Proteins

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Alanine
Ala
A
Hydrophobic and nonpolar, mostly on interior of proteins
Aliphatic

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Glycine
Gly
G
Smallest amino acid, doesn't really have an effect on hydrophobic interactions
Can be found anywhere on the protein

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Proline
Pro
P
Non-polar
Alipathic
Constrains proteins, often found at end of alpha helices; or as a kink in alpha helix

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Valine
Val
V
Non-polar and hydrophobic, usually in interior
Aliphatic

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Leucine
Leu
L
Non-polar, hydrophobic, generally in center of protein
Aliphatic
Most common amino acid

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Isoleucine
Ile
I
Non-polar and hydrophobic, interior of proteins
Aliphatic
Usually interchangable with leucine or valine

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Methionine
Met
M
Non-polar and hydrophobic
Always the first amino acid coded for by DNA to start a protein

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Serine
Ser
S
Polar, uncharged, hydrophilic
Easily hydrogen bonds

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Threonine
Thr
T
Polar, uncharged, hydrophilic

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Cysteine
Cys
C
Polar, uncharged, hydrophilic
Can form di-sulfide bonds unlike Met
Means it is often found in secreted proteins since extracellular environment allows disulfide bonds

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Asparagine
Asn
N
Polar, uncharged, hydrophilic
Common site for attachment of carbohydrates in glycoproteins

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Glutamine
Gln
Q (Qtamine)
Polar, uncharged, hydrophilic

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Phenylalanine
Phe
F
Nonpolar, aromatic, hydrophobic
Absorbs ultraviolet light
Often found in folded proteins since pi electrons stack with other aromatic systems

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Tyrosine
Tyr
Y
Polar (weakly), aromatic, uncharged
Absorbs ultraviolet radiation

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Tryptophan
Trp
W (Twiptophan)
Largest amino acid
Polar (weakly), aromatic, uncharged
Absorbs ultraviolet radiation

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Lysine
Lys
K (closest to L)
Polar, positively charged, hydrophilic
Still has some hydrophobic character to it

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Histidine
His
H
Polar, positively charged, hydrophilic
Facilitate many enzyme-catalyzed reactions

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Arginine
Arg
R
Polar, positively charged, hydrophilic
Found in nitrogen metabolism and phosphorylated substances

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Glutamate (glutamic acid)
Glu
E (Glutameke)
Acidic, polar, negatively charged, hydrophilic

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Aspartate
Asp
D (Aspardic acid)
Acidic, negatively charged, polar, hydrophilic
Maintains solubility and ionic character of proteins

Front 21

1. Define amino acid residue.

2. Which amino acid is not chiral?

Back 21

1. When an amino acid is part of a protein chain, it is known as a residue since the peptide backbone is the main structure.

2. Glycine G (Gly)

Front 22

1. What is the D,L system? Draw them.

2. Which type are all amino acids?

Back 22

2. All amino acids are L.

Front 23

Define absorbance.

Back 23

The Lambert-Beer law defines it as e*c*l where c is the concentration and l is the path length. This means that absorbance is directly related to concentration.

Aromatic compounds often have a high absorbance.

Front 24

Define cystine.

Back 24

When cysteine C (Cys) is oxidized to form a dimeric amino acid which are linked by a disulfide bond. These are strongly hydrophobic and nonpolar. They play a strong role in covalent bonds in tertiary structures.

Front 25

Define zwitterion.

Back 25

A substance that can act as either a base or an acid, has both a positive and negative charge at neutral pH. Like the peptide base of amino acids.

Front 26

1. How does forming a zwitterion affect pKa?

2. Does a positively charged amino group give up a proton more easily or less easily when a negatively charged carboxyl group is present?

Back 26

1. This lowers the pKa because zwitterions are stable. Thus, the substance wants to move towards a zwitterion.

2. The amino group has a lower pKa because the oxygen pulls some electrons away from the amino group.

Front 27

1. What is the isoelectric point?

2. How do you calculate pI?

Back 27

1. Known as pI, it is the pH at which the net electric charge is 0.

2. Take the arithmetic mean of all the pKa values. For example, in glycine, you would combine the pKa of the carboxy group and the pKa of the amino group.

Front 28

1. If the pH > pI, what charge does the amino acid have?

2. If the pH < pI, what charge does the amino acid have?

Back 28

1. Negative

2. Positive

Front 29

1. How are peptide bonds formed?

2. Do peptide bonds last long? Why?

Back 29

1. By condensation reaction, removal of water from the carboxy group and amino group. Note that peptide bonds are not favored.

2. Peptide bonds have a high activations energy but a half life of 7 years.

Front 30

1. Define oligopeptide.

2. Define polypeptide.

3. Define proteins.

Back 30

1. Few amino acids

2. Molecular weight is less than 10,000 da

3. Molecular weight is greater than 10,000 da

Front 31

Describe the convention of displaying a polypeptide/protein.

