What, no notes today? · 2019. 1. 27. · enantiomers have important functional significance because of emergent properties from the specific arrangements of atoms. • One enantiomer

What, no notes today?

• With a total of 6 electrons, a carbon atom has 2 in

the first shell and 4 in the second shell.

• Carbon has little tendency to form ionic bonds by losing

or gaining 4 electrons.

• Instead, carbon usually completes its valence shell by

sharing electrons with other atoms in four covalent bonds.

• This tetravalence by carbon makes large, complex

molecules possible.

• The complex chemistry of life requires complex

molecules.

2. Carbon atoms are the most versatile

building blocks of molecules

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

• Isomers are compounds that have the same molecular formula but different structures and therefore different chemical properties.

• For example, butane and isobutane have the same molecular formula C4H10, but butane has a straight skeleton and isobutane has a branched skeleton.

• The two butanes are structural isomers, molecules with the same molecular formula but differ in the covalent arrangement of atoms.


Fig. 4.6a

• Enantiomers are molecules that are mirror images

of each other

• Enantiomers are possible if there are four different atoms

or groups of atoms bonded to a carbon.

• If this is true, it is possible to arrange the four groups in

space in two different ways that are mirror images.

• They are like

left-handed and

right-handed

versions.

• Usually one is

biologically active,

the other inactive.


Fig. 4.6c

• Even the subtle structural differences in two

enantiomers have important functional significance

because of emergent properties from the specific

arrangements of atoms.

• One enantiomer of the drug thalidomide reduced

morning sickness,but the other isomer caused severe

birth defects. Here’s the story. 14 min.

• This is a great examples of the structure/function theme

at a molecular level.

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin CummingsFig. 4.7

https://www.youtube.com/watch?v=41n3mDoVbvk

Laboratory tests after the thalidomide disaster showed that in some

animals the 'S' enantiomer was teratogenic (caused changes but not

DNA mutations) but the 'R' isomer was an effective sedative. It is

now known that even if only one isomer (the good one) is

administered at the pH in the body, it can cause racemizing, which

means that both enantiomers are formed in a roughly equal mix in

the blood. So, even if a drug of only the 'R' isomer had been

created, the disaster would not have been averted.

Explain the connection between the sequence and

the subcomponents of a biological polymer and its

properties. [LO 4.1, SP 7.1]

Refine representations and models to explain how

the subcomponents of a biological polymer and their

sequence determine the properties of that polymer.

[LO 4.2, SP 1.3]

Use models to predict and justify that changes in the

subcomponents of a biological polymer affect the

functionality of the molecule. [LO 4.3, SP 6.1, SP

6.4]

• The basic structure of testosterone (male hormone)

and estradiol (female hormone) is identical.

• Both are steroids with four fused carbon rings, but

they differ in the functional groups attached to the

rings.

• These then interact with different targets in the body.


Fig. 4.8

• In a hydroxyl group (-OH), a hydrogen atom

forms a polar covalent bond with an oxygen which

forms a polar covalent bond to the carbon skeleton.

• Organic compounds with hydroxyl groups are alcohols

and their names typically end in -ol.


• A carboxyl group (-COOH) consists of a carbon

atom with a double bond with an oxygen atom and a

single bond to a hydroxyl group.

• Compounds with carboxyl groups are acids.


• An amino group (-NH2) consists of a nitrogen atom attached to two hydrogen atoms and the carbon skeleton.

• Organic compounds with amino groups are amines.

• The amino group acts as a base because ammonia can pick up a hydrogen ion (H+) from the solution.

• Amino acids, the building blocks of proteins, have amino and carboxyl groups.


• A phosphate group (-OPO32-) consists of

phosphorus bound to four oxygen atoms (three with

single bonds and one with a double bond).

• One function of phosphate groups is to transfer energy between organic molecules.


So what happens to your lunch?

• We are going to frame this section based on

your lunch.

• You can find a million diet advice sources.

• Here’s a good common sense one.

• http://www.nytimes.com/2015/04/21/upshot/si

mple-rules-for-healthy-

eating.html?emc=eta1&_r=0&abt=0002&abg=

0

• I would add one thing – Watch the sugar!

http://www.nytimes.com/2015/04/21/upshot/simple-rules-for-healthy-eating.html?emc=eta1&_r=0&abt=0002&abg=0

• Three of the four classes of macromolecules form

chainlike molecules called polymers.

