The Molecules of Life

Organic Compounds

• What does organic mean?– No pesticides? – Environmentally friendly farming?

– In biology, organic = carbon based molecules.

Hydrocarbons

• Hydrocarbons are long chains of carbons bonded to hydrogen atoms– C-H bond = high energy– Hydrocarbons are a good energy source

Octane is a hydrocarbon. It is one of the main components of gasoline.

Fats are mostly hydrocarbons

Hydrocarbons

• Why does our body store fat?– C-H bonds are high energy– Fat is an efficient way to store a lot of energy in a

small molecule (9 Calories/gram)– Excess calories fat

Functional Groups

• Functional groups are common groupings of atoms that give molecules predictable properties

Carboxyl group-makes molecules acidic

Amino group-makes molecules basic

Alcohol!

• All alcohols are carbon based compounds with a hydroxyl group

hydroxyl group

ethanol(drinking alcohol) Is sugar an alcohol?

Carbonyl group

• A carbonyl group consists of a carbon atom double bonded to an oxygen atom

AcetoneHave you ever used acetone?

Carboxyl group

• A carboxyl group is a carbonyl group + a hydroxyl group– Carboxyl groups make many molecules acidic. – Molecule with carboxyl group = carboxylic acid

Ethanoic acid = vinegar

Amino group

• Nitrogen bonded to two hydrogens– Makes molecules basic (opposite of acidic)

Amino acidBuilding block of proteins

Phosphate group

• Phosphate group = phosphorus bonded to four oxygen atoms– Used in DNA backbone– Used in ATP

ATP

Methyl group

• Methyl group = carbon bonded to three hydrogens– Sometimes written CH3

How many methyl groups does acetone have?

Testosterone v. Estradiol

• A few functional groups can make a big difference!

testosterone estradiol (estrogen)

Can you spot the differences?

Office Hours

• Tonight, 7:00 - 8:00– Missing work? You’re invited!– Mandatory

• Alvaro Gonzalez• Jane McCaffrey• Richard Fagan• Gavin Rudolph• Kenrick Vincent• Nate Gilbert• Stanley Yao• Ben Lieber

Polymers

• A polymer is a large molecule made of many similar building blocks strung together– Each building block is called a monomer

Proteins are polymers made of amino acids DNA is a polymer of nucleic acids

Building Polymers

• Polymers are put together by dehydration synthesis– Dehydration = lose water– Synthesis = putting together

Dehydration Synthesis

• Proteins are made by dehydration synthesis– Building blocks = amino acids

Synthesizing proteins from amino acids

Dehydration Synthesis

• Sugars can be made into polymers too– Sugars are joined by dehydration synthesis

Hydrolysis

• Hydrolysis is the disassembly of polymers by adding water back in– It is the opposite of dehydration synthesis

Hydrolysis of proteins

Hydrolysis of starches

Lactose Intolerance

• Lactose intolerance is the inability to digest milk and dairy products– Look at lactose: what kind of molecule is it?– People with lactose intolerance can’t hydrolyze

lactose.

lactose

Acids and Bases

• Water naturally ionizes into H+ and –OH ions at a low frequency– Neutral water: H+ and –OH are balanced– Acidic solution: H+ > -OH– Basic solution: -OH >H+

pH Scale

• The pH scale describes how acidic or basic a solution is– 0-14– 0 = most acidic– 7 = neutral– 14 = most basic– Each step is a tenfold decrease

in H+ ions and a tenfold increase in –OH ions

Practice!• Rate each as acidic, basic, or neutral• Rank from greatest to least concentration of H+

pH = 7 pH = 3 pH = 9

Carbohydrates

• Carbohydrates are a class of molecules that include sugars and starches– Their chemical formula is usually a multiple of

CH2O (carbon + water = carbo hydrate)– Carbohydrates are the primary energy source for

our bodies

Carbohydrates

• Simple, single unit sugars are called monosaccharides– Mono = 1– Saccharide = sugar

Glucose C6H12O6 Ribose C5H10O5

Carbohydrates

• Two monosaccharides can be linked by dehydration synthesis to form a disaccharide– Di = 2

Carbohydrates

• Polysaccharides are polymers of hundreds to thousands of simple sugars– Poly = many– Starch, glycogen, and cellulose are all polymers of

glucose molecules

Carbohydrates

• Starch is a polysaccharide used for energy storage in plants• Animals can digest starch and use it for energy. • Where do you get starch from?

