch and glycogen differ in their number and type of branching side chainsGlycogen has more branches so it can be broken

down much more rapidly than starch

CelluloseCellulose carries out a completely different function.

It provides structural support in plant cell walls.The type of glycosidic linkage between monomers of

cellulose is different from the type in starch and glycogen The hydroxyl group on carbon-1 of glucose can exist in 2

different positions These positions are referred to as alpha and beta The alpha form results in starch and glycogen, while the beta

form results in cellulose.

LipidsLike carbohydrates, lipids are composed of

carbon, hydrogen, and oxygen atomsHowever, lipids have fewer oxygen atoms and a

significantly greater proportion of carbon and hydrogen bonds

As a result, lipids are non-polar and hydrophobic (they do not dissolve in water)

Since the cell is an aqueous environment, the hydrophobic nature of some lipids plays a key role in determining their function

LipidsThe presence of many energy-rich C-H bonds

makes lipids efficient energy-storage moleculesLipids yield more than double the energy per

gram that carbohydrates doHowever, they store their energy in

hydrocarbon chains so their energy is less accessible to cells than energy from carbohydratesLipids provide longer-term energy and are

processed by the body after carbohydrate stores are used up

LipidsLipids are crucial to life in many ways:

Lipids insulate against heat lossLipids form a protective cushion around major

organsLipids are a major component of cell

membranesLipids provide water-repelling coatings for fur,

feathers, and leaves

TriglyceridesTriglycerides are

composed of 1 glycerol molecule and 3 fatty acid moleculesThe bond between the

hydroxyl group on a glycerol molecule and the carboxyl group on a fatty acid is called an ester linkage because it results in the formation of an ester functional group

1 Glycerol 3 Fatty Acids

Ester Linkages

Triglycerides: Fatty AcidsA fatty acid is a hydrocarbon chain that ends

with an acidic carboxyl group (-COOH)A saturated fatty acid has no double bonds

between carbon atomsAn unsaturated fatty acid has one or more

double bonds between carbon atomsOne double bond = monounsaturatedTwo or more double bonds = polyunsaturated

Humans can’t synthesize polyunsaturated fats and must consume them in their diet

Triglycerides: Saturated and Unsaturated Fats

The double bonds in a triglyceride affects its 3-D shape, which alters its behaviour in the body

Triglycerides containing saturated fatty acids are generally solid fats at room temperature Ex: lard and butter

Triglycerides containing unsaturated fatty acids are generally liquid oils at room temperature Ex: olive oil and canola oil

Triglycerides: HealthSaturated fat is linked with heart disease, while some

unsaturated fats, particular polyunsaturated fatty acids, are known to reduce the risk of heart disease

A food preservation process called hydrogenation involves chemical addition of hydrogen to unsaturated fatty acids of triglycerides to produce saturated fatsA by-product of this reaction is the conversion of cis

fats to trans fats, whereby remaining double bonds are converted to a trans conformation

Consumption of trans fats is associated with increased risk of heart disease

PhospholipidsPhospholipids are the main components of cell

membranesThey are similar in structure to triglycerides, but

a phosphate group replaces the third fatty acidAttached to the phosphate group is an R group

which defines the type of phospholipidThe “head” portion is polar and hydrophilicThe lower “tail” portion is non-polar and

hydrophobic

PhospholipidsIn aqueous environments phospholipids form a

lipid bilayerIn a phospholipid bilayer, the hydrophilic

heads face the aqueous solution on either side of the bilayer, while the tails form a hydrophobic interior

The inside of a cell is an aqueous environment, as is the extra-cellular fluid surrounding cellsTherefore the membranes of cells, which are made

of phospholipids, adopt this bilayer structure

Other LipidsSteroids are a group of lipids that are

composed of 4 carbon-based rings attached to each other

Steroids differ depending on the arrangement of the atoms in the rings and the types of functional group

Other Lipids: SteroidsCholesterol is a steroid that is:

A component of cell membranesPresent in the blood of animalsThe precursor of several other steroids, such as

sex hormones testosterone and estrogen.Testosterone regulates sexual function and aids in

building bone and muscle massEstrogen regulates sexual function in females and

acts to increase the storage of fatMammals make cholesterol and it also enters the

body as part of the diet

Other Lipids: SteroidsIn medicine, steroids are used to reduce

inflammationEx: Topical steroid ointments to treat skin

conditions and inhalers to treat asthma.Anabolic steroids are synthetic compounds that

mimic male sex hormonesThey are typically used to build muscle mass in

people who have cancer and AIDS, but are also frequently misused by athletes

Other Lipids: WaxesWaxes have a diversity of chemical structures, often

with long carbon-based chains, and are solid at room temperature

They are produced in both plants (ex: carnauba wax) and animals (ex: earwax, beeswax, and lanolin) In plants, waxes coat the surfaces of leaves,

preventing water and solutes from escaping and helping to repel insects

In animals, waxes are present on the skin, fur, and feathers of many species and on the exoskeletons of insects