• Polymers consist of many similar or identical building

blocks linked by covalent bonds.

• The repeated units are small molecules called

monomers.

• Some monomers have other functions of their own.

1. Most macromolecules are polymers


• The chemical mechanisms that cells use to make and

break polymers are similar for all classes of

macromolecules.

• Monomers are connected by covalent bonds via a

condensation (or dehydration synthesis) reaction.

• One monomer provides

a hydroxyl group, and

the other provides a

hydrogen and together

these form water.

• This process requires

energy and is aided

by enzymes.


Fig. 5.2a

4.A.1.a Compare the

synthesis and decomposition

of biological

macromolecules.

• The covalent bonds connecting monomers in a

polymer are disassembled by hydrolysis.

• In hydrolysis as the covalent bond is broken a hydrogen

atom and hydroxyl group from a split water molecule

attaches where the covalent bond used to be.

• Hydrolysis reactions

dominate the

digestive process,

guided by specific

enzymes.


Fig. 5.2b

Explain the connection between the sequence and the

subcomponents of a biological polymer and its properties.

[LO 4.1, SP 7.1]

Refine representations and models to explain how the

subcomponents of a biological polymer and their sequence

determine the properties of that polymer. [LO 4.2, SP 1.3]

Use models to predict and justify that changes in the

subcomponents of a biological polymer affect the

functionality of the molecule. [LO 4.3, SP 6.1, SP 6.4]

Untested:

✘ The molecular structure of specific nucleotides is beyond

the scope of the course and the AP Exam.

✘ The molecular structure of specific amino acids is beyond

the scope of the course and the AP Exam.

✘ The molecular structure of specific lipids is beyond the

scope of the course and the AP Exam.

✘ The molecular structure of specific carbohydrate polymers

is beyond the scope of the course and the AP Exam.

• Carbohydrates include both sugars and polymers.

• The simplest carbohydrates are monosaccharides

or simple sugars.

• Disaccharides, double sugars, consist of two

monosaccharides joined by a condensation reaction.

• Polysaccharides are polymers of monosaccharides.

Introduction


• Monosaccharides generally have molecular formulas that are some multiple of CH2O.

• Glucose has the formula C6H12O6, but so does fructose and galactose, They are isomers. Be able to list them.

• Most names for sugars end in -ose.

• Monosaccharides differ in the number of carbons.

• Glucose and other six carbon sugars are hexoses.

• Five carbon backbones are pentoses like ribose.

1. Sugars, the smallest carbohydrates serve as a

source of fuel and carbon sources


• Monosaccharides, particularly glucose, are a major fuel for cellular work.

• It also functions as the main transport sugar in vertebrates.

• While often drawn as a linear skeleton, in aqueous

solutions monosaccharides form rings.


Fig. 5.4

Girls are made of sugar and spice, so the

saying goes??? Very scary, that.

• Turns out fructose is quite a bad guy. Found as part of table

sugar and high fructose corn syrup (check your food labels), it

is broken down only by the liver, which turns much of it to fat

if there is too much to begin with, like there will be in a sugary

diet. Glucose, on the other hand, is broken down by all cells,

so turning it to fat is less likely. Back to the liver, this fat

causes it to become resistant to insulin, a protein hormone that

is released to help get sugar into cells. Insulin resistance is the

main problem in diabetes (type 2), obesity, heart disease and

some cancers. Every human group ever studied has shown a

positive correlation between sugar consumption and these

conditions. Stay away from sweets, especially sodas!!!

• Two monosaccharides can join to form a

dissaccharide via dehydration synthesis.

• Maltose, malt sugar, is formed by joining two glucose

molecules.

• Lactose is glucose and galactose. It is milk sugar.

• Sucrose is glucose and fructose.


Fig. 5.5a


Fig. 5.5

• Sucrose, table sugar, is the major transport form of

sugars in plants.

• Polysaccharides, aka – complex carbohydrates,

are polymers of hundreds to thousands of

monosaccharides joined by condensation.

• One function of polysaccharides is as an energy

storage macromolecule that is hydrolyzed as needed.

These are what we call starches.

• Other polysaccharides serve a structural function as

building materials for the cell or whole organism.

