topic 3: the chemistry of life

Topic 3: The Chemistry of

Life

Topic 3: The Chemistry of

Life

3.1: Chemical elements and water

3.1: Chemical elements and water★State that the most frequently

occurring chemical elements in living things are carbon, hydrogen, oxygen and nitrogen.

★State that a variety of other elements are needed by living organisms, including sulfur, calcium, phosphorus, iron and sodium

★State one role for each of the elements above



There are about 25 different elements that are essential for all life.

4 main elements that make up the majority of living matter are: hydrogen, carbon, oxygen, nitrogen

HCON

These elements are used in the molecular structures of all carbohydrates, proteins, lipids, and nucleic acids (DNA).

In addition, living organisms contain a variety of other elements which are extremely important, but are less common.



ElementExample role

in plantsExample role in

animals

Example role in

prokaryotes

Sulfur (S)

in some amino acids (building

blocks of proteins)

needed to make 2 of the 20 amino acids

that proteins contain

in some amino acids

Calcium (Ca)

co-factor in some enzymes

(speed up chemical reactions)

co-factor in some enzymes, component of bones, needed in DNA transcription

co-factor in some

enzymes

Phosphorus (P)

phosphate groups in ATP

(energy molecule)

phosphate groups in ATP, part of DNA

phosphate groups in

ATP



ElementExample role in plants

Example role in animals

Example role in

prokaryotes

Iron (Fe)

in cytochromes (enzymes in

cellular respiration-

the forming of ATP)

in cytochromes and in hemoglobin (on

red blood cells, binds with oxygen)

in cytochromes (proteins

for cell respiration)

Sodium (Na)

in membrane function

in membrane function (pumped into cytoplasm to

raise solute concentration), sending nerve

impulses

in membrane function



★Draw and label a diagram showing the structure of water molecules to show their polarity and hydrogen bond formation.

Water is the solvent of life and virtually all cells have water within (cytoplasm) and in the surrounding environment (intercellular fluid, pond water, etc)

Water is an incredibly abundant substance on Earth with many interesting properties which depend on its structure.



ARTICLE TIME!

Water Lust: Why All the Excitement When H2O is Found in Space?

Is finding water in the solar system enough to assume there is life on other planets?



Question #1: Which of the following chemical elements are part of biochemical molecules in living organisms?

A. silicon, helium, oxygen, iron

B. helium, carbon, sulfur, nitrogen

C. lead, oxygen, carbon, phosphorus

D. nitrogen, sulfur, phosphorus, iron

Answer: D, nitrogen/sulfur/phosphorus/iron



Question #2: Carbon, hydrogen, nitrogen and sulfur are elements found in living cells. Which is the least common?

A. Carbon

B. Hydrogen

C. Nitrogen

D. Sulfur

Answer: D, sulfur



Question #3: What is a role of sulfur in living organisms?

A. Formation of carbohydrates

B. Formation of proteins

C. Formations of teeth

D. Transmission of nerve impulses

Answer: B, formation of proteins



Water molecules consist of two hydrogen atoms bonded to an oxygen atom.

hydrogen atoms = slight positive charge

Hint: writing a capital H, is close to a +

oxygen atoms = slight negative charge

So water molecules have 2 poles - a positive hydrogen pole and a negative oxygen pole

This feature is called polarity.



The hydrogen and oxygen atoms in a single water molecule are held together by a polar covalent bond.

Covalent bond = sharing electrons

A bond forms between the positive pole of one water molecule and the negative pole of another.



★Outline the thermal, cohesive and solvent properties of water.

★Explain the relationship between the properties of water and its uses in living organisms as a coolant, medium for metabolic reactions and transport medium.



Name of property

Outline of the properties of water

Relationship between the properties of

water and its uses in living organisms

Cohesion

Water molecules stick to each other because of the hydrogen bonds

that form between them.

*why water forms droplets when spilled*why some organisms can "walk on water"

Strong pulling forces can be exerted to suck columns of water up to the tops of the tallest

trees in their transport systems. These

columns of water rarely break. Water is used

as a transport medium in the xylem of plants.



Youtube video: basilisk lizard running on water

These lizards are able to run on top of the water!

The relatively large surface area of their feet does does not break through the surface tension of the water as long as they keep running.

Have students pair up. Give each pair 4 items -- a regular drinking straw, a red coffee stirrer, a cup/beaker filled with water and a Sharpie marker. Have students put both the regular straw and the coffee stirrer into the cup. They should look carefully through the tubes and use the Sharpie marker to draw a line on the tube to mark the height of the water. Once students have done that, have them analyze their results. Why was there a difference in the height of the water between the regular straw and the coffee stirrer?

After some think time, ask different pairs to share. Which tube had a higher level of water in it? Was the result the same for every group? Why or why not? (lead students to the conclusion that diameter of the tube plays a huge role. If the diameter gets too large, the adhesive properties between the water and the side of the tube becomes less strong . . . causing the water not to rise as high.)

In agriculture, it is critically important that plants have incredibly small tubes within the xylem tissue that carry water and nutrients from the roots upwards into the body of the plant. If those tubes weren't small in diameter, plants would have a difficult time moving water and dissolved nutrients through their xylem tissue by capillary action. This same concept is also true in animals and humans. Our circulatory systems contain capillaries. Capillaries are incredibly small tubes that help move blood in our bodies. Since blood is mostly made of water, capillary action assists the pumping action of the heart to help keep blood moving in our blood vessels.



Question #4: Which diagram represents the polarity of a water molecule?

Answer: B



Question #5: Which diagram best illustrates the interactions between water molecules?

Answer: B



Name of property

Outline of the properties of

water

Relationship between the properties of water and

its uses in living organisms

Solvent properti

es

Different substances can

dissolve in water because of its

polarity. Particles with positive or

negative charges dissolve, like sodium ions. Enzymes also

dissolve in water.