Proteins Proteins represent an extremely diverse type of macromolecules

that can be classified into groups according to their function Some of the functions of proteins include:

Catalyzing chemical reactions Providing structural support Transporting substances in the body Enabling organisms to move Regulating cellular processes Providing defense from disease

The functions of proteins depend on their 3-D structures

Amino Acids: Monomers of Proteins

A protein is a macromolecule composed of amino acid monomers

An amino acid contains a central carbon atom that is bonded to the following four atoms or group of atoms: A hydrogen atom An amino group A carboxyl group An R group (which is also called a

side chain) The distinctive shape and properties of

an amino acid depend on its R group

Amino AcidsAll amino acids are somewhat polar, due to the

polar C=O, C-O, C-N, and N-H bondsSome amino acids are more polar than others,

depending on the polarity of the R groupThere are 20 common amino acids that make up

most proteins8 of these are essential amino acids and can’t be

produced by the human body and must be consumed as part of the diet

These are isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.

Amino AcidsIn proteins, amino acids are joined by covalent

bonds called peptide bondsForm between the carboxyl group on one amino

acid and the amino group on anotherA polymer composed of amino acid monomers is

called a polypeptideProteins are composed of one or more polypeptidesAmino acids can occur in any sequence in a

polypeptide and since there are 20 possible amino acids for each position, an enormous variety of proteins are possible

Levels of Protein Organization

The structure of a protein can be divided into 4 levels of organization

Primary structureThe linear sequence of amino acidsThe peptide bonds linking the amino acids are

the backbone of a polypeptide chainSince the peptide bonds are polar, hydrogen

bonding is possible between the C=O of one amino acid and the N-H of another amino acid.


Secondary structureThe result of the hydrogen bonds between

amino acidsA polypeptide can form a coil-like shape

(alpha helix) or a folded fan-like shape (beta pleated sheet)


Tertiary structure The 3-D shape of proteins that results from a complex process of

protein folding This folding occurs naturally as the peptide bonds and the

different R groups interact with each other and with the aqueous environment of the cell

The hydrophobic effect had a large effect on structure The polar hydrophilic groups direct towards the aqueous environment

and non-polar hydrophobic groups direct towards the interior of the proteins 3-D shape

Hydrogen bonding and electrostatic attractions between R groups of different amino acids also add stability

One class of proteins have molecular chaperones that interact with the polypeptide chain and produce the final folded protein


Quaternary structureThe association of two or more polypeptides

to form a protein

Protein DenaturationUnder certain conditions, proteins can completely

unfold in a process called denaturationThis occurs when the normal bonding between R

groups is disturbed Intermolecular bonds break, potentially affecting

the secondary, tertiary, and quaternary structuresConditions that cause denaturation include

extremes of hot and cold temperatures and exposure to certain chemicals

Once a protein loses its normal 3-D shape, it is no longer able to perform its usual function

Nucleic AcidsThere are two types of nucleic acids:

DNA (deoxyribonucleic acid) RNA (ribonucleic acid)

DNA contains the genetic information of an organism, which is interpreted and decoded into particular amino acid sequences of proteins, which carry out numerous functions in the cell

This conversion is carried out with the assistance of different RNA molecules

The amino acid sequence of a protein is determined by the nucleotide sequences of both DNA and RNA

Nucleic Acids DNA and RNA are polymers made of

thousands of repeating nucleotide monomers

A nucleotide is made up of 3 components that are covalently bonded together A phosphate group A sugar with 5 carbon atoms A nitrogen-containing base

The nucleotide make-up of DNA and RNA differs The nucleotides in DNA contain the sugar

deoxyribose The nucleotides in RNA contain the sugar

ribose

Nucleic AcidsThere are 4 different

types of nitrogenous bases in DNA:Adenine (A)Thymine (T)Guanine (G)Cytosine (C) In RNA all the same bases

are used, except thymine, which is replaced with Uracil (U)

Nucleic Acids A polymer of nucleotides is often

referred to as a strand The covalent bond between

adjacent nucleotides is called a phosphodiester bond It occurs between the phosphate

group on one nucleotide and a hydroxyl group on the sugar of the next nucleotide

A nucleic strand has a backbone made up of alternating phosphates and sugars with the bases projecting to one side of the backbone

Nucleic Acids DNA is composed of 2 strands twisted about each other to

form a double helix When unwound, it resembles a ladder The sides of the ladder are made up of alternating phosphate

and sugar molecules, and the rungs of the ladder are made up of pairs of bases held together by hydrogen bonds

