AP BIOLOGY Emergence of Organic Molecules Summer 2013 - - PDF document

Slide 1 / 131

AP BIOLOGY Emergence of Organic Molecules

www.njctl.org Summer 2013

Slide 2 / 131 Emergence of Organic Molecules

· The Early Universe & Earth · Organic Compounds · Development of Life

Click on the topic to go to that section

Slide 3 / 131

The Early Universe & Earth

Return to Table of Contents

Slide 4 / 131 The Beginning...

Many scientists have provided evidence of an event called the "Big Bang". This event is said to have occurred about 14 billion years ago.

Slide 5 / 131

Big Bang Theory

This theory states that all of the mass in the universe was once compacted into one small point. The universe was then created by a massive explosion and it has been expanding ever since.

photo: NASA

Slide 6 / 131

Big Bang Theory

Every piece of matter in the universe came from this one point ... this one explosion. Since everything is made of matter, this means that the material that makes up everything in the universe came from this one point in time.

Slide 7 / 131 Evidence Supporting the Big Bang Theory

If no one was around 14 billion years ago, then how did this theory come about? In the early 1900's, an astronomer* named Edwin Hubble, discovered that various galaxies were spreading apart by measuring their location in the sky. Due to this finding, he concluded the entire universe must be expanding.

*astronomer: a scientist who studies planets, stars, and galaxies

Slide 8 / 131 Evidence Supporting the Big Bang Theory

Scientists explain this phenomenon by claiming that the universe expanded from a single point. To visualize this, think

• f a stone that hits the

surface of the water... The water will ripple out from that one point and expand larger and larger.

Slide 9 / 131

Our Expanding Universe

The universe will continue to expand, as it always has since the Big Bang occurred. Stephen Hawking is one of the most famous physicists in the world today. He has researched and spoken on the expanding universe.

Click here to hear Stephen Hawking talk about this idea, the expanding universe

Slide 10 / 131

1 The Big Bang Theory...

A

created all the elements on the periodic table

B

expanded all matter in the universe from a single point

C

states that the universe is expanding linearly

D

is just a tv show

Slide 11 / 131

1 The Big Bang Theory...

A

created all the elements on the periodic table

B

expanded all matter in the universe from a single point

C

states that the universe is expanding linearly

D

is just a tv show

[This object is a pull tab]

Answer B

Slide 11 (Answer) / 131

2When closely examined the universe appears red. This is due to...

A

the short wavelength of red light

B

the high frequency of red light

C

the doppler effect as the universe expands

D

the high percentage of red giant stars

Slide 12 / 131

2When closely examined the universe appears red. This is due to...

A

the short wavelength of red light

B

the high frequency of red light

C

the doppler effect as the universe expands

D

the high percentage of red giant stars

[This object is a pull tab]

Answer C

Slide 12 (Answer) / 131

The age of the universe is about 14 billion years. The age of Earth is about 4.6 billion years. The early universe was almost completely made of hydrogen (H

2) and helium (He).

None of the heavier elements (above helium) existed at the dawn of the universe.

The Early Universe

Click here to see David Christian's explanation of the formation of the Universe

Slide 13 / 131

Earth formed about 10 billion years after the start of the universe, about 4.6 billion years ago. In those 10 billion years, generations of stars were born, and died. All the heavier atoms on the periodic table were created by nuclear fusion inside those stars, or when they exploded.

The Early Universe Slide 14 / 131

When the early stars died explosively (novae and supernovae), those heavier elements were scattered into space. When Earth, and its solar system, formed, it was in a cloud

• f matter which included all the naturally occurring elements

in the periodic table. No new elements have been created since Earth formed. This means that all the atoms in you and your world, other than hydrogen and helium, were once inside a star, long ago.

The Early Universe Slide 15 / 131

3 Which came first?

A

atoms

B

electromagnetic force

C

neutrons

D

quarks

Slide 16 / 131

3 Which came first?

A

atoms

B

electromagnetic force

C

neutrons

D

quarks

[This object is a pull tab]

Answer B

Slide 16 (Answer) / 131

4 Where did all the elements heavier than hydrogen and helium

come from?

A the Big Bang B the sun C stars that we see at night D stars that exploded long ago

Slide 17 / 131

4 Where did all the elements heavier than hydrogen and helium

come from?

A the Big Bang B the sun C stars that we see at night D stars that exploded long ago

[This object is a pull tab]

Answer D

Slide 17 (Answer) / 131

5 Carbon was formed in nuclear fusion reactions such as...

A

2H + He C

B

He + He + He C

C

He + Li C

D

2H + Li C

Slide 18 / 131

5 Carbon was formed in nuclear fusion reactions such as...

A

2H + He C

B

He + He + He C

C

He + Li C

D

2H + Li C

[This object is a pull tab]

Answer B

Slide 18 (Answer) / 131

The most prevelant were: · water vapor (H

2O),

· carbon dioxide (CO2), · nitrogen (N2), · hydrogen sulfide (H2S), · methane (CH4), and · ammonia (NH3).

Early Earth

Studies of volcanos suggest the early atmosphere of Earth was composed of a mix of chemical compounds.

