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O Chem 2 > Amino Acids. 2 > Flashcards

Amino Acids. 2 Flashcards

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1
Q

How are peptides distinguished from proteins?

A

Based on size- peptides contain approximately 50 amino acids or less

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2
Q

In terms of peptides, what are proteins?

A

Made up of one or more peptides arranged in a biologically functional way

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3
Q

What may proteins be bound to?

A
  • ligands like coenzymes and cofactors
  • Another protein or other macromolecule( e.g. DNA, RNA)
  • Complex macromolecular assemblies
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4
Q

What is a peptide in terms of amino acids?

A

Molecules containing 2 amino acids

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5
Q

Name a peptide with 2 amino acids

A

Dipeptide

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6
Q

Name a peptide with 3 amino acids

A

Tripeptide

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7
Q

Name a peptide with 4 amino acids

A

Tetrapeptides

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8
Q

Name a peptide with 8 amino acids

A

Octapeltides

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9
Q

Name a peptide with up to 20 amino acids

A

Oligopeptides

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10
Q

Name a peptide with less than 50 amino acids

A

Polypeptides

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11
Q

When numbering terminals in amino acids, which is the first and last terminals?

A

N-terminal= No. 1

C-terminal= last

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12
Q

How are peptides named?

A
  • Order of amino acids in a peptide
    - left(N terminal a. acid) written first, C terminal a. acid written last
  • Naming of polypeptides
    - component a. acid in peptides called moieties or residues
    - Except for C-terminal moieties, all moieties called -you instead of -ine, -are or -ic

E.g. valylglycylleucine

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13
Q

How are proteins classified?

A
  • Proteins may be classified by their composition, shape or function
  • When based on composition, proteins are classified as simple and conjugated proteins
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14
Q

Describe the composition of simple proteins

A

50% carbon

23% oxygen

16% nitrogen

7% hydrogen

0-3% sulfur

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15
Q

What happens when simple proteins are hydrolyzed?

A

Yield only amino acids when hydrolyzed

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16
Q

What is yielded when conjugated proteins are hydrolyzed?

A

Amino acids and nom-amino acid components such as prosthetic groups

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17
Q

Give 5 examples of conjugated proteins and their prosthetic groups

A

Lipoproteins- lipid

Glycoproteins- carbohydrate

Metalloproteins- Cu, Fe, Zn, Mo

Hemoproteins- heme

Flavoproteins- flavin nucleotide

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18
Q

Name the classification of protein when classified o based on solubility and shape

A
  1. Fibrous
  2. Globular
  3. Membrane
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19
Q

Describe fibrous proteins

A

Elongated, straight or twisted.

  • Generally insoluble.
  • Mainly structural in function
  • Consists of largely of a single type of secondary structure
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20
Q

Describe glomerular proteins

A
  • Compact, highly ordered pattern of folding
  • Soluble and have dynamic cellular functions e.g. enzymes, hormones
  • often contain several types of secondary structure
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21
Q

Describe membranous proteins

A

Hydrophilic amino acid, side chains, oriented outward, water insoluble

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22
Q

Where are membranous amino acid found?

A

Found associated with various membrane systems of cells

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23
Q

What are examples of globular proteins?

A

Albumin, globulin, hemoglobulin, enzymes

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24
Q

Give examples of fibrous proteins

A

Alpha-keratin, collagen, silk fibroid

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25
Q

List the functions of proteins

A
  • Catalysis(enzymes)
  • Regulation(repressors and activators)
  • Defense(antibodies, blood clotting)
  • Structural- mechanical support
  • Movement(actin and myosin)
  • Transport of molecules
  • Storage
  • Communication- membrane proteins
  • Signal transmission
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26
Q

List the 4 types of organization of proteins

A
  • Monomeric
  • Multimeric
  • Homomultimeric
  • Heteromultimeric
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27
Q

What is a monomeric protein and what structure of protein does it lead to?

A
  • a single polypeptide chain

- leads to tertiary structure

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28
Q

What is multimeric protein and what structure of protein does it lead to?

A
  • More than one peptide chain

- leads to a quaternary structure description

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29
Q

What is a homomultimeric protein?

A

All chains are the same

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30
Q

What is a heteromultimeric protein?

A

Different chains

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31
Q

What does primary structure of a protein determine?

A

Primary structure determines the 3-dimensional conformation, includes secondary, tertiary and quaternary levels

32
Q

Describe the native conformations of proteins

A
  • The most stable confirmation
  • biologically functional form of the molecule
  • lowest free energy
33
Q

What is the confirmation of proteins?

A

Spatial arrangements of all atoms in a molecule

34
Q

Every molecule of the same protein folds into the _________ ______ ____________

A

Same native conformation

35
Q

What are the 4 organizational levels of protein structure?

A
  • primary
  • secondary
  • Tertiary
  • Quaternary
36
Q

Describe primary proteins

A
  • Linear sequence of the amino acids
  • usually from N-terminal(left) to C (right)
  • automatically gives the composition
37
Q

Describe the secondary protein

A

This is the initial folding of a polypeptide chain into shapes stabilized by hydrogen bonding between NH and CO groups.

  • there is Regular arrangement,in space, of the atoms of the backbone of the protein along the long axis.
  • most common are alpha and beta pleated sheets
38
Q

What type of protein is characterized by hydrogen bonds between NH and CO groups that stabilizing an initial fold as well as alpha and beta pleated sheets.

