Molecules of Life

Sections of chapters 2, 3, 4, 5, 6, 22

Quiz II Oct. 5th

Exam II Oct. 14th

Atoms and Molecules

What are living things made of?

• Biology includes the study of life at many levels

TRACING LIFE DOWN TO THE CHEMICAL LEVEL

• In order to better understand life, in the next slide we’ll look at the macroscopic level, the ecosystem, and work our way down to the microscopic level of cells

• Cells consist of enormous numbers of chemicals that give the cell the properties we recognize as life

Ecosystem (African savanna)

Community(All the organisms in the savanna)

Population(Herd of zebras)Organism (A Zebra)

Organ systems(Circulatory system)

Organs(Heart)

Cells(Heart muscle cell)

Tissues(Heart muscletissue)

Molecules(DNA)

Atoms(Oxygen atom)

Chemicals

• Take any physical or biological system apart and you eventually end up at the chemical level

Chapter 2

SOME BASIC CHEMISTRY

Molecules

• Everything in the universe is made of atoms (Atomic theory of matter).

• Atoms can bond together to make molecules.

• Living things are made of atoms and molecules, just like any non-living thing.

• Matter is anything that occupies space and has mass

Matter: What is it?

• Matter is found on the Earth in three physical states

– Solid

– Liquid

– Gas

• All the elements are listed in the periodic table

Atomic number

Element symbol

Mass number

Figure 2.2

Atomic number

Element symbol

Mass number

Figure 2.2

Atomic number

Element symbol

Mass number

Figure 2.2

• The most common elements in living things are:

– Carbon

– Hydrogen

– Phosphorous

– Nitrogen

• What is an atom?

• Atoms are composed of subatomic particles

The Structure of Atoms

– A proton is positively charged

– An electron is negatively charged

– A neutron is electrically neutral

• Chemical reactions enable atoms to lose, gain, or share electrons in order to complete their outer shells

Chemical Bonding and Molecules

– These interactions usually result in atoms staying close together

– The atoms are held together by chemical bonds

• When an atom loses or gains electrons, it becomes electrically charged

Chemical Bonds: Ionic Bonds

– Charged atoms are called ions

– Ionic bonds are formed between oppositely charged ions

Sodium atom (Na) Chlorine atom (Cl)

Completeouter shells

Sodium ion (Na) Chloride ion (Cl)

Sodium chloride (NaCl)

• A covalent bond forms when two atoms share one or more pairs of outer-shell electrons

Chemical Bonds: Covalent Bonds

Figure 2.9

• Studied in isolation, the water molecule is deceptively simple

The Structure of Water

– Its two hydrogen atoms are joined to one oxygen atom by single covalent bonds

H

O

H

• But the electrons of the covalent bonds are not shared equally between oxygen and hydrogen

– This unequal sharing makes water a polar molecule

() ()

() ()

The Structure of Water: Polarity

• The polarity of water results in weak electrical attractions between neighboring water molecules

– These interactions are called hydrogen bonds

(b)

()

Hydrogen bond()

()()

()

()

()

()

Figure 2.11b

The Structure of Water: Hydrogen Bonds

• The polarity of water molecules and the hydrogen bonding that results explain most of water’s life-supporting properties

Water’s Life-Supporting Properties

– Water’s cohesive nature

– Floating ice

• Water molecules stick together as a result of hydrogen bonding

The Cohesion of Water

– This is called cohesion

– Cohesion is vital for water transport in plants

Microscopic tubes

• Surface tension is the measure of how difficult it is to stretch or break the surface of a liquid

– Hydrogen bonds give water an unusually high surface tension

• When water molecules get cold, they move apart, forming ice

– A chunk of ice has fewer molecules than an equal volume of liquid water

• The density of ice is lower than liquid water

– This is why ice floats

Figure 2.15

Hydrogen bond

Liquid water

Hydrogen bondsconstantly break and re-form

Ice

Stable hydrogen bonds

• Table salt, NaCl, is the result of an ionic bond between Na+ and Cl- ions.

• When salt mixes with water, this ionic bond breaks, and the separated Na+ and Cl- ions are attracted to the polar water molecules.

Water as the Solvent of Life

Ion in solutionSalt crystal

• Elements in the Human Body

– Four elements make up about 96% of the weight of the human body....

– Oxygen, Carbon, Hydrogen, Nitrogen

– Trace elements occur in smaller amounts

Molecules: what are living things made of?

Chapter 3

What is the main element that

living things are made of?

