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Basic Biochemistry

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What is Biochemistry?

• Biochemistry is the study of the chemical interactions of living things.

• Biochemists study the structures and physical properties of biological molecules.– Often are involved in the manufacture of new

drugs and medical treatments

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CHEMISTRY OF LIFECHEMISTRY OF LIFE

• ElementsElements: simplest form of a : simplest form of a substance - cannot be broken substance - cannot be broken down any further without changing down any further without changing what it iswhat it is

• AtomAtom: the actual basic unit - : the actual basic unit - composed of protons, neutrons, composed of protons, neutrons, and electronsand electrons

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THE ATOMTHE ATOM

• Just like cells are the basic unit of life, the Just like cells are the basic unit of life, the ATOMATOM is the basic unit of matter. is the basic unit of matter.

• They are very small. If placed side by side one They are very small. If placed side by side one million would stretch a distance of 1cm. million would stretch a distance of 1cm.

• The atom is made up of The atom is made up of 33 particles. particles.

ParticleParticle ChargeCharge

PROTONPROTON ++

NEUTRONNEUTRON NEUTRALNEUTRAL

ELECTRONELECTRON --

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• Electrons are not present within the atom, Electrons are not present within the atom, instead instead THEY REVOLVE AROUND THE THEY REVOLVE AROUND THE NUCELUS OF THE ATOM & FORM THE NUCELUS OF THE ATOM & FORM THE ELECTRON CLOUDELECTRON CLOUD

• Draw a helium atom. Indicate where the Draw a helium atom. Indicate where the protons, neutrons and electrons are. protons, neutrons and electrons are.

+ +-

-

PROTONSNEUTRONS

ELECTRONS

ATOMIC # = 2 (PROTONS)

ATOMIC MASS = 4 (PROTONS & NEUTRONS)

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ISOTOPESISOTOPES

• atoms of the same element that atoms of the same element that HAVE A HAVE A DIFFERENT NUMBER OF NEUTRONSDIFFERENT NUMBER OF NEUTRONS

• Some isotopes are radioactive. This means Some isotopes are radioactive. This means that their nuclei is unstable and will break that their nuclei is unstable and will break down at a down at a CONSTANT RATECONSTANT RATE over time. over time.

• There are several practical uses for There are several practical uses for radioactive isotopes:radioactive isotopes:

1.1. CARBON DATINGCARBON DATING

2.2. TRACERSTRACERS

3.3. KILL BACTERIA / CANCER CELLSKILL BACTERIA / CANCER CELLS

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COMPOUNDSCOMPOUNDS

• a substance formed by the chemical a substance formed by the chemical combination of combination of 2 or more elements2 or more elements in in definite proportionsdefinite proportions– Ex: water, salt, glucose, carbon dioxide Ex: water, salt, glucose, carbon dioxide

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• The cell is a The cell is a COMPLEX CHEMICAL COMPLEX CHEMICAL FACTORYFACTORY containing some of the containing some of the same elements found in the nonliving same elements found in the nonliving environment. environment.

• carbon (C), hydrogen (H), oxygen (O), carbon (C), hydrogen (H), oxygen (O), and nitrogen (N) are present in the and nitrogen (N) are present in the greatest percentagesgreatest percentages

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TWO TYPES OF COMPOUNDSTWO TYPES OF COMPOUNDS

• Organic - Contain C, H, and O in Organic - Contain C, H, and O in some ratio (usually referred to as some ratio (usually referred to as chemicals of life) chemicals of life)

– Carbohydrates, Proteins, Lipids, Nucleic AcidsCarbohydrates, Proteins, Lipids, Nucleic Acids

• Inorganic - usually "support" life - no Inorganic - usually "support" life - no specific ratio of C, H, and Ospecific ratio of C, H, and O

– Water (H2O), Carbon Dioxide (CO2)Water (H2O), Carbon Dioxide (CO2)

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CHEMICAL BONDSCHEMICAL BONDS

• Chemical bonds hold the atoms in a Chemical bonds hold the atoms in a molecule together. molecule together.

• There are 2 types of chemical bonds There are 2 types of chemical bonds IONICIONIC and and COVALENTCOVALENT

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IONIC BONDSIONIC BONDS

• Occur when 1 or more electrons are Occur when 1 or more electrons are TRANSFERREDTRANSFERRED from one atom to another. from one atom to another.

