B I O C H E M I S T R Y

 

Basic Chemistry and theChemical Compounds of Life

 

Regents Biology

OBJECTIVESUpon completion of this unit students will be able to: 

1. Define biochemistry.2. Differentiate empirical, molecular and structural formulas.3. List the 4 most common elements found in living things.4. Explain the differences between inorganic and organic compounds.5. Understand that water is the most important inorganic compound for organisms. 6. State the functions of carbohydrates. 7. Understand that monosaccharides (i.e., glucose) is the building block for all carbohydrates.8. Recognize the chemical formula for carbohydrates and chemical structure of glucose.9. List several examples of carbohydrates.10. Recognize that most carbohydrates end in –ose.11. Explain the difference between a ribose sugar and a deoxyribose sugar. 12. Differentiate between a monosaccharide, disaccharide, and polysaccharide.13. List three examples of polysaccharides and state their functions.14. State the functions of lipids in the body. 15. Understand that a lipid molecule is made up of 3 fatty acids and 1 glycerol molecule.16. List several examples of lipids.17. Identify the two types of nucleic acids.18. Differentiate DNA and RNA by structure and function.19. Understand that amino acids are the building blocks of proteins. 20. Recognize the chemical formula and structure of an amino acid.21. State that the chemical bond that links one amino acid to another is called a peptide bond and

that two amino acids combined is called a dipeptide.22. Explain what is meant by a dipeptide and a polypeptide and explain how they are formed.23. List five examples of polypeptides. 24. Explain in a sentence or two why there are so many possible kinds of proteins.25. Recognize that a protein structure determines its function.26. Understand the structure and function of an enzyme and that they usually end in –ase.

KEY WORDS

 1. active site2. amino acid3. amino group4. carbohydrates5. catalyst6. dehydration synthesis7. dipeptide8. disaccharide 

9.    DNA10.  enzyme 11.  hydrolysis12.  lipid13.  monosaccharides14.  nucleic acid15.  nucleotide16.  organic compound 

17.  peptide bond18.  polymer19.  polypeptide20.  polysaccharide21.  protein22.  RNA23.  starch24.  substrate 

INTRODUCTION

• The processes of life (metabolism, excretion, etc.) are, for the most part, CHEMICAL

• There are only about 100 different ATOMS AND ELEMENTS, which is what matter is made up of.

Examples CARBON, HYDROGEN, etc.

• Biochemistry is THE STUDY OF ATOMS AND MOLECULES THAT ARE IMPORTANT FOR LIFE

CHEMICAL ELEMENTS and FORMULAS• Remember that CELLS are the basic unit of life? • Well, cells as well as everything nonliving in this world, are made

up of ATOMS of elements. • There are 3 different ways to express the amount or ratios of

atoms present in a molecule: • Empirical formula – formula showing SIMPLEST proportions of

atoms in a compound– Ex.: CH

• Molecular formula – formula showing the EXACT COMPOSITION of a compound

Ex.: C2H2

• Structural formula – Shows number and kind of atoms AND how they are BONDED TO EACH OTHER – Ex.: H-C=C-H

INORGANIC vs. ORGANIC COMPOUNDS

• ALL organisms are made up of both ORGANIC and INORGANIC compounds. So what’s the difference?

 • A. Inorganic Compounds• The MOST important inorganic compound for living

things is H2O because we need it to live. – Many of the biological processes that are necessary for life take

place in water. – In fact, we are made up of over 65 percent water and can really

only survive for a few days without water!!!

• Inorganic molecules DO NOT CONTAIN CARBON

B. Organic Compounds• Of all of the atoms found on earth, there are four main ones that

are present in living things. The four main elements that are present in organic compounds are:

  ELEMENT SYMBOL

CARBON 

C

HYDROGEN 

H

OXYGEN 

O

NITROGEN N 

·      The element that is FAMOUS for being found in organic compounds is CARBON • it can bond to 4 things which makes it possible for there to be so many organic compounds.  