Carbohydrates

• Glycogen is a polysaccharide used for energy storage in humans• Stored in liver and muscles• Branched chains of glucose monomers

Carbohydrates

• Cellulose is a polysaccharide used to build the rigid cell walls of plants. – Dietary fiber – Wood

10/7/11

• Objective: To expand our knowledge of lipids

• Do now: In your notes, define a hydrocarbon and list some of its properties

• Do later: Make and study flashcards for all the bolded words from pg. 36-41

High Fructose Corn Syrup

• Normal table sugar = 50% glucose, 50% fructose

• HFCS = 55% fructose, 45% glucose

Hydrophilic v. Hydrophobic

• New words for an old idea: solubility effects• Hydrophilic = polar/dissolves in H2O• Polar functional groups: – Amino– Carbonyl– Hydroxyl– Carboxyl– Phosphate

Hydrophilic v. Hydrophobic

• Hydrophobic = non-polar/doesn’t dissolve in water

• Non-polar functional groups – Methyl (CH3)

Lipids!

• Lipids = fats, oils, steroids– Hydrophobic– Mostly made of carbon and hydrogen• mostly non-polar covalent bonds

Fats

• Fats = glycerol + 3 fatty acids– Glycerol = alcohol– Fatty acid = carboxylic acid with long hydrocarbon

chain• Hydrocarbon chains make fats hydrophobic

+ 3

Glycerol + 3 fatty acids Triglyceride (fat molecule)

Saturated v. Unsaturated Fats

• Saturated = fatty acid with no double bonds• Unsaturated = fatty acid with double bonds

Saturated v. Unsaturated Fats

• Saturated = solid at room temperature• Unsaturated = liquid at room temperature– What are some examples?

Saturated v. Unsaturated Fats

• Saturated = Straight chain packs into a solid easily

• Unsaturated = Kinks in chain keep unsaturated fat from solidifying

Science in Popular Media

• What’s right/wrong in this video?

10/10/11

• Objective: To explore the diversity of lipids and the structure of proteins

• Do now: Take a quiz and go!

• Do later: Read and outline pgs 42-44– Outlines:

• Main concepts• Important diagrams/drawings• Bolded vocabulary• Other helpful notes

Hydrogenated Oils

• Oils that are chemically hydrogenated (add hydrogen) to become saturated fats.

Hydrogenated Oils

• Why hydrogenate oils?– Solid fats create better texture in many foods– Hydrogenated oils are much less expensive than

animal fat

Hydrogenated Oils

• Is this a bad thing? – Maybe. Hydrogenation of oils creates trans fats,

which are linked to heart disease

Why fat?

• Fats contain 9 Calories/gram– Sugars & proteins = 4 Calories/gram

• Fat = more efficient energy storage than proteins/sugars– Stored in specialized fat cells

Phospholipids

• Made of glycerol, two fatty acids, and a phosphate head– Fatty acids are hydrophobic (non-polar)– Phosphate head is hydrophilic (polar)

Phospholipids

• Cell membranes are made of a bilayer of phospholipids– Hydrophobic tails on the inside – Hydrophilic heads on the outside

Steroids

• Steroids are lipids containing four fused rings– Many steroids are hormones– Cholesterol is a major component of cell

membranes

Testosterone

Estradiol

10/11/11

• Objective: To learn and model the structure of proteins

• Do now: Take out your outlines of pg. 42-44

• Do Later: Pg 49 # 5, 10, 13, 14, 18

Anabolic Steroids

• Anabolic steroids = variations of testosterone– Testosterone muscle buildup and maintenance

• Prescribed for diseases that destroy muscle

Anabolic Steroids

• Anabolic steroids increase muscle buildup after rigorous exercise

• Side effects:– Mood swings/depression– Liver damage– Cancers– High cholesterol– Suppression of natural hormones

• Shrunken testes and infertility in men• Disrupted menstrual cycle and masculine characteristics

in women

Proteins

• Review: Proteins are polymers of amino acids– Made by dehydration synthesis

Amino Acids

• 20 amino acids are commonly found in proteins– Each has a different “R group” or side chain that

affects its chemical properties

Leucine - hydrophobic Aspartic acid - acidic Serine - hydrophilic

Amino Acids

• Side chains determine chemical properties– Polar v. non-polar– Acidic v. basic v. neutral

Hydrophobic Amino Acids

• The properties of side chains can be explained by their functional groups– Hydrocarbon side chains = non-polar/hydrophobic

Valine - hydrophobic Phenylalanine - hydrophobic

Polar Acidic Amino Acids• Carboxyl groups in side chain acidic– Also polar… can you explain?