A

Secondary protein structure

39
Q

Describe a protein with a tertiary structure

A
  • The 3-D arrangement of all the atoms in the protein
  • folded globular structure
  • distant amino acids in the primary structure may be brought closer
40
Q

Describe quaternary structure

A

Association and interaction of subunits in a multimeric protein

41
Q

Describe covalent bonds in proteins

A

Not meant to be broken other than during protein degradation

42
Q

Give examples of covalent bonds

A
  • peptide bonds formed by 2 amino acids

- disulfide bonds formed by 2 cysteine residues in proteins

43
Q

What type of bonds are in proteins?

A

Covalent and non-covalent bonds

44
Q

Describe covalent bonds

A

“Weak attractive forces” specify protein folding and conformational changes

These forces may be additive, so I’m aggregate they may provide a strong stabilizing force

45
Q

Genetic diseases result from…

A

Proteins with abnormal sequences

46
Q

The 3 dimensional structure is determined by…

A

It’s primary structure

47
Q

Sequence of amino acids= what?

A

Sequence of a,IMO acids = primary structure

48
Q

What stabilizes secondary structures of proteins?

A

By hydrogen bonds involving the atoms of the peptide bond

49
Q

Describe the backbone of secondary structures

A

Regular arrangement of the atoms of the backbone of the protein along the long axis.

R groups extend outward

50
Q

Describe alpha helix as a secondary structure

A

Tightly packed and right-handed helix wound around an imaginary axis

51
Q

Describe how many residues per turn does the alpha helix of a secondary structure consist of?

A

3.6 residues per turn

52
Q

Describe where hydrogen bonds are located in relation to the alpha helix structure

A

Hydrogen bonds are parallel to the direction of the helix axis

53
Q

Where are side chains in relation to the alpha helix structure?

A

Side chains stick out from the helix

54
Q

Where are hydrogen bonds located in relation to beta pleated sheets?

A

Perpendicular hydrogen bonds between peptide bond chains and amino acid side chains

The inter-chain hydrogen bonds between NH and CO groups connect each amino acid to a single amino acid on an adjacent strand, in short H bonds are formed between two polypeptide chains

55
Q

Where are amino acid side chains located in relation to beta pleated sheets?

A

Amino acid side chains that alternate above and below the plane of the pleated sheet

56
Q

What effect does hydrogen bonding have on beta pleated sheets?

A

Stabilize the beta pleated sheets

57
Q

Contrast the clustering of polar and non-polar side chains on soluble and membrane secondary proteins

A
  • Polar amino acids cluster on the surface of soluble side chains
  • Nonpolar amino acids cluster on the surface of membrane proteins
58
Q

Describe the tertiary structure of a protein

A
  • Refers to the 3-D confirmation of a protein
  • folded globular structure
  • distant amino acids in the primary structure may be brought close together
59
Q

What is the hydrophobic core?

A

Water soluble proteins fold into 3-D structures with no polar side-chains to the inside

60
Q

How can side chains of amino acids be involved in stabilizing tertiary structure?

A
  • Formation of non-covalent associations (weak attractive forces)
  • Formation of the covalent disulfide: only covalent force involved in tertiary structure, 2 cysteine R groups- S-S link, is usually found in secreted proteins(extracellular)
  • Ionic interactions
61
Q

What are the only covalent force involved in tertiary structures?

A

The covalent disulfide bond

62
Q

Describe the effect of secondary folding structures on tertiary strutted of proteins

A

The 3-D form of a protein molecule results from distant protein-protein interactions within the same polypeptide chain(caused by folding of secondary structures)

63
Q

Describe myoglobin as a tertiary structure

A
  • Myoglobin is described in terms of tertiary structure
  • Myoglobin contains about 80% alpha-helix secondary structure
  • Myoglobin is devoid of Beta-sheet structure
64
Q

Describe quaternary structure

A
  • Consists of more than one polypeptide chain/ subunit

- refers to the spatial arrangement of subunits and the nature of their interactions

65
Q

How do subunits interact in quaternary structures?

A

Subunits interact via non-covalent bonds

- hydrogen bond, electrostatic interactions and a few hydrophobic interactions

66
Q

Give examples of quaternary structures

A

Dimmers, trimmers, tetraners and oligomers

67
Q

In quaternary structure, subunits always…

A

Combine in the same manner

68
Q

What is the denaturation of proteins?

A

The 3-D structure is changed. Noncovalent bonds and disulfide bonds are broken but not the peptide back bone

69
Q

What protein structure remains intact in denaturation?

A

Primary structure

70
Q

What happens to dietary proteins in the stomach?

A

Is denatured in the lumen of the stomach due to low pH. Stomach acid levels not low enough to cleave peptide bonds

71
Q

Denatured proteins usually cannot regain their natural configuration and precipitate. What is proof of this?

A

Once an egg is fried, you can’t uncool it

72
Q

Why can you not uncook an egg?

A

Denatured proteins usually cannot regain their natural configuration and precipitate

73
Q

Explain the denaturation of a protein in the laboratory, stating how each type of bond can be broken

A
  • Heat, 5-10M urea and salt=> breaks hydrogen bonds
  • Strong acids or bases => break ionic bonds
  • 1-2% SDS(detergent ) => to break hydrophobic interactions
  • Thiol containing compounds to reduce disulfide bonds, e.g. B-mercaptoethanol, 2-mercaptoethanol
74
Q

How does the degeneration of insulin involve denaturation of proteins?

A

The disulfide bonds of insulin are cleaved in the liver in animals

75
Q

Give some examples of how proteins can be isolated and separated

A
  • 1D gel electrophoresis
  • 2D gel electrophoresis
  • protein digestion
  • Purification
  • Isotope-Coded Affinity Tags (ICAT)

O Chem 2 (22 decks)

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