• When an atom loses an electron it is a When an atom loses an electron it is a POSITIVEPOSITIVE charge. charge.

• When an atom gains an electron it is a When an atom gains an electron it is a NEGATIVENEGATIVE charge charge

• These newly charged atoms are now called These newly charged atoms are now called IONSIONS– Example: NaCl (SALT)Example: NaCl (SALT)

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COVALENT BONDSCOVALENT BONDS• Occur when electrons are Occur when electrons are SHAREDSHARED by atoms. by atoms.

• These new structures that result from covalent These new structures that result from covalent bonds are called bonds are called MOLECULESMOLECULES

• ** In general, the more chemical bonds a ** In general, the more chemical bonds a molecule has the more energy it contains molecule has the more energy it contains

SHARING IS CARING!SHARING IS CARING!

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MIXTURESMIXTURES• Water is not always pure. It is often found as part Water is not always pure. It is often found as part

of a mixture. of a mixture. • A mixture is a material composed of A mixture is a material composed of TWO OR TWO OR

MORE ELEMENTS OR COMPOUNDS THAT ARE MORE ELEMENTS OR COMPOUNDS THAT ARE PHYSICALLY MIXEDPHYSICALLY MIXED– Ex: salt & pepper mixed, sugar and sand – Ex: salt & pepper mixed, sugar and sand – can can

be easily separated be easily separated

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SOLUTIONSOLUTIONTwo parts:Two parts:

• SOLUTE – SOLUTE – SUBSTANCE THAT IS BEING SUBSTANCE THAT IS BEING DISSOLVED (SUGAR / SALT)DISSOLVED (SUGAR / SALT)

• SOLVENTSOLVENT - the substance in which the - the substance in which the solute dissolvessolute dissolves

• Materials that do not dissolve are known as Materials that do not dissolve are known as SUSPENSIONSSUSPENSIONS. . – Blood is the most common example of a Blood is the most common example of a

suspension. suspension. – Cells & other particles remain in suspension.Cells & other particles remain in suspension.

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FORMULAFORMULA

• The chemical symbols and numbers The chemical symbols and numbers that compose a compound ("that compose a compound ("reciperecipe")")

• Structural FormulaStructural Formula – Line drawings of – Line drawings of the compound that shows the the compound that shows the elements in proportion and how they elements in proportion and how they are bondedare bonded

• Molecular FormulaMolecular Formula – the ACTUAL – the ACTUAL formula for a compoundformula for a compound

CC22HH66OO

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ACIDS & BASESACIDS & BASES• Acids: always (almost) begin with "H" Acids: always (almost) begin with "H"

because of the excess of H+ ions because of the excess of H+ ions (hydrogen)(hydrogen)

– Ex: lemon juice (6), stomach acid (1.5), acid Ex: lemon juice (6), stomach acid (1.5), acid rain (4.5), normal rain (6)rain (4.5), normal rain (6)

Facts about AcidsFacts about Acids• Acids turn litmus paper Acids turn litmus paper BLUEBLUE and usually and usually

taste taste SOURSOUR. . • You eat acids daily (coffee, vinegar, soda, You eat acids daily (coffee, vinegar, soda,

spicy foods, etc…) spicy foods, etc…)

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ACIDS & BASESACIDS & BASES• Bases: always (almost) end with -OH Bases: always (almost) end with -OH

because of the excess of hydroxide ions because of the excess of hydroxide ions (Oxygen & Hydrogen)(Oxygen & Hydrogen)– EX: oven cleaner, bleach, ammonia, sea water, EX: oven cleaner, bleach, ammonia, sea water,

blood, pure waterblood, pure water

Facts about BasesFacts about Bases

• Bases turn litmus Bases turn litmus BLUEBLUE. .

• Bases usually feel Bases usually feel SLIPPERYSLIPPERY to touch and to touch and taste taste BITTERBITTER. .

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Neutralization Reactions Neutralization Reactions

• When an acid reacts with a base to When an acid reacts with a base to produce a salt and water.produce a salt and water.

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pH SCALEpH SCALE• measures degree of measures degree of

substance alkalinity or substance alkalinity or acidityacidity

• Ranges from Ranges from 0 to 140 to 14

• 0 – 5 strong acid0 – 5 strong acid• 6-7 neutral6-7 neutral• 8-14 strong base8-14 strong base

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• The goal of the body is to maintain The goal of the body is to maintain HOMEOSTASIS (neutrality)HOMEOSTASIS (neutrality) – to do this – to do this when pH is concerned, we add weak acids when pH is concerned, we add weak acids & bases to prevent sharp changes in pH. & bases to prevent sharp changes in pH.

