Chapter 3-4- Protein Composition And Structure Flashcards
1
Q
What does protein function depend directly on?
A
The three dimensional structure of the protein which is determined by the sequence of amino acids
2
Q
What do rigid proteins function as?
A
They can function as structural elements in cells and tissues.
3
Q
What do flexible proteins function as?
A
They can act as hinges, springs, or levers that are crucial to protein function or to the assembly of protein complexes.
4
Q
Fischer projections def
A
Used to visualize the constituent atoms of a molecule. Horizontal bonds project out of the page towards you and vertical bonds project behind the page away from you.
5
Q
Sterochemical renderings def
A
Used for viewing a molecules function because they convey an immediate sense of the molecules structure and hint about its function.
6
Q
Glycine
A
G, Achiral, H
7
Q
Alanine
A
A, CH3, nonpolar
8
Q
Valine
A
V, CH(CH3)2 non polar
9
Q
Leucine
A
L, CH2CH(CH3)2
10
Q
Isoleucine
A
I, CH(CH3)CH2CH3
11
Q
Methionine
A
M, CH2CH2SCH3
12
Q
Proline
A
P, 5 member end ring with nitrogen next to the chiral carbon. Positive charge on N
13
Q
Phenylalanine
A
F, CH2-Ph
14
Q
Tryptophan
A
W, CH2-five membered ring connected to phenyl. Nitrogen in the five ring two bonds away from carbon connected to the stem. Conjugated double bonds in the five membered ring
15
Q
Serine
A
S, CH2-OH polar, alanine with an OH instead of a H.
16
Q
Threonine
A
T, CH(CH3)OH, polar, valine with an OH instead of one of the CH3 groups.
17
Q
Tyrosine
A
Y, CH2-Ph-OH, the OH is para. Phenylalanine with an OH group
18
Q
Cysteine
A
C, CH2-SH, polar. More reactive than serine. Serine with an SH instead of OH.
19
Q
Asparagine
A
N, CH2(C=O)NH2. Amide group. Polar
20
Q
Glutamine
A
Q, CH2-CH2(C=O)-NH2. Same as asparagine with an extra CH2
21
Q
Lysine
A
K, CH2-CH2-CH2-CH2-NH3+
Charges highly hydrophilic.
22
Q
Arginine
A
R, CH2-CH2-CH2-NH-C(NH2)+
Highly hydrophilic
23
Q
Histidine
A
H, CH2-five membered ring with two nitrogen’s conjugated double bonds.
24
Q
Aspartic acid
A
D, CH2-(C=O)-O- carboxylic acid, usually negatively charged in cells.
25
Glutamic acid
E, CH2-CH2-(C=O)-O-, same as aspartic acid with an extra CH2
26
What are the seven amino acids with readily ionizable side chains? And why are they important?
Tyrosine, cysteine, arginine, lysine, histidine, aspartic acid and glutamic acid. This is important because they can form ionic bonds and donate and accept protons to facilitate reactions. This is called acid-base catalysis and is important in chemical reaction for many enzymes.
27
What are essential amino acids and which are they?
Essential amino acids are the ones that are not generated in the body and must be supplied by the diet. Histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine,
The 11 others are non essential amino acids and are generated in the body.
28
Primary structure def
The amino acid sequence that constitutes a protein.
29
Secondary structure def
Folding of the polymers to form discrete three-dimensional structures with biochemical functions. Results from a regular pattern of hydrogen bonds between the NH and CO components of the amino acids in the polypeptide chain.
30
Tertiary structure def
When the R groups of amino acids that are far apart in the primary structure bond with one another. Highest level of structure that an individual polypeptide can attain.
31
Quaternary structure def
Many proteins require more than one chain to function. Can be as single as two identical polypeptide chains or as complex as dozens of polypeptide chains.
32
What groups are linked in the primary structure?
The a-carboxyl group of one amino acid and the a-amino group of another
33
What is the name of the linkage of two amino acids?
Peptide bond. Formed in the primary structure. The formation of a peptide bond expels water. The synthesis of peptide bonds requires an input of free energy.
34
What is a residue?
It is what the amino acid at the end of a polypeptide chain is called. The ends are different, a-amino group at one end and a-carboxyl group at the other.
35
Which end of the polypeptide chain is considered the beginning?
The amino end. The sequence of amino acids in a chain is written starting at the amino-terminal residue.
36
What is titin?
The largest known protein. It is a muscle protein. Consists of almost 27,000 amino acids.
37
What are disulfide bonds and how are they formed?
