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Biological Mechanisms > Lecture 2 Prep for Exam 1 > Flashcards

Lecture 2 Prep for Exam 1 Flashcards

1
Q

Peptide bond is…
A) planar and flexible
B) planar and rigid
C) nonplanar and rigid

A

B) planar and rigid

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2
Q

The majority of peptides assume ____ conformation.

A

trans

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3
Q

What is a dna’s primary structure:

a) linear sequence of amino acids
in a polypeptide chain.

b) local spatial arrangement of a polypeptide’s
backbone atoms without regard to the conformations of its side chains (e.g. α-helix, β-sheet, turns).

c) three- dimensional structure of an entire polypeptide, including its side chains

A

a…linear sequence of amino acids
in a polypeptide chain.

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4
Q

What is a dna’s secondary structure:

a) linear sequence of amino acids
in a polypeptide chain.

b) local spatial arrangement of a polypeptide’s
backbone atoms without regard to the conformations of its side chains (e.g. α-helix, β-sheet, turns).

c) three- dimensional structure of an entire polypeptide, including its side chains

A

b) local spatial arrangement of a polypeptide’s
backbone atoms without regard to the conformations of its side chains (e.g. α-helix, β-sheet, turns).

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5
Q

What is a dna’s tertiary structure:

a) linear sequence of amino acids
in a polypeptide chain.

b) local spatial arrangement of a polypeptide’s
backbone atoms without regard to the conformations of its side chains (e.g. α-helix, β-sheet, turns).

c) spatial arrangement of two or more polypeptides

d) three- dimensional structure of an entire polypeptide, including its side chains

A

d) three- dimensional structure of an entire polypeptide, including its side chains

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6
Q

What is a dna’s quaternary structure:

a) linear sequence of amino acids
in a polypeptide chain.

b) local spatial arrangement of a polypeptide’s
backbone atoms without regard to the conformations of its side chains (e.g. α-helix, β-sheet, turns).

c) noncovalent association of two or more polypeptides

d) three- dimensional structure of an entire polypeptide, including its side chains

A

c) noncovalent association of two or more polypeptides

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7
Q

How many residues does the alpha helix have per tern?

A

3.6 residues (amino acids)

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8
Q

What is the distance that the alpha helix rises per turn?

A

5.4 Angstroms

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9
Q

What is the average length of alpha helices?

A

12 residues (3 helical turns and a length of 18 angstroms)

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10
Q

How is the alpha helix stabilized?

A

hydrogen bonds within the backbone

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11
Q

What is the optimum distance for H-bonds?

A

2.8 angstroms

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12
Q

The peptide C=O bond of the second residue points along the helix axis toward the peptide N-H group of what residue?

A

(n + 4)th residue= (2+4)th residue= 6th residue

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13
Q

What are three conditions that disrupt an alpha helix?

A

electrostatic repulsion, steric repulsion and proline (if not at the end of the chain)

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14
Q

Beta sheets contain how many polypeptide strands?

A

2-22 polypeptide strands (average of 6 strands)

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15
Q

Beta sheets contain up to how many residues?

A

up to 15 (average is 6 residues)

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16
Q

Why are parallel sheets containing less than 5 strands rare?

A

Due to the longer distance between these hydrogen bonds which causes them to be weaker (as the hydrogen bonds provide the stability). Therefore, there needs to be more parallel strands than 5 in order to be stronger.

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17
Q

What is the length of each zigzag portion of a beta sheet?

A

7 Angstroms

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18
Q

What are the two common amino acids that are at the turning points in the reverse turns (beta bends)? Why are they the two common amino acids in Turns?

A

Gly or Pro are common in Turns due to glycine not having a side-chain (easier to turn) and proline already being bent.

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19
Q

Label the N- and C- terminus in the antiparallel strands

A
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20
Q

Label the N- and C- terminus in the parallel strands

A
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21
Q

Will an antiparallel beta sheet or parallel beta sheet have a longer beta turn?

A

parallel! Look at two images for comparison.

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22
Q

A motif is a combination of ______ structure present in _______ structures.

A

combination of secondary structures present in tertiary structures

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23
Q

Identify the different motifs…

A
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24
Q

What are two methods protein structure can be determined by?

