chemicals of life iii proteins and nucleic acids

Chemicals of Life IIIChemicals of Life III

Proteins and Nucleic Acids

Section OneSection One

Nucleic Acids

Some Questions…Some Questions…

Did you ever wonder why you express certain physical characteristics?

Why do all maple trees look like each other?

You can begin to answer these questions by studying the most important chemicals found in the cell nucleus.

DNA!DNA!

DNA directs cell activities from the nucleus. DNA is the substance that determines many

traits in living organisms. Let’s examine DNA more closely…

CELL

Nucleus

A Small Segment of DNAA Small Segment of DNA

DNA is a double helix.

Let’s unwind the DNA. Notice that the DNA

contains subunits. The DNA subunits are

called nucleotides.

NucleotidesNucleotides

How many different kinds of nucleotides do you see? FOUR

NucleotidesNucleotides

What letters represent the different nucleotides? A, T, C, G

Another DNA DiagramAnother DNA Diagram

Diagram of Unwound DNASingle Nucleotide

InformationInformation

The sequence of nucleotides in the DNA determines the sequence of amino acids in the proteins made by the cells.

The sequence of amino acids determines the structure and function of the protein.

Therefore, DNA controls the type of protein made by the cell.

The “A” NucleotideThe “A” Nucleotide

Let’s look closely at the nucleotide identified as A.

Adenine NucleotideAdenine Nucleotide

(Adenine)

The letter A stands for the base adenine, which is a component of this nucleotide.

All DNA nucleotides contain the five-carbon sugar deoxyribose.

All nucleotides contain a phosphate group.

Guanine NucleotideGuanine Nucleotide

(Guanine)

The letter G stands for the base guanine, which is a component of this nucleotide.

The guanine nucleotide is similar to the adenine nucleotide.

Adenine and guanine are members of bases called purines.



Identical ComponentsIdentical Components

There are two identical components in all DNA Nucleotides:

The sugar deoxyribose.The phosphate group.

The “C” and “T” NucleotidesThe “C” and “T” Nucleotides

Let’s look at the nucleotides identified by the letters C and T.

Cytosine NucleotideCytosine Nucleotide

(Cytosine)

The letter C stands for the base cytosine, which is a component of this nucleotide.


All nucleotides contain a phosphate group. (Note that the

deoxyribose and the phosphate are identical to those found in adenine and guanine.)

Thymine NucleotideThymine Nucleotide

(Thymine)

The letter T stands for the base thymine, which is a component of this nucleotide.

The thymine nucleotide is similar to the cytosine nucleotide.

Cytosine and thymine belong to a group of bases called pyrimidines.



(Note that the deoxyribose and the phosphate are identical to those found in adenine, guanine and cytosine.)

Diagrams of C, A and GDiagrams of C, A and G

(In these diagrams there are three phosphates instead of the single phosphate found in the normal nucleotide. )

Identical ComponentsIdentical Components

Because the deoxyribose sugar and the phosphate group are identical in all four nucleotides, you can use the letter R (for radical) to replace them. This simplifies the diagram.

R

DNA ProductionDNA Production

Let’s examine how nucleotides interact in the production of DNA.

DNA splits into two separate strands before a cell divides.

The bonds between the nucleotides are weak. Hydrogen bonding is the weak bond that

holds the nucleotides together. Nucleotides in the nucleus combine with DNA

when the DNA splits. DNA is a self-replicating molecule.

Diagram of DNA ProductionDiagram of DNA Production

Note that only these pairs form: Thymine & Adenine; Cytosine and Guanine.

A Simplified Animated Diagram of A Simplified Animated Diagram of DNA Replication…DNA Replication…

Bonding Between NucleotidesBonding Between Nucleotides

Why can’t adenine and cytosine or adenine and guanine combine? Think about it.

Let’s look at the bonds between the purine adenine and the pyrimidine thymine.