Slide 19 / 131

Earth was also subject to intense lightning and ultraviolet radiation. It is ironic that life arose under conditions that included bombardment by UV radiation - Today, depletion of the ozone layer that protects us from this radiation is a major environmental concern!

UV Radiation Slide 20 / 131

Early Earth atmosphere contained practically no oxygen, as this gas is not expelled during volcanic eruptions. Oxygen gas first entered the atmosphere as a byproduct of

• photosynthesis. Initial oxygen production reacted with iron,

producing banded iron formations. These geological formations have been used to date the evolution of photosynthesis to approximately 2.45 billion years ago.

Oxygen in the Atmosphere Slide 21 / 131

As Earth's crust cooled and solidified, water vapor condensed to create oceans. Water is thought to have been brought to Earth by comets in the early solar system.

Early Earth's Oceans Slide 22 / 131

6 Scientists hypothesize that Earth's early atmosphere contained

substances such as: A

• xygen, carbon dioxide and hydrogen gas

B nitrogen, oxygen, and water vapor C water vapor, methane, and oxygen D ammonia, water vapor, and hydrogen gas

Slide 23 / 131

6 Scientists hypothesize that Earth's early atmosphere contained

substances such as: A

• xygen, carbon dioxide and hydrogen gas

B nitrogen, oxygen, and water vapor C water vapor, methane, and oxygen D ammonia, water vapor, and hydrogen gas

[This object is a pull tab]

Answer D

Slide 23 (Answer) / 131

7 What is believed to have been the source of water for Earth?

A nuclear fission B chemical reactions on Earth C electrolysis D comets

Slide 24 / 131

7 What is believed to have been the source of water for Earth?

A nuclear fission B chemical reactions on Earth C electrolysis D comets

[This object is a pull tab]

Answer D

Slide 24 (Answer) / 131

Three-quarters of Earth’s surface is submerged in water. The abundance of water is the main reason the Earth is habitable.

The Blue Planet

image courtesy NASA

Slide 25 / 131

A water molecule consists of two hydrogen atoms covalently bonded to one oxygen atom. The more electronegative oxygen atom pulls the electrons from the hydrogen atoms toward it, resulting in an uneven distribution of charge.

Water Molecules

Slight Positive Charge Slight Negative Charge

Slide 26 / 131

Water: Polar Molecule

Since a water molecule has a positive end and a negative end it is called a polar molecule. This property of water causes it to act like a magnet, attracting

• ther molecules that have positive and negative poles.

Slide 27 / 131 Properties of Water

The polarity of water gives it several important properties that allowed life to emerge on Earth: · Ability to moderate temperature · Versatility as a solvent · Cohesive behavior

Slide 28 / 131 Moderate Temperature

Water has a very high specific heat. This means that a great amount of energy is needed to raise the temperature of water even a few degrees. Because of this, temperature on the Earth's surface can undergo extreme variations - between night and day, or between seasons - without its water freezing or boiling away. Why is this important in the development of life on Earth?

Slide 29 / 131

Universal Solvent

A solution is a homogeneous mixture of substances. An aqueous solution has water as the solvent. Water is sometimes referred to as the "universal solvent" because

• f its ability to dissolve most compounds.

Life's chemical reactions need to occur in solution. In water, nutrients can dissolve and chemical reactions can occur.

Solute Solvent Solvent dissolves solute in solution

Slide 30 / 131

Hydrogen Bonds

Cohesive Behavior

The polarity of water molecules causes them to be attracted to each other. Weak hydrogen bonds form between the hydrogens on one water molecule and the oxygen atoms on another to form liquid water. Attraction between water molecules is termed cohesion. Attraction between a water and a non-water molecule is termed adhesion.

Slide 31 / 131 Cohesive Behavior

This property allows:

· plants to pull water up through their roots · small insects to walk on water · and most importantly, water to bend carbon (organic) molecules into 3-D shapes.

Slide 32 / 131

8 In a water molecule, hydrogen and oxygen are bonded

together by:

A

Ionic bonds

B

Covalent bonds

C

Hydrogen bonds

D

Van der waals forces

Slide 33 / 131

8 In a water molecule, hydrogen and oxygen are bonded

together by:

A

Ionic bonds

B

Covalent bonds

C

Hydrogen bonds

D

Van der waals forces

[This object is a pull tab]

Answer B

Slide 33 (Answer) / 131

9 Which of the following best describes a hydrogen bond? A

formed through an electrostatic attraction between two oppositely charged ions

B

formed by the equal sharing of electrons between to atoms

C

the attractive force between neutral molecules

D

the attractive force between the hydrogen attached to an electronegative atom of one molecule and an electronegative atom of a different molecule

Slide 34 / 131

9 Which of the following best describes a hydrogen bond? A

formed through an electrostatic attraction between two oppositely charged ions

B

formed by the equal sharing of electrons between to atoms

C

the attractive force between neutral molecules

D

the attractive force between the hydrogen attached to an electronegative atom of one molecule and an electronegative atom of a different molecule

[This object is a pull tab]

Answer D

Slide 34 (Answer) / 131

10 Which property of water accounts for the other

properties?

