Macromolecules: Prep For Midterm 1

Front 1

Isomer

Back 1

Same chemical formula, but different arrangement of atoms.

Front 2

What is an optical isomer?
What is another name for an optical isomer?

Back 2

-When a carbon atom has four different groups attached to it, allowing for two different arrangement to be made that are mirror images of each other.

-Chirality is another name for optical isomers

Front 3

Define a sugar

Back 3

It has an aldose or ketose group at one end with a hydroxylated carbon chain.

Front 4

What do ketoses and aldoses have in common?

Back 4

They both have a carbonyl goup (a carbon atom double bonded to an oxygen atom)

Front 5

What kind of reaction links the monomers together?

Back 5

Condensation reaction, which results in a loss of water.

Front 6

What characterizes amino acid?

Back 6

-An alpha carbon
-An amine group
-A carboxyl group
-A H atom

Front 7

What characterizes the electrically charged hydrophilic side chains?

Back 7

-Either an amine group, or a deprotonated amine group (both have a posive charge.)
-COO- at the end of aspartic and glutemic acid.

Front 8

What do all of the polar but uncharged side chains have in common?

Back 8

Either an 'OH' or and 'O' in their side chain.

Front 9

Name all of the 'special' amino acids and what makes them unique

Back 9

-Cystine: Has a terminal SH group and reacts with another cystine to form a disulfide bridge.

-Proline: Has an R group that connects to it's amine group and is often called a helix breaker and is frequently found in beta turns.

-Glycine: achiral, very small so it's also often found in hairpin turns of secondary structure.

Front 10

What is the 'capital letter' of a polypeptide chain?

Back 10

The N-terminus; the amino group of the first amino acid in the chain.

Front 11

What is the punction mark of the polypeptide chain?

Back 11

The C-terminus; the carboxyl group of the last amino acid in the chain.

Front 12

Describe the flexibility of the peptide linkage between two amino acids.

Back 12

This bond is inflexible because of the resonating double bond between the carbon and oxygen and the carbon and nitrogen.

Front 13

Which atoms bond to creat the alpha helix?

Back 13

The partial negative from the C=O double bond and the partial postive from the N-H bond create the hydrogen bonding that give the alpha helix it's corkscrew shape.

Front 14

What determines tertiary structure?

Back 14

The interactions of R groups (amino acid side chains).

Front 15

How do you tell if an amino acid is of the D or L form?

Back 15

Rotate the H-group so it's facing into the page. If you read CO (carboxyl), R-group, Nitrogen group going counter clockwise (left) then it's an L form. This is the only amino acids used in proteins!

Front 16

Which series of optical isomers do most monosaccharides belong too?

Back 16

D isomers.

Front 17

How do you tell if a sugar is of a D or an L form?

Back 17

-Find the first chiral carbon working from the bottom up.
-If the hydoxide is on the right side, it's a D sugar.

Front 18

Pyran

Back 18

six MEMBERED ring

Front 19

Furan

Back 19

five MEMBERED ring

Front 20

What is the bond called that links monosaccharides together?

Back 20

Glycosidic linkages.

Front 21

In general, which carbons connect to form carbon rings?

What is the exception?

Back 21

The carbon above the CH2OH and Carbon1

-Exception is in Ketose goups when the Keto group is on C2, so it's C2 that connects with the OH or H that is attached to the Carbon above CH2OH.

Front 22

What makes a monosaccharide a (alpha) or (beta)?

Back 22

Whether the OH group on C1 is on the top or bottom. If it is on top, it's Beta, if it's on bottom, it's alpha.

Front 23

What makes up a fatty acid?

Back 23

-long nonpolar chain
-a polar carboxyl group at the head of the molecule.

Front 24

What is the difference between a fat and an oil?

Back 24

Both fall under the chemical category of triglycerides, but fats are solid at room temperature and oils are liquid.

Front 25

What makes up a triglyceride?

Back 25

One glycerol group (make up of three hydroxyl groups) and three fatty acids.

Front 26

Saturated fatty acid

Back 26

Where all of the bonds in the hydrocarbon chain are single.

Front 27

Unsaturated fatty acid

Back 27

Where there is at least one double bond between two carbons in the hydrocarbon chain.

Front 28

Polyunsaturated fatty acid

Back 28

When the hydrocarbon chain of a fatty acid has multiple sets of double bonds between different carbons.

Front 29

What is the usable energy that can do work in a system called?

Back 29

Free energy (delta G)`

Front 30

Exergonic Reaction

Back 30

- Rolling a ball down a hill
- It releases energy and goes from a state of high energy (the top of the hill) to low energy (the bottom of the hill).
- Complex molecule --> free energy + small molecules
-exergonic think explosion, something becoming small pieces.

Front 31

Endergonic Reaction

Back 31

Rolling a ball up a hill takes energy to be put into a system. Delta G would be positive.
- Small molecules + free energy --> complex molecules.

Front 32

Catalyst

Back 32

A catalyst speeds up both the forward and reverse reactions allowing equillibrium to be reached faster.

Front 33

Activation Barrier

Back 33

The amont of energy needed to start the reaction.

Front 34

Transitional State Species

Back 34

-Have higher free energy than either the reactants or products.

Front 35

Substrates

Back 35

In an enzyme catalyzed reaction, the reactants are called substrates.

Front 36

Where does the catalysis take place?

Back 36

The active site on an enzyme.

Front 37

What is formed when a substrate binds to the active site of a molecule?