Adenine and ThymineAdenine and Thymine

How many hydrogen bonds link adenine and thymine? TWO

Guanine and CytosineGuanine and Cytosine

How many hydrogen bonds link the purine guanine and the pyrimidine cytosine? THREE


Because cytosine and guanine are held together by three hydrogen bonds, they cannot combine with either adenine or thymine which form two hydrogen bonds.

Weak hydrogen bonding is responsible for the following:

DNA strands can separate. Adenine only can pair with thymine. Cytosine only can pair with guanine.

ReviewReview

Deoxyribose (a sugar), a base, and a phosphate group comprise a nucleotide.

Nucleotide subunits make up the self-replicating DNA molecule.

DNA directs cell activities and determines an organism’s traits.

Adenine and guanine are purines. Cytosine and thymine are pyrimidines.

Select The Best Matching Choice:Select The Best Matching Choice:

Answer Column:

A. Self-replicating

B. DNA subunit

C. Cytosine and thymine

D. Adenine and guanine

E. Name of a weak bond

F. DNA phosphate group

G. Name of a strong bond

H. DNA sugar

Nucleotide:Correct Answer: B

Purines:Correct Answer: D

Pyrimidines:Correct Answer: C

Deoxyribose:Correct Answer: H

Hydrogen:Correct Answer: E

DNA:Correct Answer: A

Section TwoSection Two

Proteins

ProteinsProteins

Proteins are the most abundant organic compounds that make up living cells.

Every part of every living organism contains protein.

Nucleus

CELL

Uses of ProteinsUses of Proteins

These are some of the uses of proteins: Hemoglobin to carry oxygen in blood. Secretions such as hormones and mucus. Fibers such as actin and myocin that make up muscles. Enzymes to regulate chemical reactions in the body. Antibodies to fight disease – causing organisms.

Photosynthetic plants can manufacture proteins from simple inorganic substances.

Animals and nonphotosynthetic plants must use other organisms as a source of protein.

Uses of ProteinsUses of Proteins

These are common sources of proteins for Humans:

MeatFishNutsPeas

BeansMilkCheeseEggs

Protein ComplexityProtein Complexity

Proteins are among the most complex substances found in organisms.

Let’s look at a model of a protein molecule magnified one million times…

When you first see a protein model, it may seem quite complex.

However, easily understood subunits, called amino acids, make up proteins.

StructureStructure

All amino acids have this general structure. All amino acids have an amino group, a carboxyl

group and a side chain.

C CN

H

H H O

O HR

The amino group is the nitrogen atom and the attached hydrogen atoms.

A carboxyl group contains these parts: a carbon atom, an oxygen atom and a hydroxyl group (O-H).R stands for a side chain that can contain

different combinations of carbon, hydrogen, oxygen, and nitrogen or sulfur.

Side Chains - AlanineSide Chains - Alanine

Let’s look at some amino acids to see the differences in the side chains.

C CN

H

H H O

O HC

HHH

Side Chain

Side Chains - CysteineSide Chains - Cysteine


C CN

H

H H O

O HC H

H

H

Side Chain

S

Side Chains - AsparagineSide Chains - Asparagine


C CN

H

H H O

O HC H

O

H

Side Chain

CNH

H


There are 20 different amino acids found in the human body.

Each amino acid has a different side chain that gives the amino acid specific characteristics.

The characteristics include the degree of solubility of an amino acid in various solvents and the degree to which it adsorbs (sticks) to the surface of various materials.

An Experiment…An Experiment…

The solvent rises up the paper when the two touch.

The spot on the filter paper contains four different amino acids.

Watch what happens when the paper touches the solvent in the beaker…

Amino Acid ExperimentAmino Acid Experiment

Which amino acid is the most soluble in this solvent (1-4)? Number 1 is the most soluble. It

remains dissolved in the solvent longer than the other amino acids and travels farther up the paper.

Which amino acid adheres most tightly to the paper (1-4)? Number 4 sticks tightly to the paper

and does not move as far as the other amino acids.