Back 31

Amino-terminal (N-terminal) is on the left, while carboxy-terminal (C-terminal) is on the right. The sequence is read left to right.

Front 32

1. Give a range of molecular weights for proteins in our body.

2. Give a range of length for proteins in our body.

Back 32

1. 12,000 to 3 million

2. 100 to 27,000, but the majority are < 2,000.

Front 33

1. Define multisubunit protein.

2. Define oligomeric.

3. Define protomer.

Back 33

1. A protein with two or more polypeptides associated noncovalently.

2. If at least two of the polypeptides in a multisubunit protein are identical.

3. The identical polypeptides of a oligomeric protein.

Front 34

1. How do we estimate the number of amino acid residues in a protein given molecular weight?

2. How do we get this number?

Back 34

1. Divide molecular weight by 110 da.

2. Average molecular weight is 138. However, smaller amino acids predominate, so we drop this to 128. Then we have to take into account the condensation reaction, 110 da.

Front 35

1. Define conjugated proteins.

2. Define prosthetic group.

3. Give some examples of a conjugated protein.

Back 35

1. A protein that contains permanently associated chemical components that are not amino acids.

2. The non-amino acid part of a conjugated protein.

3. Lipoprotein, glycoprotein, metalloproteins

Front 36

What is the primary structure of a protein?

Back 36

The sequence of amino acids; the description of all covalent bonds including disulfide and peptide bonds in an amino acid

Front 37

What is the secondary structure of a protein?

Back 37

Stable arrangements of amino acid residues giving rise to recurring structural patterns.

Spatial arrangement of backbone without regard to the side chain conformations.

Front 38

1. What is the tertiary structure of a protein?

2. What is the quaternary structure of a protein?

Back 38

1. Three dimensional structure of the entire polypeptide chain.

2. The spatial arrangement of two ore more subunits of polypeptides.

Front 39

1. Do proteins with different functions always have different amino acids sequences?

2. If you alter the primary structure of the amino acid, will the function of the protein change?

Back 39

1. Yes

2. Possibly.

Front 40

1. Is the amino acid sequence always the same for a particular protein?

2. Why are there diseases associated with these polymorphic proteins then?

Back 40

1. No, an estimated 20% to 30% of proteins are polymorphic, with different amino acid variations in the human genome.

2. There are critical areas of the protein, where the sequence must be conserved.

Front 41

1. Draw a peptide bond.

2. What conformation predominates? Trans or cis?

Back 41

2. Trans. Cis can happen with proline in beta chains sometimes.

Front 42

1. Define native protein.

2. Define stability as related to proteins.

Back 42

1. A protein in it's functional folded conformation.

2. The tendency for a protein to maintain a native conformation.

Front 43

1. What type of interactions predominate to fold proteins?

2. Of these, which predominates?

Back 43

1. Weak interactions like hydrogen bonding, hydrophobic and ionic interactions.

2. Hydrophobic

Front 44

1. What angle is Phi (circle with slash through it)?

2. What angle is Psi (trident)?

3. What angle is Omega (w)?

Back 44

1. C - N - Calpha - C

2. N - Calpha - C - N

3. Calpha - C - N - C (99% of the time trans)

Front 45

1. Define Ramachandran plot.

2. What is a regular secondary structure?

Back 45

1. The possible angles of Psi versus Phi for a protein configuration. Anything in blue is possible, yellow is not.

2. Has repeating angles. Two common types: alpha helix and beta sheets.

Front 46

Describe an alpha helix.

Back 46

Polypeptide backbone tightly wound around an imaginary axis with the R groups pointing outwards.

Front 47

1. Is an alpha helix right or left handed?

2. Why is an alpha helix so stable?

Back 47

1. Right handed, as your fingers curl, must trend upward. Right handed seems to be slightly more stable than left handed.

2. The amino acids on top of each other hydrogen bond. The hydrogen attached to the nitrogen group binds with the oxygen 4 amino acids away.

Front 48

1. How many amino acid residues are in every turn of an alpha helix?

2. How high is each turn of an alpha helix?

Back 48

1. 3.6 residues

2. 5.4 angstroms

Front 49

What are 5 constraints that affect the stability of an alpha helix?

Back 49

1. Intrinsic propensity of a residue to form an alpha helix.
2. Interactions between R groups 3 to 4 residues apart.
3. Bulkiness of R groups, or electrostatic repulsion
4. Occurrence of proline or glycine
5. Interactions at the end of the helix which is a dipole

Front 50

1. Why does proline affect alpha helices?

2. Why does glycine affect alpha helices?

Back 50

1. Proline causes a kink in the alpha helix with the rigid nitrogen bond. Also, there is no hydrogen on the nitrogen to participate in normal hydrogen bonds of the alpha helix.

