Biochemistry ReviewHuman Anatomy and Physiology Honors

WaterWater is a molecule

that is essential to life as we know it here on Earth.

It is a component of all living things and serves many functions.

WaterA cell is 70-90% water.

Many of the chemical reactions that are important to life occur in water.

Water has many unique properties due to the nature of its molecular composition. We will discuss 4 of these properties.

Properties of WaterHigh specific heat: It requires a lot of

heat energy to raise the temperature of water one degree Celsius. Important in regulating the temperature of living things.

High heat capacity: It requires a long period of time for water to gain or lose heat energy. Important in regulating temperature, important to aquatic organisms.

Properties of WaterUniversal Solvent: Many materials,

organic and inorganic will dissolve in water. Important in water's role as a transport medium for living things. Animal blood and the sap of plants are

primarily are composed of water carrying other dissolved materials.

Properties of WaterWater Expands as It Freezes: The solid

form of water is less dense than the liquid, and therefore ice floats! This is important in aquatic

environments because they will always freeze from the top surface down. The ice usually creates an insulating

layer from the colder air temperature, allowing the organisms below the surface of the ice to survive.

Properties of WaterHowever, this property is also

dangerous to organism with soft tissues. When the water inside their cells

freeze, it expands and destroys the cells.

Frost bite in humans is a result of this property.

Organic ChemistryOrganic compounds contain at

least one carbon atom and are found in living thingsException: carbon dioxide

Inorganic compoundsDo not contain carbonWater, salts, and many acids and bases

Chemical ElementsThe most common chemical elements

found in living things are:Carbon (C)Oxygen (O)Hydrogen (H)Nitrogen (N)

These 4 elements make up almost 90% of the mass of living things

Chemical ElementsOther important Elements

Calcium (teeth/bones)Iron (hemoglobin)Sodium (important for nerve impulses)

CarbonCarbon has 4 valence electrons it its

outer shellTherefore carbon has a strong tendency to fill its outer shell to 8 electrons by forming covalent bonds with other atoms, particularly hydrogen, oxygen, and nitrogen.

CarbonThe four single bonds one carbon atom makes

(show here bonded to hydrogen) form the four corners of a tetrahedron.

Structural formula

Ball-and-Stick Model

Space-filling Model

CarbonThe 4 electrons in the outermost shell of

carbon allow it to form complex structures (e.g., long, branched chains, ring structures).This is a major reason why carbon is the

structural backbone of organic compounds.

A compound composed only of carbon and hydrogen is called a hydrocarbon.

CarbonCarbon

molecules can even form double or triple bonds with other carbon molecules, or other molecules such as oxygen.

Monomers vs. PolymersMost of the compounds produced

and used by our cells are actually long chains of molecules strung together

These long chains are called polymers.

Monomers vs. PolymersIf you were to take a polymer and break it

down into its component parts, each piece would be a monomer, the single repeating unit of that polymer.

Two monomers together make up a dimer.

There are many different types of polymers; the type of polymer depends on the type of monomers used to make that polymer.

CarbohydratesAll carbohydrates are composed of

carbon, hydrogen, and oxygen in a 1:2:1 empirical ratio.

The general empirical formula for a carbohydrate is CH2O.If a carbohydrate has 5 carbons atoms, what

would be its empirical formula? If a carbohydrate has 12 hydrogen atoms, what

would be its empirical formula?

Most carbohydrates end with the suffix -ose (maltose, galactose, glucose)

CarbohydratesCarbohydrate

s serve as an important energy source for both plants and animals.

CarbohydratesPlants can create carbohydrates

from water and CO2 and energy from the sunThis process is called Photosynthesis6CO2 + 6H2O + Energy -> C6H12O6 + 6O2

CarbohydratesAnimals break carbohydrates made

by plants down and use them for energyThis process is called Cellular RespirationC6H12O6 + 6O2 -> 6CO2 + 6H2O + Energy

Functions of CarbohydratesProvide an energy source: Energy is

stored in the chemical bonds within the molecule and released during cellular respiration.

Usually simple sugars such as glucose and fructose.

Functions of CarbohydratesProvide energy storage:

Plants store energy in a complex carbohydrate form called starch (amylose).

Functions of CarbohydratesProvide energy storage:

Animals store energy in a complex carbohydrate in their muscle tissue and liver in a form called glycogen.

Functions of CarbohydratesStructural Building Material:

Plants build their cell walls of a complex carbohydrate material called cellulose

Functions of CarbohydratesAnimals such as arthropods build their exoskeletons of a complex carbohydrate called chitin.

Chitin is also found in the cell walls of Fungi.