Carbon Chemistry

– Has four electrons in an outer shell (can hold eight)

– Carbon can share its electrons with other atoms to form up to four covalent bonds

An atom of C

• Carbon can use its bonds to

– Attach to other carbons

– Form an endless diversity of carbon skeletons

Figure 3.2

Carbon skeletons vary in length

Carbon skeletons may be unbranched or branched

Carbon skeletons may have double bonds,which can vary in location

Carbon skeletons may be arranged in rings

• The simplest organic compounds are hydrocarbons

– These are organic molecules containing only carbon and hydrogen atoms

– The simplest hydrocarbon is methane

Figure 3.3

Structuralformula

Ball-and-stickmodel

Space-fillingmodel

• Larger hydrocarbons

– Are the main molecules in the gasoline we burn in our cars

– The hydrocarbons of fat molecules provide energy for our bodies

Figure 3.4

Molecules

• Most molecules in living things are polymers

• What type of reaction creates polymers of sugars?

• What type creates polymers of amino acids?

• What is the name of the reaction that breaks polymers into monomers?

Molecules

• There are 4 classes of compounds that are the building blocks of cells

– Carbohydrates

– Lipids (fats and oils)

– Proteins

– Nucleic acids

Carbohydrates• Repeating subunit is

H – C – O – H

which is CH2O.

• Hence carbo-hydrate

• Can occur as ring or chain

• Monosaccharides include simple sugars like glucose and fructose

Carbohydrates• Repeating subunit is

H – C – O – H

which is CH2O.

• Hence carbo-hydrate

• Can occur as ring or chain

• Monosaccharides include simple sugars like glucose and fructose

• Disaccharides (sucrose, maltose, lactose).

Polysaccharides

• Starch: long-term energy storage in plants

• Glycogen: short-term energy storage in animals

• Cellulose: structure in plants

• Chitin: structure in animals

• Polysaccharides

Figure 3.13

(a) Starch

Starch granules inpotato tuber cells

Glucosemonomer

(b) Glycogen

GlycogenGranulesIn muscletissue

(c) Cellulose

Cellulose molecules

Cellulose fibril ina plant cell wall

Carbohydrates

• Carbohydrates are polar, that is, they have an uneven charge distribution across molecule. Makes them soluble in water (hydrophilic).

• Diet: No carbohydrates are essential (you can create them in your body from other compounds you eat.)

• Energy density: 4 Cal/g.

Lipids(Fats and oils)

• 4 types

– Fatty acids

–Triglycerides

–Phospholipids

–Steroids

Lipids (fats, oils, waxes)

• The repeating subunit of a lipid is CH2:

H – C – H

• Called hydrocarbons because they are composed of mostly C and H.

• Lipids are nonpolar and are thus hydrophobic.

• Energy density: 9 Cal/g, because in carbohydrates, the O adds mass and removes high energy bonds.

Fatty Acids

Fatty Acids

• Fatty acids are used for energy, or stored

• Store a lot of energy. Why?

• Evolutionary Theory can provide a plausible explanation for why we crave fats.

Saturated fats• Saturated fats are molecules in

which the C atoms are saturated with H’s.

• Because the hydrocarbon chains line up uniformly, saturated fats are solid at room temperature (and gummy in your arteries).

• If there were any C=C (carbon-carbon double bond), it would be unsaturated.

Unsaturated fats• Unsaturated fats are liquid

at room temperature.

• Monounsaturated fats (such as olive oil) are GOOD for you, as they reduce LDL (details to follow).

Trans fats• Partially hydrogenated oils (i.e.,

trans fats) are just as bad as saturated fats (if not worse)!

• Start with a perfectly healthy vegetable oil and hydrogenate it (i.e., force H’s on it), making a new type of saturated fat.

• Crisco shortening was previously soybean oil.

Lipids

Lipids are stored primarily as triglycerides: three fatty acids attached to a small glycerol molecule.

Creating triglycerides

• When 3 fatty acids are joined to a glycerol molecule, this reaction is called ______ and produces ______.

?

Lipids in membranes

• Membranes are composed primarily of phospholipids.

• Glycerol attached to 2 fatty acids and a polar phosphate group.

• Phosphate is hydrophilic while 2 hydrocarbon chains are hydrophobic.

• Thus they form bilayers in cells, as the hydrocarbons avoid water while the phosphate heads turn towards water…

http://telstar.ote.cmu.edu/biology/downloads/membranes/index.html

Lipids: Steroids

Interconnected rings of carbon atoms

Small molecule, but big effects

Cholesterol is another example of a steroid

Lipids as messengers• Lipids can act as messengers in

the body.

• These steroid hormones are ring structures.

• Hormones send long sustained messages, regulating slow transitions (as opposed to fast nervous system)

• Ex. Puberty

• Cholesterol is important in membranes (to maintain stability)

Testosterone

Proteins• Composed of C, H, O, and N.

• The repeating subunit is an amino acid.