A

cohesion

B

adhesion

C

polarity

D

high specific heat

Slide 35 / 131

10 Which property of water accounts for the other

properties?

A

cohesion

B

adhesion

C

polarity

D

high specific heat

[This object is a pull tab]

Answer C

Slide 35 (Answer) / 131

Organic Compounds

Return to Table of Contents

Slide 36 / 131

Organic Monomers Formed

Three of the four organic molecules necessary for life to form are polymers, chains of monomers linked together by covalent bonds.

Monomers are highlighted in blue

Slide 37 / 131

Organic Monomers Review

Can you name the 3 organic molecules that are polymers? Nucleic Acids (DNA/RNA) - Proteins - Carbohydrates Can you name the monomers for each of these? Nucleotides - Amino Acids - Monosaccharides (sugars) Can you name the organic molecule that is not a polymer? Lipids/Fats

Slide 38 / 131

Source of Organic Monomers

There are two theories for the source of organic monomers. Which of these theories do you think is true? How would you go about proving one of these theories? · Arrival on Earth from space · Creation on Earth through chemical reaction

Slide 39 / 131

Organic Monomers from Space

The dust in the solar system, from which Earth formed, was rich in organic chemicals. Meteorites striking Earth would have hit with lower velocity since the atmosphere was thicker;

• rganic components would have

survived.

Slide 40 / 131

Organic Monomers from Space

We find organic chemicals in old meteorites discovered even today, such as this one. Also, it's estimated that several million kg* (5,000,000 pounds) of organic chemicals fall as cosmic dust to Earth each year.

*The Story of Life , Richard Stockton, 2003, pg. 11

Slide 41 / 131

In the 1920's, two scientists (Oparin and Haldane) proposed that

• rganic chemistry could have evolved in the early Earth's atmosphere

because it contained no oxygen. The oxygen-rich atmosphere of today is corrosive and breaks molecular bonds.

Organic Monomers From Reactions

Slide 42 / 131

In 1953, Stanley Miller used Oparin and Haldane's original idea and tested a hypothesis involving an artificial mixture of inorganic molecules. In his experiment, he stimulated the conditions thought to be found on primitive Earth. Within days, the experiment produced some of the 20 amino acids presently found in organisms, as well as other organic molecules.

Organic Monomers From Reactions

Slide 43 / 131

Stanley Miller's Experiment

the primeval sea the early atmosphere lightning rain

Slide 44 / 131

Recent experiments, improving on Miller's, have produced most of the naturally occurring organic molecules including:

Organic Monomers From Reactions

· amino acids · sugars · lipids · nucleotides

Slide 45 / 131

Absence of Oxygen in the atmosphere

• O2 would have

broken down any large organic molecules by accepting electrons.

High energy input - at that point in time, the sun was producing

massive amounts of ultraviolet radiation

Micromolecules- the inorganic molecules had to be in the

atmosphere and primitive oceans

Time - adequate time had to pass to give the molecules a chance

to form, react, and reform.

Four Conditions Required for Chemical Evolution Slide 46 / 131

11 Miller and other scientists have shown that

A simple cells can be produced in a laboratory B amino acids and sugars could be produced from inorganic molecules C cells survived in the primitive atomosphere D life on early earth required material from space

Slide 47 / 131

11 Miller and other scientists have shown that

A simple cells can be produced in a laboratory B amino acids and sugars could be produced from inorganic molecules C cells survived in the primitive atomosphere D life on early earth required material from space

[This object is a pull tab]

Answer B

Slide 47 (Answer) / 131

12 Which of the following is not a condition for the formation of

• rganic molecules?

A a long period of time B inorganic micromolecules in the system C presence of oxygen in the atmosphere D high energy input

Slide 48 / 131

12 Which of the following is not a condition for the formation of

• rganic molecules?

A a long period of time B inorganic micromolecules in the system C presence of oxygen in the atmosphere D high energy input

[This object is a pull tab]

Answer C

Slide 48 (Answer) / 131

13 Some evidence supports the theory that organic molecules and

life arose deep in the oceans on or near hydrothermal vents. These vents would replace which variable in Miller experiment?

A atmosphere B rain C

lightning

D

primeval sea

Slide 49 / 131

13 Some evidence supports the theory that organic molecules and

life arose deep in the oceans on or near hydrothermal vents. These vents would replace which variable in Miller experiment?

A atmosphere B rain C

lightning

D

primeval sea

[This object is a pull tab]

Answer C

Slide 49 (Answer) / 131

Organic Monomers Combined to Form Polymers

Polymers are formed through a process called dehydration synthesis Dehydration the process of removing water from a compound

• r molecule

Synthesis the combining of separate parts to make a new whole word breakdown

Slide 50 / 131

The process of chemical evolution relies on molecules reacting with

• ne another to form new molecules.

