Demonyo Flashcards
1
Q
- Building blocks or protein
- Acts as precursors and source of Sulfur
- Involved in many metabolic pathways such as in Glucogenesis where it is involved in glucose synthesis
A
Amino Acid
2
Q
The amino acids commonly dealt with are?
A
a- amino acids
3
Q
The name amino acid suggests that these structures have what?
A
Amine and Acid group ( amino acid and carboxylic acid group)
4
Q
How many different groups are attached to the central carbon of amino acids have and what type of carbon is it?
A
4 different groups and chiral carbon
5
Q
What arrangement does amino acid have?
A
Tetrahedral arrangement
6
Q
Because of the tetrahedral arrangement of the bonding orbitals around the a-carbon atom, the four different groups can occupy how many unique spatial arrangements and how many possible isomers?
A
2 unique spatial arrangements and 2 possible isomers
7
Q
A
8
Q
The position of the carbon atom in amino acids is? And what are attached to this carbon atom?
A
Alpha (a), NH2 and -COOH group
9
Q
Amino acids have _______ structure that vary in size, shape, charge, activity, functional groups present, hydrogen-bonding ability, and chemical reactivity
A
R = side chain
10
Q
How many amino acids are known?
A
More than 700
11
Q
Based on common “R” groups, there are how many standard amino acids?
A
20 (The Mighty Twenty)
12
Q
Nearly all amino acids in biochemistry are of the ______ -form which is the opposite of _______ which nearly always occur as the D-isomer
A
L-form ( L for Life), sugars
13
Q
True or False:
The L-designation has nothing to do with the way they rotate polarized light but is purely structural. This is based on the structure of L-glyceraldehyde
A
True
14
Q
By ________ L and D refer only to the absolute configuration of the four substitutes around the chiral carbon, not to optical properties of the molecule.
A
Fischer’s convention
15
Q
True or False:
The non-ionic form occurs in significant amounts in aqueous solutions
A
False: The non-ionic form does not occur in significant amounts in aqueous solutions
16
Q
The zwitterionic form predominates at normal pH of what?
A
pH= 7.4
17
Q
True or False:
- At 7.4 pH, the non-ionic form has lost its proton
- Has a negative charge
- with electrons of the double bond shared across the two O atoms
A
True
18
Q
True or False:
Also attached to the a-carbon is an amine group that at pH 7.4 has extra proton and so carries a negative charge
A
False: Also attached to the a-carbon is an amine group that at pH 7.4 has extra proton and so carries a positive charge
19
Q
The amino acid residues in protein molecules are exclusively what?
A
L-isomers
20
Q
Cells are able to specifically synthesize the ________ of amino acids because the active sites of enzymes are asymmetric, causing the reaction they catalyze to be _______.
A
L-isomers, stereospecific
21
Q
The 20 common amino acids are a-amino acids they have a ______ group and _____ group
A
Carboxyl group, amino group
22
Q
The 20 common amino acids differ from each other in their ______ or ______
A
Side chain or R groups
23
Q
Other than the 20 amino acids there are many less common ones. Some are ______ modified after a protein has been synthesized; other are amino acids present in living organisms but not as _______ of proteins.
A
residues, constituents
24
Q
What are the uncommon amino acids?
A
5-Hydroxylysine, 4 Hydroxyproline - found mainly in collagen and gelatin proteins
Thyroxine - is iodinated AA found only in thyroglobulin in the thyroid gland
gamma carboxyglutamic acid - is found in proteins involved in blood clotting
25
Uncommon amino acids are _____ not found in proteins
Derivatives
( L-Chloramphenicol, Epinephrine, Histamine, Ornithine, Citrulline, Serotonin, gamma Aminobutyric acid (GABA) , b-Alanine)
26
What are the Biologically Active Amino Acid Derivatives
gamma Aminobutyric acid (GABA), Histamine, Dopamine, Thyroxine
27
Uncommon Amino Acid function as a derivative of Proline, found in plant cell wall proteins
4-hydroxyproline
28
Uncommon Amino Acid function found in collagen, a fibrous protein in connective tissues
5-hydroxylsine
29
Uncommon Amino Acid function is a constituent of myosin, a contractile of muscles
6-N0 methyllysine
30
Uncommon Amino Acid function that is found in blood clotting protein prothrombin and in certain other proteins that bind a ca2+ as part of their biological function
gamma - carboxyglutamate
31
Uncommon Amino Acid function as a derivative of four Lysine residue, which is found in the fibrous protein elastin
Desmosine
32
Uncommon Amino Acid function:
- a special case
- rare amino acid residue that is introduced during protein synthesis rather than created through a post synthetic modification
- contains selenium rather than the sulfur of cysteine
- derived from serine, is a constituent of just a few known proteins
Selenocysteine
33
Uncommon Amino Acid function as key intermediates (metabolites) in the biosynthesis of arganine and in the urea cycle
Ornithine and Citrulline
34
All amino acids show optical activity except for ______
Glycine (no chiral carbon)
35
This isomer has the ability to rotate the plane of polarized light to the right
Dextrorotatory (+)
36
This isomer has the ability to rotate the plane of polarized light to the left
Levorotatory (-)
37
True or False:
Both isomers can rotate the plane of polarized light by different magnitude but in same directions.