• These are called These are called BUFFERSBUFFERS

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Elements in Living Organisms

• The most common elements found in living organisms include:

–Carbon (C)–Oxygen (O)–Nitrogen (N)–Hydrogen (H)–Phosphorus (P)–Sulfur (S)

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Periodic Table of the Elements (excerpt)

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Biochemistry: where chemistry and biology meet head-on

• Living things require millions of chemical reactions within the body, just to survive.

• Metabolism = all the chemical reactions occurring in the body.

• Organic molecules: – usually associated with living things. – always contain CARBON.– are “large” molecules, with many atoms– always have covalent bonds (share electrons)

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Plant Metabolism

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Primary Metabolites

• Primary metabolites are compounds that are commonly produced by all plants and that are directly used in plant growth and development.

• The main primary metabolites are carbohydrates,lipids, proteins, and nucleic acids.

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Macromolecules of Cells

• Macro = large

• 4 types of macromolecules in cellular biology

1. Carbohydrates2. Lipids3. Proteins

4. Nucleic Acids (DNA & RNA)

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Macromolecule #1: Carbohydrates

• Sugars and groups of sugars

• Purposes: energy and structure

• Includes three types:– Monosaccharide (1 sugar – quick energy)– Disaccharide (2 sugars – short storage)– Polysaccharide (many sugars – energy

long storage & form structures)

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Carbohydrates

• Carbohydrates are the sugars made up of glucose and its isomers

• Carbohydrates come in many different sizes:• Monosaccharides made up of one sugar unit

(glucose or fructose)• Disaccharides made up of two sugar units

(sucrose is a glucose and a fructose)• Polysaccharides are polymers made up of more

than two sugar units

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Monosaccharides (simple sugars) Monosaccharides (simple sugars)

• all have the formula C6 H12 O6 all have the formula C6 H12 O6

• all have a single ring structure all have a single ring structure – (glucose is an example) (glucose is an example)

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Disaccharides (double sugars) Disaccharides (double sugars)

• all have the formula C12 H22 O11 all have the formula C12 H22 O11

• sucrose (table sugar) is an example sucrose (table sugar) is an example

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Harvesting Sucrose

Sugar Cane Maple Syrup

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Refining Sucrose

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Macromolecule #1: Carbohydrates• Polysaccharide Examples:

– Glycogen—glucose polymer stored for future energy needs. Found in liver, muscle and sperm, etc.

– Cellulose—glucose polymer used to form fibers for plant structures. Humans can’t digest (fiber). Most abundant organic molecule.

– Chitin—glucose polymer for exoskeletons of some crustaceans & insects.

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Polysaccharides

• Structural polysaccharides are used to support plants

• Storage polysaccharides are used to store energy for later use by the plant

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Structural Polysaccharides

• The most common structural polysaccharide in plants is cellulose. It makes up 40 to 60% of the cell wall. It is also the most common polymer on earth

• Cellulose is extremely strong due to its chemical organization. It is made of a long chain of beta-glucose molecules – 100 to 15,000 glucose molecules

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CARBOHYDRATESCARBOHYDRATES

• Living things use carbohydrates as a key Living things use carbohydrates as a key source of source of ENERGYENERGY! !

• Plants use carbohydrates for structure Plants use carbohydrates for structure ((CELLULOSECELLULOSE) ) – include sugars and complex carbohydrates include sugars and complex carbohydrates

(starches) (starches) – contain the elements carbon, hydrogen, and contain the elements carbon, hydrogen, and

oxygen (the hydrogen is in a 2:1 ratio to oxygen (the hydrogen is in a 2:1 ratio to oxygen) oxygen)

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Polysaccharides Polysaccharides

• Formed of three or more simple sugar units Formed of three or more simple sugar units • Glycogen - animal starch stored in liver & muscles Glycogen - animal starch stored in liver & muscles • Cellulose - indigestible in humans - forms cell walls Cellulose - indigestible in humans - forms cell walls • Starches - used as energy storage Starches - used as energy storage

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Cotton Boll – Pure Cellulose

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Polysaccharides

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Polysaccharides

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Gluey Polysaccharides • Pectins are mainly polymers of galacturonic acid.• Hemicelluloses are highly variable and are not

related to cellulose.• Grass hemicelluloses are high in xylose, with

small amounts of arabinose, galactose, and urionic acids. But pea family (Fabaceae) are high in arabinose, galactose and urionic acid, but low in xylose.