2. Polysaccharides, the polymers of sugars, have

storage and structural roles


• Starch is a storage polysaccharide composed entirely of

glucose monomers.

• One non-branched form of starch, amylose, forms a helix. When they crystalize they become resistant to digestion and good for your gut microbes!

• Branched forms, like amylopectin, are more complex.


Fig. 5.6a

• Animals also store glucose in a polysaccharide

called glycogen. Still all glucose monomers.

• Glycogen is highly branched, like amylopectin.

• Humans and other vertebrates store glycogen in the liver and muscles, but only have about a one day supply.


Insert Fig. 5.6b - glycogen

Fig. 5.6b

So do other carbs affect blood sugar?

• Yes they do. They hydrolyze quickly in the

mouth and small intestine to release glucose into

the blood stream. Some hydrolyze faster than

others (why?), and this is indicated by what is

called their glycemic index.

• Resistant starches, like in oats, green bananas, and

cooled potatoes, are those that don’t break down

so fast and so are good for your gut bugs!

• http://www.health.harvard.edu/healthy-

eating/glycemic_index_and_glycemic_load_for_1

00_foods

http://www.health.harvard.edu/healthy-eating/glycemic_index_and_glycemic_load_for_100_foods

• While polysaccharides can be built from a variety of

monosaccharides, glucose is the primary monomer

used in polysaccharides.

• One key difference among polysaccharides develops

from 2 possible ring structure of glucose.

• These two ring forms differ in whether the hydroxyl group attached to the number 1 carbon is fixed above (beta glucose) or below (alpha glucose) the ring plane.


Fig. 5.7a


Fig. 5.7

• Starch is a polysaccharide of alpha glucose

monomers.

• Structural polysaccharides form strong building

materials.

• Cellulose makes up the cell wall of plant cells. Be

able to list starch, glycogen and cellulose.

• Cellulose is also a polymer of glucose monomers, but

using beta rings.


Fig. 5.7c

• While polymers built with alpha glucose form helical structures, polymers built with beta glucose form straight structures.

• This allows H atoms on one strand to form hydrogen bonds with OH groups on other strands.

• Groups of polymers form strong strands, microfibrils, that are basic building material for plants and animals.

• This is a great example of your favorite

theme.



Fig. 5.8

Another good thing about fiber….

• There are good and bad guys in our gut, collectively

referred to as our microbiome. The good guys help in one

simple way by outnumbering the bad guys. In general,

the good guys can eat fiber and resistant starches, the bad

guys can’t. So if you feed your good guys they will keep

outnumbering the bad guys, and that is good for you

• Retrogradation is a process by which amylose and

amylopectin, normally broken down very quickly to make

blood sugar shoot up, get bonded together when things

like potato or pasta dries and cools. This makes them

harder to digest so they make it past the small intestine

into the colon and feed the good guys!

4.A.1.a.4 Why is starch easily digested by

animals, while cellulose isn’t?

4.A.1.a how does the structure of

<polysaccharides, proteins, nucleic

acids> influence the function of those

molecules?

• Another important structural polysaccharide is

chitin, used in the exoskeletons of arthropods

(including insects, spiders, and crustaceans).

• Chitin is similar to cellulose, except that it contains a

nitrogen-containing group on each glucose.

• Pure chitin is leathery, but the addition of calcium

carbonate hardens the chitin.

• Chitin also forms

the structural

support for the

cell walls of

many fungi.


Fig. 5.9

• Lipids as a group are an exception among

macromolecules because the group does not include

polymers.

• The unifying feature of lipids is that they all have

little or no affinity for water.

• This is because their structures are dominated by

nonpolar covalent bonds.

• Lipids are highly diverse in form and function.

Introduction



• Glycerol consists of a three carbon skeleton with

a hydroxyl group attached to each.

• A fatty acid consists of a carboxyl group attached

to a long carbon skeleton, often 16 to 18 carbons

long.

Fig. 5.10a

• The many nonpolar C-H bonds in the long

hydrocarbon skeleton make fats hydrophobic.

• In a fat, three fatty acids are joined to glycerol by

an ester linkage, creating a triglyceride.


Fig. 5.10b

Fish: Healthy or Hazardous?