False: Both isomers can rotate the plane of polarized light by the same magnitude but in opposite directions.
38
When an amino acid is dissolved in water it exist in solution as a ______ or _______
Dipolar ion or Zwitterion
39
Zwitterion is German for
Hybrid Ion
40
Zwitterion can act as an ____ as a _____ and an ____ as a _____
acid, proton donor, base, proton acceptor
41
Substances like Zwitterion having dual nature are amphoteric and are often called what?
Ampholytes
42
Titration has a plot that has 2 distinct stages corresponding to?
Deprotonation pf two different groups on glycine
43
At the midpoint of any titration point of _____ is reached where the pH is equal to the _____ of the protonated group being titrated
inflection, pk2
44
Convenient notations for proton concentration and the equilibrium constant for ionization, respectively
pH and pK
45
Measure of the tendency of a group to give up a proton
pK
46
47
Functions of Amino Acid
- Synthesis of proteins the body needs
- precursors of nitrogen
- some function as chemical messengers/ neurotransmitters
- glucose synthesis
- some for detoxification reactions
48
What are the nonpolar, all phatic R groups in the Mighty 20?
Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine
49
What are the Aromatic R groups in the Mighty 20?
Phenylalanine, Tyrosine, Tryptophan
50
What are the Positively charged R groups in the Mighty 20?
Lysine, Arginine, Histidine
51
What are the polar, uncharged R groups in the Mighty 20?
Serine, Threonine, Cysteine, Asparagine, Glutamine
52
What are the negatively charged R groups in the Mighty 20?
Aspartate, Glutamate
53
In chemical reactions most often the amino acid will be drawn with the carboxyl group as?
-COOH
54
In chemical reactions most often the amino acid will be drawn with the amine group as?
NH2
55
Appearance of molecules at what physiological pH?
pH= 7.4
56
What is considered the more correct form to draw amino acids?
Zwitterion
57
Identify the amino acid:
- a- carbon is Not a chiral center because it has 2 H groups attached to it
- the R-group provides little steric hindrance
- proteins can bed or rotate easily where this amino acid forms part of their structure
Glycine (G, Gly)
58
Identify the amino acid based on its major function:
- major inhibitor neurotransmitter in the brain
- hyperpolarizes the neuron and hence decrease its activity
Glycine (G, Gly)
59
A change in a cell’s membrane potential that makes it more negative. Opposite of depolarization
Hyperpolarization
60
Glycine can be modified by addition of what?
A fatty acid (myristate - 14 carbons)
61
It is the most important amino acid to learn
Glutamate (E, Glu)
62
Identify the amino acid (2):
-R-group contains carboxylic acid
-normal pH at 7.4, the carboxyl group carries a negative charge, and are very water soluble
- amide bond can be formed with the carboxylic acid of the r-group
- r-groups are more soluble in water, or more hydropyllic than those of the nonpolar amino acids because they contain functional groups that form hydrogen bonds with water
Glutamate and Aspartate
63
Identify the amino acid based on its major function:
- major excitatory neurotransmitter of the brain
- very important in a region of the brain which influences memory
Glutamate (E, Glu)
64
Region of the brain which influences memory
Hippocampus
65
Asparagine can be converted into Aspartate by ________
Hydrolyzing the amide bond
66
The R groups of both Asparagine and Glutamine are quite______, having a slightly positive charge
polar
67
Relationship between the molecules and the sequence
Q END
68
The small polar, positive charge can be used to advantage when studying the function of proteins using a genetic technique called __________. With this technique, the activity of the native protein is compared with one which has had one amino acid changed
single point substitution
69
True or False:
If the change is subtle, and it has a small effect on the activity of the protein, then it becomes clear that the amino acid of interest is critical to the function of the protein
False: If the change is subtle, and it has a large effect on the activity of the protein, then it becomes clear that the amino acid of interest is critical to the function of the protein
70
True or False:
If the protein retains its function, then these amino acids are NOT critical for protein's functions and vice versa
True
71
Ketone formation from amino acids and a very important reaction that some amino acid can undergo in the body is removal of ammonia
Deamination
72
The ___________ is formed when ammonia is removed from a-carbon and replaced with a ketone group
a- ketoglutaric acid
73
Removing _______ from Glutamate and replacing it with a _________, the carbon skeleton of Glutamate can be metabolized for energy
Ammonia, keto group
74
Significance of a-ketoglutaric acid is that it is a molecule in the energy generating and carbon shuffling cycle in mitochondria which is?