   

TYPES OF ORGANIC COMPOUNDS·      There are 4 types of organic compounds. They are:  ORGANIC

COMPOUNDSCOMPOSITION FUNCTION(S)

CARBOHYDRATES C, H, OSOURCE OF

ENERGY

LIPIDS C, H, OCUSHIONING, INSULATION,

ENERGY

NUCLEIC ACIDS 

C, H, O, N, PDIRECT AND

CONTROL ACTIVITIES

PROTEINS 

C, H, O, NSTRUCTURE AND

FUNCTION

A. CARBOHYDRATES

I. Structure & Function• Carbohydrates are comprised of CARBON,

HYDROGEN, AND OXYGEN in a ratio of 1:2:1.– Ex. Glucose C6H12O6

• The chemical names of carbohydrates usually end in –OSE (i.e., glucose, sucrose, etc.)

• MONOSACCHARIDES are the simple sugars

     ·      Sugars are biologically important because they CONTAIN LARGE AMOUNTS OF ENERGY; nearly all organisms use glucose as a source of energy.

NAME FORMULA TYPE FUNCTIONS

Glucose C6H12O6 MONOSACCHARIDE ENERGY

Maltose C11H22O11 DISACCHARIDE “ “

Lactose C11H22O11 Disaccharide “ “

Sucrose C11H22O11 Disaccharide “ “

Cellulose POLYMER POLYSACCHARIDE TOUGH OUTER STRUCTURE

Glycogen POLYMER Polysaccharide STORES EXCESS SUGAR IN HUMANS

Starch POLYMER Polysaccharide STORES EXCESS SUGAR IN PLANTS

 Some up-close-and-personal looks at some Carbohydrates: 

  GLUCOSE 

  SUCROSE 

A. CARBOHYDRATESII. Dehydration Synthesis

• Sugar molecules can be bonded together by a process called DEHYDRATION SYNTHESIS

• Synthesis means “PUTTING TOGETHER” and dehydration means “REMOVING WATER”.

• Dehydration synthesis makes ORGANIC COMPOUNDS that the organism needs, – such as GLYCOGEN & PROTEINS.

• We use it for ALL complex organic compounds.

• By joining two simple sugars, a DISACCHARIDE is formed:

A. CARBOHYDRATESPolysaccharides

• Polysaccharides are LONG CHAINS OF REPEATING SUGAR UNITS

• can be formed by DEHYDRATION SYNTHESIS • Organisms store excess sugar in the form of polysaccharides:

1. PLANTS – STARCH2. HUMANS – GLYCOGEN (IN LIVER AND

MUSCLES) • Polysaccharides can also be used to form tough, structural parts of

organisms:1. PLANTS - CELLULOSE2. INSECTS - CHITIN

CARBOHYDRATESIII. Hydrolysis

• Just as sugar molecules can be joined together, they can be broken apart.

• Hydrolysis: WATER BEING ADDED TO SPLIT UP A COMPLEX MOLECULE THAT WAS FORMED FROM DEHYDRATION SYNTHESIS

B. LIPIDSI. Structure & Function

• Lipids are commonly called FATS, OILS AND WAXES

• Lipids are comprised of CARBON, HYDROGEN, AND OXYGEN, as carbohydrates are.

• The only difference is that THE RATIOS ARE DIFFERENT– AS A RESULT FATS YIELD MORE ENERGY

• A molecule of fat is formed from the combination of FATTY ACIDS AND GLYCEROL

• Lipids functions– BEING A RESERVE ENERGY SUPPLY – PART OF THE CELL MEMBRANE

• Lipids contain TWICE as much energy as the same amount of carbohydrate!

• Mammals also use lipids for CUSHIONING AND INSULATION

B. LIPIDSII. Saturated vs. Unsaturated Fats

• Saturated fat: ALL CARBON-TO-CARBON BONDS ARE SINGLE BONDS

C-C-C-C-C-C-C-C-C-C-C-C-C•  Unsaturated fat: ONE OR MORE PAIRS OF CARBON

ATOMS ARE JOINED BY A DOUBLE OR TRIPLE BOND

• Unsaturated fats are liquid at room temperature and are healthier for you than saturated fats which are solid at room temperature

C. PROTEINSI. Structure & Function

• Proteins are compounds that CONTAIN CARBON, HYDROGEN, OXYGEN AND NITROGEN

• The functions of proteins are:– STRUCTURAL PARTS OF CELLS AND BODY

TISSUES (HAIR, NAILS, CARTILAGE)– PIGMENTS IN BLOOD, SKIN, EYES, AND

CHLOROPHYLL– HORMONES (CHEMICAL MESSENGERS)– ENZYMES

C. PROTEINSII. Amino Acids

• Amino acids are THE BUILDING BLOCKS OF PROTEINS• Each amino acid is called a MONOMER. The structure of an

amino acid is:

• There are 20 different amino acids that are found as part of proteins.