1

2

3

4

Amino Acid ExperimentAmino Acid Experiment

Identify amino acid number 2 by comparing it with the key above. The answer is VALINE!

This process is paper chromatography. There are other types of chromatography

that use starch or silica gel as the adsorbent medium.

When determining the amino acid composition of a protein, chromatography is a very important tool.

1

2

3

4

glycine

cysteine

histidine

tryptophan

valine

Dehydration SynthesisDehydration Synthesis

Let’s see how amino acids combine to make proteins.

Amino acids combine in the presence of an enzyme during dehydration synthesis.

C CN

H

H H O

O HR

C CN

H

H H O

O HR

H2O

Dehydration SynthesisDehydration Synthesis

The compound produced from the dehydration synthesis of two amino acids is a dipeptide.

Water is also produced during the reaction. The bond between the carbon atom and the nitrogen atom is a

peptide bond. A polypeptide is a long chain of amino acids containing many

peptide bonds. Proteins can contain two or more polypeptide chains.

C CN

H

H H O

R

C CN

H H O

O HRH2O Peptide Bond

Digestion of ProteinsDigestion of Proteins

Protein can contain thousands of peptide bonds that link thousands of amino acids.

When you digest protein, the peptide bonds must be broken so your body can absorb the amino acids.

This process is hydrolysis. Many hydrolysis reactions

take place to produce polypeptides, then dipeptides, and finally amino acids.

Dipeptide HydrolysisDipeptide Hydrolysis

Protein hydrolysis requires water and an enzyme called protease.

C CN

H

H H O

R

C CN

H H O

O HRH2O

C CN

H

H H O

O HR

C CN

H

H H O

O HR

Your body now can absorb the amino acids.

ReviewReview

Protein is made of amino acid subunits. There are 20 kinds of amino acids. An amino acid contains a carboxyl group, an amino

group, and a side chain that varies from one amino acid to the next.

There can be thousands of amino acids in a protein. During dehydration synthesis, peptide bonds link

amino acids to form protein. During hydrolysis, the enzyme protease breaks the

peptide bonds in proteins.

Quiz: Fill In The Blanks…Quiz: Fill In The Blanks…

Thousands of ______________ make up the protein actin that is responsible for muscle contraction. These subunits are linked together by ____________ bonds, that form during _____________ synthesis. The protein can be broken down during the process of ____________. These processes require the presence of enzymes.

amino acids

peptidedehydration

hydrolysis

Section ThreeSection Three

Enzymes: Organic Catalysts

Enzyme ReactionsEnzyme Reactions

Let’s begin an investigation of enzymes by studying this reaction:

2H2O2 2H2O + O2

Hydrogen Water OxygenPeroxide

If hydrogen peroxide is stored in a sealed bottle for a long time, you hear a slight hiss when you open the bottle. This is caused by the gas named oxygen.

If you store hydrogen peroxide for a long time, it loses its properties.

Over a long period of time, hydrogen peroxide slowly breaks down into water and oxygen gas. Therefore, it loses its properties.

Hydrogen PeroxideHydrogen Peroxide

When you use hydrogen peroxide to clean a wound, it bubbles when it contacts blood. These are bubbles of oxygen gas.

The substance in blood that causes the hydrogen peroxide to bubble is a chemical called catalase.

Hydrogen Peroxide ExperimentHydrogen Peroxide Experiment The diagram shows two containers of hydrogen

peroxide. Container B contains a small amount of catalase. Compare their reaction rates (bubbles of oxygen

produced).

ContainerA

ContainerB

(with catalase)

Catalase causes hydrogen peroxide to break down faster. A substance that changes the rate of reaction is a catalyst.


A catalyst is a substance that alters the rate of a chemical reaction while undergoing no change itself.

A catalyst can be organic or inorganic. Organic catalysts are chemicals that contain both hydrogen and carbon atoms.

