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Biochemistry > Biochem Protein Lecture 9 > Flashcards

Biochem Protein Lecture 9 Flashcards

1
Q

α helix + β sheet conformations joined by connecting segments are considered…

A

Globular Proteins

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2
Q

These folding patterns (motifs/folds) are particularly stable arrangement of several elements of secondary structure and the connections between them

A

Supersecondary Structures

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3
Q

These may be simple or complex Examples are an α-β loop and a β barrel

A

Motifs

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4
Q

These are defiend as two or more stable, globular units; present when there are > 100 aa residues

A

Domains

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5
Q

How many domains do small proteins have?

A

One domain (the protein itself)

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6
Q

The burial of hydrophobic R groups requires two layers of ___ structure (folding rule for polypeptides, hydrophobic interaction make large contribution to stability)

What creates the two layers?

A

Secondary Structure

Simple motifs (β-α-β)

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7
Q

Know the structures of beta barrel, etc.

A

!

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8
Q

A folding rule for polypeptides in simple motif: when occurring in the same protein, alpha helices and beta sheets are found in the same or different structural layers?

A

Different

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9
Q

A folding rule for polypeptides in simple motifs: the polypeptides that are adjacent to each other in the primary sequqnce are usually stacked ____ to each other in the secondary structure

A

Adjacent

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10
Q

In hemoglobin structure, deoxy means no Oxygen binded to heme, oxy is opposite

A

Double check this

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11
Q

Note: urea disrupts hydrophobic interactions)

A

! She said this specifically in class

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12
Q

Connections between elements of secondary structure CAN/CANNOT form knots or cross

A

CANNOT form knots or cross

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13
Q

The β conformation is most stable when individual segments are twisted slightly in a ______ hand sense

A

Right Hand Sense

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14
Q

Consider two parallel β strands, in proteins, the crossover is always _____ handed which is shorter, bends through smaller angles making it easier to form

A

Right handed

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15
Q

When many segments of β parallel strands are connected, the twisting of the β sheets leads to twisting of the structure. ______ and twisted _____ results

A

β barrel and twisted β sheet result

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16
Q

The α/β barell arises from repetitions of the βαβ loop motif. The α/β barrel is found in many ________

A

Enzymes

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17
Q

Domains which show similar folding patterns are described as having the same

A

“Motif”

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18
Q

Structural Classification of Proteins database (SCOP) divides protein structures into ___ classes

What are they?

A

4 Classes

1) All α
2) All β
3) α/β (interspersed)
4) α + β (α + β regions are somewhat spaced)

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19
Q

Fewer than _______ motifs (folds) may exist in all proteins

A

1000

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20
Q

Proteins with very similar primary sequence and/or similar structure and function are in the same protein ______

A

Family

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21
Q

Proteins with the same major structural motif and some functional similarities (but little primary sequence similarity) are part of the same ________

A

Superfamily

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22
Q

As mentioned in previous lecture, quaternary structure refers to the interaction between polypeptide chains in a protein where each chain has its own secondary and tertiary structure

A

!

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23
Q

This term means a multisubunit protein

A

Multimer

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24
Q

This means a multimer with just a few subunits

This means a multimer where the repeating structural unit is a multimer

A

Oligomer

Protomer

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25
Q

What interactions may contribute to the bonding between chains in quaternary structure

A

Hydrophobic, H-bonding, salt, metal-ligand and disulfide interactions`

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26
Q

The first oligomeric protein 3-D structural determination was conducted on

A

Hb

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27
Q

The protein in red blood cells that is responsible for oxygen transport

A

Hb

28
Q

What is the Mr of hemoglobin?

A

64,500

29
Q

How many polypeptide chains and how many heme prosthetic groups are in Hb?

A

4 polypeptide chains and 4 heme prosthetic groups

30
Q

What state is iron in in Hb?

A

Ferrous (Fe2+)

31
Q

Globin consists of two ____ chains and two ___ chains

A

α, β

32
Q

In globin, do β and α refer to secondary structure?

Hemoglobin is a _____ or a _____ of αβ protomers

A

No.

Tetramer or a dimer

33
Q

How many residues are in the β and α chains of globin?

A

141 in α

146 in β

34
Q

Identical subunits of multimers are arranged this way

A

Symmetrical Patterns

35
Q

Oligimers can have two types of symmetry, what are they?

