BIOCHEMISTRY

Living things are made up of inorganic and organic compounds.

Compounds that do NOT contain both carbon and hydrogen are INORGANIC COMPOUNDS.

The principal inorganic compounds in living things are water, salts and inorganic acids and bases.

ORGANIC COMPOUNDS are compounds that contain both carbon and hydrogen.

WHAT IS THE MOST IMPORTANT INORGANIC COMPOUND FOR ALL

LIVING THINGS?

WRITE ITS CHEMICAL FORMULA

WATER H2OThe most important liquid in the world

You can live for a month without food but only 2 – 3 days without waterAll vegetation disappears without water

West Africa – the size of the US is becoming a dessert because of lack of rain

The Human Body is 80 – 90% water

Our water supply is NOT unlimited

Today we have about the same quantity of drinkable water that was available when Columbus set foot on our shores

Biochemistry – carbon based chemistry

Carbon is a unique element because of its remarkable ability to form covalent bonds that are strong and stable

The simplest compound that can be formed from carbon is methane CH4

The ability of carbon to combine with itself allows carbon atoms to form all kids of chain-like and ring-shaped molecules making the number of potential organic compounds almost infinite.

Carbon has the ability to form millions of different large and complex structures. No other element even comes close to matching carbon’s versatility

Most organic compounds occur naturally

Classes of organic molecules found in living things:

•carbohydrates

•proteins

•lipids

•Nucleic acids

Organic compounds can be used to assemble other molecules such as proteins, DNA, starch and fats.

The chemical energy stored in bonds can be used as an energy source for life processes.

Many of the molecules in living cells are so large that they are known as macromolecules, which means “giant molecules.” Macromolecules are made from thousands or even hundreds of thousands of smaller molecules.

Macromolecules are formed by a process known as polymerization - large compounds are built by joining smaller ones together.

The smaller units, or monomers, join together to form polymers.

The monomers in a polymer may be identical, like the links on a metal watch band, or the monomers may be different, like the beads in a multicolored necklace. The diagram below illustrates the formation of a polymer from more than one type of monomer.

Carbohydrates

Compounds made up of carbon, hydrogen, and oxygen atoms, usually in a ratio of 2:1 hydrogen:oxygen.      Living things use carbohydrates as their main source of energy.

The breakdown of sugars, such as glucose, supplies immediate energy for all cell activities.

Plants and some animals also use carbohydrates for structural purposes

As shown below, the monomers in starch polymers are sugar molecules

Living things store extra sugar as complex carbohydrates known as starches.

a.)  monosaccharides (simple sugars, the monomer) •all have the formula C6 H12 O6 •all have a single ring structure•Ex. Include: glucose, galactose, (a component of milk), & fructose (found in fruits).

Name this molecule

GLUCOSE

Note: the names of sugars end in ‘ose’

b.) disaccharides (double sugars) •all have the formula C12 H22 O11 •sucrose (table sugar) is an example

c.) Polysaccharides (formed of three or more simple sugar units)

We store excess sugar as a polysaccharide called glycogen. When the level of glucose in your blood runs low, glycogen is released from your liver. The glycogen stored in your muscles supplies the energy for muscle contraction and, thus, for movement.Plants make a polysaccharide called cellulose. Cellulose fibers give plants much of their strength and rigidity. It is the major component of both wood and paper.

How are complex carbohydrates formed and broken down?

1.) Dehydration synthesis -- combining simple molecules to form a more complex one with the removal of water Ex. monosaccharide + monosaccharide ---->

disaccharide + water

(C6H12O6 + C6H12O6 ----> C12H22O11 + H2O

-- polysaccharides are formed from repeated dehydration syntheses of water

2.) hydrolysis -- the addition of water to a compound to split it into smaller subunits

(also called chemical digestion)