Most chemical reactions in living organisms take place with water. Water

is the medium for metabolic (within cells)

reactions. Many substances can be dissolved in the water of the blood of animals and the sap of plants. Water

can be used as a transport medium.



Name of property

Outline of the properties of water

Relationship between the properties of

water and its uses in living organisms

Thermal properties: heat capacity

Water has large heat capacity - large

amounts of energy needed to raise its temperature. The

energy is needed to break some of the hydrogen bonds. Think: On a cold

night, a large body of water won't be as

cold as the air.

Blood, mainly composed of

water, carries heat from warmer parts

of the body to cooler parts.

Blood is used as a transport medium

for heat.



Name of property


water



Thermal properti

es: boiling point

The boiling point of water (100°C) is high, because to change it from a liquid to a gas

all of the hydrogen bonds

between the water molecules

have to be broken.

Almost everywhere on Earth that has life,

water is below boiling/above freezing.

As a liquid, rather than solid/gas, it can act as the medium for metabolic reactions.

Discuss lake effect - what do students think it means?

Lake effect snows occur when a mass of sufficiently cold air moves over a body of warmer water, creating an unstable temperature profile in the atmosphere.

As a result, clouds build over the lake and eventually develop into snow showers and squalls as they move downwind. The intensity of lake effect snow is increased when higher elevations downwind of the lake force the cold, snow-producing air to rise even further.

The most likely setting for this localized type of snowfall is when very cold Arctic air rushes over warmer water on the heels of a passing cold front, as often happens in the Great Lakes region during winter.

Winds accompanying Arctic air masses generally blow from a west or northwest direction, causing lake effect snow to fall on the east or southeast sides of the lakes.

For us, it signifies the strength of Lake Michigan's effect on the temperature of the area. During winter, the lake keeps us warmer and, during summer, we are cooler.

http://www.weather.com/encyclopedia/winter/temp.html

http://www.weather.com/encyclopedia/winter/precip.html#snow

http://www.weather.com/glossary/a.html#arcticair



Name of property


water



Thermal propertie

s: the cooling effect of evaporati

on

Hydrogen bonds must be broken

for water to evaporate. The

heat energy needed to break

the bonds is taken from the liquid water,

cooling it down.

Evaporation of water from plant leaves

(transpiration) and from the human skin

(sweat) has useful cooling effects.

Water can be used as a coolant.



Question #1: Which of the following chemical elements are part of biochemical molecules in living organisms?

A. silicon, helium, oxygen, iron

B. helium, carbon, sulfur, nitrogen

C. lead, oxygen, carbon, phosphorus

D. nitrogen, sulfur, phosphorus, iron

Answer: D, nitrogen/sulfur/phosphorus/iron



Question #2: Carbon, hydrogen, nitrogen and sulfur are elements found in living cells. Which is the least common?

A. Carbon

B. Hydrogen

C. Nitrogen

D. Sulfur

Answer: D, sulfur



Question #3: What is a role of sulfur in living organisms?

A. Formation of carbohydrates

B. Formation of proteins

C. Formations of teeth

D. Transmission of nerve impulses

Answer: B, formation of proteins



Question #4: Which diagram represents the polarity of a water molecule?

Answer: B



Question #5: Which diagram best illustrates the interactions between water molecules?

Answer: B



Question #6: What property of water makes it a good evaporative coolant?

A. High latent heat of evaporation

B. Relatively low boiling point

C. Volatility

D. Transparency

Answer: A, high latent heat of evaporation



Question #7: Blood is a water-based transport medium. Which property of water makes it a good transport medium?

A. Transparency

B. It has its greatest density at 4°C

C. High specific heat

D. Versatility as a solvent

Answer: D, versatility as a solvent

3.2: Carbohydrates, lipids, proteins3.2: Carbohydrates, lipids, proteinsLiving things are composed of an amazing array of molecules.

We can start to make sense of all of these molecules by classifying them into a molecule type.

Molecules of the same type have certain qualities in common .

3.2: Carbohydrates, lipids, proteins3.2: Carbohydrates, lipids, proteinsSome biochemically important molecules and their subcomponents/building blocks

MoleculeSubcomponents/building

blocksExample molecules

Carbohydrates

monosaccharides

disaccharidespolysaccharide

s

glucose/galactose/fructose

maltose/lactose/sucrosestarch/glycogen/

cellulose

Lipidsglycerol and fatty acids

triglycerides, phospholipids

Proteins (polypeptide

s)amino acids enzymes, antibodies

Nucleic acids

Nucleotides DNA, RNA

3.2: Carbohydrates, lipids, proteins3.2: Carbohydrates, lipids, proteins★Distinguish between organic and inorganic compounds.

Organic compounds: contain carbon found in living organisms

ALL organic molecules contain carbon, but not all carbon containing molecules are organic (ex: carbon dioxide is not organic)

Many of the carbons found in food you eat (carbs) will be eliminated from your body as carbon dioxide that you breathe out.

Inorganic compounds: do not contain carbon

3 types of organic compounds that are found in large amounts in living organisms:

Carbohydrates, lipids, and proteins

The molecules of many organic compounds are large and so are called macromolecules.

They are built up using small and relatively simple subunits.

3.2: Carbohydrates, lipids, proteins3.2: Carbohydrates, lipids, proteins

★Identify amino acids, glucose, ribose and fatty acids from diagrams showing their structure (specific names of amino and fatty acids not expected).


Amino Acids: Generalized structure because it can be one of 20 amino acids (look for central carbon)


Glucose: A monosaccharide, identified by its 6-carbon sugar (look for hexagon)


Ribose: A monosaccharide, identified by its 5-carbon sugar (look for pentagon).


Fatty Acids: Number of carbon atoms and bonding between carbon atom varies - both pics have same number of carbons, one is just condensed

3.2: Carbohydrates, lipids, proteins

3.2: Carbohydrates, lipids, proteins

★List 3 examples each of monosaccharides, disaccharides and polysaccharides.