Carbohydrates Carbohydrates can be arrainged as

monomers, dimers or polymers.A monomer of carbohydrate is called

a monosaccharide. (single sugar)A dimer of carbohydrate is called a disaccharide.

A polymer of carbohydrate is called a polysaccharide.

Monosaccharides are the building blocks for all other polysaccharides!

Glucose and FructoseGlucose and Fructose are Isomers of each

other

Glucose FructoseWhat is the empirical formula for each of these molecules?

DisaccharidesDisaccharides are formed by joining two

monosaccharides.Table sugar, sucrose, is a disaccharide

made up of glucose and fructoseMaltose is a disaccharide made up of

two glucose monomers. It is used in brewing.

Lactose is made up of glucose and galactose. It is the carbohydrate found in milk.

Polysaccharides Polysaccharides are formed by joining

multiple monosaccharides into a long chain of sugars. Examples:Amylose (starch storage in plants) Glycogen (starch storage in animals)Cellulose (structural support in plants)Chitin (structural support in insects and

fungi)

LipidsLipids are complex molecules

composed of carbon, hydrogen, and oxygen.

Most lipids are non-polar and are hydrophobic because they contain hydrocarbon chains.

If there are double or triple bonds in the hydrocarbon chain the lipids are said to be “unsaturated”

Functions of LipidsEnergy storage: Fats and oils.Waterproofing: Waxes and oilsInsulation: Fat layers (blubber)Cushioning: Fat layers (soles of your

feet)Regulating metabolic processes:

SteroidsBuilding component of cell

membranes: Phospholipids

Representative Lipids Found in the BodyNeutral fats – found in subcutaneous

tissue and around organsPhospholipids – chief component of cell

membranesSteroids – cholesterol, bile salts,

vitamin D, sex hormones, and adrenal cortical hormones

Fat-soluble vitamins – vitamins A, E, and K

Lipoproteins – transport fatty acids and cholesterol in the bloodstream

TriglyceridesA triglyceride is

composed of an alcohol called glycerol covalently bonded to three fatty acid molecules.

TriglyceridesExcess energy available from

food/photosynthesis is stored as triglycerides

Can be broken down later to yield energy when needed

Fats and oils contain twice as many energy stored per unit of weight as carbohydrates

Saturated vs. Unsaturated FatsWhen double bonds form in hydrocarbon

chains it causes them to bend. In unsaturated fats this prevents the

molecules from being able to “stack” or “pack” themselves tightly, thus they remain in a liquid state at room temperature such as oils.

Saturated vs. Unsaturated FatsIf the hydrocarbon chains are saturated,

the chains are straight and pack themselves close together forming a solid at room temperature (animal fat, butter, tallow, lard).

ProteinsProteins are composed primarily of

carbon, hydrogen, nitrogen, and oxygen. Some contain sulfur.

They are all composed of structural monomers called amino acids.

Their differences from organism to organism is due to differences in the DNA which contains the instructions for their formation. Ex. Eye color, Blood type

Functions of ProteinsStructure: Building structural

components of organismsExamples: collagen, elastin, keratin, microtubules, microfilaments)

Functions of ProteinsRegulation of

metabolic processes: Hormones (insulin)

Functions of ProteinsCarrying out of metabolic processes: Enzymes

Membrane component: Carrier proteins, Protein pumps, Transport of materials through membrane phospholipid layers

Functions of ProteinsSelf and non-self recognition: Major

histocompatibility complexes (Tissue rejection, immune responses).

Membrane receptors: Hormone receptors and neurotransmitter receptors.

Levels of Protein StructureProteins are very complex molecules

and their shape or structure determines their function.

Most proteins have 4 levels of folding, primary, secondary, tertiary and quaternary, so that the final protein is a complex folded chain of molecules which can provided many structural functions.

If any level of structure is changed it can create faulty or nonfunctioning proteins!

Levels of Protein StructureThe Primary Level is

determined by the number of amino acids, the type of amino acids, and the sequence of the amino acids in the polypeptide chain.

Levels of Protein StructureThe Secondary Level is due to interactions

between amino acids in the chain.This is usually due to hydrogen bonding

between oxygen and hydrogen atoms in different amino acids.

Levels of Protein StructureTwo general forms

are created.Alpha helix, a spiral

structure, common in globular proteins

Beta pleated sheet structure, common in structural proteins.

Levels of Protein StructureThe Tertiary Level is due

to the “folding over” of the alpha helical or beta pleated sheet structure on itself.

This configuration is due to interactions between amino acid side groups, such as:hydrogen bonding hydrophobic

interactions ionic bonding

interactionsdisulfide bridges

Levels of Protein StructureThe Quaternary

Level of structure is due to the interactions of more than one polypeptide chain to form the complete, functional protein.