Tricarboxylic acid cycle (TCA cycle)
75
Is a part of the citric acid cycle, and is where Aspartate may enter the citric acid cycle - its carbon skeleton used for generating energy
Oxaloacetic acid
76
- Sodium salt of amino acid glutamate
- used as flavor enhancer
- may work to stimulate glutamate receptors in the tongue
- some people may react to this and develop ______ Symptom Complex
MSG - Monosodium glutamate
77
Identify the amino acid:
- This molecule is important in proteins because it has no charge on its R-group
- r- group is an acyl group
- regions of proteins with lots of these types of amino acids are lipid soluble regions of protein
- important basis for learning several of the other amino acids
- can be removed from the a-c through deamination
Alanine (A, Ala)
78
-Is very important in metabolism. In the liver it can be made into glucose for transport to the muscle. In the muscles the reverse process can take place - glucose is broken down to provide energy without using oxygen
- can be shuffled into the citric acid cycle so that its carbon skeleton can be used in making new molecules for energy production
- high concentration is toxic to the muscles
Pyruvic Acid
79
True or False:
Pyruvic acid in high concentration is toxic to the muscles and therefore an AMINE group from Glutamate (E, Glu) can be transferred to Pyruvate to form Alanine (A, Ala).
Alanine (A, Ala) is then transported into the blood back to the liver where it is converted back to pyruvate by removing ammonia.
The pyruvate is then made into glucose (gluconeogenesis) and transported back into the muscles. In this way, the muscles not only remove the acid but also ammonia, both of which are toxic.
True
80
Identify the amino acid:
- an aromatic amino acid
- Its symbol is "F" is phonetic sound of "ph"
- it is very hydrophobic in proteins
- essential amino acid in humans, because of the difficulty to make the ring structure, hence obtain this amino acid from diet
- used for depression, attention deficit , ADHD, and a skin disease called VITILIGO
Phenylalanine (F, Phe)
81
-An inherited disorder that increases the levels of a substance called phenylalanine in the blood
- Classic _____ is the most severe form
- without treatment develop permanent intellectual disability\
- treated by dietary modification - not eating foods high in phenylalanine e.g. cheese, eggs, meat, fish, milk
Phenylketonuria (PKU)
82
_____ is the enzyme responsible for the first step in processing Phenylalanine. inability to metabolize phenylalanine because of a lack of this enzyme cannot make TYROSINE and end up with an excess of phenylalanine which is excreted into urine after being modified into a ________
Phenylalanine Hydroxylase (PAH), Ketone
83
Identify the amino acid:
- is synthesized from Phenylalanine
- is used to make several types of hormones that transmit signals in the brain - neurotransmitters and a pigment called melanin - which gives hair and skin their color
- can also be broken down into smaller molecules that are used to produce energy
- in proteins, strongly hydrophobic
- aromatic rings absorb light at 290 NM and used as an indirect measure of protein concentration
- in protein, its r-group can be phosphorylated by forming an ester bod between the hydroxyl group and phosphoric acid
Tyrosine
84
The enzyme responsible in the synthesis of Tyrosine from Phenylalanine is
Phenylalanine hydroxylase (PAH)
85
In the conversion of Phenylalanine to Tyrosine:
- 2 additional substances are need: ______ and a co-enzyme named ______
- the coenzyme is converted to _______
- _____ oxygen atom is added to the _______ group of Phenylalanine to form Tyrosine and on the the H2 to form water
Oxygen, Tetrahydrobiopterin
Dihydrobiopterin
One, Phenyl Group
86
Is a benzene ring with one or more hydroxyl groups attached. Tyrosine is the precursor for forming a group of neurotransmitters which includes dopamine, noradrenaline, and adrenaline for this.
Catecholamines
87
An enzyme in the synthesis of Catecholamines that added to the meta position to the benzene ring of Tyrosine
Hydroxyl group
88
An enzyme in the synthesis of Catecholamines that has O standing for OH
Dihydroxyphenylalanine (DOPA)
89
An enzyme in the synthesis of Catecholamines that is the enzyme in the synthesis of Tyrosine to DOPA and catalyzes the formation of hydroxyl group on Tyrosine to form DOPA
Tyrosine hydroxylase
90
In the synthesis of Catecholamines the conversion of DOPA to Dopamine by?