★State one function of glucose, lactose and glycogen in animals, and of fructose, sucrose and cellulose in plants



Examples

Example of use in

animals

Example of use in plants

Monosaccharides

glucose

galactose

fructose

Glucose is carried by

the blood to transport energy to

cells throughout

the body (think

chemical fuel)

Fructose is used to

make fruits sweet-tasting,

attracting animals to disperse

seeds in the fruit


Examples

Example of use in

animals


Disaccharides

maltose

lactose

sucrose

Lactose is sugar in

milk, that provides energy to

young mammals until they

are weaned

Sucrose is carried by leaves to

other locations of the plant - transports

energy


Examples

Example of use in

animals


Polysaccharides

starch

glycogen

cellulose

Glycogen is used as a

short-term energy store in

liver and in muscles

Cellulose is used to

make strong fibers that are used to construct the plant cell wall


ARTICLE TIME!

Grassoline at the Pump

If you were just appointed as an environmental advisor to the president in 2013, would you tell him it would be wise to invest in cellulosic biofuels? Explain.

Question #8: Which of the following is an organic compound made by all plants?

A. Carbon dioxide

B. Lactose

C. DNA

D. Oxygen

Answer: C, DNA


Question #9: Which molecule is shown below?

A. Glucose

B. Galactose

C. Ribose

D. Sucrose

Answer: C, ribose


Question #10: Which of the following terms correctly describe the molecule below?

I. Monosaccharide

II. Ribose

III. Carbohydrate

A. I only B. I and III only

C. II and III only D. I, II, III

•Answer: B, I and III only


Question #11: Which describes these molecules correctly?

Answer: D

I II

A riboseamino acid

B glucoseamino acid

C ribose fatty acid

D glucose fatty acid


Question #12: Which of the following is a function of cellulose in plants?

A. Formation of cell walls

B. Formation of mitochondria

C. Storage of energy

D. Storage of fat

Answer: A, formation of cell walls


Question #13: What is the difference between galactose and lactose?

A. Galactose is a sugar found in milk but lactose is not found in milk.

B. Lactose is an enzyme and galactose is a hormone.

C. Lactose is the product of anaerobic respiration in humans and galactose is the product of anaerobic respiration in yeast.

D. Lactose is a disaccharide and galactose is a monosaccharide.

Answer: D

★Outline the role of condensation and hydrolysis in the relationships between monosaccharides, disaccharides and polysaccharides; between fatty acids, glycerol and triglycerides; and between amino acids and polypeptides.

This can be dealt with using equations with words or chemical formulas


Many organisms, including animals, rely on the foods they eat to gain the building block molecules which make up their own larger molecules.

When animals eat foods, the food is digested (or hydrolyzed) into the building blocks.

After these building blocks are transported to body cells, they are bonded together to form larger molecules once again.


Hydrolysis Reactions: Large molecules, like polypeptides/polysaccharides/triglycerides, can be broken down into smaller molecules.

Water molecules are used up in hydrolysis reactions

Hydrolysis reactions always split larger molecules into smaller subcomponents and USE water molecule(s) as one of the reactants


Hydrolysis Reactions

polypeptides + water → dipeptides or amino acids

polysaccharides + water → disaccharides or m monosaccharides

glycerides + water → fatty acids + glycerol


3 Questions for homework - write in your notebook

1. Explain why water makes a good coolant for animals.

Explain why it is harder to break down a polysaccharide than a monosaccharide. Give an example.

In a paragraph, discuss the properties that make water a universal molecule for all living things.


1. Explain why water makes a good coolant for animals.

Evaporation from the animals skin (sweat) has useful cooling effects. The heated water from the blood, evaporates from the body, cooling the animal off.

2. Explain why it is harder to break down a polysaccharide than a monosaccharide. Give an example.

Polysaccharides are complex, larger sugars, whereas monosaccharides are smaller sugars. An example of a polysaccharide is cellulose, which the human body has a hard time breaking down, in comparison to a simple sugar like glucose.

3. In a paragraph, discuss the properties that make water a universal molecule for all living things.

Water is a polar molecule, which means it has both a negative and positive charge. Cohesion is a property of water that allows water molecules to stick to each other, because of the opposite charges. Water is also an excellent solvent, meaning many substances can dissolve in water, like enzymes. In addition, water has several thermal properties, such as: a large heat capacity, a high boiling point, and the ability to act as a coolant.

Condensation reactions: two molecules are joined together to form a larger molecule.

Water is formed during these reactions, thus it is a product!

Condensation reactions are total reverse of hydrolysis reactions (simply reverse the arrow in one chemical equation and get the exact opposite, either hydrolysis or condensation)


Condensation Reactions

dipeptides or amino acids → polypeptides + water

disaccharides or monosaccharides → polysaccharides + + water

fatty acids + glycerol → glycerides + water


Water Lust Mel-Con HINTS:

Miss Hickey's Short hand:

SP - spelling is wrong

MI - main idea

Para - paragraph

Conc - conclusion

When you discuss: the article, need to introduce title, author!


No rhetorical questions - anywhere!

Student examples:

What is life exactly?

Why not have life on Mars?

How would water contribute to life in space?

No HCON - we use that in class, not a real thing - need to spell all of it out in your essay


Water is NOT AN ELEMENT - it is a compound!

Student examples:

Water is the element of life.

One of the most important elements on Earth is water.

Remember to keep your evidence/links focused back onto the main idea.

Lots of students are forgetting to discuss life on other plants, and just focusing on water in general


Introduction: Many students rattle off facts, in both the intro and conclusion. Needs to flow more, not be so staccato.

Student example of middle of intro:

Earth requires water itself. Water can also remain a liquid over a variety of temperatures. While also absorbing infrared radiation.

Example Better Paragraph:

Question #14: What chemical reaction is taking place when a dipeptide becomes two amino acids?