Nucleotide bases always pair together in the same way: Thymine (T) pairs with Adenine (A) Guanine (G) pairs with Cytosine (C) These bases are said to be complementary to each other

RNA is single-stranded

Section 1.3 Biochemical Reactions

The chemical reactions that are associated with biological processes can be grouped in several types

The four main types of chemical reactions that biological molecules undergo in the cell are:NeutralizationOxidation-reductionCondensationHydrolysis

Neutralization (Acid-Base) Reactions

In the context of biological systems, acids and bases are discussed in terms of their behaviour in water

An acid is a substance that produced hydrogen ions, H+, when it dissolves in water It increases the concentration of hydrogen ions in an

aqueous solutionA base is a substance that produces hydroxide ions,

OH-, when it dissolves in water It increases the concentration of hydroxide ions in an

aqueous solution

The pH scale ranks substances according to the relative concentration of their hydrogen ions Substances that have a pH lower

than 7 are classified as acids Substances that have a pH

higher than 7 are classified as bases

Substances that have a pH of 7 (that is, they have an equal concentration of hydrogen and hydroxide ions) are classified as neutral



When an acid chemically interacts with a base, they undergo a neutralization reaction that results in the formation of a salt (an ionic compound) and water

The acid loses its acidic properties and the base loses its basic properties i.e. their properties have been cancelled out, or

neutralized


The normal pH of human blood ranges from 7.35-7.45 If blood pH increases to 7.5 it can cause dizziness and

agitation This condition is called alkalosis

If blood pH decreases to 7.3-7.1 it can cause disorientation, fatigue, severe vomiting, brain damage, and kidney disease This condition is called acidosis

Blood pH that falls below 7.0 or rises beyond 7.8 can be fatal


To maintain optimum pH ranges, organisms rely on buffers Substances that resist changes in pH by releasing hydrogen

ions when a fluid is too basic and taking up hydrogen ions when a fluid is too acidic

Most buffers exist as specific pairs of acids and bases Ex: One of the most important buffer systems in human

blood involves the pairing of carbonic acid, H2CO3(aq), and hydrogen carbonate ion, HCO3

-(aq)

Oxidation-Reduction Reactions

Another key type of chemical reaction is based on the transfer of electrons between molecules When a molecule loses electrons it becomes oxidized and

has undergone a process called oxidation Electrons are highly reactive and do not exist on their own

or free in the cell so when a molecule undergoes oxidation, the reverse process must occur in another molecule

When a molecule accepts electrons from an oxidized molecule, it becomes reduced and has undergone a process called reduction

Because oxidations and reductions occur at the same time, the whole reaction is called an oxidation-reduction reaction, or redox reaction

Oxidation-Reduction Reactions

A common type of redox reaction is a combustion reactionEx: In the combustion of propane in your barbeque, the

propane becomes oxidized and the oxygen is reducedThis reaction releases a lot of energy that is used to

cook food on the barbeque.Redox reactions also occur in cells, such as cellular

respirationSugars such as glucose are oxidized through a series

of redox reactions to produce carbon dioxide and water.

Condensation and Hydrolysis Reactions

The assembly of all four types of biological macromolecules involves a condensation reaction between the monomers of each polymer

In a condensation reaction, an H atom is removed from a functional group on one molecule, and an OH group is removed from another moleculeThe two molecules bond to form a larger molecule and

waterCondensation reactions are also called dehydration

reactions because the reaction results in the release of water

Condensation and Hydrolysis Reactions

The breakdown of macromolecules into their monomers involves the addition of water to break the bonds between the monomers

In a hydrolysis reaction, an H atom from water is added to one monomer, and an OH group is added to the monomer beside that one

The covalent bond between these monomers breaks and the larger molecule is split into two smaller molecules

Condensation

Enzymes Catalyze Biological Reactions

A certain amount of energy is required to begin a reaction, which is referred to as the activation energy of a reaction If the activation energy for a reaction is large, the reaction will

occur very slowlyOne of the methods to speed up reactions is to increase the

temperature of the reactants However, the temperatures that chemical reactions would

need to reach in order to proceed quickly enough to sustain life are so high that they would permanently denature proteins

This is why long-lasting high fevers are so dangerous, as the high temperature can cause major disruptions to cellular reactions

Enzymes Catalyze Biological Reactions

A catalyst is a substance that speeds up a chemical reaction but is not used up by the reaction Catalysts function by lowering the activation energy of a

reactionCells manufacture specific proteins that act as catalysts,

called enzymes Ex: In red blood cells an enzyme called carbonic anhydrase

enables carbon dioxide and water to react to form about 600,000 molecule of carbonic acid each second!

