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Biochemistry > Chapter 4 Protein Structure > Flashcards

Chapter 4 Protein Structure Flashcards

1
Q

Proteins

A
  • are polymers of amino acids and consist of one or more polypeptides
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2
Q

Alpha amino protein at physiological pH

A
  • The amino group and carboxylate groups are attached to a central carbon known as an alpha carbon
  • The alpha amino carbon builds proteins
  • At physiological pH the carboxyl group is unprotonated and the amnio group is protonated, which means the amino acid bears both a positive and negative charge
    -Worth noting that the R group attached to the amino acid decides if the amino acid will be polar, nonpolar, or charged
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3
Q

Glycine is the simplest amino acid

A
  • This is because glycine has hydrogen as its side chain instead of an R group and it is also a non-polar amino acid and not optically active. It is also most commonly found in animal proteins.
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4
Q

How are amino acids classified?

A
  • Amino acids are classified based on the overall chemical characteristics of their R groups (side chains) such as non-polar, polar but uncharged, or charged.
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5
Q

Hydrophobic amino acids( look at Anki for photos)

A
  • Nonpolar side chains that interact very weakly or not at all
    -Alanine(Ala, A)
    -Valine (Val, V)
  • Phenylalanine(Phe, F)
    -Tryptophan( Trp, W)
    -Leucine (Leu, L)
    -Isoleucine(Ile, I)
  • Methionine (Met,M)
    -Proline (Pro,P)
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6
Q

Polar amino acids

A
  • The side chains can interact with water because they contain hydrogen-bonding groups
  • Serine (Ser, S)
    -Threonine (Thr, T)
  • Tyrosine (Tyr, Y)
    -Cysteine (Cys, C)
    -Asparagine(Asn, N)
    -Glutamine( Gln, Q)
    -Histidine (His, H)
    -Glycine (Gly, G)
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7
Q

Charged amino acids

A

-virtually always charged under physiological conditions
- Aspartate(Asp,D)
-Glutamate (Glu, E)
-Lysine(Lys,K)
-Arginine(Arg,R)

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8
Q

Amino acids that have pilar and (+) charged R groups

A
  • Lysine (Lys,K) and Arginine (Arg,R) are referred to as basic amino acids due to PKA
  • when pH is lower than pka= acid
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9
Q

Amino acids that have polar and (-) charged R groups

A
  • Aspartate( Asp,D) and Glutamate (Glu,E)
  • pH is higher than pka= predominate species is conjugated base
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10
Q

pKa values of ionizable groups in amino acids

A
  • C-terminus - COOH( carboxate) pka: 3.5
    -Asp -CH2COOH pka: 3.9
    -Glu -CH2CH2COOH pka:4.1
  • His pka: 6.0
    -Cys pka:8.4
  • N-terminus pka:9.0
    -Tyr pka: 10.5
  • Lys pka:10.5
    -Arg pka:12.5
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11
Q

How to estimate the net charge of a peptide at physiological pH

A
  • review sample calculation 4.1
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12
Q

Relative abundance of amino acids in proteins

A
  • leucine is the most abundant
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13
Q

Average MW of an amino acid

A
  • The average MW of an amino acid is 110 Da
  • To estimate the number of amino acids, divide by 110 da
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14
Q

How are peptide bonds formed?

A

-Once amino acids are polymerized to form a polypeptide chain from the condensation of the carboxylate group of one amino acid with the amino group of another. The resulting amide bond links the alpha-amino group with one of the amino acids and the alpha carboxylate group with another.
-Peptide bonds link the amino acid residues in a polypeptide

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15
Q

Amino acid residue

A
  • Are the amino acids connected by the peptide because only the residual atoms remain
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16
Q

Amino and carboxyl-terminal residues

A
  • The N-terminus is the residue with the free amino group on the left of the polypeptide
  • The C-terminus is the residue with the free carboxylate group on the right.
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17
Q

Chain directionality of a polypeptide bond

A
  • A polypeptide bond has two ends that are chemically distant from each other known as the N-terminus and C-terminus
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18
Q

Properties of the peptide bond

A
  • Peptide bond in the polypeptide backbone has two resonance forms this is due the partial (40%) double character but no rotation about the C-N bond
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19
Q

Why rotation around N-C-C is restricted (box is alpha)

A
  • The rotation around the N-C-alpha-C is limited due to steric contraints
  • The polypeptide backbone must adaot to a secondary structure to minimize steric strain
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20
Q

Properties of the peptide bond

A
  • Peptide bond in the polypeptide backbone has two resonance forms this is due to the partial (40%) double character but no rotation about the C-N bond
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21
Q

Four levels of protein structure

A
  • Primary Structure: is the sequence of amino acid residues
    -Secondary Structure: The spatial arrangement of the polypeptide backbone
    -Tertiary Structure: The three-dimensional structure of an entire polypeptide, including all the side chains
    -Quaternary structure: The spatial arrangement of polypeptide chains in a protein with multiple subunits
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22
Q

How the alpha-helix is specifically formed, stabilized, and ways to represent it

A
  • In this conformation, the polypeptide backbone twists in a right-handed fashion so that the hydrogen bonds form between CO and NH groups four residues farther along.
    -There are 3.6 AA residues per turn of the helix
  • The H bonds help stabilize the alpha helix
    -DNA and myoglobin are examples of alpha helix
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23
Q

How the -pleated sheet is specifically formed, stabilized, and ways to represent it

A

-The beta pleated sheet is a type of secondary structure that consists of aligned strands of a polypeptide whose hydrogen-bonding requirements are met by bonding between neighboring strands
- Beta sheets are stabilized by interstrand hydrogen bonding
- The beta-sheet is represented as broad, flat, and has arrows to show directionality.