Reacting together also involves breaking molecules apart. This process is called Hydrolysis: Hydro (water) Lysis (splitting)

Hydrolysis

Slide 51 / 131

14 Which is true about dehydration synthesis?

A

• ne monomer loses a hydrogen atom, the other loses a

hydroxyl group B electrons are shared between the joined monomers C water is formed when monomers join D covalent bonds are formed between monomers E all of the above are true

Slide 52 / 131

14 Which is true about dehydration synthesis?

A

• ne monomer loses a hydrogen atom, the other loses a

hydroxyl group B electrons are shared between the joined monomers C water is formed when monomers join D covalent bonds are formed between monomers E all of the above are true

[This object is a pull tab]

Answer E

Slide 52 (Answer) / 131

15 The results of dehydration synthesis can be reversed by A condensation B hydrolysis C polymerization D adding an amino group

Slide 53 / 131

15 The results of dehydration synthesis can be reversed by A condensation B hydrolysis C polymerization D adding an amino group

[This object is a pull tab]

Answer B

Slide 53 (Answer) / 131

16 The following equation is an example of:

A

dehydration synthesis

B

hydrolysis

C5H12 + H2O C3H7OH + C2H6 Slide 54 / 131

16 The following equation is an example of:

A

dehydration synthesis

B

hydrolysis

C5H12 + H2O C3H7OH + C2H6

[This object is a pull tab]

Answer B

Slide 54 (Answer) / 131

17 The following equation is an example of:

A

dehydration synthesis

B

hydrolysis

C5H12 + C3H7OH C8H18 + H2O Slide 55 / 131

17 The following equation is an example of:

A

dehydration synthesis

B

hydrolysis

C5H12 + C3H7OH C8H18 + H2O

[This object is a pull tab]

Answer A

Slide 55 (Answer) / 131

Hydrocarbons form the framework from which the 4 different classes of macromolecules (large molecules) have been derived.

Biological Macromolecules

· Carbohydrates · Nucleic Acids · Proteins · Lipids

Slide 56 / 131

The general formula for a carbohydrate is

CxH2xOx

Some possible formulas for carbohydrates are:

Formula for Carbohydrates

Carbohydrates have equal amounts of carbon and oxygen atoms, but twice as many hydrogen atoms. · C6H12O6 · C8H16O8 · C9H18O9

Slide 57 / 131

The simplest sugars. Examples include glucose and fructose. In solution, they form ring-shaped molecules. The basic roles of simple sugars are as:

• fuel to do work,
• the raw materials for carbon backbones
• the monomers from which larger

carbohydrates are synthesized.

Monosaccharides Slide 58 / 131

Sugars all have several hydroxyl (OH-) groups in their structure that makes them soluble in water.

C

Glucose Fructose (monosaccharides)

Carbohydrate Solubility

Note: the names of sugars typically end in "ose".

Slide 59 / 131

Cells link 2 simple sugars together to form disaccharides Disaccharide formation is another example of a dehydration reaction, the same reaction used to create proteins The most common disaccharide is sucrose (glucose + fructose)

Disaccharides Slide 60 / 131

18 Which of the following is an example of a monosaccharide? A sucrose B

glucose

C fructose D B & C

Slide 61 / 131

18 Which of the following is an example of a monosaccharide? A sucrose B

glucose

C fructose D B & C

[This object is a pull tab]

Answer D

Slide 61 (Answer) / 131

19 Saccharides are soluble in water because... A They are nonpolar molecules B They can form hydrogen bonds C

Carbon is highly electronegative

D

They are unsaturated

Slide 62 / 131

19 Saccharides are soluble in water because... A They are nonpolar molecules B They can form hydrogen bonds C

Carbon is highly electronegative

D

They are unsaturated

[This object is a pull tab]

Answer B

Slide 62 (Answer) / 131

20 What is another name for simple carbohydrates?

A sugars B saccharides C monosaccharides D all of the above

Slide 63 / 131

20 What is another name for simple carbohydrates?

A sugars B saccharides C monosaccharides D all of the above

[This object is a pull tab]

Answer D

Slide 63 (Answer) / 131

Polysaccharides are polymers of glucose. Different organisms link monosaccharides together, using dehydration reactions, to form several different polysaccharides. The most important 3 are starch, glycogen, and cellulose.

Polysaccharides Slide 64 / 131

Polysaccharides: Starch

Starch is used for long term energy storage in plants. Can be branched or unbranched.

Slide 65 / 131 Polysaccharides: Glycogen

Glycogen has the same kind of bond between monomers as starch but it is always highly branched. It is used for long term energy storage in animals. It's used in muscles to provide a local supply of energy when needed. Glycogen is broken down to

• btain glucose.

Slide 66 / 131 Polysaccharides: Cellulose

Cellulose has a different kind of bond between monomers, forming chains that are cross- linked by hydrogen bonds. Cellulose is a carbohydrate used to make cell walls in plants.

Slide 67 / 131

In order for cells to obtain energy from polysaccharides, they must be first broken down into monosaccharides. Hydrolysis occurs, breaking the polysaccharide into glucose molecules.

Getting Energy Slide 68 / 131

21 The fundamental unit of polysaccharides is

A fructose B glucose C sucrose D A and B

Slide 69 / 131

21 The fundamental unit of polysaccharides is

A fructose B glucose C sucrose D A and B

[This object is a pull tab]

Answer B

Slide 69 (Answer) / 131

22 Starch and glycogen are both used for energy storage. Which of the

following is not true of these two polysaccharides?

