Biochemistry Chp 4

Front 1

What is the Henderson-Hasselbalch Equation? (Must Memorize!)

Back 1

pH = pKa + log ([A-]/[HA])

A- = conj. base

HA = weak acid

Front 2

Unlikemost organic polymers what specific conformation do protein molecules adopt?

Back 2

A 3-D conformation

Front 3

What is the protein's 3-D natural conformation called?

Back 3

Native fold

Front 4

What is the relation between Entropy and the Folding of proteins?

Back 4

One comes at the cost of the other.

They are opposites

Front 5

Does Enthalpy help with folding? How?

Back 5

Yes

Front 6

What are the 4 favorable interactions in proteins?

Back 6

1. Hydrophobic Effect

2. Hydrogen Bonds

3. London Dispersion

4. Electrostatic Interactions

Front 7

What is the Hydrophobic Effect?

Back 7

Releaseof water molecules from the structured solvation layer around the molecule asprotein folds increases the net entropy

Front 8

What is the solvation layer?

Back 8

A solvation shell is the solvent interface of any chemical compound or biomolecule that constitutes the solute. If the solute is water, it's often called a hydration shell.

Front 9

What are Hydrogen Bonds?

Back 9

H bonding to N, O, or F

*Interactionof N-H andC=O ofthe peptide bond in proteins leads to local regular structures such as a-helicesand b-sheets

Front 10

What are London Dispersion Forces?

Back 10

Results when the electrons in two adjacent atoms occupy positions that make the atoms form temporary dipoles

*Medium-rangeweak attraction between all atoms contributes significantly to the stability inthe interior of the protein

Front 11

What are Electrostatic Interactions?

Back 11

Long-rangestrong interactions between permanently charged groups

*Salt-bridges,esp. buried in the hydrophobic environment strongly stabilize the protein

Front 12

What is a salt bridge?

Back 12

a link between electrically charged acidic and basic groups, especially on different parts of a large molecule such as a protein

Front 13

What are the 4 Levels of Protein Structure?

Back 13

1. Primary

2. Secondary

3. Tertiary

4. Quaternary

Front 14

What is the Primary Structure of a protein?

Back 14

the linear sequence of amino acids

Front 15

What type of protein structure involves Alpha Helices?

Back 15

Secondary

Front 16

What type of protein structure involves Beta Sheets?

Back 16

Tertiary Structure

Front 17

What type of protein structure involves 2 or more assembled subunits of proteins?

Back 17

Quaternary

Front 18

Which of the 4 favorable interactions in proteins is most important to the alpha helix? (secondary structure)

Back 18

H-Bonding

Front 19

Where is the peptide bond found?

Back 19

Between C of one amino acid's carbonyl

and the N of another amino acid's amino group

H

l

* C---N

ll

O

Front 20

What makes a peptide bond stronger than a single bond, but weaker than a double bond?

Back 20

Resonance

*also makes bond a bit shorter than single bond

Front 21

Phi (Φ) is used to denote the bond between which two atoms?

Back 21

Between the Alpha Carbon and its Amide Nitrogen

*remember: phi has an "h" which resembles the "n" in Nitrogen

Front 22

Psi (ψ) is used to denote the bond between which two atoms?

Back 22

Between the Alpha Carbon and its Carbonyl Carbon

*remember: psi has 3 points on top of symbol and COO- has 3 atoms

Front 23

Can a peptide bond rotate?

Back 23

No because the peptide structure is in a plane

(resonance)

Front 24

Can the bonds around the Alpha Carbon (Φ and ψ) rotate?

Back 24

Yup to the Yes!

Front 25

What angle do Φ and ψ make when a polypeptide chain is fully extended?

Back 25

180 degrees (dihedral angle)

Front 26

What is a Dihedral Angle?

Back 26

the angle between two intersecting planes

*In chemistry it is the angle between planes through two sets of three atoms, having two atoms in common

Front 27

What makes Φ and ψ combinations favorable and unfavorable?

Back 27

Favorable: Chance to form H-bonds

Unfavorable: Steric Hindrance of backbone side chains

Front 28

What does a Ramachandran plot show?

Back 28

The distribution of Φ and ψ dihedral angles

Front 29

What are the two common arrangements of the secondary protein structure?

Back 29

Alpha Helix

Beta Sheet

Front 30

What stabilizes the alpha sheet?

Back 30

H-bonds

Front 31

What stabilizes beta sheets?

Back 31

H-bonds between adjacent strands

Front 32

What are the 2 sub-types of beta sheets?

Back 32

Antiparallel and Parallel

Front 33

Any irregular arrangement of a polypeptide chain is called what?

Back 33

Random coil

Front 34

The Helical backbone is held together byhydrogen bonds between the backbone amides and carbonyl O of an n and n+what amino acid?

Back 34

n+4

Front 35

How many residues does a right-handed helix have per turn?

Back 35

3.6

Front 36

How many Angstroms (Å) does a right-handed helix have per turn?

Back 36

5.4 Å

Front 37

Do the side chains on an alpha helix point into the helix or out?

Back 37

Out

Front 38

What charge does the N Terminus of a polypeptide chain have?

Back 38

Positive

Front 39

What charge does the C Terminus of a polypeptide chain have?

Back 39

Negative

Front 40

FOR MCAT!

A sequence with many Pro and Gly will most likely not form what secondary structure?

Back 40

Alpha Helix

Front 41

What is the most favorable amino acid in an alpha helix?

Back 41

Alanine

Front 42

What does Proline do to an alpha helix?

Back 42

It breaks it! because of the rotation around the N--Ca bond (phi) is impossible

Front 43

What does Glycine do to an alpha helix?

Back 43

It breaks it! because the tiny R-group on Gly supports other conformations

Front 44

Which bond of an amino acid has a strong dipole moment?

Back 44

Peptide Bond

(Carbonyl O is neg

Amide H is pos)

Front 45

Do side chains point up or down in a beta strand?

Back 45

Trick Question! They alternate pointing up and down

Front 46

Which is more robust (stable): Parallel or Antiparallel Beta Sheets?

Back 46

Antiparallel

Front 47

Why are Antiparallel Beta Sheets more stable?

Back 47

H-bonds are linear

Front 48

Why are Parallel Beta Sheets less stable?

Back 48

H-bonds are bent

Front 49

Are antiparallel or parallel beta sheets more extended?

Back 49

Antiparallel by 0.5 Angstroms between two amino acids

Front 50

What are Beta Turns?

Back 50

Secondary Structure: 180 degree turns in a polypeptide chain

Front 51

Over how many amino acids does a beta turn go?

Back 51

4

Front 52

What holds a beta turn in place?

Back 52

An H-bond

Front 53

In which position will you find proline and glycine in a beta turn?

Back 53

Proline in 2nd position

Glycine in 3rd position

Front 54

Mostpeptide bonds notinvolving proline are in what configuration >99.95% of the time?

Back 54

Trans

Front 55

Forpeptide bonds involvingproline, about what percent are in the cisconfiguration and where are they found?

Back 55

~6%

In Beta Turns

Front 56

What is Circular Dichroism (CD) Analysis?

Back 56

A way to measure circularly polarized light from secondary structures

Front 57

On CD analysis, why are alpha helices in the negative region?

Back 57

Because of L proteins and right-handed Helices