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MABS Biochemistry > lecture 7 > Flashcards

lecture 7 Flashcards

structure function relationships in proteins

1
Q

what are the major structural classifications of proteins?

A

globular, fibrous, and transmembrane

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2
Q

what are globular proteins?

A

usually soluble in aqueous medium and resemble irregular balls

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3
Q

what are fibrous proteins?

A

geometrically linear, arranged around a single axis, and have a repeating unit structure

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4
Q

what are transmembrane proteins?

A

proteins that have one or more regions aligned to cross the lipid membrane

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5
Q

how many levels of protein structure are there?name them and define.

A

primary, secondary, tertiary, and quaternary

primary is linear sequence of aa joined through peptide bonds

secondary is the recurring structures that occur in short localized regions like the alpha helix and beta pleated sheet

tertiary is the overall 3-D conformation of a protein

quaternary is the association of polypeptide subunits in a geometrically specific manner

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6
Q

what forces are involved in protein folding?

A

noncovalent interactions (H-bonds, ionic bonds, hydrophobic interactions, van der waals)

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7
Q

what bonds join amino acids?

A

peptide bonds

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8
Q

what are the general requirements for a 3-D structure?

A

1) binding that is specific
2) flexibility and rigidity
3) external surface that is appropriate like cytoplasmic proteins that need to have polar amino acids on the surface to remain soluble
4) conformation must be stable
5) protein must have a structure that can be degraded when it damaged

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9
Q

name an example of a globular protein? a fibrous protein? transmembrane protein?

A

myoglobin, collagen, integral protein

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10
Q

how are amino acids joined to form a primary structure?

A

peptide bonds, these are amide linkages between alpha carboxyl group of 1 aa and the alpha group of another

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11
Q

what are the characteristics of peptide bonds?

A

1) resistant to denaturing conditions like heating and high concentrations of urea, 2)they have a partial double bond character that is rigid and planar
3) they are also uncharged but polar but can participate in H-bonds

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12
Q

how does the primary structure read?

A

from N-terminus(free -NH3) to the C-terminus(free -COO^-), left to right and when naming all amino acids have their suffixes changed to -yl with exception to C-terminal amino acid

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13
Q

how many amino acids are in an oligopeptide?polypeptides?Proteins?

A

10-15 amino acids; more than 15 amino acids; more than 50 amino acids

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14
Q

why are amino acids called residues?

A

because it is the portion of the amino acid remaining after the atoms of water are lost in the formation of the peptide bond.

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15
Q

what is the alpha helix of the secondary structure?

A

Spiral structure consisting of a tightly packed, coiled polypeptide core, with the –R groups extending outward from the central axis

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16
Q

how is the alpha helix stabilized?how?

A

through extensive H-bonding; they extend upward and are parallel to the spiral from the carbonyl oxygen of one peptide bond to the -NH group of a peptide linkage 4 residues ahead in the polypeptide

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17
Q

how many acids comprise a turn of the alpha helix?

A

3.6 amino acids

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18
Q

where are secondary structures important?

A

hair and skin, and their rigidity is determined by the # of disulfide bonds between the constituent polypeptide chains. It is a common secondary structural element of globular proteins, membrane-spanning domains, and DNA-binding proteins.

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19
Q

which amino acid is known as a “helix breaker”?

A

proline because of the nitrogen in its cyclical structure and cannot fit within an alpha helix

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20
Q

what is the Beta pleated sheet?

A

is composed of two or more peptide chains (Beta strands) or segments of polypeptide chains in which the peptide bond components are involved in H-bonds

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21
Q

As we all know that that H-bonds are involved in the formation of the secondary structure, explain how?

A

the carbonyl oxygen of one peptide bond is H-bonded to the nitrogen of a peptide bond on an adjacent strand

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22
Q

explain the characteristics of the beta pleated sheet?

A

the surfaces appear pleated, they can be parallel running in the same direction or anti parallel with polypeptide running in the opposite direction

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23
Q

optimal H bonding occurs in which secondary structure?

A

when sheet is bent pleated to form beta pleated sheets

24
Q

what is significant about antiparallel strands?

A

they are often the same polypeptide chain folded back on itself with simple hairpin turns

25
Q

what it significant about parallel sheets?

A

they tend to have hydrophobic residues on both the sides of the sheets and they tend to have a hydrophobic and a hydrophilic side

26
Q

what are B-bends?

A

these are part of the secondary structure used to reverse the direction of a polypeptide chain and are found on the surface of protein molecules; they often include charged residues, composed of 4 amino acids like proline and glycine and are stabilized by ionic and H-bonds

27
Q

what percentage of the globular protein is secondary structure?