Ex. disaccharide + H2O ---> monosaccharide + monosaccharide

C12H22O11 + H2O ---> C6H12O6 + C6H12O6

3. Lipids (Fats) : Ex. fats, oils, waxes, steroids -- lipids chiefly function in energy storage, protection, and insulation -- contain carbon, hydrogen, and oxygen but the H:O is not in a 2:1 ratio lipids tend to be large molecules -- an example of a neutral lipid is below

-- neutral lipids are formed from the union of one glycerol molecule and 3 fatty acids

-- fats -- found chiefly in animals

-- oils and waxes -- found chiefly in plants

-- oils are liquid at room temperature, waxes are solids

-- lipids along with proteins are key components of cell membranes

-- steroids are special lipids used to build many reproductive hormones and cholesterol

Cooking oils, such as corn oil, sesame oil, and peanut oil, contain polyunsaturated lipids

If there is at least one carbon-carbon double bond in a fatty acid, the fatty acid is said to be unsaturated.

Lipids whose fatty acids contain more than one double bond are said to be polyunsaturated.

If the terms saturated and polyunsaturated seem familiar, you have probably seen them on food package labels.Lipids such as olive oil, which contains unsaturated fatty acids, tend to be liquid at room temperature

Nucleotides

Nucleic acids -

macromolecules containing hydrogen, oxygen, nitrogen, carbon, and phosphorus.

consist of three parts:a 5-carbon sugar

a phosphate group

a nitrogenous base

Nucleic acids are polymers assembled from individual monomers known as nucleotides

PHOSPHATE

5-CARBON SUGAR

NITROGENOUS BASE

A. DNA (deoxyribonucleic acid)

-- contains the genetic code of instructions that direct a cell's behavior through the synthesis of proteins -- found in the chromosomes of the nucleus (and a few other organelles)

--contains the sugar deoxyribose

The nitrogenous bases are:

Adenine Guanine Cytosine Thymine

B. RNA (ribonucleic acid)

-- directs cellular protein synthesis

-- found in ribosomes & nucleoli

--contains the sugar ribose

-- the nitrogenous bases are:

Adenine Guanine Cytosine Uracil

PROTEINS

-- contain the elements carbon, hydrogen, oxygen, and nitrogen -- polymers of molecules called amino acidsAmino acids contain an amino group (–NH2) on one

end of a central carbon and a carboxyl group (–COOH) on the other end.

There are more than 20 different amino acids found in nature. All 20 amino acids are identical in the regions where they may be joined together by covalent bonds. This uniformity allows any amino acid to be joined to any other amino acid—by bonding an amino group to a carboxyl group.

The portion of each amino acid that is different is a side chain called an R-group.

Dehydration synthesis of a dipeptide

amino acid + amino acid ----- dipeptide + water

Hydrolysis of a dipeptide

dipeptide + H2O ---> amino acid + amino acid

Polypeptide (protein)

Examples of proteins include

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

•insulin•hemoglobin

•enzymes.

Chemistry isn’t just what life is made of—chemistry is also what life does. Everything that happens in an organism—its growth, its interaction with the environment, its reproduction, and even its movement—is based on chemical reactions.

Energy is released or absorbed whenever chemical bonds form or are broken. Because chemical reactions involve breaking and forming bonds, they involve changes in energy

Some chemical reactions release energy, and other reactions absorb energy. Energy changes are one of the most important factors in determining whether a chemical reaction will occur.      Chemical reactions that release energy often occur spontaneously. Chemical reactions that absorb energy will not occur without a source of energy. An example of an energy-releasing reaction is hydrogen gas burning, or reacting, with oxygen to produce water vapor

The instructions for arranging amino acids into many different proteins are stored in DNA. Each protein has a specific role.       

Major Protein Functions

•regulate cell processes

•fight diseases

•transport substances into or out of cells

•control the rate of reactions•Buffer -- helps keep body pH constant

•energy

form bones and muscles•Growth and repair –

Catalysta substance that speeds up the rate of a chemical reaction

Enzymes •proteins•biological catalysts

•speed up chemical reactions that take place in cells •very specific

catalyze only one chemical reaction

•enzyme’s name derived from the reaction it catalyzes

•Most enzyme names end in ‘ase’

•present in the cell in small amounts & reusable•they are not altered during their reactions

How do enzymes do their jobs?Enzymes provide a site where reactants can be brought together to reactThe reactants of enzyme-catalyzed reactions are known as substrates

Recall that each protein has a specific, complex shape.The substrates bind to a site on the enzyme called the active siteThe active site and the substrates have complementary shapes.