They are the most common type of cross-link and they are formed by the oxidation of a pair of cysteine residues. The resulting unit of the two linked cysteines is called a cystine. Disulfide bonds can occur between cysteine residues in the same polypeptide chains or they can link two separate chains together.
38
Who discovered the amino acid sequence of insulin and why was it so important?
Frederick Sanger discovered it in 1953. This was important because it was the first time that it was shown that a protein has a precisely defined amino acid sequence consisting only of L amino acids linked by peptide bonds.
39
Why is knowing the amino acid sequence of a protein important?
The amino acid sequence determines the three dimensional structure of a protein. Also, the knowledge of the sequence is essential to explaining its function. Alterations in amino acids I sequence can produce abnormal function and disease such as sickle cell anemia and cystic fibrosis, which are caused by a single change of an amino acid in a protein.
40
What are the two configurations for a planar peptide bond? And which is most common?
There is the trans configuration where the two a-carbon atoms are on opposite sides of the peptide bond and cis, where the two a-carbons are on the same side of the peptide bond. Almost all peptide bonds in proteins are trans due to steric clashes between the R groups in the cis configuration.
41
What allows the proteins to fold in many ways?
The freedom of rotation about the bonds between the amino group and the a-carbon and the a-carbon and the carbonyl group allows to the proteins to fold in many ways. These two bonds are purely single bonds and aren’t as rigid as the peptide bonds, which can then rotate about these bonds.
42
What is steric exclusion?
The fact that two atoms cannot be in the same place at the same time, restricts the number of possible peptide conformations and is thus a powerful organizing principle.
43
What are the two periodic structures that polypeptide chains can fold into in the secondary structure and how to they form?
Alpha helices and beta pleated sheets and they are formed by a regular pattern of hydrogen bonds between the peptide NH and CO groups of amino acids that are often near one another in the linear sequence
44
Alpha helix terms and meanings.
The pitch of the alpha helix is the length of one complete turn along the helix axis.
The screw sense of a helix can be clockwise (right handed) or counter clockwise (left handed). Clockwise are energetically more favourable because there are less steric clashes. Screw sense refers to the direction in which a helical structure rotates with respect to its axis.
45
Which amino acids disrupt the alpha helices and why?
Amino acids with branching at the a-carbon such as, valine, threonine, isoleucine, disrupt because of steric clashes.
Serine, aspartic acid, and asparagine also disrupt because their side chains contain hydrogen donors or acceptors in close proximity to the main chain.
Proline is also an alpha helix breaker because is lacks an NH group and because its ring structure prevents it from assuming the right angle.
46
What are beta sheets composed of?
They are composed of two or more polypeptide chains called B strands. A B strand is almost fully extended rather than tightly coiled as in alpha helix. The side chains of adjacent amino acids in beta sheets point in opposite directions. The two beta sheets are linked together by hydrogen bonds.
47
What are the two common fibrous proteins?
a-keratin and collagen
a-keratin is the primary component of wool and hair and it consists of two right-handed a-helices intertwined to form a left-handed super helix called a coiled coil
Collagen is the main fibrous component of skin, bone, tendon, cartilage and teeth
48
Alpha keratin facts
It is a member of a super family of proteins referred to as coiled-coil proteins. Two or more helices and entwine to form a very stable structure with long length. The two helices are cross linked by weak interactions such as van der wails forces and ionic interactions. Possible disulfide bonds with the presence of neighbouring cysteine residues.
49
Collagen facts.
Contains three helical polypeptide chains, each nearly 1000 residues long. Glycine appears at every third residue and the sequence gly-pro-pro recurs frequently.
50
Give an example of a globular protein and how they are special
Myoglobin is a globular protein and they have a compact three-dimensional structure and are water soluble. Because of their more intricate three dimensional structure, they perform most of the chemical transactions in the cell.
51
What is myoglobin, where is it found, and what does it do?
Myoglobin is a single polypeptide chain of 153 amino acids and is an oxygen binding protein found in the heart and skeletal muscle. It appears to facilitate the diffusion of oxygen from the blood to the mitochondria. It can do this with the oresence of heme, a helper group containing iron. It is water-soluble.
52
What is the simplest sort of quaternary structure?
A dimer- consisting of two identical subunits.
53
Intrinsically disordered proteins def
A class of proteins which completely or I part, do not have a discrete three dimensional structure under physiological conditions. They assume a defined structure upon interaction with different partners yielding different biochemical functions. Especially important in signalling and regulatory pathways.