A. Condensation

B. Hydrolysis

C. Denaturation

D. Polymerization

Answer: B, hydrolysis


★State 3 functions of lipids

★Compare the use of carbohydrates and lipids in energy storage


Both lipids and carbohydrates are very efficient molecules for energy storage.

Lipids are biochemically important molecules that serve many functions.

Triglyceride lipids in solid form are fats.

In liquid form, triglycerides are oils.


Functions of Lipids:

1. Energy storage: in the form of fat in humans and oil in plants.

2. Heat insulation: a layer of fat under the skin reduces heat loss (think of layer of blubber of arctic animals)

3. Buoyancy: lipids are less dense than water so helps animals to float.


Both lipids and carbohydrates have advantages as energy storage compounds.

Carbohydrates are usually used for energy storage over short periods and lipids for long-term storage.


Advantages of lipids:

1. Lipids contain more energy per gram than carbohydrates so stores of lipids are lighter than stores of carbohydrates that contain the same amount of energy.

2. Lipids are insoluble in water, so they do not cause problems with osmosis in cells.


Advantages of carbohydrates:

1. Carbohydrates are more easily digested than lipids so the energy store by them can be released more rapidly.

2. Carbohydrates are soluble in water so are easier to transport to and from the store.


QUIZ TOMORROW!

3 Questions for homework - write in your notebook

1. Discuss the importance of 3 trace elements for living organisms.

2. Determine the difference between organic and inorganic - give an example of each.

3. Outline condensation and hydrolysis reactions using a different example of each.


QUIZ TODAY!

1. Discuss the importance of 3 trace elements for living organisms.

Sulfur is needed to make several amino acids, which are building blocks for proteins. Phosphorus is a component of ATP, which is an energy molecule in both plants and animals. Sodium helps with membrane transport in cells.


2. Determine the difference between organic and inorganic - give an example of each.

Organic contains carbon, inorganic does not have carbon

EX: DNA is organic - part of living things, primarily made of carbon

EX: Water is not organic - not living and doesn't have carbon


3. Outline condensation and hydrolysis reactions using a different example of each.

Condensation: produces water, builds up molecules

Equation:

Hydrolysis: loses water, breaks down molecules

Equation:


Tag Team Debate for the GRASSOLINE article

Introduction Round: In a tag team debate, each team will represent one side of the topic question. Each team has a set amount of time (10 minutes) to present its point of view. When it's time for the team to state its point of view, one speaker from the team takes the floor. That speaker can speak for no more than 1 minute, and must "tag" another member of the team to pick up the argument before his or her minute is up.


Free Style Round: After both teams have stated their case, it is now open for a free style/tag team debate. Rather than your team having the whole floor like in the introduction round, teams are allowed to jump in with comments against the other team.

2 debaters (one from each side) will be at the front of the room, counter-attacking/holding a discussion/asking each other questions for the other to answer

At any point, team members in the audience can raise their hand to be picked by their teammate at the front of the room - at which point they can "tag" each other, and switch spots.


NOTE: This activity is worth points. If you do not participate, you will receive a ZERO for the day.

THAT MEANS your team needs to remember to be respectful, and tag teammates (only if they volunteer) that have not had a chance to speak.

If you never raise your hand to debate, teammates won't pick you - it is not their fault, and you will receive a zero.

We are going to SKIP 3.3, 3.4, 3.5 - which is all DNA, and SHOULD be review from freshman biology.

We will pick up these topics of DNA much later, after the genetics topic.

★Define enzyme and active site.

★Explain enzyme-substrate specificity.

3.6: Enzymes3.6: Enzymes

Enzymes are globular proteins which act as catalysts of chemical reactions.

Enzymes are long chains of amino acids, with a 3-dimensional shape...think of a flexible metal wire that someone bends many times into a globular shape.

This complex shape is NOT random, it is very specific.


Most enzymes are specific - they catalyze (speed up) very few different reactions.

They therefore only have a very small number of possible substrates.

Substrate = Reactant

The substrates bind to a special region on the surface of the enzyme called the active site.


The active site of an enzyme has a very intricate and precise shape.

It also has distinctive chemical properties.

Active sites match the shape and chemical properties of their substrates.

Molecules of substrate fit the active site and are chemically attracted to it.

Other molecules either do not fit or are not chemically attracted, and therefore do not bind to the active site.


Analogy 1: Glove fits on a hand.

The active site of an enzyme matches the substrate in a similar way to the way a glove (active site) fits over a hand (substrate).


Analogy 2: Lock and key.

The enzyme's active site (lock) and the substrate (key).

Because the 3-dimensional shape of the internal portion of the lock is complex and specific, only one key will fit.

The same principle is generally true for enzymes and their substrates - they are specific for each other.


Enzymes are catalysts - they influence the rate of reactions.

As a general rule, a set of reactants in the presences of an enzyme will form product(s) at a faster rate than without the enzyme.

Enzymes cannot force reactions to occur that would not otherwise occur.

The real role of an enzyme in a reaction is to lower the energy level needed to start the reaction.


This energy is referred to as the activation energy of the reaction.

Thus, enzymes lower the activation energy of reactions.

Enzymes are not considered reactants and are not used up in the reaction.

An enzyme can function as a catalyst many, many times.


Enzymes so dramatically increase the rate of many reactions that they sometimes appear to be absolutely necessary for the reaction.

As already stated, enzymes cannot cause a reaction, only increase its rate.

At temperatures typical of living organisms, many reactions would have a reaction rate that is so low without enzymes, life as we know it would not be possible.


★Explain the effects of temperature, pH and substrate concentration on enzyme activity.

★Define denaturation

★Explain the use of lactase in the production of lactose-free milk.


Factors affecting enzyme activity:

1. Effect of Temperature

Both the enzyme and its substrate float freely in a fluid environment.

Because they are in constant motion, the rate of that motion is dependent on the temperature of the fluid.


Enzyme activity increases as temperature increases, often doubling with every 10°C rise.