A

x-ray crystallography and twp-dimensional NMR spectroscopy

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25
Q

What is the online data bank that is the Repository for Structural Information?

A

Protein Data Bank (PDB)

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26
Q

What was the significance of the Nature Article?

A

The AI tool called AlphaFold has predicted the structure of nearly the entire human proteome and predicted the proteomes for other organisms. It transformed the primary sequence to 3D

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27
Q

Most proteins can be classified as what structure names?

A

alpha, beta, alpha/beta

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28
Q

Alpha proteins have what type(s) of strands?

A

All antiparallel

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29
Q

Beta proteins have what type(s) of strands?

A

parallel and antiparallel

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30
Q

How do the human retinol binding protein and the Beta barrel distribute vitamin A?

A

Vitamin A is hydrophobic, and at the top of the barrel there is water. Therefore, the huamn retinol binding protein (that is bounded to vitamin A) will be distributed down and throughout the beta barrel due to the hydrophobic effect. Hydrophobic effect occured with the two droplets of oil due to water wanting to bond with the least amount of surface area of the oil droplets, therefore, the oil droplets clumped together and the h-bonds then formed around the clumped oil droplets (instead of individual droplets).

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31
Q

A quaternary structure of Transthyretin (homo-tetramer) has how many subunits and polypeptides?

A

4 identical subunits (all of the same polypeptide)

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32
Q

The complex of Transthyretin tetramer and retinol binding protein/retinol is an example of what structure?

A

A quaternary structure

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33
Q

Anything less than ______ gets filtered by the kidney

A

less than 30 kdal

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34
Q

What are some advantages of a quaternary structure?

A

-defects can be repaired by simply replacing the flawed subunit
-provides the structural basis for the regulation of their activities (allosteric or cooperative binding)

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35
Q

Fibrous proteins such as keratin and collagen have repeating _____ structures

A

secondary structures

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36
Q

alpha-keratin is rich in what type of amino acids/bonds

A

cysteine residues (disulfide bonds)

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37
Q

What is the only covalent bond that can occur in quaternary structure?

A

disulfide bond (2 cys)

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38
Q

A domain is a globular cluster of secondary/supersecondary structures usually found in polypeptides with __X____ residues

a) >100
b) > 200
c)>300

A

> 200 residues

side note…*What is the difference between domains and tertiary structures? Tertiary structures of a protein is the overall 3D structure of the protein and it is formed by the folding of the protein’s primary and secondary structures and can include embedded secondary structures, super secondary structures and domains. Many globular proteins have DOMAINS which are locally folded parts of the tertiary structure. A proteins with multiple functions can have more than one domain, each playing a specific role.

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39
Q

Most domains consist of ___ to ___ residues

A

40 to 200

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40
Q

what is the average diameter of a domain?

A

25 angstrom

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41
Q

What structure is the following? (primary, secondary, tertiary, etc.) What will you have if you unfold the structure?

A

-quaternary structure

-You will have 4 polypeptide chains.

42
Q

For alpha keratin:

Which is the secondary structure?

And what is alpha keratin prevalently found in ?

A

-the coiled coil of two alpha helices is the secondary structure
-alpha keratin is found in the outer epidermis, hair, horn, nails and feather

43
Q

What type of agent (reducing or oxidizing) do you need if you have curly hair, and you want to make it straight?

A

You need a reducing agent such as ammonium thioglycolate

44
Q

What type of agent (reducing or oxidizing) do you need if you have straight hair, and you want to make it curly?

A

You need an oxidizing agent such as hydrogen peroxide

45
Q

Explain what is going on in the following image:

A

Hydrogen bonds are forms with hair making the curly hair straight…therefore, when the water dries, the H2 bonds are then gone, and the hair goes back to being curly

46
Q

Explain what is going on in the following image:

A

An oxidizing agent reacts with the sulfhydryl (-SH) groups to yield disulfide bonds. These strong covalent bonds help with creating permanent waves

47
Q

What is the most abundant vertebrate protein?