The fit is so precise that the active site and substrates are often compared to a lock and key

LOCK & KEY THEORY

Enzyme-Substrate Complex This space-filling model shows how a substrate binds to an active site on an enzyme

It is thought that, in order for an enzyme to affect the rate of a reaction, the following events must take place. 1. The enzyme must form a temporary association with the substance or substances whose reaction rate it affects. These substances are known as substrates. 2. The association between enzyme and substrate is thought to form a close physical association between the molecules and is called the enzyme-substrate complex. 3. While the enzyme-substrate complex is formed, enzyme action takes place.

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

Enzyme activity is affected by a number of factors including:

a. the concentration of enzyme

•increasing enzyme concentration will increase the enzyme reaction rate

b. the concentration of substrate

•As the substrate concentration increases, the enzyme reaction rate increases. However, at very high substrate concentrations, the enzymes become saturated with substrate and a higher concentration of substrate does not increase the reaction rate.

c. the pH•Each enzyme has an optimal pH that helps maintain its three-dimensional shape

•Changes in pH may denature enzymes by altering the enzyme's charge.

Enzyme Substrate Concentrations

How Substrate Concentration Affects Reaction Rate

Additional factors affecting enzyme activity:

c. the temperature

•However, the temperature rises above a certain point, the heat will denature the enzyme, causing it to lose its three-dimensional functional shape by denaturing its hydrogen bonds

•A higher temperature generally results in an increase in enzyme activity

•Cold temperature, on the other hand, slows down enzyme activity

Hypothetical relationships between temperature and enzyme activity for a human and for a thermophilic(heat loving) bacteriaEnzymes produced by human cells generally work best at temperatures close to 37°C, the human body’s core temperature

How does pH affect an enzyme? Catalase is an enzyme that helps decompose the toxic hydrogen peroxide that is produced during normal cell activities. The products of this reaction are water and oxygen gas. The pressure of the oxygen gas in a closed container increases as oxygen is produced. Any increase in the rate of the reaction will cause an increase in the pressure of the oxygen.The purple line on the graph represents the normal rate of the reaction in a water solution of hydrogen peroxide and catalase. The red line represents the rate of reaction when an acid is added to the solution. The blue line represents the rate of reaction when a base is added to the solution.

                   1.Applying Concepts  What variable is plotted on the x-axis? What variable is plotted on the y-axis?2.Interpreting Graphics  How did the rate of reaction change over time in the control reaction?3.Inferring  Suggest an explanation for the change in the control reaction at about 40 seconds.4.Interpreting Graphics  How does the presence of a base affect the rate of the reaction? How does the presence of an acid affect the rate?5.Drawing Conclusions  What effect do acids and bases have on the enzyme catalase?6.Going Further  Predict what would happen if vinegar were added to a water solution of hydrogen peroxide and catalase.

2H2O2 O2 + 2H2O

The pressure of oxygen gas is a measure of the amount of oxygen produced. The slope of the graphs is an indication of the rates of the reactions 1. Time is plotted on the x axis and pressure of oxygen on the y axis

2. The rate was very rapid at first and then dropped off dramatically after about 40 seconds3. Hydrogen peroxide was used up or the reaction is reversible

4. A base inhibits the enzyme so that it is less effective. An acid may deactivate the enzyme so that the reaction cannot take place5. It would be valid because the blue line shows that the pressure of oxygen evened out when the base was added. That effect suggests that the rate of reaction slowed b/c any increase in the rate would cause an increase in the pressure of the oxygen.6. B/c vinegar is an acid, it would inhibit and possible destroy the catalyst.