Collisions between substrate (reactants) and active site happen more at higher temperatures due to faster molecular motion.

However, reactions that use enzymes do have a maximum temperature they can work at.


At high temperatures enzymes are denatured and stop working.

Denaturation: changing the structure of an enzyme (or other protein) so that it can no longer carry out its function (usually permanent).

Enzymes become denatured at high temps because heat causes vibrations inside enzymes which break bonds needed to maintain the structure of the enzyme.


3.6: Enzymes3.6: EnzymesQuestion #15: What is denaturation?

A. A structural change of a protein that results in the loss of its biological properties.

B. A change in the genetic code of an organism.

C. A change in the amino acid sequence of a protein causing a disruption of its 3D shape.

D. The process by which amino acids are broken down and ammonia is released.

Answer: A, structural change of a protein

3.6: Enzymes3.6: EnzymesQuestion #16: What happens as an enzyme becomes denatured?

A. The enzyme works faster

B. The enzyme works slower

C. The enzyme can perform a new role

D. The enzyme can make the reverse reaction proceed faster.

Answer: B, the enzyme works slower

2. Effect of pH

Review from freshman biology:


ACID BASE

0 7 14

H+ OH-

*lower the #, more acidic

*higher the #, more basic

The pH of a solution is dependent on the # of H+ (hydrogen ions) compared to OH- (hydroxide ions).

Any substance that gives off hydrogen ions, like HCL, is an acid and results in a solution lower than 7.

Any substance that gives off hydroxide ions, for example NaOH, is a base and results in a solution higher than 7.

Pure water has a neutral pH of 7 (H+ = OH-)


The optimum pH at which enzyme activity is fastest is different for each enzyme.

Many of the enzymes active in the human body are active when in an environment that is near neutral.

Few exceptions: pepsin, an enzyme active in the stomach, used to speed up digestions, is active in a highly acidic environment.


As pH increases or decreases from the optimum (varies depending on enzyme), enzyme activity is reduced.

Both acids and bases can denature enzymes.


ARTICLE TIME!

Panic Attacks as a Problem of pH

Rising Acidity in the Ocean: The Other CO2 Problem

Compare and contrast the pH dependency of humans and ocean organisms.


3. Effect of substrate concentration

Enzyme activity increases as substrate concentration increases.

Random collisions between substrate and active site happen more frequently when there are more substrates floating around.

BUT there is a limit.


The limit is due to the fact that enzymes have a maximum rate at which they can work.

At high substrate concentrations most of the active sites are occupied, so raising the substrate concentration has little effect on enzyme activity.

There are only so many locks (active sites) for the keys (substrates)


3.6: Enzymes3.6: EnzymesR

ate

of

en

zym

e-

cata

lyze

d r

eact

ion

Use of lactase in lactose-free milk:

Lactose is the sugar that is naturally present in milk.

Almost all humans are born with the ability to digest lactose.

We are born able to produce the enzyme lactase in our digestive tract.


Lactase is the enzyme that digests the disaccharide lactose into two monosaccharides.

lactose glucose + galactose

Hydrolysis!

The monosaccharides easier to absorb in the bloodstream.


lactase

Lactose intolerance: Most people lose the ability to produce lactase as they get older, most adults no longer produce a significant amount of lactase.

Normal milk/milk products enter their digestive tract and are not digested.

Instead, bacterial colonies in their intestines feed directly on the lactose (sugar).

This leads to such symptoms as cramping, excessive gas, and diarrhea.


Lactose intolerance has been shown to have an extremely high incidence in some ethnic groups (Asian) and be relatively low in others (European).

There are more adults on Earth with lactose intolerance than there are without it.

Thus, it can be argues that lactose intolerance has become the norm for adults.


Milk and milk products can be pre-treated with lactase.

Thus, the final product contains the enzyme for people who don't make enough of it.

The nutrients in the milk are not affected, but the person is able to absorb the sugars because they have been predigested.


Reasons for biotechnology companies to sell lactase to food manufacturing companies:

Some people are lactose intolerant and cannot drink more than about 250ml of milk per day unless it is lactose-reduced.

Galactose and glucose are sweeter than lactose, so less sugar needs to be added to sweet foods containing milk - like milk shakes or fruit yogurt.



ARTICLE TIME!

Worrying About Milk

Is drinking cow's milk destructive to human health?

Lead-in to next article/essay on the evolution of the enzyme lactase in the human population.

http://www.scientificamerican.com/podcast/episode.cfm?id=just-how-big-a-deal-is-milk-drinkin-11-02-23


3.6: Enzymes3.6: EnzymesQuestion #15: What is denaturation?

A. A structural change of a protein that results in the loss of its biological properties.

B. A change in the genetic code of an organism.

C. A change in the amino acid sequence of a protein causing a disruption of its 3D shape.

D. The process by which amino acids are broken down and ammonia is released.

Answer: A, structural change of a protein

3.6: Enzymes3.6: EnzymesQuestion #16: What happens as an enzyme becomes denatured?

A. The enzyme works faster

B. The enzyme works slower

C. The enzyme can perform a new role

D. The enzyme can make the reverse reaction proceed faster.

Answer: B, the enzyme works slower

3.6: Enzymes3.6: EnzymesQuestion #17: The graph below shows the effect of substrate concentration on enzyme activity. What conclusion can be drawn about section X of the graph?

Copy down graph, multiple choice questions on next slide.

3.6: Enzymes3.6: EnzymesA. The enzyme has started to denature and the reactions slows down.

B. The reaction has finished and the substrate has been used up.

C. The enzyme is saturated and is working at its maximum reaction rate.

D. Some of the enzyme has been consumed and the reaction has reached a plateau.

Answer: C, enzyme is working at max reaction rate

Question #18: Which of the following will cause an enzyme to permanently lose its properties?