Enzymes are organic catalysts found in living cells; these are sometimes referred to as biological catalysts. Enzyme names always end in “ase”.

Catalase is an example of an enzyme found in blood.

CatalaseCatalase

Let’s study the action of catalysts more closely:

2H2O2 2H2O + O2

catalase

Two molecules of hydrogen peroxide break down to form two molecules of water and one molecule of oxygen. A small number of catalase molecules speeds up this reaction.

CatalaseCatalase

Watch the breakdown of 5000 molecules of hydrogen peroxide:

Hydrogen Peroxide

Water Oxygen

5000 0 0

Hydrogen Peroxide

Water Oxygen

0 5000 2500

Let’s Graph This ReactionLet’s Graph This Reaction

The graph shows the breakdown of hydrogen peroxide to water and oxygen over five hours.

Notice that the number of hydrogen peroxide molecules decreases over the five-hour period.

Breakdown of Hydrogen Peroxide to Water and Oxygen

0

1000

2000

3000

4000

5000

6000

1 2 3 4 5 6

Time in Hours

Nu

mb

er

of

Hy

dro

ge

n P

ero

xid

e

Mo

lec

ule

s

0 1 2 3 4 5

Graph of Hydrogen PeroxideGraph of Hydrogen Peroxide

What is the number of hydrogen peroxide molecules found at the beginning of the reaction? __________

What is the number of hydrogen peroxide molecules found after 1 hour? ___________

What is the number of hydrogen peroxide molecules found after 5 hours? ___________

Breakdown of Hydrogen Peroxide to Water and Oxygen

0

1000

2000

3000

4000

5000

6000

1 2 3 4 5 6

Time in Hours

Nu

mb

er

of

Hy

dro

ge

n P

ero

xid

e

Mo

lec

ule

s

0 1 2 3 4 5

5000

3000

1000

QuestionsQuestions

Which period of time represents the most rapid breakdown of hydrogen peroxide?

a) The third to fourth hour.

b) The first to third hour.

c) The first two hours.Answer: C – About 3000 molecules of hydrogenperoxide break down in the first two hours.

What happens to the number of water and oxygen molecules as hydrogen peroxide breaks down? It ______________.increases

Catalase EnzymeCatalase Enzyme

This hydrogen peroxide reaction does not occur in a short period of time without the enzyme catalase.

If you start with only 500 molecules of catalase, how many molecules do you think remain after 5 hours? _________500

The enzyme is not used up in the reaction! Let’s look at a table of our results…

TableTable

Time In

Hours

Number of MoleculesCatalase Hydrogen

PeroxideWater Oxygen

0 500 5000 0 0

1 500 3000 2000 1000

2 500 2000 3000 1500

3 500 1500 3500 1750

4 500 1200 3800 1900

5 500 1000 4000 2000

QuestionQuestion

Using ONLY the table on the previous slide, determine which of the following statements is true.

a) The breakdown of hydrogen peroxide is most rapid after one hour.

b) Catalase is an enzyme.

c) 2000 molecules of hydrogen peroxide break down during the first hour.

Answer: C – The most rapid breakdown of hydrogenPeroxide occurs in the first hour. B is also correct,but you cannot determine this from the informationin the table.

CatalaseCatalase

Catalase is the enzyme in this reaction. If catalase is not present, how many molecules of

hydrogen peroxide would break down after five hours?

a) Very few.

b) 4000.

c) 5000.

Answer: A – An enzyme speeds up a chemicalreaction. Although catalase is needed in this reaction, it is not

used up or changed. Enzymes are needed in very small quantities.

SubstrateSubstrate

The substance that the enzyme works on is called the substrate. What is the name of the substrate in the catalase reaction? _________________hydrogen peroxide

The hydrogen peroxide (substrate) combines with catalase (enzyme) to form water and oxygen (products).