A

collagen

48
Q

What type of structure does collagen form?

a) single helix structure
b) triple helix structure
c) double helix structure

A

b) triple helix structure

49
Q

Where is the covalent bond found in the triple helix structure of collagen? (This linkage from this reaction allows for the side chains in collagen to be covalently crosslinked)

a) between his and activated lys
b) between activated lys and his
c) between lys and Glu

A

a) between his and activated lys

50
Q

What is collagen almost entirely free from/of?

a) His residues
b) Glu residues
c) Cys residues

A

c)

51
Q

What is the amino acid composition of collagen?

a) 30% Gly and 4-Hyp, 15-30% Pro, and others
b) 30% Gly, 15-30% Pro and 4-Hyp, and others
c) 15-30% Gly, 30% Pro and 4-Hyp, and others
d) 15-30% Gly and Pro, 30% 4-Hyp, and others

A

b)

52
Q

What is the significance of this residue in regard to collagen?

A

It makes up to 15-30% of collagen

53
Q

What coenzyme is needed for this rxn?

A

Ascorbic vitamin C…without this then the Prolyl hydroxylase will not be able to function and can lead to SCURVY!!!

54
Q

Define scurvy disease? What type of disease is it? What low activities and low amounts result from it?

A
55
Q

Explain mechanism of induced fit for enzymes:

A

The active site can change its shape even more to bind that substrate perfectly

56
Q

What is the role of lactase?

A

It breaks lactose down into smaller parts that are body can then digest.

57
Q

Are enzymes used multiple times in a reaction and then filtered out of our body? Or can they be used indefinitely?

A

Indefinitely as they are catalysts (which is why we do not include them in reactants or end products or reaction equations

58
Q

What is the role of lipase and where is it found?

A

enzymes that help digest fats…Lipase is secreted from the pancreas via a duct that empties into the GI tract at the duodenum…therefore, it acts on food that has already been partially digested in the stomach

59
Q

What is the role of amylase and where is it found?

A

helps change starches into sugars. It can be found in the salivary glands, pancreas, small intestine and liver…it is secreted from the pancreatic duct into the duodenum

60
Q

What is the role of protease and where is it found?

A

enzymes that break down proteins…it is found in blood serum (thrombin, plasmin, Hageman factor, etc.)

61
Q

What is the role of cofactors/coenzymes?

A

They help bind to the substrate or to the active site and help the enzyme either build or break down substrates into products

62
Q

What typically are cofactors?

A

metal ions (Fe2+)

63
Q

What typically are coenzymes?

A

organic molecules (vitamins)

64
Q

What are the two factors that heavily influence/affect enzymes and their function?

A

The pH and temperature

65
Q

What is the role of trypsin?

A

found in the small intestine, breaks proteins down into amino acids.

66
Q

What is the role of maltase?

A

also found in saliva; breaks the sugar maltose into glucose.

67
Q

Differences between the “lock and key” and “induced fit” methods

A

The active site is not static in induced fit unlike the lock and key method. Additionally, the binding site is flexible for induced fit while the binding is stronger for the lock and key method due to a catalytic group weakening the substrate bonds either by the nucleophilic or electrophilic attack for the induced fit model. No weakening of the substrate bonds occurs for the lock and key model.

Also note for the induced fit model that there is a transition state that develops prior to the reactants undergoing changes and the active site of the enzyme containing two components as well.

68
Q

What forces allow for reversible binding?

a) covalent
b) noncovalent
c) both

A

b) noncovalent forces

69
Q

Do you want to have a large or small K sub m for having a strong binding of ES?

A

small K sub m will indicate the stronger the binding

70
Q

Do we want ____ Kon and ____ Kof to get lower Kd?

a) fast, slow
b) slow, fast
c) fast and fast
d) slow and slow

A

a) fast, slow

71
Q

What is the average molecular weight of an amino acid?

A

110 daltons

72
Q

how do calculate the average MW of a protein?