I. Hydrolysis

II. Freezing to -20°C

III. Dissolving it in water

• A. I only B. II only

• C. I and II only D. I and III only

Answer: A, only hydrolysis

3.6: Enzymes3.6: EnzymesQuestion #19: What is lactase used for?

A. It is used to make sugar-free milk.

B. It hydrolyzes lactose to glucose and fructose

C. It decreases the acidity of the milk.

D. It improves the digestion of milk by some people

Answer: D, improves digestion of milk

Question #20: Which of the following graphs shows the relationship between substrate concentration and enzyme activity with a fixed concentration of enzyme?

Answer: C

3.7: Cell Respiration3.7: Cell Respiration

★Define Cell Respiration

★State that, in cell respiration, glucose in the cytoplasm is broken down by glycolysis into pyruvate, with a small yield of ATP


All living cells need a continual supply of energy.

Most of these processes require energy in the form of ATP (adenosine triphosphate).

ATP = energy molecule

ATP diffuses into any part of the cell and releases energy.


Cells break down (metabolize) their organic nutrients by way of slow oxidation (release of energy).

A molecule, such as glucose, is acted on by a series of enzymes.

The enzymes catalyze a series of reactions in which the covalent bonds are broken (oxidized) one at a time.


Each time a covalent bond is broken, a small amount of energy is released.

Ultimate goal: release energy in a controlled way to trap the energy in the form of ATP molecules.

Cell respiration: the controlled release of energy from organic compounds in cells to form ATP.

3.7: Cell Respiration3.7: Cell RespirationGlycolysis: FIRST step of cell respiration.

Glyco = sugar lysis = split

1. Glucose enters a cell through the plasma membrane, floats in the cytoplasm.

2. One enzyme modifies the glucose slightly. A 2nd enzyme modifies this molecule even more.

3.7: Cell Respiration3.7: Cell Respiration3. Then a series of reactions splits the 6-carbon glucose into 2 equal 3-carbon molecules.

Each of these 3-carbon molecules is called a pyruvate.

Some of the covalent bonds in the glucose were broken during this series of reactions.

The energy that was released from breaking the bonds forms a small number of ATP molecules.


VERY simplified version of glycolysis:

• Total yield of ATP: 2 ATP are used to initiate reaction, and 4 made = 2 ATP gained


Quick review:

ATP: 3 phosphates (TRI)

ADP: 2 phosphates (DI)

Renewable cycle of ATP formation and breakdown:

Used energy: ATP --> ADP

Energy ready: ADP --> ATP


Our cells make energy as they need it by adding a phosphate to ADP to ATP

This cycle of forming/breaking down ATP relieves the cells of having to store all of the ATP it needs.

There isn't enough room in cells to store all the energy they need everyday - our cells would be huge!


★Explain that, during anaerobic cell respiration, pyruvate can be converted in the cytoplasm into lactate, or ethanol and carbon dioxide, with no further yield of ATP.

★Explain that, during aerobic cell respiration, pyruvate can be broken down in the mitochondrion into carbon dioxide and water with a large yield of ATP.


Cell Respiration: A variety of biochemical pathways that can be used to metabolize (break down) glucose.

All of the pathways start with glycolysis.

Anaerobic Respiration: Making ATP without oxygen

Fermentation: The breakdown of organic molecules to produce ATP production in an anaerobic way

3.7: Cell Respiration3.7: Cell Respiration2 main anaerobic (without oxygen) pathways:

1. Alcoholic fermentation (AF)

Yeast (single-celled fungus) uses AF to generate ATP.

Yeast starts with glycolysis: takes in/breaks down glucose, net gain of 2 ATP.

Products are 2 pyruvate molecules.


Yeast, then converts both 3-carbon pyruvate molecules to molecules of ethanol.

Ethanol is a 2-carbon molecule, so a carbon atom is "lost" in this conversion.

The "lost" carbon atom is given off in a carbon dioxide molecule.


Both the ethanol and carbon dioxide that are produced are waste products - Good for us!

CO2 helps bread dough to rise.

The ethanol waste used in drinking alcohol production.


VERY simplified version of Alcoholic Fermentation:


Alcoholic Fermentation:


Question #21: How do cells capture the energy released by cell respiration?

A. They store it in molecules of carbon dioxide.

B. They produce glucose.

C. The energy is released as pyruvate.

D. They produce ATP

Answer: D, produce ATP

3.7: Cell Respiration3.7: Cell RespirationQuestion #22: Which of the following is part of the process of cellular respiration?

A. Exchange of gases across the surface of alveoli

B. Exchange of gases across the surface of capillaries

C. Glycolysis

D. Changes in the volume of the thoracic cavity

Answer: C, glycolysis

3.7: Cell Respiration3.7: Cell RespirationQuestion #23: Which of the following is the best definition of cell respiration?

A. A process needed to use energy, in the form of ATP, to produce organic compounds

B. A process used to provide oxygen to the atmosphere

C. A controlled release of energy, in the form of ATP, from organic compounds in cells

D. A controlled release of energy in the production of food from organic compounds.

Answer: C, controlled release of energy, ATP

3.7: Cell Respiration3.7: Cell Respiration2. Lactic Acid Fermentation (LAF)

Organisms that use an aerobic (w/oxygen) cell respiration pathway sometimes find themselves in a situation where they cannot supply enough oxygen to their cells.

EX: heavy exercise, feeling cramps!

If this is the case, then some of the glucose will follow the anaerobic pathway, called LAF

3.7: Cell Respiration3.7: Cell RespirationLactic Acid Fermentation:

3.7: Cell Respiration3.7: Cell RespirationLactic acid levels can be monitored in the bloodstream by athletes preparing for competition.

If an athlete shows no lactic acid in their bloodstream after training, then not demanding enough.

If the amount of lactic acid is too high, the training program can be decreased.

3.7: Cell Respiration3.7: Cell RespirationDONT WRITE: already in your notes!

Sum up anaerobic cell respiration:

If no oxygen is available, the pyruvate remains in the cytoplasm and is converted into a waste product that can be removed from the cell.