• Some of the most interesting hemicelluloses are not actually used structurally, but rather are exuded from stems, leaves, roots, or fruits in a sticky mixture called a gum

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Pectin and Hemicellulose

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Gum Arabic from Acacia senegal

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Storage Polysaccharides

• The most important storage polysaccharides are amylose and amylopectin. Amylose is a long chain of alpha-glucose, several hundred to several thousand molecules long. Amylopectin is more complex, often made up of 50,000 molecules.

• These two polymers are both used in making starch grains. Most starch grains are about 20% amylose and 80% amylopectin, but this varies with the plant.

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Inulin – another storage carbohydrate

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Jerusalem artichoke

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How are complex How are complex carbohydrates formed and carbohydrates formed and

broken down?broken down?

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Dehydration Synthesis Dehydration Synthesis

• Combining simple molecules to form a more Combining simple molecules to form a more complex one with the complex one with the removal of waterremoval of water – ex. monosaccharide + monosaccharide ----> ex. monosaccharide + monosaccharide ---->

disaccharide + waterdisaccharide + water– (C6H12O6 + C6H12O6 ----> C12H22O11 + H2O(C6H12O6 + C6H12O6 ----> C12H22O11 + H2O

• Polysaccharides are formed from repeated Polysaccharides are formed from repeated dehydration syntheses of water dehydration syntheses of water – They are the stored extra sugars known as starchThey are the stored extra sugars known as starch

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Hydrolysis Hydrolysis

• Addition of Addition of WATERWATER to a compound to to a compound to SPLITSPLIT it into smaller subunits it into smaller subunits

–(also called chemical digestion) (also called chemical digestion)

–ex. disaccharide + H2O ---> ex. disaccharide + H2O ---> monosaccharide + monosaccharidemonosaccharide + monosaccharide

C12 H22 O11 + H2 O ---> C6 H12 O6 + C6 H12 C12 H22 O11 + H2 O ---> C6 H12 O6 + C6 H12 O6O6

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Macromolecule #2: Lipids• Insoluble in water (think oil & water)

4 types: – 1-triglycerides (fats & oils)

• (long-term energy storage, insulation)– 2-phospholipids (primary component of cell

membrane)– 3-steroids (cell signaling)

• cholesterol molecules modified to form sex hormones. (e.g. testosterone, estrogen, etc.)

– 4-waxes (protection, prevents water loss)• Used mainly by plants, but also bees, some furry

animals and humans.

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Triglycerides

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Phospholipids

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Steroids

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Waxes

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Lipids (Fats)Lipids (Fats)• Fats, oils, waxes, steroids Fats, oils, waxes, steroids • Chiefly function in Chiefly function in energy storage, protection, and energy storage, protection, and

insulation insulation • Contain carbon, hydrogen, and oxygen but the Contain carbon, hydrogen, and oxygen but the

H:O is not in a 2:1 ratio H:O is not in a 2:1 ratio • Tend to be Tend to be largelarge molecules -- an example of a molecules -- an example of a

neutral lipid is below neutral lipid is below

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• Neutral lipids are formed from the union of Neutral lipids are formed from the union of one one glycerol molecule and 3 fatty acids glycerol molecule and 3 fatty acids

• 3 fatty acids + glycerol ----> neutral fat (lipid) 3 fatty acids + glycerol ----> neutral fat (lipid) • Fats -- found chiefly in Fats -- found chiefly in animalsanimals • Oils and waxes -- found chiefly in Oils and waxes -- found chiefly in plantsplants • Oils are liquid at room temperature, waxes are Oils are liquid at room temperature, waxes are

solids solids • Lipids along with proteins are key components of Lipids along with proteins are key components of

cell membranescell membranes • Steroids are special lipids used to build many Steroids are special lipids used to build many

reproductive hormones and cholesterolreproductive hormones and cholesterol

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Oils• Oils occur in all parts of a plant, but are most

common in seeds. Some seeds have so much oil that it can be commercially harvested. The most commonly used oils are cotton, sesame, safflower, sunflower, olive, coconut, peanut, corn, castor bean, and soybean oils.