decarboxylic DOPA
91
- The amine form of dihydroxyphenylalanine
- neurotransmitter in the brain
- controls the pressure of blood through the kidneys
Dopamine
92
Are used to stimulate Dopamine release to control attention deficit disorder - used for social purposes because they quickly create dependence and schizoid behavior
Amphetamines
93
Dopamine is converted to Noradrenaline by hydroxylating the _______
B-carbon
94
Another name for Noradrenaline is ________ and similarly Adrenaline is called _________
Norepinephrine , Epinephrine
95
- is an important hormone and neurotransmitter
- is released as a hormone by the adrenal medulla as part of the flight and fight response
- main neurotransmitter of the sympathetic nervous system
- phenylethanolamine
(2)
Noradrenaline and Adrenaline
96
Inner part of the adrenal gland, controls hormones that help a person cope with physical and emotional stress
Adrenal medulla
97
Noradrenaline is converted to Adrenaline by adding a ______ group to the _____ group of Noradrenaline
Methyl, Amine
98
Ethanol with an amine group and phenyl group
Ethanolamine
99
In forming Adrenaline, a methyl group is transferred to the ______
Nitrogen
100
Enzyme that describes the reaction, and the N indicates that the transfer was to the nitrogen group
Phenylethanolamine – N – methyl transferase (PNMT)
101
Identify the amino acid:
- similar to Tyrosine but you can see a W in its ring structure
Tryptophan (W, TRP)
102
In the procedure for hydroxylation and decarboxylation to form serotonin (5-hydroxytryptamine):
The R-group is hydroxylated at ________ of the ring structure
Then 5-hydroxytryptophan is _____ to form serotonin
C5, decarboxylated
103
- A very important neurotransmitter in the brain
- involved in spinal reflexes, sleep-wake cycle, flow of sensory afferents and habituation
- decrease in this has been implicated in the depressive phase of some manic depressive disorders
5-hydroxytryptamine (serotonin)
104
Is an inhibitor of serotonin receptors, The use of this substance causes vivid hallucinations
Lysergic acid diethylamine (LSD)
105
A drug which activates serotonin receptors in the brain, had been used to give people a sense of well being
Prozac
106
Glutamic acid is decarboxylated at the ________
a-carbon
107
CH3CH2CH2COOH
Butyric acid
108
True or False
In decarboxylation of glutamic acid, the carbon with the carboxyl group has lower priority now than the carbon with the amine group
False: In Tryptophan, the carbon with the carboxyl group has lower priority now than the carbon with the amine group
109
In decarboxylation of glutamic acid, the carbon with the carboxyl group becomes _______ and the carbon with the amine group becomes the ________
a-carbon, y-carbon
110
Decarboxylation of glutamic acid by the enzyme ______ forms y-amino butyric acid (GABA)
Glutamic acid decarboxylase
111
-major inhibitory neurotransmitter in the brain
- has both amine group and an acid group and considered an amino acid
- it is not an a-amino acid, therefore is not used in making proteins
GABA
112
Enhances the action of GABA
Benzodiazapines (Valium)
113
Identify the amino acid:
- Is decarboxylated to give Histamine
- r-group can change its charge at around physiological pH = 7.4
- is the only amino acid in proteins whose charge on the R-group is changed around physiological pH
Histidine (H, HIS)
114
- Is a very important molecule for our body's defense against infection
- released from mast cells
- people suffering from strong allergy responses release too much of this
Histamine
115
Identify the amino acid: (2)
- have hydroxyl group in their r-group
Serine (S, SER)
Threonine (T, THR)
116
Serine is _____ with a hydroxyl group attached to it. For Threonine, with a hydroxyl and methyl group added to it
Alanine
117
In phosphorylation of Serine and Threonine :
The _____ make these two of the most important amino acids in protein
Having this means they can form an _______ with ______
This is important because it means that where the protein has no charge at a Serine or Threonine, once phosphorylated is has a massive ________ charge.
This changes the shape of the protein and affects its function in this way they are similar to ________
Hydroxyl groups
Form an ester bond, Phosphoric acid
Negative
Tyrosine
118
True or False:
In Glycosylation of Amino Acids ether bonds can be formed by condensing it with another hydroxyl group
True
119
When sugar, having multiple hydroxyl groups, can be attached to proteins at Serine or Threonine by what type of ether bond?
O-glycosidic bond
120
Beside Serine or Threonine, what is another amino acid to which sugars can attach is? Where n-glycosidic bond is formed
Asparagine
121
These 2 amino acids both contain sulfur
Cysteine (C, CYS) and Methionine (M, MET)
122
Identify the amino acid:
- an alanine with sulfuhydryl group
- can be oxidized to form a disulfide bridge (important in determining the shape of the protein)
Cysteine (C, CYS)
123
What is removed when oxidation of 2 cysteine occurs
Removal of Hydrogen
124
The mucous formed is very viscous because the protein component of the mucous makes a large number of disulfide bonds is given as treatment.
Asthma
125
Identify the amino acid:
- used in proteins to transfer the methyl group (METHYL TRANSFERASES)
- very-non polar in proteins and hence is lipophilic
- important ins synthesis of carnitine or melatonin
- essential amino acid that cannot be synthesized in the body
Methionine (M, Met)
126
A rare deficiency when present, may lead to reduced growth rate, along with liver damage, muscle loss, edema, skin lesions, and lethargy
Methionine deficiency
127
Identify the amino acid:
- the r-group is consists of 4 carbons
- the charge is carried by a terminal amine
- has a second primary amino group at the end position of its aliphatic chain
Lysine (K, Lys)
128
Identify the amino acid:
- contains guanidium group
- 4 carbon in its r-group, but one carbon is part of the guanidium group, cccnc as r-group
- used in making UREA in the liver where the body removes NH3 which in high level is toxic to human beings
Arginine (R, Arg)
129
This structure appears in the Nucleoside Base Guanine which is found in DNA
Guanidium group
130
In addition to Alanine, what are 3 amino acids that also carry no charge?