Waste in humans: lactate (lactic acid)

Waste in yeast: ethanol and carbon dioxide


Aerobic (with oxygen) cell respiration (CR): the most efficient pathway to produce ATP.

Any cell containing mitochondria (plants and animals) uses aerobic CR as its primary CR pathway.

This pathway also begins with glycolysis.


Inside the mitochondrion, the 2 pyruvates breaks down into carbon dioxide and water.

A large amount of ATP is produced as a result of these reactions.


VERY simplified version of Aerobic Respiration:

3.7: Cell Respiration3.7: Cell RespirationWhy is Aerobic CR more efficient than Anaerobic CR?

Anaerobic pathways do not completely oxidize (release energy) the glucose molecule.

This is why ethanol/lactic acid are produced - both represent portions of the original glucose that were not oxidized.

Aerobic cell respiration leaves no such by-products and results in a high yield of ATP.


Question #24: Which process produces the most ATP per molecule of glucose?

A. Anaerobic respiration in a yeast cell

B. Aerobic respiration in a bacterial cell

C. Glycolysis in a human liver cell

D. The formation of lactic acid in a human muscle cell.

Answer: B, aerobic respiration

3.7: Cell Respiration3.7: Cell RespirationQuestion #25: What happens during the pathway of glycolysis?

A. Glucose is broken down into pyruvate

B. Carbon dioxide is produced

C. More ATP is consumed than it is produced

D. Lactic acid is produced.

Answer: A, glucose broken down into pyruvate


Question #26: Which of the following processes produces CO2?

I. Glycolysis

II. Alcohol (ethanol fermentation)

III. Lactic acid production

A. I only B. II only

C. I and II only D. I, II, and III

Answer: B, alcohol/ethanol fermentation

Question #27: This diagram shows a biochemical pathway in a yeast cell, which of the following correctly identifies a compound in the diagram?

A. I is fat

B. II is pyruvate

C. III is lactate

D. IV is carbon dioxide

I

II

III IV


A. I is fat

B. II is pyruvate

C. III is lactate

D. IV is carbon dioxide

Answer: B, II is pyruvate

3.8: Cell Photosynthesis3.8: Cell Photosynthesis

★State that photosynthesis involves the conversion of light energy into chemical energy.

★State that light from the Sun is composed of a range of wavelengths (colors).


★State that chlorophyll is the main photosynthetic pigment.

★Outline the differences in absorption of red, blue and green light by chlorophyll


What you SHOULD know:

Humans use oxygen to produce energy molecules, a by product/waste is carbon dioxide

Plants use carbon dioxide to produce energy molecules, a by product/waste is oxygen

ARTICLE TIME!

Forests in the Gas

This article was published close to 20 years ago. Since then, do you think our forests will continue to succeed in a world of increasing CO2 or eventually reach a plateau?


3.8: Cell Photosynthesis3.8: Cell PhotosynthesisPlants and other photosynthetic organisms produce foods that begin food chains.

We count on the Sun to be a constant energy source for both warmth and food production for all of planet Earth.

Photosynthesis is the process used by plants and some other organisms to produce all their own organic substances (food), using only light energy and simple inorganic substances.

3.8: Cell Photosynthesis3.8: Cell PhotosynthesisThe sunlight that strikes our planet must be converted from light energy into a form of chemical energy during photosynthesis

The most common chemical energy produced from photosynthesis is the molecule glucose.

Remember, glucose is also the most common molecule that organisms use for fuel in the process of cell respiration!


The vast majority of plant leaves appear green to our eyes.

Plants contain a variety of different pigments.

The photosynthetic pigment that dominates in most plant species is the molecule chlorophyll, which is green.


Plants make use of the same part of the electromagnetic spectrum that our eyes are able to see.

We call this the visible portion of the spectrum.

Sunlight is called white light, but it is actually made up of a wide range of wavelengths, including red, green, and blue.


You can see these colors when you let sunlight pass through a prism.

The prism separates the colors because each of the colors is a different wavelength and is refracted in the prism to a slightly different angle.

Some substances called pigments can absorb light.

3.8: Cell Photosynthesis3.8: Cell PhotosynthesisThe main pigment used to absorb light in photosynthesis is chlorophyll.

The structure of chlorophyll allows it to absorb some colors or wavelengths of light better than others.

Red and blue light are absorbed more than green.

The green light that chlorophyll cannot absorb is reflected - making most chloroplasts and plant leaves look green.


Upper leaf section, these cells are very active in photosynthesis as is shown by the large number of chloroplasts.

3.8: Cell Photosynthesis3.8: Cell PhotosynthesisSubstances can do one of only two things when they are struck by a particular wavelength (color) of light; they can:

1. absorb that wavelength - if so, energy is being absorbed and may be used.

2. reflect that wavelength - if so, the energy is not being absorbed and you will SEE that color.

3.8: Cell Photosynthesis3.8: Cell PhotosynthesisWhen a plant leaf is hit by sunlight, the red and blue wavelengths of light are absorbed by chlorophyll and used for photosynthesis.

Almost all the energy of the green wavelengths is reflected, not absorbed.

Would plants grow best under red, blue or green light?

Red or blue, definitely not green light!

3.8: Cell Photosynthesis3.8: Cell PhotosynthesisLittle known facts:

The advice to wear light-colored clothing in warm months is good advice based on the principle that lighter colors reflect more energy and therefore keep you cooler.

In the fall, the colors leaves turn have been there all along absorbing light energy, but were hidden by the dominant pigment chlorophyll.


★State that light energy is used to produce ATP, and to split water molecules (photolysis) to form oxygen and hydrogen.

★State that ATP and hydrogen (derived from photolysis of water) are used to fix carbon dioxide to make organic molecules.


Photosynthesis produces sugar molecules as a food source for the plant.

Sugars, such as glucose, are held together by covalent bonds.