Back 37

An enzyme-substrate complex (ES)

Front 38

Adding an enzyme does not change what between the reactants and products?

Back 38

The difference in free energy between the reactants and products. (delta G)

Front 39

Explain the relationship between enzymes and the equillibrium of a reaction

Back 39

An enzyme will speed the forward and reverse reactions so that equillibrium is reached more quickly, but it will not change the equillibrium itself.

Front 40

How large is the activation site of an enzyme?

Back 40

About 6-12 residues.

Front 41

Give three ways that enzymes cause their substrates to enter into the transition phase.

Back 41

1. They orient the substrates so that they can covalently bond more easily.
2. They can put strain on the bonds making them more unstable and reactive to say, water.
3. They can temporarily add chemical groups to substrates, making the substrate more chemically reactive.

Front 42

What types of bonds are invloved in the binding of the substrate to the enzyme?

Back 42

- H bonds, hydrophobic interactions, attraction/repulsion between electrically charged groups.

Front 43

induced fit

Back 43

A change in enzyme shape due to substrate binding.

Front 44

prosthetic groupings

Back 44

non amino acid molecules that are permanently bound to enzymes.

Front 45

Which regard to enzymes, what is the saturation phenomenon?

Back 45

By adding more and more substrate, more of the enzymes are occupied with the reaction. But when all of the enzymes are used up, the reaction will not proceed any faster even if more reactants are added.

Front 46

Define an inhibitor and give an example.

Back 46

An inhibitor binds to the active site of an enzyme and slows down the enzyme catalyzed reaction.

Front 47

Competitive inhibitors

Back 47

A molecule that binds non-covalently to the active site of the enzyme and competes with the substrate for the position. Once the concentration of the natural substrate has decreased, the competitive inhibitor detaches itself.

Front 48

Non-competitve inhibitor

Back 48

Binds to a site on the enzyme that is not the active site. This causes the enzyme to change its shape and temporarily inhibits the substrate from binding to the active site. As with competitive inhibitors, they can unbind.

Front 49

Allostery

Back 49

The change in enzyme shape due to non-competitive inhibitors.

Front 50

Difference between the active and inactive form of an enzyme

Back 50

Active form has the proper shape for substrate binding.

Inactive form can bind to an inhibitor but not to the substrate.

-ALLOSTERIC ENZYMES CAN CONVERT BETWEEN THE ACTIVE AND NON-ACTIVE FORMS.

Front 51

Activator

Back 51

Stabalizes the active form of an enzyme.

Makes it more likely that the active form will occur.

Front 52

Regulatory subunits

Back 52

- Part of the enzyme where activators/inhibitors bind to.

Front 53

Name the two allosteric modifiers and the subunit on which they bind.

Back 53

-Allosteric inhibitors bind in the non-active form on the regulatory subunit and make it so the active form does not occur.

-Allosteric activators bind to the the activator site on the the active enzyme in the regulatory subunit and stabalize the active form.

Front 54

Feedback inhibition

Back 54

When there is a surplus of the final product in a reaction, sometimes this final product will allosterically inhibit the enzyme that catalyzed the commitment step, thereby halting the production of the product.

Front 55

amino acids with electrically charged positive side chains

Back 55

Histidine

Arginine

Lysine

Front 56

Amino acids with electrically charged negative side chains

Back 56

Aspartic Acid

Glutamic Acid

Front 57

Amino Acids with polar side chains

Back 57

Glutamine

Asparagine

Serine

Threonine

Tyrosine

Front 58

Describe the chain form of glucose

Back 58

It is an aldose, so Carbon 1 has a double bonded Oxygen and a single bonded hydrogen. Carbon 3 has the H bonded on the right side instead of the left side.

Front 59

Describe the ring form of D isomer ribose.

Back 59

It is a furan, so it is a five membered ring. Carbon 2 and 3 have the OH pointed down, and the Oxygen forms the peak of the pentagon. Don't forget the Hydrogen that extends down from Carbon 4.

Front 60

What is the difference between the ring form of ribose and deoxyribose?

Back 60

Deoxyribose is also a furan with an oxygen at the peak of the pentose, but it's carbon 2 has the H pointed down. The C1 and C2 both have the H pointed down. In ribose, the C1 has the H pointed down and C2 and C3 have OH pointed down.

Front 61

Black=
Red=
Blue=
White=
Green=

Back 61

Black is the Carbon atom
White is the hydrogen atom
Red is the oxygen atom
blue is the nitrogen atom
green is the R group

Front 62

When R groups are on opposite sides of an amino acid chain, what configruation is it?

Back 62

Trans configuration.

Front 63

Describe the ring formation of fructose

Back 63

It is a furanose (five membered), but it is also a hexose. Carbon 1 shoots downward from Carbon 2 on the right most point of the monosaccharide. Carbon 6 shoots up from carbon 5 like with glucose. C2 and C3 both have their OH's pointed up.

Front 64

Describe how glucose goes from a chain to a ring form?

Back 64

The hydroxyl group on C5 binds to C1. The double bond to oxygen becomes a single bod and a partial negative forms, attracting an H and forming the hydroxyl group on C1

Front 65

Which is the anomeric carbon in a ketose?

Back 65

C2

Front 66

Distance between residues in a Beta strand

Back 66

3.5 anstroms

Front 67

distance between residues in a alpha helix

Back 67

1.5 anstroms

Front 68

how many residues appart are the H bond interactions in an alpha helix

Back 68

4.