- The r-groups in this class of amino acids are non-polar and hydrophobic
- side chains tend to cluster together within proteins, stabilizing protein structure by means of hydrophobic interactions
Valine (V, Val), Leucine (L, Leu), Isoleucine (I, Ile)
131
What amino acid can be remembered because its R-group is an inverted V in structure
Valine
132
Identify the amino acid:
- r -group circles around forming a bond with the amine group
- structure looks like a p lying on its face
- ring makes the amino acid very rigid
Proline (P, Pro)
133
True or False
The secondary amino group of proline residues is held in a rigid conformation that reduces the structural flexibility of polypeptide regions containing proline
True
134
Are made from strings of amino acids linked together by amide bonds between the a -carboxyl and the a- amino groups
Proteins
135
When amide bonds occur between amino acids (linkage)
Peptide bonds
136
The amino acids used in forming peptide bonds are the ______ and _______
20 a - L -amino acids and cysteine
137
The _____ of amino acids determine the structure and the properties of the peptide or proteins
Sequence
138
Carboxyl group + amino group form a strong covalent bond releasing water in the process
Condensation reaction
139
Amino acids join together in a long chain: N terminal end to C terminal end
A polypeptide
140
True or False:
Proteins contain only one polypeptide chain
False: Proteins may contain one or more polypeptide chains
141
True or False:
The double bond between the C and the H is actually shared across the bond between the C and the O
False: The double bond between the C and the O is actually shared across the bond between the C and the N
142
True or False:
It is easy to rotate the C-N bond because of its double bond nature
False: It is very difficult to rotate the C-N bond because of its double bond nature
143
True or False:
The O and the H are in the trans - position and all four molecules lie in the same plane
True
144
True or False:
Due to the slight un-pairing of electrons between the C and the O due to the sharing of the double bond with the N, the O has a slightly positive charge, and the electron of the H - atom spends most of its time in the bond between the N and the O which gives C - atom a slightly negative charge
False: Due to the slight un - pairing of electrons between the C and the O due to the sharing of the double bond with the N, the O has a slightly negative charge, and the electron of the H – atom spends most of its time in the bond between the N and the H which gives the H – atom a slightly positive charge
145
True or False:
The C, H, O, N atoms are able to take part in hydrogen bonding very readily
True
146
True or False:
The a - C are trans - and lie in the same plane as the four atoms of the peptide bonds
True
147
True or False:
The a-c trans two bonds are single bonds, and there is free rotation about them
True
148
True or False:
The angle of rotation about the bond between the N and the a-c is called psi bond angle and between the C and the a-c, the phi bond angle
False: The angle of rotation about the bond between the N and the a-c is called phi bond angle and between the C and the a-c, the psi bond angle
149
Identify the Classification of Proteins according to Chemical Structure:
- yield only amino acids upon complete hydrolysis
- proteins with no prosthetic group (non-protein part)
- albumin, globulin, keratin, collagen, elastin
Simple Proteins
150
Identify the Classification of Proteins according to Chemical Structure:
- simple protein combined with a non-protein or prosthetic group
- apoprotein (protein part)
- hemoglobin, lipoprotein
Compound or Conjugated Proteins
151
Identify the Classification of Proteins according to Chemical Structure:
- substances resulting from the decomposition of simple and compound proteins by the action of heat and other physical forces or by hydrollic agents
- peptones, proteases and peptides
Derived protein
152
Identify the Classification of Proteins according to shape or physical form:
- consists of several helical peptide chains twisted together to form a stiff rod
- generally insoluble in body fluids and give strength to tissues
- highly resistant to digestion by proteolytic enzymes
- collagen of connective tissues, keratin, myosin, elastin and fibrin
Fibrous protein
153
Identify the Classification of Proteins according to shape or physical form:
- consists of chain of amino acids that are coiled and tightly packed together in a spherical or ellipsoidal shape
- casein in milk, egg albumin, serum albumin, myoglobin, and hemoglobin
Globular protein
154
Identify the important fibrous protein:
- structural scaffold inside the cell
- keratin in hair, horns and nail
Intermediate filaments of the cytoskeleton
155
Identify the important fibrous protein:
- bind cells together to make tissues
- secreted from cells and assemble in long fibers
Extracellular matrix
156
Extracellular matrix that is a fiber with a glycine every third amino acid in the protein
Collagen
157
Extracellular matrix that is unstructured fibers that gives tissues an elastic characteristic
Elastin
158
True or False:
For Structural proteins:
Keratin - hair and nails
Collagen - supports ligaments, tendons, and skin
Silk - coconuts and spider webs
True
159
True or False:
In stabilizing cross-links, cross linkages can be between 3 parts of a protein or between 3 subunits
False: In stabilizing cross-links, cross linkages can be between 2 parts of a protein or between 2 subunits
160
True or False:
Disulfide bonds (S-S) form between adjacent -SH groups on the amino acid cysteine
True
161
Identify the Classification of Protein according to state of degradation:
- refers to the original protein structure without any change in physiochemical properties
Native protein
162
Identify the Classification of Protein according to state of degradation:
- Refers to a protein that has changed its physical, chemical, and biological properties characterized by an unfolding of the molecule from the pervious configuration due to splitting of peptide linkages and crosslinks that connect the peptide chains.