• The long chain unsaturated fats in Omega 3 oils found in fish can actually lower blood cholesterol, but they also may contain harmful mercury. Always be careful where fish are involved.

http://www.youtube.com/watch?v=VnTBkICWIO8

• The major function of fats is energy storage.

• A gram of fat stores more than twice as much energy as a gram of a polysaccharide (9C/g vs. 4C/g)

• Plants use starch for energy storage when mobility is not a concern but use oils when dispersal and packing is important, as in seeds.

• Humans and other mammals store fats as long-term energy reserves in adipose cells.

• Fat also functions to cushion vital organs.

• A layer of fats can also function as insulation.

• This subcutaneous layer is especially thick in whales, seals, and most other marine mammals.


4.A.1.a.3 Explain how the structure of

lipids determines the polarity of the

molecule.

4.A.1.a.3 If the chemistry of water occurs

in aqueous solution, why are lipids useful

in biological systems?

• Phospholipids have two fatty acids

attached to glycerol and a phosphate

group at the third position.

• The phosphate group carries a

negative charge.

2. Phospholipids are major components of

cell membranes



Fig. 5.12

• The interaction of phospholipids with water is

complex.

• The fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head.

• Steroids have a carbon skeleton consisting of four

fused carbon rings, very different than triglycerides.

• Different steroids are created by varying functional groups

attached to the rings.

3. Steroids are lipids that include

cholesterol and certain hormones


Fig. 5.14

• Cholesterol, an important steroid, is a component in

animal cell membranes.

• Cholesterol is also the precursor from which all

other steroids are synthesized.

• Many of these other steroids are hormones, including the

vertebrate sex hormones.

• Sunshine helps convert cholesterol in your skin to

vitamin D.

• While cholesterol is clearly an essential molecule,

high levels of cholesterol in the blood may

contribute to cardiovascular disease.


• Proteins are instrumental in about everything that

an organism does.

• These functions include catalyzing reactions, structural

support, storage, transport of other substances,

intercellular signaling, movement, and defense against

foreign substances.

• Protein enzymes are of overwhelming importance in a

cell and regulate metabolism by selectively accelerating

chemical reactions.

• Humans have tens of thousands of different proteins,

each with their own structure and function.

Introduction


4.A.1.a how does the structure of <polysaccharides,

proteins, nucleic acids> influence the function of those

molecules?

4.A.1.a.2 Explain how the sequence of amino acids in a

protein determines each level of that protein’s structure.

4.A.1.a.2 Explain how the conditions of the environment

that a protein is in affect the structure and function of that

protein.

• All protein polymers are constructed from the

same set of 20 monomers, called amino acids.

• Polymers of proteins are called polypeptides.

• A protein consists of one or more polypeptides

folded and coiled into a specific shape, generally

either fibrous or globular. See what you

remember from the 9th grade – watch this. 4

min., or this, 6 min. with a bit more detail.


https://www.youtube.com/watch?v=qBRFIMcxZNM

https://www.youtube.com/watch?v=wvTv8TqWC48

• Amino acids consist of four components attached

to a central carbon, the alpha carbon.

• These components include a

hydrogen atom, a carboxyl

group, an amino group, and

a variable R group

(or side chain).

• Differences in R groups

produce the 20 different

amino acids.

1. A polypeptide is a polymer of amino

acids connected in a specific sequence



• One group of amino acids has hydrophobic R

groups. Don’t try to memorize these, just get the

general idea of differences in R groups. What if

one of these was substituted for another in a

protein?

• The last group of amino acids includes those with

functional groups that are charged (ionized) at

cellular pH.

• Some R groups are bases, others are acids.


Fig. 5.15c

• Amino acids are joined together when a

dehydration reaction removes a hydroxyl group

from the carboxyl end of one amino acid and a

hydrogen from the amino group of another.

• The resulting covalent bond is called a peptide bond.


Fig. 5.16

• A protein consists of one or more polypeptides that

have been precisely folded and coiled into a unique

shape, again, generally fibrous or globular.

• It is the order of amino acids that determines what the

three-dimensional conformation will be.

2. A protein’s function depends on its specific

conformation (that means shape)


Fig. 5.17

• A protein’s specific structure determines its

function.

• In almost every case, the function depends on its

ability to recognize and bind to some other

molecule like two pieces of a puzzle.