A

breakdown of these molecules produces carbon dioxide

B

they contain easily hydrolyzed bonds

C

they are products of photosynthesis

D

synthesis of these molecules is endergonic

Slide 70 / 131

22 Starch and glycogen are both used for energy storage. Which of the

following is not true of these two polysaccharides?

A

breakdown of these molecules produces carbon dioxide

B

they contain easily hydrolyzed bonds

C

they are products of photosynthesis

D

synthesis of these molecules is endergonic

[This object is a pull tab]

Answer C

Slide 70 (Answer) / 131

23 Cellulose is found in plants but not animals,

because...

A

It is produced by chloroplasts

B

It is the structural molecule of cell walls

C

It requires more energy to produce; plants receive unlimited energy from sunlight

D

It provides the green coloration to plants

Slide 71 / 131

23 Cellulose is found in plants but not animals,

because...

A

It is produced by chloroplasts

B

It is the structural molecule of cell walls

C

It requires more energy to produce; plants receive unlimited energy from sunlight

D

It provides the green coloration to plants

[This object is a pull tab]

Answer B

Slide 71 (Answer) / 131

Nucleic acids are compounds consisting of carbon, hydrogen,

• xygen, nitrogen, and phosphorus.

Nucleic Acids

The two main types of nucleic acids are DNA and RNA Nucleic acids are chains of nucleotides linked together by phosphodiester bonds. nucleotide nucleotide nucleotide Nucleic Acid

Slide 72 / 131

Nucleotides have three parts: a sugar a base (a nitrogen compound) a phosphate

Parts of a Nucleotide Slide 73 / 131

Sugars

Ribonucleic Acid (RNA) uses the sugar ribose, while Deoxyribonucleic Acid (DNA) uses the sugar deoxyribose. Here's the difference. Ribose Deoxyribose

Slide 74 / 131 Slide 75 / 131 Slide 76 / 131

Each strand is unique due to its sequence of

• bases. In this way, genetic information is stored

in the sequence of nucleotides. Since the bases are not part of the sugar or the bond, the base sequence is independent of

• them. Any base sequence is possible.

Nucleotides Slide 77 / 131

24 The creation of a phosphodiester bond involves the

removal of ____ from the nucleotides:

A

phosphates

B

glucose

C

water

D

nucleic acids

Slide 78 / 131

24 The creation of a phosphodiester bond involves the

removal of ____ from the nucleotides:

A

phosphates

B

glucose

C

water

D

nucleic acids

[This object is a pull tab]

Answer C

Slide 78 (Answer) / 131

25 Which of the following is not a component of a nucleotide?

A phosphate group B nitrogenous base C 5-carbon sugar D glucose

Slide 79 / 131

25 Which of the following is not a component of a nucleotide?

A phosphate group B nitrogenous base C 5-carbon sugar D glucose

[This object is a pull tab]

Answer D

Slide 79 (Answer) / 131

26 Which base is found in RNA but not DNA?

A Cytosine B Uracil C Guanine D Adenine

Slide 80 / 131

26 Which base is found in RNA but not DNA?

A Cytosine B Uracil C Guanine D Adenine

[This object is a pull tab]

Answer B

Slide 80 (Answer) / 131

27 Adenine would be characterized as a purine.

True False

Slide 81 / 131

27 Adenine would be characterized as a purine.

True False

[This object is a pull tab]

Answer TRUE

Slide 81 (Answer) / 131

Slide 82 / 131 Slide 82 (Answer) / 131

29 Pyrimidines are bases with single carbon rings.

True False

Slide 83 / 131

29 Pyrimidines are bases with single carbon rings.

True False

[This object is a pull tab]

Answer TRUE

Slide 83 (Answer) / 131

30 Guanine and adenine do not pair because...

A They create different numbers of hydrogen bonds B

They are both purines

C

They are not found in the same nucleic acid

D

They both have a single ring

Slide 84 / 131

30 Guanine and adenine do not pair because...

A They create different numbers of hydrogen bonds B

They are both purines

C

They are not found in the same nucleic acid

D

They both have a single ring

[This object is a pull tab]

Answer A

Slide 84 (Answer) / 131

RNA

RNA is usually single stranded. As a result, it can take on many different shapes. Hydrogen bonds form between different bases, and between bases and water. These bonds cause RNA to form different shapes. Different sequence of bases = different shapes

A U C G Slide 85 / 131

RNA World Hypothesis

The RNA world hypothesis proposes that self-replicating RNA molecules were the precursors to early life. Evidence to support this hypothesis includes the observation that many of the most critical components of cells, are composed of RNA or substances closely related to RNA. In early life, RNA is believed to have played many roles that have now been taken over by more specific molecules. RNA's role is still essential, but more limited than it once was.

Function Then Now catalyze reactions RNA Proteins store energy RNA's phosphate group ATP store genetic information RNA DNA

Slide 86 / 131

DNA is double-stranded. It only forms one shape: the double-helix. Pair bonding between nucleotides still occurs, but in DNA it is between guanine (G) and cytosine (C) and between adenine (A) and thymine (T)

DNA

Adenine Thymine Cytosine Guanine

A T C G Slide 87 / 131

Proteins are compounds consisting of carbon, hydrogen and

• xygen, nitrogen, and sometimes sulfur.