A

half, the remainder is described as having a loop or coil formation. Not random, just less regular

28
Q

what are motifs?

A

patterns of secondary structures that construct the globular proteins. They serve as the primary core of the molecule and are connected by loops at the surface of the protein. They formed by close packing of the side chains and can be associated with a particular function like the helix loop helix found in transcription factors

29
Q

what is the tertiary structure?significance?

A

the folding pattern of secondary structural elements into a 3-D conformation and final 3-D form. They create specific and flexible binding sites for ligands, maintain residues on the surface appropriate for cellular location, flexible and dynamic fluctuations to allow ions and water to diffuse through

30
Q

which protein structure is the final 3-D conformation?

A

tertiary structure and it is fully functional

31
Q

name some common structural motifs?

A

helix loop helix, beta alpha beta, beta meander, beta barrel

32
Q

what is the definition of a tertiary structure?

A

the folding pattern of secondary structural elements into a 3-D conformation

33
Q

what are protein domains?

A

independent folding units in the tertiary structure of a protein that consist of secondary structural elements and superstructural elements that collect together

34
Q

what type of specific functions do individual domains perform?

A

catalytic site and ligand binding site

35
Q

what is the major driving force in folding domains?

A

hydrophobic interactions

36
Q

what are some examples fo protein domains?

A

horseshoe, solenoid, barrel, propeller, layer sandwich, super roll, sandwich, prism

37
Q

with respect to the secondary structure of a protein, how are H-bonds oriented?

A

they are perpendicular to the polypeptide backbone with patterns different between parallel and antiparallel

38
Q

what is unique to the stabilization of tertiary structure?

A

1) the unique 3-D structure is determined by its amino acid sequence
2) the interactions between side chains guide the folding of the polypeptide to form structure
3) interactions cooperate in stabilizing the tertiary structure

39
Q

what are the interactions that cooperate to stabilize the tertiary structure?

A 
there are 4:
disulfide bonds
hydrophobic interactions
H bonds
ionic interactions
40
Q

why are the disulfide bonds significant in tertiary structure?

A

because not all cysteine residues in proteins are involved in disulfide bonds. They can be separated from each other by other amino acids in the primary sequence or on two different polypeptide chains and help to prevent denaturing of the protein in the extracellular environment

41
Q

what type of bonds hold together disulfide bonds?

A

covalent bonds

42
Q

what is the energy state of a fully folded functional protein?

A

low energy state, the energy can be derived from Gibbs Free Energy G=H-TS

43
Q

what determines the 3-D shape of functional protein?

A

interactions between the side chain of amino acids

44
Q

what type of pathways are involved in protein folding?

A

nonrandom, ordered pathways; occurs within seconds to minutes

45
Q

what facilitates protein folding?name an example?

A

a molecular chaperone like a heat shock protein (HSP)

46
Q

what is the result in Protein denaturation?

A

the unfolding and disorganization of secondary and tertiary structures WITHOUT hydrolysis of peptide bonds; it may or may not be reversible and the denatured proteins are often insoluble and precipitate out of solution

47
Q

what are some examples of denaturing agents?

A

heat, organic solvents, strong acids or bases, detergents, and ions of heavy metals

48
Q

what is the effect of entropy on an unfolded protein?

A

entropy increases

49
Q

what is the quaternary structure?

A

polypeptide units of 2 or more that can be structurally identical or unrelated.

50
Q

How are the subunits of quaternary structure held together?

A

by non-covalent interactions, i.e. H-bonds, ionic bonds, hydrophobic interactions and these subunits function independently of each other and work cooperatively.

51
Q

T/F, all proteins have a quaternary structure?

A

F, many proteins consist of a single polypeptide chain that may be structurally identical or unrelated

52
Q

name out the steps involved in protein folding?

A

1) formation of secondary structures
2) formation of domains
3) formation of the final protein monomer

53
Q

what is the significance of protein modification/posttranslational modification?

A

this can happen after synthesis where a few amino acids in the primary sequence can be enzyme catalyzed where you can add a chemical group, oxidize, or modify a specific amino acid

54
Q

what purpose do protein modifications serve?

A

a regulatory function, target or anchor the protein in membranes, enhance protein association and target it for degradation

55
Q

name examples of protein modification?

A

carbohydrate addition (O/N glycosylation), lipid addition (palmitoylation, myristoylation, prenylation), regulation (phosphorylation, acetylation, ADP ribosylation) and modified amino acids like oxidation and carboxylation that facilitate cross linking attachment

MABS Biochemistry (54 decks)

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