- This happens when proteins are subjected to heat, acid, or other conditions that disturb their stability.
Denatured Protein
163
- The peptide bond allows for rotation around it and therefore the protein can fold and orient the R groups in favorable positions
- Weak non-covalent interactions will hold the protein in its functional shape – these are weak and will take many to hold the shape
- The shape of proteins is determined by the sequence of the amino acids
Protein Folding
164
In protein folding, the final shape is called the ______ and has the lowest free energy possible
Conformation
165
- is the process of unfolding the protein
- can be down with heat, pH or chemical compounds
- In the chemical compound, can remove and have the protein renature or refold
Denaturation
166
True or False:
Primary structure is unchanged by denaturing
True
167
The side chains will help determine the conformation in an aqueous solution
Globular proteins
168
Noncovalent bonds can form interactions between individual polypeptide chains
Multiple Peptides
169
In Multiple Peptides it is where proteins interact with one another
Binding Site
170
In Multiple Peptides it is each polypeptide chain of large protein
Subunit
171
In Multiple Peptides it is protein made of 2 subunits. Can be same or different subunits
Dimer
172
- a basic structural unit of a protein structure
- part of protein that can fold into a stable structure independently
- can impart different functions to proteins
- proteins can have one to many of this depending on protein size
Domains
173
- protein can form large versions of this
- can form long chains if the protein has 2 binding sites - link together as a helix or a ring
- actin fibers in muscles and cytoskeleton - is made from thousand of actin molecules as a helical fiber
Protein Assemblies
174
- muscle contraction
- motor proteins within the cell
- allow cell components to move from place to place
Motion
175
For motion, specifically muscle contraction, these 2 make up muscle fibers
Actin and Myosin
176
For motion, specifically motor proteins within the cell, move the cell
Flagella
177
For motion, specifically motor proteins within the cell, move contents around the cell
Cilia
178
In Different Subunits Proteins, Hemoglobin has ____ a globin subunits and ____ b globin subunits
2, 2
179
Is called when they have similarities in amino acid sequence and 3-D structure
Protein Families
180
Identify the Classification of Proteins according to biological functions:
- Enzymes are proteins that direct and accelerate thousands of biochemical reactions in such processes as digestion, energy capture, and biosynthesis.
- One example is the enzyme Phenylethanolamine – N – methyl transferase (PNMT) – enzyme in the formation of adrenaline.
Enzymic proteins (Catalytic action proteins)
181
Identify the Classification of Proteins according to biological functions:
- Proteins are involved in all cell movements.
- For example, actin, tubulin and other proteins comprise the cytoskeleton. Cytoskeletal proteins are active in cell division, endocytosis, exocytosis and the amoeboid movement of white blood cells.
Aids in Movement (Contractile Proteins)
182
In metabolism this speeds ups chemical reactions
Biological catalysts
183
Digestive enzymes aid in hydrolysis:
Lipase
Amylase
Lactase
Protease
Molecular Biology:
Polymerase
Ligase
Industry:
Dairy, baby food, rubber, beer, photography, contact lens cleaner
.
184
Identify the Classification of Proteins according to biological functions:
- Functions as carrier of molecules or ions across membranes or between cells.
- Examples of membrane proteins include, Na+ , K+ , ATPase and the glucose transporter.
- Hemoglobin, which carries oxygen to the tissues from the lungs, and the lipoproteins LDL and HDL, which transport lipids from the liver and intestines to other organs.
- Transferrin and ceruloplasmin are serum proteins that transport iron and copper respectively.
Transport proteins
185
Identify the Classification of Proteins according to biological functions:
- Some proteins provide protection and support.
- have very specialized properties.
- Example, Collagen (major component of connective tissues) and fibroin (silk protein) have significant mechanical strength.
- Example, Elastin, the rubberlike protein found in elastic fibers, is found in several tissues in the body (e.g. blood vessels and skin) that must be elastic to function properly
Structural Proteins
186
When channel and carrier proteins in the cell membrane and allows substances to enter and exit the cell
Transport
187
A transport molecule in the blood that transport oxygen in the blood
Hemoglobin
188
Identify the Classification of Proteins according to biological functions:
- Proteins that serve as reservoir of certain nutrients.
- For example, ovalbumin in bird eggs and casein in mammalian milk are rich sources of organic nitrogen during development.
- Plant proteins such a zein perform a similar role in germinating seed.
- Ferritin is one example of storage protein that stores iron.
Storage proteins
189
Identify the Classification of Proteins according to biological functions:
- Binding a hormone molecule or a growth factor to cognate receptors on its target cell changes cellular function.
- Examples of peptide hormones include insulin and glucagon, both of which regulate blood glucose level.