• The most common seed oil fatty acids are oleic acid (one double bond), linoleic acid (two double bonds), and linolenic acid (three double bonds). Linoleic and linolenic are essential fatty acids – we can’t make them ourselves.

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Olive Oil

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Waxes• Waxes are complex mixtures of fatty acids linked

to long-chain alcohols. Waxes comprise the outermost layer of leaves, fruits, and herbaceous stems and are called EPICUTICULAR waxes. Waxes embedded in the cuticle of the plant are cuticular waxes. Cutin is another wax in the cuticle and it makes up most of the cuticle. Suberin is a similar wax that is found in cork cells in bark and in plant roots. Both help prevent water loss by the plant.

• Structures of waxes vary depending on which plant produced them.

• Waxes are usually harder and more water repellant than other fats.

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Bayberry Wax

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Jojoba Wax

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Macromolecule #3: Proteins• The building blocks of proteins are AMINO

ACIDS. There are only 20 types of Amino Acids.

• There are millions of different proteins, and they are all built from different combinations of the 20 amino acids.

• Amino acids join together to form peptides, polypeptides, and polypeptide chains.

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Macromolecule #3: Proteins• Probably the most complicated of all biological

molecules. • Serve the most varied purposes, including:

Support structural proteins (e.g., keratin, collagen)

Enzymes speed up chemical reactions

Transport cell membranes channels, transporters in blood

(e.g., Hemoglobin)

Defense antibodies of the immune system

Hormones cell signaling (e.g., insulin)

Motion contractile proteins (e.g., actin, myosin)

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CollagenCollagen

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Antibodies

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Cellular Transport

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actin & actin & myosin fibers myosin fibers

in musclesin muscles

Motion

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PROTEINSPROTEINS• contain the elements carbon, hydrogen, contain the elements carbon, hydrogen,

oxygen, and nitrogen oxygen, and nitrogen

• composed of MANY amino acid subunitscomposed of MANY amino acid subunits

• It is the arrangement of the amino acid that It is the arrangement of the amino acid that forms the primary structure of proteins. forms the primary structure of proteins.

• The basic amino acid form has a The basic amino acid form has a carboxyl carboxyl groupgroup on one end, a on one end, a methyl groupmethyl group that only that only has one hydrogen in the middle, and a has one hydrogen in the middle, and a amino groupamino group on the other end. on the other end.

• Attached to the methyl group is a Attached to the methyl group is a RR groupgroup. .

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AN R GROUP IS ANY GROUP AN R GROUP IS ANY GROUP OF ATOMS – THIS CHANGES OF ATOMS – THIS CHANGES THE PROPERTIES OF THE THE PROPERTIES OF THE PROTEIN!PROTEIN!

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FUNCTIONAL GROUPSFUNCTIONAL GROUPS

• There are certain groups of atoms that are There are certain groups of atoms that are frequently attached to the organic molecules frequently attached to the organic molecules we will be studying, and these are called we will be studying, and these are called functional groupsfunctional groups. .

• These are things like These are things like hydroxyl groupshydroxyl groups which form which form alcoholsalcohols, , carbonyl groupscarbonyl groups which form which form aldehydesaldehydes or or ketonesketones, , carboxyl groupscarboxyl groups which form which form carboxylic carboxylic acidsacids, and , and amino groupsamino groups which form which form aminesamines. .

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Major Protein Functions Major Protein Functions

• Growth and repair Growth and repair

• Energy Energy

• Buffer -- helps keep body pH Buffer -- helps keep body pH constant constant

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Dipeptide Dipeptide • formed from two amino acid subunits formed from two amino acid subunits

• Formed by the process of Formed by the process of Dehydration Dehydration SynthesisSynthesis

• amino acid + amino acid ----- dipeptide + amino acid + amino acid ----- dipeptide + waterwater

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Hydrolysis of a dipeptide Hydrolysis of a dipeptide

• Breaking down of a dipeptide into amino Breaking down of a dipeptide into amino acidsacids

• dipeptide + H2O ---> aminoacid + amino dipeptide + H2O ---> aminoacid + amino acidacid

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Polypeptide (protein) Polypeptide (protein)

• composed of composed of three or morethree or more amino acids amino acids linked by synthesis reactions linked by synthesis reactions

• Examples of proteins include Examples of proteins include insulin, insulin, hemoglobin, and enzymes. hemoglobin, and enzymes.

• ** There are an extremely large number of ** There are an extremely large number of different proteins. different proteins.