2. Glycine is so tiny that it has more flexibility and forms a different coiled structure.

Front 51

Describe a beta strand.

Back 51

Zigzag polypeptide chains that resemble sheets. Hydrogen bonding happens between the hydrogen attached to the nitrogen and the carbonyl group. The R groups alternate pointing up and pointing down.

Front 52

Describe the two types of beta strands.

Back 52

Antiparallel is where the polypeptides run antiparallel to each other.

Parallel is where the polypeptides run parallel to each other.

Front 53

Describe a beta turn.

Back 53

A four amino acid sequence connection between anti-parallel strands of a beta pleated sheet. Allows a 180 degree turn. Typically involve either proline P (pro) or glycine G (gly) since P participates in cis bonds and glycine is super small. It is a non-repetitive structure.

Front 54

Describe an omega loop.

Back 54

It is a non-repetitive structure that is compact and globular. R groups are inside.

Front 55

What is circular dichroism (CD) spectroscopy?

Back 55

Plots absorption spectrums for proteins. Thus, we can determine if the proteins are properly folded, estimate the percentage of the protein that is folded in the common secondary structures and monitor transitions between folded and unfolded states.

Front 56

1. Define fibrous protein.

2. Define globular proteins.

Back 56

1. Polypeptide chains arranged in long strands or sheets. Generally a single secondary structure and a simple tertiary structure.

2. Polypeptide chains folded into a spherical or globular shape. Several types of secondary structures usually. Typically enzymes or regulatory proteins.

Front 57

Describe alpha-keratin.

Back 57

Found only in mammals, this is a type of intermediate filament. Two right handed alpha helices are wound together in a left handed alpha helix. The interior of this helix is full of hydrophobic R groups. These interactions and disulfide bonds help stabilize the structure.

Front 58

1. Define dimer as it relates to alpha-keratin.

2. Define protofilament.

3. Define protofibril.

4. Define microfibril.

Back 58

1. Two polypeptide strands wound around each other in a left-handed helix.
2. 3 of these dimers strung together.
3. 12 of these dimers strung together, or 4 protofilaments packed together.
4. 8 of these protofibrils strung packed together.

Front 59

How does a perm work?

Back 59

Reduce the disulfide bonds, curl the hair and reform the disulfide bonds. Now, when original alpha helix formations form, these new disulfide bonds will torque the hair.

Front 60

Describe collagen.

Back 60

A strong tensile fiber found in tendons or bone matrix. Consists of 3 alpha chains (not helices) which are left handed, supertwisted together right-handedly. Has 3 amino acids residues per turn and the sequence is usually glycine, proline then 4-Hyp (an uncommon amino acid).

Front 61

Why does having Vitamin C protect you against scurvy?

Back 61

Scurvy is the weakening of collagen strength, which eventually causes death. Both Pro and 4-Hydroyproline are needed in collagen. Alpha-ketoglutarate is consumed converting Pro -> 4-Hyp, but it is also consumed in another reaction with iron. Vitamin C is needed to reduce the heme iron so that the enzyme can work again.

Front 62

What type of covalent crosslinking does collagen have?

Back 62

Not disulfide bonds, but lysyl oxidase bonds which use Lys and HyLys (5-hydroxylysine)

Front 63

Describe the structure of silk.

Back 63

Silk is made of fibroin protein. Almost all of it is in the beta conformation (anti-parallel). Silk does not stretch, but will bend since there are extensive hydrogen bonds between the sheets.

Front 64

1. What are the effects of non-polar R groups in tertiary structure?

2. Charged polar R groups?

3. Uncharged polar R groups?

Back 64

1. Interior, hydrophobic interactions.

2. Exterior, ionic interactions.

3. Either, hydrogen bonding,

Front 65

Describe myoglobin.

Back 65

Small globular protein. 153 amino acids, 16.7 kDa and has 8 alpha helices. Hydrophobic proteins packed in core (only room for 4 water molecules), peptide bonds in trans, and proline present at many of the turns and 1 at strategic kink in an alpha helix. 3/4 residues per turn.

Front 66

Define motif.

Back 66

Also known as supersecondary structure or fold, it is a recognized folding pattern involving two or more elements of secondary structure and connections between. Has functional significance. Examples are B-a-B loop or a-a corner.

Front 67

Define x-ray diffraction.

Back 67

Place a crystal of protein (limitation of crystal) between x-ray and source and measure the reflections using mathematical Fourier transforms. Can be applied to proteins too large for NMR.

Front 68

Define NMR.

Back 68

Works on proteins dynamically. When a magnetic field is applied, some atoms give rise to a magnetic dipole which shows up on a graph. Using computers, we can then use this info along with van der Waals radii, etc to plot the 3-D structure of the protein.

Front 69

Define domain.