• Amino acids can be linked together in any sequence and in chains of varying length.

The R group is variable or RANDOM

C. PROTEINSIII. The Peptide Bond

• Two amino acids may be bonded together by DEHYDRATION SYNTHESIS TO MAKE A DIPEPTIDE

• The bond that forms is called a PEPTIDE BOND• It forms between THE AMINO GROUP OF ONE AMINO

ACID AND THE CARBOXYL GROUP OF THE NEXT• A chain of amino acids is called a POLYPEPTIDE. All proteins

are made up of POLYPEPTIDES (CHAINS OF AMINO ACIDS).

ENZYMES ARE PROTEINS…………..• Enzymes are PROTEIN SUBSTANCES THAT

MAKE CHEMICAL REACTIONS OF LIVING ORGANISMS POSSIBLE

• Enzymes enter into a chemical reaction TEMPORARILY—JUST LONG ENOUGH TO MAKE IT HAPPEN

• Enzymes are CATALYSTS, WHICH MEANS THEY ARE NOT CHANGED DURING A REACTION, – THEY ARE USED AGAIN AND AGAIN (RECYCLED)

• The substance that an enzyme acts on is called its SUBSTRATE

• Enzymes usually end with the suffix -ASE. – Examples: maltase, amylase, lactase and protease

How Enzymes Work• The ability of enzymes act as CATALYSTS depends on

their SHAPE• There is a region on the surface of an enzyme called the

ACTIVE SITE– The substrate molecules fit the shape of the active site– when the substrate comes into contact with the active site, it

forms a TEMPORARY UNION CALLED THE ENZYME-SUBSTRATE COMPLEX

• ENZYME-SUBSTRATE COMPLEX– the enzyme may cause the substrate to separate into two

molecules– may also join two molecules (using two substrates)

• The theory of enzyme action where the enzyme and substrate fit together at an active site is called the LOCK-AND-KEY MODEL

LOCK AND KEY MODEL• THE SHAPE OF THE ACTIVE SITE OF THE ENZYME ONLY

FITS THE SHAPE OF CERTAIN SUBSTANCES • EACH ENZYME CAN ONLY CATALYZE CERTAIN

SUBSTRATES

D. NUCLEIC ACIDS• Nucleic acids contain the elements CARBON, HYDROGEN,

OXYGEN, NITROGEN and PHOSPHORUS.

• There are two kinds of nucleic acids which were originally found in the part of the cell called the nucleus:– DNA – DEOXYRIBONUCLEIC ACID– RNA – RIBONUCLEIC ACID

• DNA is the hereditary material passed from one generation to the next during reproduction.

• RNA works with DNA to direct and control the development and activities of all cells of an organism.

• The building blocks of nucleic acids are NUCLEOTIDES.

D. NUCLEIC ACIDSI. Structure of DNA and RNA

• The general structure of a nucleic acid molecule is that of A LONG CHAIN OF REPEATING UNITS

• In DNA, there are 4 different bases that can be attached to the chain: – ADENINE (A), GUANINE (G), CYTOSINE (C),

THYMINE (T)• The sequence of bases acts as a CODE or TEMPLATE

– determines what proteins will be made in the cell. – The proteins then determine the nature of the cell what

activities the cell will undertake.• The entire DNA molecule is coiled into a DOUBLE

HELIX. – By repeated coilings DNA is “packed” and is able to fit into

tiny structures within the cell.

• An RNA molecule is similar to a DNA molecule, but it has some differences.

• The structure of an RNA molecule is different than the structure than a DNA molecule by:

• RNA CONSISTS OF A SINGLE STRAND OF BASES

• THE SUGAR IN RNA IS RIBOSE

• THYMINE IS REPLACED WITH URACIL