• For example, antibodies bind to particular foreign

substances that fit their binding sites.

• Enzymes recognize and bind to specific substrates,

facilitating a chemical reaction.

• Neurotransmitters pass signals from one cell to another

by binding to receptor sites on proteins in the membrane

of the receiving cell.


More protein functions

• Structural proteins: Collagen, Keratin, Silk

• Transport proteins: membrane “pumps” (e.g.-

Na/K Pump), hemoglobin

• Hormones: insulin, HGH

• Movement: actin and myosin, tubulin

• Proteins in the news: gluten and casein

• The folding of a protein from a chain of amino acids occurs spontaneously, but with the help of other proteins called Chaperonins. We’ll come back to them later.

• Three levels of structure: primary, secondary, and tertiary structure, are used to organize the folding within a single polypeptide.

• Quaternary structure arises when two or more polypeptides join to form a protein.


• The primary structure of a

protein is its unique sequence of

amino acids.

• Lysozyme, an enzyme that

attacks bacteria, consists on a

polypeptide chain of 129

amino acids.

• The precise primary structure

of a protein is determined by

inherited genetic information.

• Primary structure will then

determine how it folds after it

is formed.


Fig. 5.18

• Even a slight change in primary structure can

affect a protein’s shape and ability to function.

Here’s the classic example:

• In individuals with sickle cell disease, abnormal

hemoglobins, oxygen-carrying proteins, develop

because of a single amino acid substitution.

• These abnormal hemoglobins crystallize,

deforming the red blood cells and leading to

clogs in tiny blood vessels.


Fig. 5.19


• The secondary structure of a protein results from

hydrogen bonds at regular intervals along the

polypeptide backbone.

• Typical shapes

that develop from

secondary structure

are coils (an alpha

helix) or folds

(beta pleated

sheets). Both give

the molecule

structural support.

• Link to animation.


Fig. 5.20

../Animations/Animation 5.4.3 Secondary St.MOV

Linus Pauling• One of only a few to

have won two Nobel

Prizes in science - the

first was for his

discovery of the alpha

helical nature of many

proteins.

• Pauling did his work at

Cal-Tech

Tertiary structure refers to

irregular shapes determined by a

variety of interactions among R

groups and between R groups and

the polypeptide backbone,

including disulfide bridges.

Link to animation. 1 min.

../Animations/Animation 5.4.4 Tertiary Str.MOV

Tertiary Structure

• These irregular

foldings are due to

many different types of

bonds between R

groups. The H bonds

which determine

secondary structure are

not between R groups.

• Quaternary structure results from the aggregation of two or

more polypeptide subunits.

• Collagen is a fibrous protein of three polypeptides that are

supercoiled like a rope. Collagen and silk are fibrous.

• This provides the structural strength for their role in

connective tissue.

• Hemoglobin is a

globular protein

with two copies

of two kinds

of polypeptides.

• Hemoglobin and

insulin are globular.


Fig. 5.23

../Animations/Animation 5.4.5 Quaternary S.MOV

Here’s gluten. What is it found in? Why

have you heard of it?

Here’s some gluten tidbits

• In baking, fats interfere with gluten development

process. Cookies are more crumbly than bread

because they've got more fat in them. What

happens is that the fat molecules surround and

literally shorten the strands of gluten so that they

can't stretch out as much. That's where we get the

name "shortening" as well as shortbread cookies.

• Kneading dough and tossing pizza dough gives

the chains more time to form, so they stick

together better. Pizza and bagels –lots of gluten.

http://culinaryarts.about.com/od/cookierecipes/r/shortbredcookie.htm

• A protein’s shape, and therefore its function, can change

in response to the physical and chemical conditions.

• Alterations in pH, salt concentration, temperature, or

other factors can unravel or denature a protein.

• These forces disrupt the hydrogen bonds, ionic

bonds, and disulfide bridges that maintain the

protein’s shape.

• Some proteins can return to their functional shape after

denaturation, but others cannot, especially in the

crowded environment of the cell.

• A cooked egg is an example of a denatured protein.


4.A.1.a.2 Explain how the conditions of

the environment that a protein is in

affect the structure and function of that

protein.

Documents

What, no notes today? · 2019. 1. 27. · enantiomers have important functional significance because of emergent properties from the specific arrangements of atoms. • One enantiomer