• The bases for variability include differences The bases for variability include differences in the number, kinds and sequences of in the number, kinds and sequences of amino acids in the proteins amino acids in the proteins

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Proteins

• Proteins make up most of the remaining biomass of living plant cells.

• A protein consists of one or more polypeptides made up of amino acids. Plants make amino acids from the products of photosynthesis through a very complex process involving the acquisition of N, usually in the form of NH4, and involving the use of large amounts of energy, in the form of ATP and NADPH.

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Structural Proteins

• Structural proteins make up 2 to 10% of the cell wall in plants. Expansins help increase the surface area of cell walls. Extensins help protect or repair damaged cell walls. The plant cell membrane is about 50% structural proteins.

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Storage Proteins

• Storage proteins are used mostly in seeds and are used as source of nutrition for the early development of seedlings. Storage proteins used in seeds vary considerably between plant species. Corn produces a storage protein called ZEIN. Wheat produces a storage protein called GLIADIN

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Macromolecule #4: Nucleic Acids• Nucleotides: building blocks of nucleic acids.

– Each nucleotide contains • (a) phosphate molecule, • (b) nitrogenous base, and • (c) 5-carbon sugar

• Several types of nucleic acids, including:– DNA: deoxyribonucleic acid

• Genetic material, double stranded helix– RNA: ribonucleic acid

• Genetic material, single stranded– ATP: adenosine triphosphate

• High energy compound

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The 4th type of biochemical

macromolecules are the NUCLEIC ACIDSThe types of Nucleic Acids

we will study are:–DNA (DeoxyriboNucleic Acid)

–RNA (RiboNucleic Acid)

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NUCLEIC ACIDS

THERE ARE 2 TYPES OF THERE ARE 2 TYPES OF NUCLEIC ACIDSNUCLEIC ACIDS

DNADNA RNARNA

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DNADNA

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“DNA” is short for DeoxyriboNucleic

Acid• Now you know why they just call it DNA!

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Nucleic Acids

1) DNA• Is our genetic material. Chromosomes are

made of DNA.• Chromosomes contain the “recipes” to make

proteins for your body.

2) RNA• Reads the DNA “protein recipes” and makes

the proteins for your body.

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NUCLEIC ACIDS

Nucleic Acids are chains Nucleic Acids are chains (polymers) made of (polymers) made of

monomers. Nucleic acids are monomers. Nucleic acids are made up of made up of

Which are nitrogen bases…Which are nitrogen bases…something we will learn more something we will learn more

about when we study DNAabout when we study DNA

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The shape of a nucleic acid is:

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Nucleotide Structure

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Nucleic Acids

Each nucleic acid is made up Each nucleic acid is made up of…of…

THINK: “PONCH”THINK: “PONCH”

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Nucleic acidsThe nucleic acids in food are not considered a substance that the body uses to gain

energy.

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ENERGY So…So…

BIG 4 MACROMOLECULES

Number of Calories it provides/g

Carbohydrates 4

Proteins 4

Lipids 9

Nucleic Acids 0

TEST: TEST: Are you smart? If you eat a sandwhich with 46 grams of carbs and 24 grams of protein and 10 grams of fat, how much energy

will you gain?

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NUCLEIC ACIDSNUCLEIC ACIDS

• in all cellsin all cells

• composed of composed of NUCLEOTIDESNUCLEOTIDES

• store & transmit store & transmit heredity/geneticheredity/genetic information information

• Nucleotides consist of 3 parts:Nucleotides consist of 3 parts:

• 1. 1. 5-Carbon Sugar5-Carbon Sugar

• 2. 2. Phosphate GroupPhosphate Group

• 3. 3. Nitrogenous BaseNitrogenous Base

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Nucleic Acids• The most complex

biological polymers are the nucleic acids that make up RNA and DNA. The basic content of bases (adenine, thymine, guanine and cytosine) are similar in all plants

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DNA (deoxyribonucleic acid) DNA (deoxyribonucleic acid) • contains the genetic code of instructions contains the genetic code of instructions

that direct a cell's behavior through the that direct a cell's behavior through the synthesis of proteins synthesis of proteins

• found in the chromosomes of the nucleus found in the chromosomes of the nucleus (and a few other organelles) (and a few other organelles)

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RNA (ribonucleic acid) RNA (ribonucleic acid) • directs cellular protein synthesis directs cellular protein synthesis

• found in ribosomes & nucleoli found in ribosomes & nucleoli

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CHEMICAL REACTIONS CHEMICAL REACTIONS

• a process that a process that changeschanges one set of one set of chemicals into another set of chemicalschemicals into another set of chemicals

• REACTANTSREACTANTS – elements or compounds – elements or compounds that enter into a chemical reactionthat enter into a chemical reaction

• PRODUCTSPRODUCTS – elements or compounds that – elements or compounds that are produced in a chemical reactionare produced in a chemical reaction

• Chemical reactions always involve the Chemical reactions always involve the breaking of bonds in reactantsbreaking of bonds in reactants and the and the formation of new bonds in products.formation of new bonds in products.