• Central C is attached to

– amine group

– carboxyl group (acid)

– H atom

– R-group (varies depending on amino acid)

Peptide bonds• When 2 amino acids are joined,

the N from one’s amino group attaches to the C of the other’s carboxyl group.

• Forms a peptide bond.

• What is this process called?

• What is released?

• To join 3 amino acids, how many water are released?

• When many amino acids are joined in a chain, a protein (polypeptide) is formed.

• Your body has tens of thousands of different kinds of proteins

• Proteins do many different jobs, some are hormones, some are enzymes, some are structural

• The arrangement of amino acids makes each one different, differently shaped proteins have different functions.

• Primary structure

– The specific sequence of amino acids in a protein

1 510 15

20253035

4045

5055

6065

70

75 80 85

9095

100

105110 115

120125

129

Amino acidFigure 3.21

• A slight change in the primary structure of a protein affects its ability to function

– The substitution of one amino acid for another in hemoglobin causes sickle-cell disease

Figure 3.22

(a) Normal red blood cell Normal hemoglobin

12 3

4 56

7. . . 146

(b) Sickled red blood cell Sickle-cell hemoglobin

2 314 5

67. . . 146

Protein Structure• The shape (structure) of a

protein is intimately linked to its function.

• In their role as enzymes, they act as keys to make reactions occur.

• Primary structure: the linear sequence of amino acids in a chain.

• Secondary structure: the shape the chain takes (sheet or coil).

• Tertiary structure: how those sheets or coils form a 3-dimensional structure.

• Quaternary structure: using 2 or more tertiary structures to create a more complex 3-D structure.

• One more visual example…

Proteins have four levels of structure

Figure 3.23

Hydrogen bond

Pleated sheet

Amino acid

(a) Primary structure

Hydrogen bond

Alpha helix

(b) Secondary structure

Polypeptide(single subunit)

(c) Tertiary structure

Completeprotein,with fourpolypeptidesubunits

(d) Quaternary structure

http://www.stolaf.edu/people/giannini/flashanimat/proteins/protein%20structure.swfhttp://www.stolaf.edu/people/giannini/flashanimat/proteins/hydrophobic%20force.swf

Facts about proteins• Enzymes (proteins) are very

fragile: If you change just one amino acid in the linear sequence (primary structure), you may impair the function of the enzyme.

• Proteins are affected by pH and temperature. If subjected to high stress (extreme temperature or pH), and protein may denature (permanently change its shape).

The structure of proteins is very important!

• Diet: Proteins include eight essential amino acids

– Different vegetables contain different ones; BUT no single vegetable contains all eight of them

Essential amino acids

Corn and other grains

Methionine

Valine

(Histidine)Threonine

Phenylalanine

Leucine

Isoleucine

Tryptophan

Lysine

Beans and other legumes

– Meats, however, do contain all eight

Summarizing Proteins

• Composed of 20 different amino acids

• Amino acids joined by peptide bonds

• Very complex 3-dimensional structure

• Extremely important as enzymes

• Energy density: 4 calories/gram

Nucleic Acids• Not important in nutrition, but

famous because of DNA, RNA, and ATP.

• Composed of nitrogenous base (5 types), pentose sugar (2 types), and a phosphate group.

• They form chains of sugars attached to phosphates (with the nitrogenous base dangling.

• DNA is double-stranded: the nitrogenous bases in adjacent strands attach to each other.

• Some nucleic acids are also important in energetics. ATP is the ‘currency’ used in the cell to get things done.

Nucleic acids

• Nucleic acids are polymers of nucleotides

• Nucleotides have three parts:

– Sugar

– Phospate

– Nitrogen base

•

ATP (adenosine triphosphate)

Energetics and Respiration

How do living things work?

Order and Physical Laws• Organisms require energy to

maintain order in their bodies.

• Without using energy to maintain order, life would be impossible.

• Why?

• Because of the 2nd Law of Thermodynamics:

• Entropy (disorder) increases.

Order and Physical Laws• Restated in terms of chemical

reactions: No energy transformation is 100% efficient.

• What does that mean?

• It means energy is lost as heat every time it changes forms.

• For example… when:

Sugar ATP

glycogen fat

fat glycogen

• 2nd Law of Thermodynamics:

• Entropy (disorder) increases.

Example of 2nd Law of Thermodynamics

• Consider a car that is powered by gasoline.

• Most of the energy in the gasoline is not used to propel the car forward, play the stereo, AC, etc.

• Rather it is wasted (lost) as heat.

• Much of the machinery under your hood is designed to cool the engine, not propel it!

Example #2

• Consider breakfast.

• If you eat a 500 calorie breakfast, less than 200 calories are actually used to produce ATP’s.

• The rest is lost as heat.