Information:Information: Enzymes in living cells:

Control the rate of biochemical reactions in the cell. Are required in very small quantities. Remain unchanged in chemical reactions. Can be used over and over again. Sometimes require the presence of coenzymes (nonprotein

molecules). Living cells contain hundreds of different enzymes,

each regulating reactions that: Build large molecules needed by the cell (dehydration

synthesis). Break down large molecules into smaller ones (hydrolysis).

The chemical that combines with the enzyme (E) is called a substrate (S).

EnzymesEnzymes

Enzymes are large proteins that have different shapes.

The red figure represents an enzyme. Weak chemical bonds that hold the molecule together determine the shape of this protein.

Enzyme Molecule (E)

Enzyme Activity vs. TemperatureEnzyme Activity vs. Temperature

What do you think happens to the enzyme if you increase the temperature of the enzyme solution?

The enzyme loses its shape and breaks apart when it reaches a high temperature.

As an enzyme’s shape changes, it becomes less and less active.


Enzymes are large proteins that have different shapes.

Weak chemical bonds hold proteins in their special shapes.

High temperatures destroy enzymes. Shape is important in determining the activity

of enzymes.

High Temperatures Destroy High Temperatures Destroy Enzymes - DiagramsEnzymes - Diagrams

Heat is increased, whichdistorts the shape of theenzyme.

Substrate can no longerfit into active site onenzyme, rendering ituseless.

ReviewReview

Hydrogen peroxide slowly breaks down to form oxygen gas and water.

A catalyst is a substance that changes the rate of a chemical reaction.

Enzymes are organic catalysts. The enzyme catalase increases the rate of hydrogen

peroxide breakdown. A substrate is the substance on which an enzyme

works. The shape of an enzyme determines its activity rate.

Quiz: Fill In The Blanks…Quiz: Fill In The Blanks…

An inorganic substance that changes the rate of a chemical reaction is a(n) ____________. An organic substance that acts this way is a(n) ____________. The ___________ of this substance is very important in determining the rate of reaction. The compound on which the organic substance acts is the ____________.

catalystenzyme

shape

substrate

Section FourSection Four

Enzyme Action

ReviewReview

The cell requires enzymes to control the rate of chemical reactions.

An enzyme works by “combining” with a substrate to produce a product.

The ability of an enzyme to combine with a substrate depends on several factors.

Enzyme ActionEnzyme Action

Enzyme molecules (E) randomly collide with substrate molecules.

The substrate (S) fits into a special place on the enzyme. This location is the active site.

This combination of enzyme and substrate is the enzyme-substrate complex (ES).

Because the substrate must fit the enzyme, a substrate generally has its own specific enzyme. This is enzyme specificity.

After the enzyme combines with the substrate, product (P) forms.

This is the lock-and-key model of enzyme action.

Enzyme ActionEnzyme Action

Enzyme Molecule (E)

Substrate (S)

Product (P)

Product (P)

Product (P)

(THREE PRODUCTS)

Enzyme Action – Another DiagramEnzyme Action – Another Diagram

Enzyme Activity – Animated Enzyme Activity – Animated DiagramDiagram

Equation of Enzyme ActionEquation of Enzyme Action

This equation can represent a model of enzyme action.

E + S ES P E = enzyme; S = substrate; ES = enzyme-substrate

complex; P = product. Which contains the active site? _________ The complex formed during an enzyme reaction is

_________ The chemical not used up in the reaction is ________ Which symbol(s) show the specificity of enzymes?

_________

E

ESE

ES


Temperature affects enzyme activity. Changes in temperature alter the shape of the

enzyme. This makes it difficult for the substrate to

combine with the enzyme to form an enzyme-substrate complex.

Fewer enzyme-substrate complexes produce fewer products.

Factors That Affect EnzymesFactors That Affect Enzymes

These are some of the factors that affect the amount of product produced in reactions that involve enzymes: Temperature pH Concentration of substrate Concentration of enzyme

Effect of Temperature on Enzyme Effect of Temperature on Enzyme ActivityActivity

40302010 50

Effect of pH on Enzyme ActivityEffect of pH on Enzyme Activity

753 9 10 111

Effect of Increasing Substrate Effect of Increasing Substrate Concentration on Enzyme ActivityConcentration on Enzyme Activity

ReviewReview

Enzymes work best at a specific pH and temperature.