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• In a reaction, energy is either In a reaction, energy is either TAKEN IN (TAKEN IN (ENDOTHERMICENDOTHERMIC) or ) or GIVEN OFF (GIVEN OFF (EXOTHERMICEXOTHERMIC) )

• Can you think of an everyday Can you think of an everyday example of each type of reaction?example of each type of reaction?

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Enzymes and Enzyme Action Enzymes and Enzyme Action • catalystcatalyst: inorganic or organic substance : inorganic or organic substance

which which speeds up the ratespeeds up the rate of a chemical of a chemical reaction without entering the reaction itself reaction without entering the reaction itself

• enzymesenzymes: organic catalysts made of protein : organic catalysts made of protein

• most enzyme names end in -ase most enzyme names end in -ase

• enzymes lower the energy needed to start a enzymes lower the energy needed to start a chemical reaction. (chemical reaction. (activation energyactivation energy) )

• begin to be destroyed above 45øC. (above begin to be destroyed above 45øC. (above this temperature all proteins begin to be this temperature all proteins begin to be destroyed) destroyed)

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It is thought that, in order for an enzyme to affect the rate of It is thought that, in order for an enzyme to affect the rate of a reaction, the following events must take place.a reaction, the following events must take place.

1.1. The enzyme must form a The enzyme must form a temporary associationtemporary association with the with the substance or substances whose reaction rate it affects. substance or substances whose reaction rate it affects. These substances are known as These substances are known as substratessubstrates. .

2.2. The association between enzyme and substrate is The association between enzyme and substrate is thought to form a thought to form a close physical associationclose physical association between the between the molecules and is called the molecules and is called the enzyme-substrate complexenzyme-substrate complex. .

3.3. While the enzyme-substrate complex is formed, enzyme While the enzyme-substrate complex is formed, enzyme action takes place. action takes place.

4.4. Upon completion of the reaction, the enzyme and Upon completion of the reaction, the enzyme and product(s) product(s) separateseparate. The enzyme molecule is now . The enzyme molecule is now available to form additional complexes. available to form additional complexes.

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Enzymes

• Enzymes catalyze biochemical reactions. Most proteins in living cells are enzymes.

• Pure enzymes that maintain their activity when removed from plants are commercially important to us.

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Papaya – Papain and Chymopapain

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Pineapple - Bromelain

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How do enzymes work?How do enzymes work?

• substratesubstrate: molecules upon which an : molecules upon which an enzyme acts enzyme acts

• the enzyme is shaped so that it can only the enzyme is shaped so that it can only lock up with a lock up with a specific substratespecific substrate molecule molecule

enzymeenzyme

substrate -------------> productsubstrate -------------> product

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"Lock and Key Theory"

• each enzyme is specific for each enzyme is specific for one and ONLY one and ONLY one substrateone substrate (one lock - one key) (one lock - one key)

• this theory has many weaknesses, but it this theory has many weaknesses, but it explains some basic things about enzyme explains some basic things about enzyme functionfunction

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Factors Influencing Rate of Enzyme Factors Influencing Rate of Enzyme Action Action

1. 1. pH pH - the optimum (best) in most living things - the optimum (best) in most living things is close to 7 (neutral)is close to 7 (neutral)

• high or low pH levels usually slow enzyme high or low pH levels usually slow enzyme activityactivity

• A few enzymes (such as gastric protease) A few enzymes (such as gastric protease) work best at a pH of about 2.0work best at a pH of about 2.0

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2. 2. TemperatureTemperature - strongly influences enzyme - strongly influences enzyme activity activity

• optimum temperature for maximum enzyme optimum temperature for maximum enzyme function is usually about 35-40 C. function is usually about 35-40 C.