54
Metamorphic proteins def
Another class of proteins that do not adhere to the paradigm and they appear to exist in an ensemble of structures of approximately equal energy that are in equilibrium. Small molecules may bind to a particular member of the ensemble, resulting in a complex that had a biochemical function that differs from:that of another complex formed by the same metamorphic protein bound to a different partner.
55
How is a peptide bond stable if the free energy of hydrolysis of proteins is negative?
Because the energy barrier tat must be crossed in order to go from the polymerized state to the hydrolyzed state is large even though the reaction is thermodynamically favourable.
56
Why might an amino acid have a variety of pKa values?
Depending on the chemical environment inside the protein, the pKa of an amino acid can change
57
Why is rotation about the peptide bond prohibited? What are the consequences of the lack of rotation?
The peptide bond has a partial double bond character, preventing rotation. This lack of rotation constrains the conformation of the peptide backbone and limits possible structures.
58
What is meant by the term polypeptide backbone?
The nitrogen-acarbon-carbonyl carbon repeating unit.
59
Define the term side chain in the context of amino acid or protein structure
Side chain is the functional group attached to the a carbon of an amino acid.
60
Differentiate between amino acid composition and amino acid sequence
Amino acid composition refers to the amino acids that make up the protein. The order is not specified. Amino acid sequence is the same as primary structure- the sequence of amino acids from the amino terminal to the carboxyl terminal of the protein.
61
What are the benefits of knowing the primary structure of a protein?
The primary structure determines the tertiary structure so knowing it helps to know the function of the protein. Knowledge of the primary structure of mutated proteins enables a n understanding if the basis of some diseases. Primary structure can reveal the evolutionary history of the protein.
62
List some of the differences between alpha helix and beta strand.
The helix is condensed, coiled, with the R groups bristling outward from the axis of the helix. The distance between two adjacent amino acids is 1.5A. The beta strand is a fully extended polypeptide chain, and the side chains of adjacent amino acids point in opposite directions. The distance between adjacent amino acids is 4.5 A. Both structures are stabilized by hydrogen bonding between components of the polypeptide backbone.
63
What are the levels of protein structure and describe the type of bonds characteristic of each level.
Primary structure- peptide bond
Secondary structure- local hydrogen bonds between components of the polypeptide backbone and
Tertiary structure- various types of non covalent bonds between R groups that are far apart in the primary structure so knowing
Quaternary structure- various non covalent bonds between R groups on the surface of subunits.
64
Tertiary structure description
Refers to the spacial arrangement of amino acid residues that are far apart in the sequence
65
Supersecondary structure description
Combinations of secondary structure that are present in many proteins.
66
Domain description
Compact regions that may be connected by a flexible segment of polypeptide chain
67
Subunit description
Basic component of quaternary structure so knowing
68
Quaternary structure description
Refers to the arrangement of subunits and the nature of their interactions.
69
Folding funnel description
An energy landscape
70
Molten globule description
Structure characterized by dynamic hydrophobic interactions.
71
Metamorphic protein description
Proteins that exist in an ensemble of structures of approximately equal energy that are in equilibrium.
72
Intrinsically disordered protein
Proteins that in whole or in part lack discrete three dimensional structure under physiological conditions.
73
Prion description
Cause of spongiform encephalopathies, which is a group of conditions that cause brain dysfunction
74
Why are the amino acids that make up the loops of proteins hydrophilic?
Because the loops are found on the surface of the proteins, exposed to the environment. Many proteins exist in aqueous environments so the loops are hydrophilic to interact with water.
75
Why is glycine such a highly conserved amino acid residue in the evolution of proteins?
Because glycine has the smallest side chain of any amino acid and spits size is often critical in allowing polypeptide chains to make tight turns or to approach one another closely.
76
What type of amino acids will you find in hydrophobic membranes and why do the proteins usually take on an alpha helix structure in the hydrophobic environment of the interior of a membrane?
The amino acids will be hydrophobic in nature. The alpha helix is suitable for crossing a membrane because all of the amide hydrogen atoms and carbonyl oxygen atoms of the peptide backbone take part in intrachain hydrogen bonds, stabilizing these polar atoms in a hydrophobic environment.
77
The alpha and beta subunits of hemoglobin bear a remarkable structural similarity to myoglobin but in the subunits of hemoglobin, residues that are hydrophilic in myoglobin, are hydrophobic. Why is this?
Hemoglobin exists as a tetramer, whereas myoglobin is a monomer. The hydrophobic residues on the surface of hemoglobin subunits probably take part in van der waals interactions with similar regions of the other subunits and are shielded from the aqueous environment by these interactions.