A

Rotational Symmetry and Helical symmetry

36
Q

This type of oligomeric symmetry occurs when individual subunits can be superimposed on others by rotation about one or more rotational axes

This type of oligomeric symmetry occurs when subunits can be superimposed by helical rotation

A

Rotational Symmetry

Helical Symmetry

37
Q

For rotational symmetry, subunits pack to form

For helical symmetry, structures are more open ended with subunits added in a _____

A

Closed structures

Spiraling Array

38
Q

X-ray crystal structure determinations have shown that there are several forms of rotational symmetry that occur in proteins.

A

!

39
Q

This type of rotational symmetry involves rotation about a single axis. Symmetry is defined as _____

A

Cyclic Symmetry

Cn (C for cyclic and n for the number of subunits related by the axis)

40
Q

The αβ protomers of Hb have ___ symmetry

A

C2

41
Q

This type of rotational symmetry is a more complicated form of rotational symmetry, a two fold rotational axis intersects an n-fold axis at right angles.

The symmetry is

A

Dihedral Symmetry

Dn

42
Q

Cyclic and dihedral symmetry are most common true or false

A more complicated symmetry than these is

An example of this is the

A

True

Icosahedral Symmetry

Human Polio Virus

43
Q

This means the loss of 3-D structure sufficient to cause a loss of protein function

A

Denaturation

44
Q

Under most conditions, denatured proteins exist in ______ states

A

Partially Folded

45
Q

Most proteins can be denatured by

A

Heat

46
Q

When proteins are denatured by heat, there tends to be a sudden or gradual loss of structure over a narrow range?

What does this suggest?

A

Sudden

Folding is cooperative

47
Q

This term means that loss of structure in one part of a protein destabilizes other parts

A

Cooperativity

48
Q

Are the effects of heat on proteins readily predictable?

A

No.

49
Q

What are two other ways of denaturing protein than heat?

A

pH extremes

The use of chemical agents

50
Q

What do pH extremes do to protein?

What do chemical agents do?

A

Alter the net charge and disrupt H bonding

Disrupt hydrophobic interactions

51
Q

What are examples of chemical agents that can denature proteins?

A

Organic Solvents (alcohol, acetone),

solutes like urea or guanidine hydrochloride

detergents

52
Q

Certain globular proteins which have been denatured regain their native structure and biological activity if returned to conditions where the native conformation is stable. What is this process called?

A

Renaturation

53
Q

What molecule was used as an example of protein renaturation?

A

Ribonuclease A

54
Q

Treating ribonuclease A with ura and mercaptoethanol resulted in complete loss off the enzyme’s catalytic activity. What happened when urea and mercaptoethanol were removed?

A

It regained its tertiary structure including the same disulfide bond positions. Catalytic activity was restored

55
Q

What did the ribonuclease A experiment show?

A

The aa sequence of a polypeptide chain has al the information required to fold the chain into its native 3 D structure

56
Q

Do some proteins require folding assistance?

A

Yes

57
Q

Polypeptides rapidly fold by what type of process?

E coli cells can make a complete biologically active protein molecule containing 100 aa residues in about 5 seconds at 37 degrees

A

Stepwise

58
Q

The rapid, stepwise folding of proteins indicates that principles must guide protein folding in their native states.

The thermodynamics of protein folding can be described by a

A

Free-energy tunnel

59
Q

In the free energy tunnel, what is at the top?

As the folding proceeds, the narrowing of the funnel represents a INCREASE/DECREASE in the number of conformational species present

A

The number of folded states (and the conformational Entropy)

Decrease

60
Q

At the bottom of the free energy funnel, what is there?

A

A single native conformation (or a small set of them)

61
Q

Defects in protein folding account for wide range of genetic disorders.

In this one, there are defects in CFTR, a membrane bound protein which acts as a channel for chloride ions

A

Cystic Fibrosis (CFTR= cystic fibrosis transmembrane conductance regulator)

62
Q

The most common mutation of cystic fibrosis is a deletion of the ___ residue in position 508 in CFTR, resulting in improper folding

A

Phe

63
Q

Proteins that interact with partially folded or improperly folded polypeptides. They promote the correct folding pathways or provide microenvironments where folding can occur

A

Molecular Chaperones

64
Q

Two well studied chaperones are

A

Hsp70 and Chaperonins

65
Q

This chaperone is a heat shock protein that is more abundant in temperature stressed cells

They bind to regions rich in ____ residues and prevent inappropriate aggregation

A

Hsp70

Hydrophobic

66
Q

These chaperones are elaborate protein complexes that are required to fold cullular proteins that don’t fold spontaneously

A

Chaperonins

Biochemistry (27 decks)

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