• reactions proceed slowly below optimal reactions proceed slowly below optimal temperatures temperatures

• above 45 C most enzymes are denatured above 45 C most enzymes are denatured (change in their shape so the enzyme active (change in their shape so the enzyme active site no longer fits with the substrate and the site no longer fits with the substrate and the enzyme can't function)enzyme can't function)

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3. 3. ConcentrationsConcentrations of Enzyme and of Enzyme and Substrate Substrate

• ** When there is a fixed amount of ** When there is a fixed amount of enzyme and an excess of substrate enzyme and an excess of substrate molecules -- the rate of reaction will molecules -- the rate of reaction will increase to a point and then level off. increase to a point and then level off.

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Plant Secondary Metabolites• Plants make a variety of less widely distributed

compounds such as morphine, caffeine, nicotine, menthol, and rubber. These compounds are the products of secondary metabolism, which is the metabolism of chemicals that occurs irregularly or rarely among plants, and that have no known general metabolic role in plants.

• Secondary metabolites or secondary compounds are compounds that are not required for normal growth and development, and are not made through metabolic pathways common to all plants.

• Most plants have not been examined for secondary compounds and new compounds are discovered almost daily.

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Plant Secondary Metabolites

• Secondary compounds are grouped into classes based on similar structures, biosynthetic pathways, or the kinds of plants that make them. The largest such classes are the alkaloids, terpenoids, and phenolics.

• Secondary compounds often occur in combination with one or more sugars. These combination molecules are known as glycosides. Usually the sugar is a glucose, galactose or rhamnose. But some plants have unique sugars. Apiose sugar is unique to parsley and its close relatives.

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Functions of Secondary Compounds

• The most common roles for secondary compounds in plants are ecological roles that govern interactions between plants and other organisms.

• Many secondary compounds are brightly colored pigments like anthocyanin that color flowers red and blue. These attract pollinators and fruit and seed dispersers.

• Nicotine and other toxic compounds may protect the plant from herbivores and microbes.

• Other secondary compounds like rubber and tetrahydrocannabinil (THC) from cannabis plants have no known function in plants.

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Alkaloids• Alkaloids generally include alkaline substances

that have nitrogen as part of a ring structure. More than 6500 alkaloids are known and are the largest class of secondary compounds. They are very common in certain plant families, especially:

• peas – Fabaceae • sunflower – Asteraceae• poppy – Papaveraceae • tomato – Solanaceae • dogbanes – Apocynaceae• milkweeds - Asclepiadaceae• citrus – Rutaceae.

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Terpenoids

• Terpenoids are dimers and polymers of 5 carbon precursors called isoprene units (C5 H8).

• Terpenoids often evaporate from plants and contribute to the haze we see on hot sunny days. They are expensive to make; they often take 2% of the carbon fixed in photosynthesis; carbon that could otherwise be used for sugars.

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Phenolics• Compounds that contain a fully unsaturated six

carbon ring linked to an oxygen are called phenolics.

• Salicylic acid (basic part of aspirin) is a simple phenol.

• Myristicin is a more complex phenol that provides the flavor of nutmeg.

• Flavonoids are complex phenolics. They are often sold in health food stores as supplements to vitamin C. The most commonly available flavonoid is rutin from buckwheat.

• Anthocyanins are a type of flavonoid that give flowers red and blue pigments.

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More Phenolics

• Some phenolics form polymers.• Tannins are astringent to the taste. They give

dryness (astringency) to dry wines. They can also be used to tan leather. They often give water a tea-colored look. Tannins are common in pines and oaks.

• Lignin is a major structural component of wood. The exact structure of lignin is complex and not known.

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Minor Secondary Metabolites• Mustard oil glycosides are nitrogen-sulfur containing

compounds that occur in cabbage, broccoli, horseradish, watercress and other members of the mustard family (Brassicaceae). They give the group its characteristic taste and odor.

• Cyanogenic glycosides occur in several families of plants, but are especially common in roses (Rosaceae) and peas (Fabaceae). They are sugar containing compounds that release cyanide gas when hydrolyzed.

• Cardiac glycosides effect vertebrate heart rate. Especially common in milkweeds Asclepiadaceae.

• The parsley/carrot family Apiaceae is noted for having aromatic and poisonous 17 carbon polyacetylenes, though a few species have alkaloids like Coniium.

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Mustard Oil

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THE BIG PICTURETHE BIG PICTURE

Chemistry is essential for Chemistry is essential for life…life…