• Living cells and automobile engines use the same basic process to make chemical energy do work

Figure 5.3a

Fuel rich inchemicalenergy

Heatenergy

Waste productspoor in chemicalenergy

Gasoline

Oxygen

CombustionKinetic energyof movement

Carbon dioxide

Water(a) Energy conversion in a car

Heatenergy

Food

Oxygen

Cellularrespiration

Energy for cellular work

Carbon dioxide

Water

(b) Energy conversion in a cell

Fuel rich in Chemical energy

Waste products poor in chemical energy

Heatenergy

Gasoline

Oxygen

CombustionKinetic energyof movement

Carbon dioxide

Water(a) Energy conversion in a car

Types of energy

• kinetic energy (moving objects)

1. moving car, moving baseball

2. hits something, stops, energy converted in sound, heat, light, etc.

3. fire burning

• potential energy (stored energy)

1. E.g. coiled spring, object at high location, gasoline

2. chemical energy is form of potential energy

Metabolism

• Living things maintain order through essential chemical reactions called metabolism.

– Organic molecules are converted into other organic molecules.

– Energy is released by oxidizing reduced carbon compounds (that is, breaking lots of C-H bonds).

Metabolism

Oxidation

• Both living creatures and fire consume oxygen. The oxygen reacts with the fuel (wax in the candle, or sugars in us) to produce CO2 and H2O. This process is called oxidation. In our bodies we oxidize glucose:

• C6H12O6 (glucose) + 6O2 6CO2 + 6H20

Differences between fire and metabolism

• Fire consumes everything: with enough oxygen, everything is oxidized randomly and chaotically.

• But Metabolism is controlled and ordered. Energy is stored in ATP molecules in your cells as the food molecules are oxidized slowly in many small steps. And each small step requires an enzyme.

• How does your body control which molecules get oxidized, when, and where?

• By producing the enzymes capable of certain reactions ONLY when those reactions are needed.

What enzymes do

• Chemical reactions require a push to get going.

• The push is called activation energy.

• Enzymes reduce the activation energy needed.

•http://www.lewport.wnyric.org/jwanamaker/animations/Enzyme%20activity.html

Facts about enzymes

• Lock and key idea: enzymes must have their own perfect 3-D shape.

Example: alcohol dehydrogenase

Facts about enzymes

• Enzymes are not used up in chemical reactions. They can be reused over and over, and will continue to exist until your body destroys them.

• Enzymes have very specific functions. Each step of a chemical pathway requires a different enzyme.

Facts about enzymes

• Enzymes cannot get more energy out of a reaction, they just make reaction more likely to occur.

Facts about enzymes

• Enzymes are temperature sensitive, since proteins denature at high temperatures and lose their shape.

Enz

yme

activ

ity

Facts about enzymes

• Enzymes are sensitive to pH for the same reason.

Metabolism

• Living things require energy and materials to stay alive.

– Energy and materials to maintain their structure and function

– Energy and materials to reproduce

• Where does that energy come from?

Food webs and energy pyramids

Autotrophs and heterotrophs

• Autotrophs

– Make their own food/fuel

• Heterotrophs

– Need to consume food/fuel produced by autotrophs

• All organisms need to acquire materials from their environment, but each type needs different materials

Autotrophs

• Most make their own fuel by a process called photosynthesis

• Have chlorophyll

• Convert CO2 and H2O to C6H12O6 + O2

• Use solar energy to do this

Heterotrophs

• Must consume food for fuel

Respiration

• All eukaryotic cells burn fuel (glucose) to make ATP

• ATP can then be used as an energy source anywhere in the cell or body.

• Burning fuel requires O2

• In cells the process is called respiration

Respiration• Respiration occurs in mitochondria

• Respiration occurs in controlled steps each step requires an enzyme

• Glycolysis:

Glucose is split into 2 molecules – can occur without O2, produces 2 ATP molecules

• Krebs Cycle and Electron transport chain:

Require O2, produce 34 ATP molecules.

•C6H12O6 + O2 + ADP + P → CO2 + H2O + 36 ATP

Respiration Overview

Glycolysis (sugar-breaking)

Fermentation

No O2 If O2 is present

Aerobic Respiration

Krebs CycleElectron Transport Chain

Glucose

Respiration

• Other food we eat can also be burned for energy

Oxygen Cycle• Respiration

C6H12O6 + O2→ CO2 + H2O

• Photosynthesis

CO2 + H2O → C6H12O6 + O2

• What’s wrong with this picture?

• Do plants use Oxygen? If so, what for?

Energy vs. Materials

• Common elements in living things?

• Where do living things get these?

– Plants

– Animals

Energy vs. Materials

• It takes energy to stay alive

• What is the ultimate source of energy for all living things?