The best temperature for most enzymes is body temperature (approximately 37°C).

The best pH for most enzymes is the pH of cells (approximately 7).

Relative concentrations of enzyme and substrate determine the amount of product produced.

Questions…Questions…

Enzymes function most effectively at:

a) 20°C

b) 30°C

c) 37°C

d) 45°C Enzymes break down at:

a) 10°C

b) 37°C

c) 40°C

d) 50°C


Enzyme action is greatest as the pH approaches:

a) 7

b) 9

c) 12

d) 6 The rate of enzyme action can be decreased by:

a) changing the pH to 7.

b) changing the temperature to 37°C.

c) decreasing the amount of substrate.


If an enzyme action is high, it can be made faster by:a) raising the temperature above 40°C.b) raising the pH above 8.c) raising the enzyme concentration.d) none of these.

Which factor has the most specific effect on the rate of enzyme activity?

a) pH.b) temperature.c) substrate concentration.d) enzyme concentration.

Section FiveSection Five

Testing Your Knowledge

This Is A Test of What You Have This Is A Test of What You Have Learned…Learned…

There are 10 questions on this test.Try to correctly answer all of the

questions.If you miss a question, watch the screen

for an explanation of the correct answer.


Answer Column:

A. Purine nucleotide

B. Name of weak bond

C. Organic catalyst

D. Pyrimidine nucleotide

E. Protein subunit

F. Substrate

G. Name of protein bond

H. Side chain

Guanine:Correct Answer: AGuanine and adenine are purine nucleotides found in DNA. Cytosine and thymine are pyrimidine nucleotides found in DNA.

Peptide:Correct Answer: GA peptide bond forms when two amino acids react during the dehydration synthesis of a protein.


Answer Column:

A. Purine nucleotide

B. Name of weak bond

C. Organic catalyst

D. Pyrimidine nucleotide

E. Protein subunit

F. Substrate

G. Name of protein bond

H. Side chain

Amino Acid:Correct Answer: EA protein consists of many linked amino acid subunits. Proteins in humans contain 20 different kinds of amino acids.

Enzyme:Correct Answer: CAn enzyme is an organic catalyst that regulates chemical reactions in organisms.

Select The Best Choice To Select The Best Choice To Complete Each Analogy:Complete Each Analogy: A nucleotide is to DNA as an amino acid is to

____________.

A. deoxyribose

B. protein

C. pyrimidine

D. catalyst

E. substrate

protein

Nucleotides (adenine, cytosine, guanine or thymine) are the basic units of DNA, just as amino acids are the basic units of a protein. The best answer, therefore, is protein.

Select The Best Choice To Select The Best Choice To Complete Each Analogy:Complete Each Analogy: A ____________ is to an active site as a key is

to a lock.A. peptideB. proteinC. substrateD. productE. molecule

substrate

The best answer is substrate because the shape of a substrate perfectly fits the active site of its enzyme, just as the shape of a key fits its lock.

Fill In The Blanks…Fill In The Blanks…

Proteins are composed of _____________ acids, of which there are twenty different kinds. Enzymes are special proteins that affect the ____________ of biological reactions. Concentration of enzyme and substrate, pH and _____________ are all factors affecting the activity of enzymes. If an enzyme loses its shape, it becomes incapable of binding to a(n) ____________ molecule and carrying out its function.

amino

rate

temperature

substrate

Chemicals of Life IIIChemicals of Life III~Proteins and Nucleic Acids~

chemicals of life iii proteins and nucleic acids

Documents

dna nucleotides

nucleotides t

different nucleotides

phosphate group

dna subunits

different kinds of nucleotides

deoxyribose sugar

carbon sugar deoxyribose