It required energy to create those covalent bonds and the source of that energy can ultimately be traced back to the Sun.

3.8: Cell Photosynthesis3.8: Cell Photosynthesis1st stage of photosynthesis: (light dependent reactions)

Some of the energy absorbed by chlorophyll is converted from light energy to chemical energy to produce ATP.

Also, light energy is also used to accomplish a reaction called photolysis of water.

Photolysis of water: A water molecule is split into its component elements: hydrogen and oxygen.

3.8: Cell Photosynthesis3.8: Cell PhotosynthesisThe oxygen that is split away during the photolysis of water is released from the plant leaf as a waste product.

That's great for us - plants release oxygen into the atmosphere.

For the plant, the useful products formed during this state of photosynthesis are ATP and hydrogen.

3.8: Cell Photosynthesis3.8: Cell Photosynthesis2nd stage of photosynthesis: (light independent reactions)

Carbon dioxide is absorbed from the environment for use in photosynthesis.

The carbon from it is used to make a wide range of organic substances (like glucose).

The conversion of carbon in a gas to a carbon in solid compounds is called carbon fixation.


Carbon fixation involves the use of hydrogen from photolysis and energy from ATP.

Summary: photosynthesis can be described as a series of reactions in which carbon dioxide and water are fixed into glucose, and oxygen is produced as a by-product (waste).


Photosynthesis chemical equation:

Carbon dioxide molecules are reactants

Oxygen and sugar molecules are products

6CO2 + 6H2O → C6H12O6 + 6O2


★Explain that the rate of photosynthesis can be measured directly by the production of oxygen or the uptake of carbon dioxide, or indirectly by an increase in biomass.

★Outline the effects of temperature, light intensity and carbon dioxide concentration on the rate of photosynthesis.


Measuring rates of photosynthesis:

Production of oxygen

Aquatic plants release bubbles of oxygen when

they carry out photosynthesis. If these bubbles are

collected, their volume can be measured.



Uptake of carbon dioxide

Leaves take in CO2 from the air or water around them, but this is difficult to measure directly. If CO2 is absorbed from water, the pH of the

water rises. This can be monitored with pH

indicators or with pH meters.



Increases in biomass

If batches of plants are harvested at a series of

times and the biomass of the batches is

determined, the rate of increase in biomass gives

an indirect measure of the rate of photosynthesis

in the plants.


Remember photosynthesis has carbon dioxide as a reactant, and oxygen as a product.

Cell respiration has oxygen as a reactant and carbon dioxide as a product.

But plants do both!

They do NOT cancel each other out.


Plants do not have muscle and other ATP-demanding tissues as do animals, so their need for ATP is far below animals.

Thus, cell respiration in plants is much lower.

Opposite is true for photosynthesis.


Photosynthetic rate is highly dependent on many environmental factors like intensity of light and air temp.

During the day, the rate of photosynthesis may be very high, and so the rate of carbon dioxide taken in, and the rate of oxygen being released will both be very high.


At night, the rate of photosynthesis may drop to zero.

At that time, a given plant may be giving off carbon dioxide and taking in oxygen to maintain its relatively low and consistent rate of cell respiration.

3.8: Cell Photosynthesis3.8: Cell PhotosynthesisGraph shows oxygen given off and taken in by a plant over 48 hours.

When the line intersect is at 0, the oxygen generated by photosynthesis is equal to the oxygen needed for cell respiration.

3.8: Cell Photosynthesis3.8: Cell PhotosynthesisEffect of changing light intensity

3.8: Cell Photosynthesis3.8: Cell PhotosynthesisEffect of changing temperature

3.8: Cell Photosynthesis3.8: Cell PhotosynthesisEffect of changing carbon dioxide concentration


Question #28: Which 2 colors of light does chlorophyll absorb most?

A. red and yellow

B. green and blue

C. red and green

D. red and blue

Answer: D, red and blue

3.8: Cell Photosynthesis3.8: Cell PhotosynthesisQuestion #29: Oxygen is produced during photosynthesis. What is the source of this oxygen inside the plant?

A. Air spaces in the leaf

B. Carbon dioxide

C. Water

D. Glucose

Answer: C, water

3.8: Cell Photosynthesis3.8: Cell PhotosynthesisQuestion #30: Which of the following colors of light is absorbed the most by chlorophyll?

A. Blue

B. Green

C. Yellow

D. Orange

Answer: A, blue


Question #31: What is light energy used for during photosynthesis?

A. To produce carbon dioxide

B. To produce water molecules

C. To produce ATP

D. To break down sugar molecules

Answer: C, to produce ATP

3.8: Cell Photosynthesis3.8: Cell PhotosynthesisQuestion #32: How can the rate of photosynthesis of a plant be directly measured?

A. By measuring the rate of oxygen produced

B. By measuring the rate of carbon dioxide produced

C. By measuring the rate of plant growth

D. By measuring the rate of light absorbed

Answer: A, measure rate of O2 produced

Question #33: A plant is exposed to increasing light intensity from very dim to bright light, while the carbon dioxide concentration and temperature are kept at an optimum level. What will happen to the rate of oxygen production?

A. It will increase exponentially

B. It will remain constant

C. It will decrease to a minimum level

D. It will increase to a maximum level

Answer: D, increase to a maximum level

3.8: Cell Photosynthesis3.8: Cell PhotosynthesisQuestion #34: Which type of light is least useful for photosynthesis in terrestrial plants?

A. Blue

B. Green

C. White

D. Red

Answer: B, green

3.8: Cell Photosynthesis3.8: Cell PhotosynthesisQuestion #35: What is the source of oxygen released into the air as a product of photosynthesis?

A. Chlorophyll

B. Carbon dioxide only

C. Water only

D. Both water and carbon dioxide

Answer: C, water only

topic 3: the chemistry of life

Documents

following chemical elements

nitrogenhconthese elements

main elements

different elements

elements above3

role of sulfur

chemical reactionscofactor

living organisms