Proteins also called peptides

also called polypeptides.

Proteins

Proteins are chains of amino acids linked together by peptide bonds. There are 20 amino acids used to construct the vast majority of

• proteins. While there are a few others that are sometimes

used, these 20 are the "standard" amino acids. All life on Earth uses virtually the same set of amino acids to construct its proteins.

Slide 88 / 131

amine group (NH3) side chain carboxyl group (COOH) Amino Acids always include an amine group (NH3), a carboxyl group (COOH) and a side chain that is unique to each amino acid.

Components of Amino Acids

The side chain (sometimes called the R-group) determines the unique properties of each amino acid. Here it is symbolized by the letter "R".

Slide 89 / 131

The 3 in the light blue box are basic ("amine" group in the side chain). The 2 in the magenta box are acidic ("carboxyl" group in the side chain). The 8 amino acids in orange are nonpolar and hydrophobic.The

• thers are polar and hydrophilic.

The unique side chains are shown in blue. The common "amine" group (NH3) and "carboxyl" group (COOH) are shown in black.

http://www.bioss.ac.uk/~dirk/genomeOdyssey/go_1955_to_66.html

Amino Acids Slide 90 / 131

31 Glucose molecules are to starch as ___________ are to

proteins. A

• ils

B fatty acids C amino acids D waxes

Slide 91 / 131

31 Glucose molecules are to starch as ___________ are to

proteins. A

• ils

B fatty acids C amino acids D waxes

[This object is a pull tab]

Answer C

Slide 91 (Answer) / 131

32 Which component of amino acids varies between the 20 different

kinds? A Amine group B Carboxyl group C Hydroxyl group D R-group

Slide 92 / 131

32 Which component of amino acids varies between the 20 different

kinds? A Amine group B Carboxyl group C Hydroxyl group D R-group

[This object is a pull tab]

Answer D

Slide 92 (Answer) / 131

33 Which of the following statements is best supported by the chart?

A

The DNA sequence of horses and donkeys are identical for the cytochrome c gene.

B

Penguins have an increase number of hydrophillic amino acids in their cytochrom c protein.

C

Snakes and horses use entirely different amino acids in their cytochrome c structure

D

The gene for cytochrome c protein is snakes is most similiar to the gene for this protein in penguins Horse Donkey Chicken Penguin Snake Horse 1 11 13 21 Donkey 1 10 12 20 Chicken 11 10 3 18 Penguin 13 12 3 17 Snake 21 20 18 17

Answer

Slide 93 / 131 Protein Shape and Structure

Shape is critical to the function of a protein. A protein's shape depends on four levels of structure: · Primary · Secondary · Tertiary · Quaternary

Slide 94 / 131

The primary structure of a protein is the sequence of amino acids that comprise it. Each protein consists of a unique sequence.

Proteins: Primary Structure

Alanine Lysine Valine Leucine Serine Leucine Leucine Alanine Lysine Alanine Serine Lysine

• r
• r
• r...

Slide 95 / 131

Secondary Structure

Secondary Structure is a result of hydrogen bond formation between amine and carboxyl groups of amino acids in each polypeptide chain. Depending on where the groups are relative to one another, the secondary structure takes the shape

• f an alpha helix or a pleated

sheet. Note: R-groups do not play a role in secondary structure.

Slide 96 / 131

alpha helix pleated sheets

Secondary Structure Slide 97 / 131

Tertiary Structure

Tertiary Structure is the

• verall 3-D shape of the
• polypeptide. This 3-D shape

determines the protein's function. It results from the clustering of hydrophobic and hydrophilic R- groups and bonds between them along the helices and pleats.

Slide 98 / 131 Denaturation

Changes in heat, pH, and salinity can cause proteins to unfold and lose their functionality, known as denaturation. This egg's protein has undergone denaturation and loss of solubility, caused by the high rise in the temperature of the egg during the cooking process.

Slide 99 / 131 Quaternary Structure

Some proteins have a Quaternary Structure. Quaternary structure consists

• f more than one

polypeptide chain interacting with each other through hydrogen bonds and hydrophobic/hydrophilic interactions.

Slide 100 / 131

34 The tertiary structure of a protein refers to:

A its size

B the presence of pleated sheets

C its over all 3D structure D the number of R-groups it contains

Slide 101 / 131

34 The tertiary structure of a protein refers to:

A its size

B the presence of pleated sheets

C its over all 3D structure D the number of R-groups it contains

[This object is a pull tab]

Answer C

Slide 101 (Answer) / 131

35 The __________ structure of a protein consists of a chain of

amino acids assembled in a specific order. A primary B secondary C tertiary D quaternary

Slide 102 / 131

35 The __________ structure of a protein consists of a chain of

amino acids assembled in a specific order. A primary B secondary C tertiary D quaternary

[This object is a pull tab]

Answer A

Slide 102 (Answer) / 131

36 Scientists alter a valine molecule to prevent hydrogren bonding of atoms in the R group. This would not effect ____________ of a protein.

