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68 Cards in this Set

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  • Back
Same chemical formula, but different arrangement of atoms.
What is an optical isomer?
What is another name for an optical isomer?
-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
Define a sugar
It has an aldose or ketose group at one end with a hydroxylated carbon chain.
What do ketoses and aldoses have in common?
They both have a carbonyl goup (a carbon atom double bonded to an oxygen atom)
What kind of reaction links the monomers together?
Condensation reaction, which results in a loss of water.
What characterizes amino acid?
-An alpha carbon
-An amine group
-A carboxyl group
-A H atom
What characterizes the electrically charged hydrophilic side chains?
-Either an amine group, or a deprotonated amine group (both have a posive charge.)
-COO- at the end of aspartic and glutemic acid.
What do all of the polar but uncharged side chains have in common?
Either an 'OH' or and 'O' in their side chain.
Name all of the 'special' amino acids and what makes them unique
-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.
What is the 'capital letter' of a polypeptide chain?
The N-terminus; the amino group of the first amino acid in the chain.
What is the punction mark of the polypeptide chain?
The C-terminus; the carboxyl group of the last amino acid in the chain.
Describe the flexibility of the peptide linkage between two amino acids.
This bond is inflexible because of the resonating double bond between the carbon and oxygen and the carbon and nitrogen.
Which atoms bond to creat the alpha helix?
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.
What determines tertiary structure?
The interactions of R groups (amino acid side chains).
How do you tell if an amino acid is of the D or L form?
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!
Which series of optical isomers do most monosaccharides belong too?
D isomers.
How do you tell if a sugar is of a D or an L form?
-Find the first chiral carbon working from the bottom up.
-If the hydoxide is on the right side, it's a D sugar.
six MEMBERED ring
five MEMBERED ring
What is the bond called that links monosaccharides together?
Glycosidic linkages.
In general, which carbons connect to form carbon rings?

What is the exception?
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.
What makes a monosaccharide a (alpha) or (beta)?
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.
What makes up a fatty acid?
-long nonpolar chain
-a polar carboxyl group at the head of the molecule.
What is the difference between a fat and an oil?
Both fall under the chemical category of triglycerides, but fats are solid at room temperature and oils are liquid.
What makes up a triglyceride?
One glycerol group (make up of three hydroxyl groups) and three fatty acids.
Saturated fatty acid
Where all of the bonds in the hydrocarbon chain are single.
Unsaturated fatty acid
Where there is at least one double bond between two carbons in the hydrocarbon chain.
Polyunsaturated fatty acid
When the hydrocarbon chain of a fatty acid has multiple sets of double bonds between different carbons.
What is the usable energy that can do work in a system called?
Free energy (delta G)`
Exergonic Reaction
- 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.
Endergonic Reaction
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.
A catalyst speeds up both the forward and reverse reactions allowing equillibrium to be reached faster.
Activation Barrier
The amont of energy needed to start the reaction.
Transitional State Species
-Have higher free energy than either the reactants or products.
In an enzyme catalyzed reaction, the reactants are called substrates.
Where does the catalysis take place?
The active site on an enzyme.
What is formed when a substrate binds to the active site of a molecule?
An enzyme-substrate complex (ES)
Adding an enzyme does not change what between the reactants and products?
The difference in free energy between the reactants and products. (delta G)
Explain the relationship between enzymes and the equillibrium of a reaction
An enzyme will speed the forward and reverse reactions so that equillibrium is reached more quickly, but it will not change the equillibrium itself.
How large is the activation site of an enzyme?
About 6-12 residues.
Give three ways that enzymes cause their substrates to enter into the transition phase.
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.
What types of bonds are invloved in the binding of the substrate to the enzyme?
- H bonds, hydrophobic interactions, attraction/repulsion between electrically charged groups.
induced fit
A change in enzyme shape due to substrate binding.
prosthetic groupings
non amino acid molecules that are permanently bound to enzymes.
Which regard to enzymes, what is the saturation phenomenon?
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.
Define an inhibitor and give an example.
An inhibitor binds to the active site of an enzyme and slows down the enzyme catalyzed reaction.
Competitive inhibitors
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.
Non-competitve inhibitor
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.
The change in enzyme shape due to non-competitive inhibitors.
Difference between the active and inactive form of an enzyme
Active form has the proper shape for substrate binding.

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

Stabalizes the active form of an enzyme.

Makes it more likely that the active form will occur.
Regulatory subunits
- Part of the enzyme where activators/inhibitors bind to.
Name the two allosteric modifiers and the subunit on which they bind.
-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.
Feedback inhibition
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.
amino acids with electrically charged positive side chains


Amino acids with electrically charged negative side chains
Aspartic Acid

Glutamic Acid
Amino Acids with polar side chains




Describe the chain form of glucose
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.
Describe the ring form of D isomer ribose.
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.
What is the difference between the ring form of ribose and deoxyribose?
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.
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
When R groups are on opposite sides of an amino acid chain, what configruation is it?
Trans configuration.
Describe the ring formation of fructose
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.
Describe how glucose goes from a chain to a ring form?
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
Which is the anomeric carbon in a ketose?
Distance between residues in a Beta strand
3.5 anstroms
distance between residues in a alpha helix
1.5 anstroms
how many residues appart are the H bond interactions in an alpha helix