Back 69

Describes structural patterns in a protein. Part of a polypeptide chain that is independently stable or could undergo movement as a single entity with respect to the entire protein. Different domains often have different functions.

Front 70

Define Rossman fold.

Back 70

1. A type of motif that has dinucleotide binding (for DNA).

2. Includes a B-a-B loop that then has a bunch of beta segments attached to it's neighbor by an alpha helix segment. Found in enzymes, often with a binding site.

Front 71

List 5 rules for protein folding.

Back 71

1. Hydrophobic R groups bured in core.
2. B and a found in different layers.
3. Segments close to each other in sequence are usually close together in folded.
4. Connections of elements do not typically for knots or crossover
5. B most stable with slight right twist.

Front 72

1. What are the categories in the Structural Classification of Proteins?

2. Define protein family.

Back 72

1. All a, all B, a/B (integrated) and a + B (alpha and beta somewhat seperated).

2. Proteins similar in primary structure of tertiary structure and function.

Front 73

Define superfamilies.

Back 73

Protein families with similar function that use the same motif. Probably evolutionarily related.

Front 74

Why did domains evolve?

Back 74

They are stable folding patterns, which can tolerate amino acid changes. They support function, thus often domains are conserved through evolution, not specific primary structure.

Front 75

1. Define multimer.

2. Define oligomer.

3. Define protomer.

Back 75

1. Multisubunit protein.

2. Multimer with just a few subunits.

3. Repeating structural units in a multimeric protein.

Front 76

Go into more detail about quaternary structure and symmetries.

Back 76

Subunits are symmetrically arranged and associate non-covalently.

Rotational or helical symmetry means that subunits can be superimposed on others by rotation around some axis.

Front 77

List four forces that stabilize protein structure.

Back 77

1. Electrostatic forces

2. Hydrogen bonding forces

3. Hydrophobic forces

4. Chemical crosslinks

Front 78

1. What are salt bridges?

2. Define hydropathies.

Back 78

1. Electrostatic interactions between two ionic groups of opposite charges within a protein.

2. Combined hydrophilic and hydrophobic tendencies of individual residues. High value means more likely interior.

Front 79

1. Define denaturation.

2. What are some things that cause denaturation?

Back 79

1. Loss of 3D structure enough to affect function. Cooperative process, has a sigmoidal curve, denaturation happens all at once.

2. Extreme heat, pH or salt concentrations.

Front 80

Define renaturation.

Back 80

If a denatured protein is returned to conditions that are favorable for function, sometimes the protein will return to the stable native conformation.

Ribonuclease A can be renatured. Has 4 disulfide bonds that can be broken and remade.

Front 81

Describe the two hypotheses of protein folding.

Back 81

1. Folding process is hierarchical. First comes a and B structures, then ionic interactions help things, etc.

2. Folding is initiated by a spontaneous collapse of the polypeptide into a compact state (molten globule)

Front 82

Describe a free energy funnel.

Back 82

Free energy decreases as you move down the graph, shows how a protein folding would act. Decreases entropy and increases proteins in native conformation as move down. There is also a reduction of possible conformations.

Front 83

Define molecular chaperone.

Back 83

Proteins that interact with partially folded or improperly folded proteins. Prevent aggregation, assist in assembly, and allow refolding. Examples include Hsp70, GroEL/GroES and enzymes.

Front 84

Define Hsp70.

Back 84

A molecular chaperone abundant in cells stressed by elevated temperatures. Bind to hydrophobic regions to prevent aggregation, block folding until translocated through membrane, and assist in general assembly. ATP dependent.

Front 85

Define GroEL and GroES chaperones.

Back 85

Fold proteins that do not fold spontaneously. Up to 10% of proteins in E.coli need this. They work together and are ATP dependent.

Front 86

Define PDI.

Back 86

Protein disulfide isomerase is an enzymatic molecular chaperone that rearranges disulfide bonds.

Front 87

Define PPI.

Back 87

Peptide prolyl cistrans isomerase is an enzymatic molecular chaperone that converts between cis and trans isomers of proline.

Front 88

1. Define amyloid.

2. Define amyloidoses.

Back 88

1. A protein that has been secreted in a misfolded state and has been made into an insoluble extracellular fiber.

2. Diseases associated with amyloids.

Front 89

1. Define primary amyloidosis.

2. Define secondary amyloidosis.

Back 89

1. Independent of any other disease, like immunoglobin light chain accumulation.

2. Accompanied by a long term illness like RA, tuberculosis, cancer.

Front 90

1. How can amyloidosis affect diabetes?

2. Alzheimer's?

3. Parkinson's?

Back 90

1. Amylin forms on pancreatic islets cells, eventually destroying them.

2. Amyloid plagues, presenillin build up in extracellular spaces while tau fibers build in intracellular neuron spaces.

3. Intracellular fibers called Lewy bodies build up.