24
Q

How are the beta strands connected to form sheets

A
  • The beta strands are connected by hydrogen bonds to form the beta sheets.
  • A single beta-sheet may contain 2 to more than 12 polypeptides
25
Q

What is the difference between turns and loops

A
  • Antiparallel beta sheets align in opposite directions are easily connected with turns
  • Parallel beta-sheets align in the same direction and are connected by loops
26
Q

Anti-parallel and parallel beta sheets

A

-Anti-parallel beta sheets are neighboring chains that run in opposite directions and whose residues form two hydrogen bonds with neighboring strands.
-Parallel beta sheets are neighboring chains that run in the same direction.

27
Q

What beta-sheet is the most stable

A
  • Antiparallel Beta sheets are slightly more stable than the parallel beta sheets due to having a more optimal hydrogen bonding pattern.
28
Q

How proteins differ in composition

A

This depends on the number of amino acid residues, the number of polypeptide chains, and molecular mass

29
Q

Tertiary structure

A
  • Is a three-dimensional structure of an entire polypeptide, including its side chains.
  • TPI(triose phosphate isomerase) is a type of protein a typical globular protein that has a polypeptide backbone
  • Their advantages are being able to provide the lock and key function for enzymes or receptors on a cell
30
Q

all-alpha protein

A
  • Growth hormone is an example of alpha protein and has loops that serve as binding sites and they also have hydrophobic interactions
31
Q

all-beta protein

A

an example is alpha-beta crystallin and contains beta sheets, and has strands that are anti-parallel and no helix

32
Q

Alpha/beta protein

A
  • Flavodoxin is an example of this protein and this is also where the beta sheets expand.
33
Q

Layers in proteins and the location of nonpolar residues

A

(primary, secondary,tertiary and quaternary)
- Nonpolar residues are found in the protein’s interior

34
Q

Stabilizing force in the tertiary structures

A
  • ion pairs that form ionic bonds. ( ionic interactions)
35
Q

Protein Doman

A
  • is a polypeptide segment that has folded into a single structural unit with a hydrophobic core
36
Q

Principles of globular proteins

A

There are 2 layers of the secondary structure known as hydrophobic core and hydrophilic surface
- Hydrophobic core is typically rich in secondary structure and has H bonds that minimize hydrophilicity of the polar backbone groups
-Hydrophilic surface: is typical with a irregular structure and has polar backbone groups of loops that can form H-bonds with water

37
Q

Correlation of a residues hydrophobicity with location

A
  • The greater a residues hydrophobicity is, the more likely it is found in the protein’s interior
  • the more positive the value the more hydrophobic
38
Q

Disulfide bonds in proteins

A

-Extracellular proteins are stabilized by disulfide bonds (-s-s)

39
Q

Metals in stabilization of proteins

A

-Zinc fingers are domains in which Zn2+ is coordinated to Cys/His or only cys

40
Q

Characteristics of protein folding in vivo

A
  • Is a newly synthesized polypeptide begins to fold as it leaves the ribosome it may require molecular chaperones or post-translation processing
41
Q

Characteristics of protein folding in vitro

A
  • is a full length polypeptide that is denatured and then allowed to renature, it is a not a random process
42
Q

Molecular chaperone

A

-is a protein that binds to unfold or misfold proteins in order to promote their normal folding

43
Q

Anfinsens postulate

A
  • Anfinsen found that a primary structure AA sequence determines the tertiary structure
44
Q

Driving force of protein folding/ largest force

A

-is the hydrophobic effect which stabilizes the structure of a protein.

45
Q

Protein folding

A
  • The wide mouth of the funnel represents high energy and high entropy and the narrow end represents low energy and low entropy.
46
Q

What determines the proteins structure

A

-The amino acid sequence

47
Q

Quatenary structure

A
  • is a spatial arrangement of more than one polypeptide chain in protein
48
Q

Nomenclature used to describe the different types of quaternary structures

A

if chains are identical use Homodimer, Homotrimer, Homotetramer, and if the chains are not identical then use the word hetero.

49
Q

What is a subunit

A
  • a individual chain
50
Q

Different techniques used to separate proteins

A

-Column chromatography
-Size-exclusion chromatography
-Ion-exchanged chromatography

51
Q

size-exclusion chromatography

A
  • also known as gel filtration
    -Separation is based on size, larger proteins will be eluded from spaces inside the beads and pass through the column faster than smaller proteins which stay at the top of the column.
  • Proteins are gradually separated and can be recovered by collecting the solution that exits the column
52
Q

Ion-exchange chromatography

A
  • it is a process for separating proteins in solution based on differences in net charge
  • (-) charged proteins bind to (+) charged solid supports and (+) charged proteins bind to (-) charged solid support.
    -Cation exchange supports (-) charged and Anion-exchange supports (+) charged
  • Whether using a cation or anion exchange, the addition of NaCl can elute bound proteins and the counter ions either Na+ or Cl- will be exchanged for the bound proteins and then be released.
53
Q

SDS Page

A
  • known as sodium dodecyl sulfate-polyacrylamide gel electrophoresis
  • SDS page is used to verify the purification of a protein
54
Q

Components of SDS-page

A
  • BME(-mercaptoethanol)
  • SDS
55
Q

What occurs during SDS-page

A

-SDS is added to a denature protein and adds a (-) charge
- 1 SDS binds uniformly along the chain every 2 amino acid residues, the proteins will have the same charge-to-mass ratio and can be separated on the basis of mass or size

Biochemistry (10 decks)

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