A

(# of amino acids) * 110

73
Q

Calculate the average MW of 200 amino acids

A
74
Q

Where do nonpolar residues occur? Select from below which are non polar…

a) Val
b) Arg
c) His
d) Leu
e) Ile
f) Met
g) Lys
h) Asp
i) Glu
j) Phe
k) Asn
l) Ser
m) Thr

A

Nonpolar residues occur mostly in the interior of a protein, out of contact with the aqueous solvent

a) Val
d) Leu
e) Ile
f) Met
j) Phe

75
Q

Where do charged polar residues occur? Select from below which are polar…

a) Val
b) Arg
c) His
d) Leu
e) Ile
f) Met
g) Lys
h) Asp
i) Glu
j) Phe
k) Asn
l) Ser
m) Thr

A

charged polar residues Arg, His, Lys, Asp, and Glu are
usually located on the surface of a protein in contact with
the aqueous solvent…this is due to the charged polar residues wanting to form electrostatic bonds with the surface of H2O

b) Arg
c) His
g) Lys
h) Asp
i) Glu

76
Q

Where do uncharged polar groups occur? Which are the uncharged polar groups below?

a) Asn
b) Arg
c) His
d) Gln
e) Tyr
f) Met
g) Lys
h) Asp
i) Glu
j) Phe
k) Asn
l) Ser
m) Thr

A

a) Asn
d) Gln
e) Tyr
I) Ser
m) Thr

77
Q

Is the folded and unfolded/denatured form of a protein its active form?

A

folded!

78
Q

________ ________ has the greatest influence on protein stability

Why is this?

A
79
Q

Hydrogen bonds make _________ contributions to protein stability.

a) only minor contributions
b) major contributions

A
80
Q

How many kJ mol^-1is the difference in hydrogen bonding free energies between the native and unfolded states

A
81
Q

Do unfolded proteins form any sort of bonds?

A

They form hydrogen bonds with water molecules

82
Q

define protein stability

A

the difference in energy between folded and unfolded

83
Q

What is occurring at the arrow?

A

Ionic interactions (i.e. ion pair or salt bridge)

84
Q

Ionic interactions (i.e. ion pair or salt bridge) have _________ contributions to the stability of a native protein.

a) minor
b) major
c) both

A

a) minor

85
Q

If you have an electrostatic interaction (a positive and minus charge)…and you have them close together…is there more or less entropy? Is it enthalpy favorable?

A

Since the two charges are in close proximity, there is a loss of entropy of the side chains due to ion-pair formation (aka salt bridge formation) and enthalpy is favorable.

86
Q

If you have an electrostatic interaction (a positive and minus charge)…and you have them further apart …is there more or less entropy? Is it enthalpy favorable?

A

Since the distance does not allow the two charges to form a salt bridge, now H+ binds with water…therefore, enthalpy is unfavorable in this situation and there is more entropy…think of hydrophobic effect similarly where S increases

87
Q

Why is it rare of disulfide bonds to exist in intracellular proteins?

A

Due to the cytoplasm having a reducing environment due to glutathione

88
Q

Explain what a zinc infer is and what is its purpose and what it contributes to…

A
89
Q

What can zinc fingers do with DNA, RNA and proteins?

A
90
Q

What are the 5 ways that proteins can be denatured by?

A

heat, acid/base, detergents, reducing agents and chaotropic agents

91
Q

What enzyme is responsible for turning fruits brown? How can this browning of fruit be avoided?

A

Polyphenol oxidases (PPO)

92
Q

For the melanin that results from the polyphenol oxidases with fruits…it is a(n)

a) reducing agent
b) oxidizing agent
c) electrophile
d) nucleophile

A

c) electrophile

93
Q

How many disulfide bonds are present in this active protein? How many cysteines?

A

4 disulfide bonds

8 cysteine residues

94
Q

Explain the process by which denatured proteins can be renatured…

A
95
Q

Protein renaturation occurs only when…

A

the primary structure is intact

96
Q

What does protein primary structure dictate?

A

its three dimensional structure

97
Q

What is the role and significance of molecular chaperones? What do they prevent?

A

They assist in protein folding!

98
Q

What are molecular chaperones?

a) ATPases
b) ligands
c) polymers

A

a) atpases

99
Q

What is the significance of Hsp?

A

They are important chaperones that are required to recover heat-denatured proteins or to prevent misfolding under conditions of environmental stress

100
Q

Hsp synthesis is ______ at elevated temperatures

A

increased

101
Q

What is Hsp90/s relation to cancer?

A

Hsp90 stabilizes a number of proteins required for tumor growth…thus it is an excellent target for cancer therapy

Biological Mechanisms (9 decks)

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