A

the secondary structure

B

the tertiary structure

C

the quaternary structure

D

it would effect all the structural levels

Slide 103 / 131

36 Scientists alter a valine molecule to prevent hydrogren bonding of atoms in the R group. This would not effect ____________ of a protein.

A

the secondary structure

B

the tertiary structure

C

the quaternary structure

D

it would effect all the structural levels

[This object is a pull tab]

Answer A

Slide 103 (Answer) / 131

Structure Summary

Level Structure Notes Primary bonds between amino acids single chain of amino acids Secondary hydrogen bonds between amine and carboxyl groups alpha helix, pleated sheet Tertiary clustering of hydrophobic

• r hydrophilic R groups

disulfide bonds Quaternary attractions between multiple peptide chains not present in all proteins

Slide 104 / 131 Types of Proteins

Structural hair, cell cytoskeleton Contractile as part of muscle and

• ther motile cells

Storage sources of amino acids Defense antibodies, membrane proteins Transport hemoglobin, membrane proteins Signaling hormones, membrane proteins Enzymatic regulate speeds of chemical reactions Type Function

Proteins have 7 different roles in an organism.

Slide 105 / 131

37 Hormones are an example of what class of protein?

A structural B defense C transport D signaling

Slide 106 / 131

37 Hormones are an example of what class of protein?

A structural B defense C transport D signaling

[This object is a pull tab]

Answer D

Slide 106 (Answer) / 131

38 Hemoglobin is an example of what class of proteins?

A Transport B Signaling C Enzymatic D Structural

Slide 107 / 131

38 Hemoglobin is an example of what class of proteins?

A Transport B Signaling C Enzymatic D Structural

[This object is a pull tab]

Answer A

Slide 107 (Answer) / 131

Lipids are the one class of large biological molecules that do not consist of polymers.

Lipids

Main functions of lipids include · energy storage · the major component of cell membrane · involved with metabolic activities

Slide 108 / 131

Lipids are either hydrophobic or amphiphilic.

Amphiphilic

hydrophobic hydrophilic

Amphiphilic molecules have a hydrophobic "tail" and a hydrophilic "head". So one of its ends is attracted to water, while the other end is repelled.

Slide 109 / 131

Triglicerides are hydrophobic. They are constructed from two types of smaller molecules: a single glycerol and three fatty acids Fatty acids are carboxylic acids with a very long chain of carbon atoms. They vary in the length and the number and locations of double bonds they contain

Triglicerides: Hydrophobic Lipids

a fatty acid

CH2OH

CH2OH CH2OH

glycerol

C C C C C H H H H H H H H H H C C C

COOH

C H H H H H H H

Slide 110 / 131

3 fatty acids added to glycerol produce a trigliceride

Triglicerides Slide 111 / 131

Phospholipids have 2 fatty acids and 1 phosphate group. The phosphate end is polar and hydrogen bonds with water. The fatty acids are made of long chains of carbon and hydrogen, making them non-polar. As a result, the phosphate end is hydrophilic and the fatty- acid end is hydrophobic. Overall, phospholipids are amphiphilic.

Phospholipids: Amphiphilic Lipids Slide 112 / 131

Steroids are lipids with backbones which form rings. Cholesterol is an important steroid as are the male and female sex hormones, testosterone and estrogen.

Steroids Slide 113 / 131

39 Lipids can be _____. A hydrophobic B

hydrophilic

C amphiphilic D hydrophobic and amphiphilic E

hydrophilic and amphiphilic

Slide 114 / 131

39 Lipids can be _____. A hydrophobic B

hydrophilic

C amphiphilic D hydrophobic and amphiphilic E

hydrophilic and amphiphilic

[This object is a pull tab]

Answer D

Slide 114 (Answer) / 131

40 A phospholipid is an example of a/an _____.

A hydrophobic molecule B hydrophilic molecule C amphiphilic molecule D hydrophobic and amphiphilic molecule

Slide 115 / 131

40 A phospholipid is an example of a/an _____.

A hydrophobic molecule B hydrophilic molecule C amphiphilic molecule D hydrophobic and amphiphilic molecule

[This object is a pull tab]

Answer C

Slide 115 (Answer) / 131

Development of Life

Return to Table of Contents

Slide 116 / 131

The chemical reactions in early protobionts would eventually create sugars, and then ribonucleic acid (RNA). RNA has been shown to be capable of some of the key functions enabling life: · replication: making identical copies of itself · metabolism: storing energy for chemical reactions · catalyzation: dramatically speeding up favored chemical reactions Once these three functions were developed, evolution accelerated.

From Micromolecules to Macromolecules Slide 117 / 131

Abiogenesis is the study of how biological life could arise from organic molecules through natural processes. In particular, the term usually refers to the processes by which life on Earth may have arisen.

Abiogenesis

3.5 Billion year old cyanobacteria are the

• ldest and simplest life forms ever discovered.

Slide 118 / 131

This topic is outside the scope of the AP test, but if you need further evidence for the formation of living things from chemical components, you can view the work of Jack W. Szostak who has shown ways in which organic molecules could have assembled into a complex sphere capable of self replication and producing energy.