Examples:Hemoglobin, used to

bind oxygen to red blood cells for transport.

Collagen, a structural protein used through the body.

Levels of Protein Structure

When Protein folding goes wrong…Sickle-cell anemia is due to a

change in protein structure at the primary level.

Once the change is made at the primary level it has an effect on all subsequent levels.

When Protein folding goes wrong…This results in the formation of an

irregular hemoglobin protein that cause the molecule to take on an irregular form which in turns affects its normal function and the shape of the erythrocytes (red blood cells).

Nucleic AcidsNucleic acids such and DNA and RNA serve

as the blueprints for proteins – the instructions for arraigning amino acids into a primary protein sequence.

Nucleic acids are composed of carbon, hydrogen, oxygen, nitrogen, and phosphorous

Nucleic AcidsThey are carriers of the genetic code

(recipe book for proteins)There are two types: DNA

(deoxyribonucleic acid) and RNA (ribonucleic acid)

Molecules responsible for heredityNucleic acids are again polymers. The monomer unit od a nucleic acids is a

nucleotide.

Nucleic AcidsThese monomers are composed of:

A monosaccharide (deoxyribose in DNA or ribose RNA)

A phosphate groupA nitrogenous base

Nucleic Acids: DNAThe nitrogenous bases found in DNA

are:Adenine AThymine TGuanine GCytosine C

Nucleic Acids: RNAThe nitrogenous bases found in RNA

are:Adenine AGuanine GCytosine CUracil U, which replaces thymine.

Complementary Base PairingWhen two strands of DNA

join to form the alpha helix, it is due to hydrogen bonding between the complimentary purine and pyrimidinde bases on each complimentary strand.

Adenine forms hydrogen bonds with Thymine.

Guanine forms hydrogen bonds with Cytosine.

This is called Complimentary Base Pairing.

DNA StructureThe strands begin to form a spiral due to the

hydrogen bonding of the complementary base pairs.

Comparing DNA and RNADNA bases

(A,T,G,C)Deoxyribose sugarOriginal

information for making proteins

One form or typeFound primarily in

the nucleus forms chromosomes during cell division

Large moleculeDouble Stranded

RNA bases (A,U,G,C)

Ribose sugarWorking copy for

making proteinsVariety of forms:

m-RNA, t-RNA, r-RNA

Found in nucleus and through the cell

Smaller moleculesSingle Stranded

pH pH is a measure of the acidity or basicity of

a solution. Acids have a pH of 0-7Bases have a pH of 7-14Neutral solutions have a pH of 7, right in

the middle between acidic and basic.When acids and bases of equal strength are

mixed, they cancel each other out; this is called Neutralization

Note: basic solutions are also sometimes called “alkaline”

pH Acids and bases can burn biological tissue

severely. Therefore the pH of various cellular fluids

in the body is tightly controlled in a system called acid-base homeostasis.

If a biological solution becomes to acidic, the body will work to make it more basic.

If a biological solution becomes to basic, the body will do the opposite.

Large differences, however, can overwhelm this process and be devastating.

pH Blood is actually slightly basic, with

a pH near 7.365. Gastric (stomach) fluids are highly acidic (pH 1).

Acid reflux occurs when gastric (stomach) fluid enters the esophagus (throat), causing burning and cell death, and thus the pain associated with acid-reflux disease.

[H3O+] pH Example

Acids

1 X 100 0 HCl 1 x 10-1 1 Stomach acid1 x 10-2 2 Lemon juice1 x 10-3 3 Vinegar1 x 10-4 4 Soda1 x 10-5 5 Rainwater1 x 10-6 6 Milk

Neutral 1 x 10-7 7 Pure water

Bases

1 x 10-8 8 Egg whites1 x 10-9 9 Baking soda1 x 10-10 10 Tums® antacid1 x 10-11 11 Ammonia

1 x 10-12 12 Mineral lime - Ca(OH)2

1 x 10-13 13 Drano®

1 x 10-14 14 NaOH

Adenosine Tri-Phosphate (ATP)ATP or Adenosine Tri-Phosphate is an

important molecule because it is the molecule which stores energy for chemical and mechanical processes in the body.

The energy in ATP is stored within the high energy phosphate bonds. If a phosphate bond is formed, energy is

stored. If a phosphate bond is broken energy is

released.ATP is a modified form of the nucleotide

Adenine.

Adenosine Tri-Phosphate (ATP)ATP is like a “rechargable battery”

because it can be recycled and used over and over again.

If the terminal phosphate-phosphate bond is broken, energy is released, and the resulting molecule is called Adenosine Di-Phosphate, or ADP.

ATP -> ADP + Pi + Energy

ADP + Pi + Energy -> ATP