- Growth hormone, stimulates cell growth and division (growth factors are polypeptides that control animal cell division and differentiation) – examples include platelet – derived growth factor (PDGF) and epidermal growth factor (EGF)
Regulatory or signal proteins
190
Protein function when intercellular messengers that influence metabolism
Hormones
191
Hormone that regulates the amount of glucose in the blood and in cells
Insulin
192
Hormone that its presence determines the height of an individual
Human growth hormone
193
Part of the Regulation function of protein that is built into the membrane of nerve cells and detect chemical signals released by other nerve cells
Receptor Proteins
194
Identify the Classification of Proteins according to biological functions:
- A wide variety of proteins are protective.
- Examples found in vertebrates include keratin, the protein found in skin cells that aids in protecting the organism against mechanical and chemical injury.
- Another example, the blood clotting proteins fibrinogen and thrombin, prevent blood loss when blood vessels are damaged.
- The immunoglobulins (or antibodies), are produced by lymphocytes when foreign organisms such as bacteria invade an organism (binding antibodies to an invading organism is the first step in its destruction).
Defense Proteins
195
Identify the Classification of Proteins according to biological functions:
- The capacity of a living organism to survive a variety of abiotic stresses is mediated by certain proteins.
- Example, cytochrome P450 – a diverse group of enzymes found in animals and plants that usually convert a variety of toxic organic contaminants into less toxic derivatives.
- Example, cells are protected from radiation by DNA repair enzymes (e.g. o6 – methylguanine methyl transferase – transfers the methyl group from O6 – methylguanine to a cysteine residue in the enzymes active site).
Stress Response Proteins
196
Part of the Defense function of proteins that combat bacteria and viruses
Antibodies
197
Identify the Classification of Proteins according to biological functions:
- Example, Tryptophan – rich sensory protein (TspO) are a family of proteins that are involved in transmembrane signaling.
- These are proteins that connect the system to the surrounding (e.g. smell, touch, hear feel heat, see and detect light.
Sensory proteins
198
The primary structure of a protein is the complete set of ______ within a protein
Covalent bonds
199
True or False:
Enzymes play an important role in Metabolism, Diagnosis, and Therapeutics
True
200
- The sequence of amino acid residues from the N-terminal to the C-terminal
- the order in which the amino acids are linked together
- one dimensional first step in specifying the three dimensional structure of a protein
Primary Structure
201
True or False:
H-bonds form between:
1) atoms involved in the peptide bond
2) peptide bond atoms and R groups
3) R groups
True
202
Molecules that contain a special pocket or cleft
Active sites
203
True or False:
In every protein, the correct 3 – D structure is not needed for correct functioning.
False: In every protein, the correct 3 – D structure is needed for correct functioning.
204
The interaction between amino acid residues determines the protein's ______ and its functional role and relationship to other proteins
3-D structure
205
where ENZYME slightly changes shape when the SUBSTRATE binds
Enzyme/substrate complex
206
- genetic disease
- red blood cells cannot bind oxygen efficiently
- due to its sickle shape they tend to become trapped in small blood vessels, cutting off circulation and thereby causing organ damage
- stem from a change in one amino acid residue in the sequence of the primary structure
Sickle Cell Anemia
207
Where the substrate is processed
Enzyme/product complex
208
True or False:
According to research, it is possible to replace any chosen amino acid residue in a protein with another specific acid residue
True
209
Explains enzyme specificity and loss of activity when enzymes denature:
- Active site has rigid shape
- only substrates with matching shape can fit: have reaction
-does not work for all enzymes
Lock (enzyme)-and-key (substrate) model
210
- centers on the 3-D shape of the peptide bonds
- the most commonly observed types of secondary structure are the a -helix and the b - pleated sheet
- Both α – helix and β – pleated sheet patterns are stabilized by hydrogen bonds between the carbonyl and N – H groups in the polypeptide backbone.
Secondary Structure
211
- Apoproteins: enzyme without its non protein moiety(prosthetic)
- Inactive
- needs a coenzyme to activate
Apoenzyme
212
- Occur when there is strong hydrogen bonding between the carbonyl (C=O) group and the amide (N – H) group of the nearest amino acid with which in can interact
- This occurs because the amino acids chain twists in a spiral to bring the carbonyl group of 1 – amino acid adjacent to the amine group of the amino acid 3 – amino acids away from it.
-Therefore, each amino acid will form hydrogen bonds with 2 other amino acids ( one with an amino acid 3 positions above it in the chain, and the other with an amino acid 3 positions below in the chain.
-An a - helix can occur as a left or right handed helix and this gives the protein its optical activity (whether it rotates polarized light to the right or the left) in solution – a left hand a - helix is rare.
- If a protein is made up predominantly of a - helix – then it is a fibrous protein (e.g. a - keratin found in hair, nails, scales, wool and hooves are good examples).