Enzymes facilitate almost all chemical reactions in organisms, and each type of reaction is carried out by its own characteristic enzyme

Enzymes Bind with a Substrate

Like other proteins, enzymes are composed of long chains of amino acids folded into particular 3-D shapes, with primary, secondary, tertiary, and often quaternary structures

Most enzymes have globular shapes, with pockets or indentations on their surfaces called active sitesThe unique shape and function of an active site

are determined by the sequence of amino acids in that section of the protein


An active site on an enzyme interacts in a specific manner with the reactant of a reaction, called the substrate

During the reaction, the substrate joins with the enzyme to form an enzyme-substrate complex

The substrate fits closely into the active site because enzymes can adjust their shapes slightly Intermolecular bonds, such as hydrogen bonds, form between the

enzyme and the substrate as the enzyme adjusts its shape This change in shape is called induced fit


Enzymes lower the activation energy of the reaction by changing the substrate, its environment, or both

To accomplish this, the active site may: Contain amino acid R groups that cause bonds in the

substrate to stretch or bend, making the bonds weaker and easier to break

Bring two substrates together in the correct position for a reaction to occur

Transfer electrons to and from the substrate (reduce or oxidize it), destabilizing it and making it more likely to react

Add or remove hydrogen ions to or from the substrate (i.e. act as an acid or base), destabilizing it and making it more likely to react


Once the reaction takes place, the products of the reaction are released and the enzyme is able to accept another substrate and begin the process again This cycle is known as the catalytic cycle

Some enzymes require the presence of other molecules or ions, known as coenzymes, to catalyze a reaction

Some enzymes require the presence of metal ions, such as iron or zinc, which are referred to as cofactors This is why your body requires small amount of minerals

and vitamins to stay healthy

Enzyme ClassificationEnzymes are classified according to the type of reaction

they catalyzeThe shape of an enzyme must match its substrate exactly,

so most enzymes catalyze only one specific reactionThere are thousands of different enzymes to catalyze the

numerous reactions that take place within an organism, each with a specific name to identify it

The names of many enzymes consist of the first part of the substrate’s name, followed by the suffix “-ase” Ex: The enzyme that catalyzes the cleavage of the glycosidic

linkage in lactose is named lactase.

Enzyme Activity and Surrounding Conditions

Enzyme activity is affected by any change in conditions that alters the enzyme’s 3-D shape

Temperature and pH are two important factors When temperatures are too low, the bonds that determine

enzyme shape are not flexible enough to enable substrate molecules to fit properly

When temperatures are too high, the bonds are too weak to maintain the enzyme’s shape

The optimal temperature and pH ranges of most enzymes are fairly narrow Most human enzymes work best within the pH range of 6-8.

There are exceptions though (ex: stomach enzymes)

Enzyme Activity and Surrounding Conditions

The number of substrates available also affects the rate of enzyme activity

If there are too few substrates present, enzymes and substrates will encounter each other much less frequently, and the rate of reaction will decrease

Therefore, enzyme activity increases as substrate concentration increasesThis is true up to a point where the enzymes are

working at maximum capacity, after which adding more substrate will not affect the rate of the reaction

Enzyme Activity Regulation

Inhibitors are molecules that interact with an enzyme and reduce its activityThey reduce the enzyme’s ability to interact with

its substrateThis can occur by two different mechanisms:

Competitive inhibitionNon-competitive inhibition

Competitive InhibitionThese inhibitors interact with the active site of

the enzymeWhen both the substrate and inhibitor are

present, they will compete to occupy the active site

When the inhibitor is present in high enough concentration, it will out-compete the substrate and block it from bindingThis prevents the reaction that the enzyme usually

catalyzes from occurring

Non-competitive InhibitionThese inhibitors bind to an allosteric site, altering the

conformation or 3-D shape of the enzyme, which decreases the activity of the enzyme

Many biochemical reactions are grouped together in pathways where the product of one reaction acts as a substrate for the enzyme that catalyzes the next reaction in the pathway These pathways are regulated by feedback inhibition The product of the last reaction in a pathway is a non-

competitive inhibitor of the enzyme that catalyzes the reaction at the beginning of the pathway

This ensures that the products of a pathway are not produced unnecessarily

Enzyme Activity Regulation

Activator molecules can also bind to an allosteric site In this case, the conformation of the enzyme alters

in such a way as to cause an increase in enzyme activity

The regulation of enzyme activity by activators and inhibitors binding to allosteric sites is called allosteric regulation

welcome to biology!

Documents

interactions of atoms

atoms interactions

neutronsall atoms

moleculessome atoms

atoms electronegativityoxygen

polar molecules interactions

carbonbasedcarbon atoms

interactions of cells