Aspartic acid Glutamic acid

Polar Basic Amino Acids

• Amino groups in side chain basic

Lysine Arginine

Polar Neutral Amino Acids

• Other polar functional groups polar/neutral

Serine - polar Glutamine - polar

Peptides

• Proteins are also called peptides– Two covalently linked amino acids are a dipeptide• C-N bond = peptide bond

– A longer protein is a polypeptide

Polypeptide

Protein Structure

• Proteins have four levels of structure– Primary– Secondary– Tertiary– Quaternary

Actin – muscle protein

10/13

• Objective: To understand the structure of proteins by building them!

• Do now: Pick a partner for your protein project and select a mini-toober!

• Do later: Biomolecules assignment on the masteringbiology.com site (due Tuesday)

Primary structure

• The primary structure of a protein is the order in which amino acids are linked together– Just like amino acids, proteins have an amino end

(N-terminus) and a carboxyl end (C-terminus)

Primary Structure

• Our bodies have about 20,000 unique proteins– Proteins range from 100s to 1000s of amino acids

in length

• How do we make these from only 20 amino acids?– Each protein has a unique sequence of amino

acids, or primary structure

Secondary Structure

• Proteins fold into structures called – Alpha helices

– Beta sheets

Alpha helices

• Alpha helices are coils of polypeptides– 3.5 amino acids/turn– Held together by hydrogen bonds

Review: Hydrogen Bonds in Proteins

• A hydrogen bond forms between:– A lone pair (on nitrogen or oxygen)– A hydrogen atom bonded to a nitrogen or oxygen

Where are the hydrogen bond donors (H-N or H-O) and acceptors (lone pairs)?

Alpha helices

• Alpha helices are stable because they maximize hydrogen bonds in a protein– All donors point in one direction, all acceptors point

in the other, and maximum H-bonds are made

Alpha Helices

• Fun fact:– Alpha helices only coil in one direction– Clockwise or to the right as you go up.• “right handed helix”

Beta sheets

• Beta sheets are parallel strands of polypeptides– They are also held together by hydrogen bonds

Beta Sheets

• Silk is made of stacked beta sheets– Hydrogen bonds make silk extremely strong– Stronger than steel fibers of equal weight

Spider silk Spider silk bulletproof vest

10/14/11

• Objective: To practice protein model building and explore secondary and tertiary structure

• Do Now: – Parents: Take a syllabus from the front of the room– Students: Take a mini-toober (either yours or a

loaner if your partner has yours)

Kruppel-like factor 4

• Today we will be building Kruppel-like factor 4– Protein composed of 3 zinc fingers– Transcription factor – regulates whether certain

genes are turned on or off

Zinc Fingers

• Klf-4 is composed of 3 zinc fingers– Each zinc finger is made of one alpha helix and a 2

stranded beta sheet– Held together by charge attraction between a Zn+

ion and lone pairs on the side chains of the amino acids histidine and cysteine

Zinc fingers

• Practice building your own Klf-4 model– You can use Jmol or the sample model to help you,

or you can just approximate the structure

• Have each family member build at least one of the 3 zinc fingers– One right handed alpha helix (about 3 coils)– One two stranded beta sheet (3 amino

acids/strand)

10/18

• Do now:In your notes:– Define primary and secondary structure• How do they differ?

• Do Later: Research protein choices and list your top 3

Antiparallel beta sheets

• Antiparallel beta sheets are made of strands going in different directions– One goes C-terminus to N-terminus– One goes N-terminus to C-terminus

Parallel beta sheets

• Parallel beta sheets are made of strands going in the same direction

Antiparallel v. Parallel

• Antiparallel beta sheets are more stable because they line up H-bonds perfectly

Beta Barrel

• Beta strands can also form ‘barrels’– Pretty cool.

Review time!With a partner:

• What kind of bonding is most important to primary structure?

• What kind of bonding is most important to secondary structure?

Tertiary Structure

• The elements of secondary structure fold together to form the tertiary structure

Tertiary structure

• Tertiary structure is stabilized by solubility effects– Hydrophobic and hydrophilic interactions

Hemagglutinin – flu protein

Tertiary Structure

• Hydrophobic effects– Proteins exist in watery environments– Hydrophobic side chains bury themselves in the

core of proteins

Hydrophobic side chains

Tertiary Structure

• Hydrophilic effects– Hydrophilic side chains dissolve in water, so they

are found on the outside of a protein

Hydrophilic side chains

Tertiary Structure

• Disulfide bonds– Tertiary structure is also sometimes held together

by disulfide bonds– Two cysteine residues can link together by forming

a Sulfur-Sulfur bond

Quaternary Structure

• Many proteins are made of multiple separate polypeptide chains – These are called subunits– Multiple subunits = quaternary structure

hemoglobin

Quaternary Structure

• How are subunits held together?– Hydrophobic surfaces– Fit together like puzzle pieces