Abiogenesis

Jack Szostak Harvard Medical School Nobel Prize for Physiology 2009

Click here to see Szostak Lab's animations that show the steps in forming a pre-biotic complex sphere

Slide 119 / 131

Membranes are an arrangement

• f phospholipids that gather

together and make a closed shape. Membranes act as a wall or a barrier separating the outside and the inside of the closed shape. This is the natural condition of phospholipids when placed in aqueous solution.

Primitive Cells: The Start of Animated Earth Slide 120 / 131

This occurs because of the unique chemical properties of

• phospholipids. They are amphiphilic : containing a portion that

is hydrophobic and a portion that is hydrophilic.

Primitive Cells: The Start of Animated Earth

Polar head that will attract water Non-polar hydrocarbon tail that will repel water

Slide 121 / 131 Primitive Cells: The Start of Animated Earth

Within an enclosed volume, more complex chemistry can proceed; leading to protobionts: the precursors to life.

Slide 122 / 131

Within the inner environment of the protobiont, the processes of chemistry created ever more complex: · Proteins · Carbohydrates · Lipids · Nucleic Acids Simple metabolism evolved to increasingly complex levels based on the principles of organic chemistry.

From Micromolecules to Macromolecules Slide 123 / 131

Last Universal Common Ancestor (LUCA)

Protobionts became ever more complex until they included all the large biological molecules, including both RNA and DNA and the enzymes needed to maintain and use them. This led to what is called Last Universal Common Ancestor (LUCA). As you'll learn throughout this course, the common features of life on Earth are so profound that all life must have evolved from a single ancestor. "A universal common ancestor is at least 102860 times more probable than having multiple ancestors…"

Saey, Tina (5 June 2010). "Life has common ancestral source". Science News 177 (12): 12. doi:10.1038/465168a

Slide 124 / 131

LUCA

Some of the common features of all life on Earth that make a universal ancestor a logical necessity includes the following: ALL LIFE on Earth uses the IDENTICAL: · Universal Genetic code that makes all life's structures possible · Base pair coding in DNA (ATCG)and RNA (AUCG) · DNA and RNA polymerases, enzymes that make polymers · mRNA for sending genetic messages · tRNA for gathering amino acids · Ribosomes for assembling proteins · L-isomers of amino acids · 20 Amino acids that are used to build all proteins · Glucose as the ultimate energy source (very few exceptions exist) · Lipid bilayer for making cell membranes · Cellular division for growth · Sodium and Potassium ion pumps for creating potential · ATP as the "currency" of energy to power all their systems · ATP Synthase to power the production of ATP AND MANY, MANY MORE SIMILARITIES!

Slide 125 / 131 LUCA

None of these features of life on Earth had to be exactly this way. There are alternative ways to solve each problem. Question: How would it come to be that all life uses all these common features if there was not a universal ancestor? Take a moment and come up with an alternate theory to LUCA.

Slide 126 / 131

LUCA

Earth is 4.6 billion years old

+

The environment is too hostile for life until 3.9 bya

+

The earliest fossil evidence for life is 3.5 bya = The evolution of LUCA occurred between 3.9 and 3.5 bya.

Slide 127 / 131

Cells

Fossilized stromatolites (layered rocks that form when certain prokaryotes bind thin layers of sediment together) provide evidence that the first organisms

• n Earth were prokaryotic cells.

The earliest stromatolites have been dated to 3.5 BYA. These cells were/are very limited in their capabilities to perform the functions of life.

http://www.life.umd.edu/classroom/bsci124/img/ bacteria.jpg

Slide 128 / 131

Cells

Early prokaryotic cells are the simplest packet of chemicals capable of doing all the functions that define life. Life is defined as a set of conditions that separate abiotic (non-life) from the biotic (living). There are 7 conditions. Can you name them? · Organization/Order: Composed of units/cells · Adaptations: Populations evolving to their environment · Response to the environment: Individual response to stimuli · Regulation: Mantaining an internal condition ( homeostasis) · Energy processing: Using energy from environment · Growth and development: Immature to mature form · Reproduction: Producing offspring, heredity

Slide 129 / 131

41 The creation of membranes from phospholipids

__________________. A allowed for a more complex chemistry B allowed bacteria to flourish C allowed lipids to make glycoproteins D allowed more amino acids to form

Slide 130 / 131

41 The creation of membranes from phospholipids

__________________. A allowed for a more complex chemistry B allowed bacteria to flourish C allowed lipids to make glycoproteins D allowed more amino acids to form

[This object is a pull tab]

Answer A

Slide 130 (Answer) / 131

42 Evidence for a last universal common ancestor among life

• n Earth is:

A they all rely on photosynthetic reactions

for energy

B they all utilize ATP C they all reproduce through mitosis D they are all aerobic

Slide 131 / 131

42 Evidence for a last universal common ancestor among life

• n Earth is:

A they all rely on photosynthetic reactions

for energy

B they all utilize ATP C they all reproduce through mitosis D they are all aerobic

[This object is a pull tab]

Answer B

Slide 131 (Answer) / 131