Amino Acids. 2 Flashcards
1
Q
How are peptides distinguished from proteins?
A
Based on size- peptides contain approximately 50 amino acids or less
2
Q
In terms of peptides, what are proteins?
A
Made up of one or more peptides arranged in a biologically functional way
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
4
Q
What is a peptide in terms of amino acids?
A
Molecules containing 2 amino acids
5
Q
Name a peptide with 2 amino acids
A
Dipeptide
6
Q
Name a peptide with 3 amino acids
A
Tripeptide
7
Q
Name a peptide with 4 amino acids
A
Tetrapeptides
8
Q
Name a peptide with 8 amino acids
A
Octapeltides
9
Q
Name a peptide with up to 20 amino acids
A
Oligopeptides
10
Q
Name a peptide with less than 50 amino acids
A
Polypeptides
11
Q
When numbering terminals in amino acids, which is the first and last terminals?
A
N-terminal= No. 1
C-terminal= last
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
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
14
Q
Describe the composition of simple proteins
A
50% carbon
23% oxygen
16% nitrogen
7% hydrogen
0-3% sulfur
15
Q
What happens when simple proteins are hydrolyzed?
A
Yield only amino acids when hydrolyzed
16
Q
What is yielded when conjugated proteins are hydrolyzed?
A
Amino acids and nom-amino acid components such as prosthetic groups
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
18
Q
Name the classification of protein when classified o based on solubility and shape
A
- Fibrous
- Globular
- Membrane
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
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
21
Q
Describe membranous proteins
A
Hydrophilic amino acid, side chains, oriented outward, water insoluble
22
Q
Where are membranous amino acid found?
A
Found associated with various membrane systems of cells
23
Q
What are examples of globular proteins?
A
Albumin, globulin, hemoglobulin, enzymes
24
Q
Give examples of fibrous proteins
A
Alpha-keratin, collagen, silk fibroid
25
List the functions of proteins
- 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
26
List the 4 types of organization of proteins
- Monomeric
- Multimeric
- Homomultimeric
- Heteromultimeric
27
What is a monomeric protein and what structure of protein does it lead to?
- a single polypeptide chain
| - leads to tertiary structure
28
What is multimeric protein and what structure of protein does it lead to?
- More than one peptide chain
| - leads to a quaternary structure description
29
What is a homomultimeric protein?
All chains are the same
30
What is a heteromultimeric protein?
Different chains
31
What does primary structure of a protein determine?
Primary structure determines the 3-dimensional conformation, includes secondary, tertiary and quaternary levels
32
Describe the native conformations of proteins
- The most stable confirmation
- biologically functional form of the molecule
- lowest free energy
33
What is the confirmation of proteins?
Spatial arrangements of all atoms in a molecule
34
Every molecule of the same protein folds into the _________ ______ ____________
Same native conformation
35
What are the 4 organizational levels of protein structure?
- primary
- secondary
- Tertiary
- Quaternary
36
Describe primary proteins
- Linear sequence of the amino acids
- usually from N-terminal(left) to C (right)
- automatically gives the composition
37
Describe the secondary protein
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
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.
Secondary protein structure
39
Describe a protein with a tertiary structure
- 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
Describe quaternary structure
Association and interaction of subunits in a multimeric protein
41
Describe covalent bonds in proteins
Not meant to be broken other than during protein degradation
42
Give examples of covalent bonds
- peptide bonds formed by 2 amino acids
| - disulfide bonds formed by 2 cysteine residues in proteins
43
What type of bonds are in proteins?
Covalent and non-covalent bonds
44
Describe covalent bonds
“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
Genetic diseases result from...
Proteins with abnormal sequences
46
The 3 dimensional structure is determined by...
It’s primary structure
47
Sequence of amino acids= what?
Sequence of a,IMO acids = primary structure
48
What stabilizes secondary structures of proteins?
By hydrogen bonds involving the atoms of the peptide bond
49
Describe the backbone of secondary structures
Regular arrangement of the atoms of the backbone of the protein along the long axis.
R groups extend outward
50
Describe alpha helix as a secondary structure
Tightly packed and right-handed helix wound around an imaginary axis
51
Describe how many residues per turn does the alpha helix of a secondary structure consist of?
3.6 residues per turn
52
Describe where hydrogen bonds are located in relation to the alpha helix structure
Hydrogen bonds are parallel to the direction of the helix axis
53
Where are side chains in relation to the alpha helix structure?
Side chains stick out from the helix
54
Where are hydrogen bonds located in relation to beta pleated sheets?
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
Where are amino acid side chains located in relation to beta pleated sheets?
Amino acid side chains that alternate above and below the plane of the pleated sheet
56
What effect does hydrogen bonding have on beta pleated sheets?
Stabilize the beta pleated sheets
57
Contrast the clustering of polar and non-polar side chains on soluble and membrane secondary proteins
- Polar amino acids cluster on the surface of soluble side chains
- Nonpolar amino acids cluster on the surface of membrane proteins
58
Describe the tertiary structure of a protein
- 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
What is the hydrophobic core?
Water soluble proteins fold into 3-D structures with no polar side-chains to the inside
60
How can side chains of amino acids be involved in stabilizing tertiary structure?
- 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
What are the only covalent force involved in tertiary structures?
The covalent disulfide bond
62
Describe the effect of secondary folding structures on tertiary strutted of proteins
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
Describe myoglobin as a tertiary structure
- Myoglobin is described in terms of tertiary structure
- Myoglobin contains about 80% alpha-helix secondary structure
- Myoglobin is devoid of Beta-sheet structure
64
Describe quaternary structure
- Consists of more than one polypeptide chain/ subunit
| - refers to the spatial arrangement of subunits and the nature of their interactions
65
How do subunits interact in quaternary structures?
Subunits interact via non-covalent bonds
| - hydrogen bond, electrostatic interactions and a few hydrophobic interactions
66
Give examples of quaternary structures
Dimmers, trimmers, tetraners and oligomers
67
In quaternary structure, subunits always...
Combine in the same manner
68
What is the denaturation of proteins?
The 3-D structure is changed. Noncovalent bonds and disulfide bonds are broken but not the peptide back bone
69
What protein structure remains intact in denaturation?
Primary structure
70
What happens to dietary proteins in the stomach?
Is denatured in the lumen of the stomach due to low pH. Stomach acid levels not low enough to cleave peptide bonds
71
Denatured proteins usually cannot regain their natural configuration and precipitate. What is proof of this?
Once an egg is fried, you can’t uncool it
72
Why can you not uncook an egg?
Denatured proteins usually cannot regain their natural configuration and precipitate
73
Explain the denaturation of a protein in the laboratory, stating how each type of bond can be broken
- 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
How does the degeneration of insulin involve denaturation of proteins?
The disulfide bonds of insulin are cleaved in the liver in animals
75
Give some examples of how proteins can be isolated and separated
- 1D gel electrophoresis
- 2D gel electrophoresis
- protein digestion
- Purification
- Isotope-Coded Affinity Tags (ICAT)