Helical Structure
213
Active enzyme with non protein component
Holoenzyme
214
the -CO group of residue n is _______ to the -NH group of residue
H-bonded
215
- non-protein chemical compound that is bound/reacted (loose or tight) to an enzyme
- required for catalysis
Cofactor
216
A helical structure, the most common conformation is a _______ where where phi = ___ degrees and psi = ___ degrees
Right handed helix, -48, -57
217
Types of cofactors
- Coenzymes
- Prosthetic groups
218
True or False:
Left handed alpha helix is more stable than the right handed
False: Right handed alpha helix is more stable than the left handed
219
- non protein component that is LOOSELY bound to apoenzyme by NON-COVALENT BOND
- examples are VITAMINS or compounds derived from vitamins
Coenzyme
220
In the constraints in Helical Structure:
The presence of pro and gly offers constraints to formation of an _______
a-helix
221
non protein component that is TIGHTLY bound to the apoenzyme by a COVALENT BOND
Prosthetic group
222
In the constraints in Helical Structure:
______ introduces a destabilizing link in an a-helix. The N of this can not participate in H-bonding
Proline
223
In the constraints in Helical Structure:
In proline, the N atom is part of the rigid ring and rotation about the ______ bond is not possible
N-Ca bond
224
Enzymes may recognize and catalyze:
- A single substrate
- Group of similar substrates
- Particular type of bonds
225
In the constraints in Helical Structure:
________ is infrequently found in an a-helix because it tends to form coiled structures different from an a-helix
Glycine
226
Types of enzyme specificity
- Absolute
- Group
- Linkage
227
- extensive hydrogen bond network with their neighbors in which the N-H groups in the backbone of one strand establish hydrogen bonds with the C=O groups in the backbone of the adjacent strands
- Silk is a very good example
Secondary: Beta pleated sheet
228
- Catalyzes one type of reaction for a SINGLE SUBSTRATE
- example: urease catalyzes only hydrolysis of urea
Absolute
229
True or False;
a - structures are helical and involve H – bonding within the amino acid chain.
Β – structures are sheet structures and involve H – bonding between chains.
True
230
- Catalyzes one type of reaction for SIMILAR SUBSTRATES
- example: Hexokinase adds phosphate group to hexoses
Group
231
A type of B sheet that run in an opposite direction of its neighbor. Aligned at the N-terminus to C-terminus and the other is oriented at C-terminus to N-terminus.
Anti- parallel
232
- Catalyzes one type of reaction for a SPECIFIC TYPE OF BOND
- Examples: Chymotrypsin catalyzes the hydrolysis of peptide bonds
Linkage
233
A type of B sheet that run in the same direction with longer looping sections between them. The bend in the protein can occur so that the chains are in the same orientation (N-terminus to C-terminus aligned with another strand from N-terminus to C-terminus).
Parellel
234
All chemical reactions require some amount of energy to get them started or first push to start a reaction
Activation energy/energy of activation
235
- Refers to the unique 3 – D conformations that globular proteins assume as they fold into their native (biologically active) structures
- is the overall shape of the protein
-structure formed by bending and twisting of the polypeptide chain
-Formation of domain: section of protein structure sufficient to perform a particular chemical or physical task
-linear sequence of amino acids is folded into a compact globular structure
Tertiary Structure
236
What is the mechanism of the action of enzymes
- enzymes INCREASE reaction rate by DECREASING activation energy (inversely proportional)
- Enzyme-substrate interactions
-Formation of enzyme substrate complex (lock and key model and induced fit model)
237
Three amino acids that have considerable influence over the tertiary structure
Cysteine, Proline, Glycine
238
4 types of interactions that stabilizes tertiary structure
-Hydrophobic interactions (hydrophobic amino acid side chains into the interior of the protein shielding them from water)
- Disulfide bonds
- Hydrogen bonds
- Electrostatic interactions between charged amino acid side chains
239
enzymes______reaction rate by ________activation energy, making it efficient.
Increase, Decreasing
240
- Final assemblage of protein chains to form a physiologically active protein.
- E.g. HEMOGLOBIN – is the assemblage of four (4) proteins and two (2) of the units are coded for by one (1) gene and the other two (2) from a different gene.
- The number of subunits in a protein leads to the protein being described as a monomer, dimer, trimer, tetramer,…
Quaternary Structure
241
- Flexible, not rigid
- shape of enzyme, active site, and substrate adjust to maximize the fit to improve catalysis
- more consistent with wider range of enzymes
Induced fit model
242
part 3 enzymes
243
How does an enzyme react to a substrate to form complex
enzyme and substrates COMBINE (step 1)
244
What is formed when enzyme and substrate is combined
enzyme-product complex
245
How is the enzyme product complex formed (step 2)
Enzyme substrate complex is being processed ---> transition state (breakdown) ---> formation of enzyme product substrate
246
What is the next step (3) of the enzyme process?
the enzyme and product SEPARATE
247
What does the enzyme do after the process?
it can regenerate and get another substrate which repeats the whole process
248
What affects enzyme activity
- Environment
- cofactors and coenzymes
- enzyme inhibitors
249
What specific environmental condition makes an enzyme at risk
- extreme temperatures (High temperatures which causes an enzyme to DENATURE)
- pH that is above or below normal pH (normal: 7) which also makes enzymes DENATURE but it DEPENDS on the enzyme (some like acidic or basic conditions)
- substrate concentration
250
What specific cofactors and coenzymes are needed for enzyme activity
- inorganic substances (zinc, iron) and vitamins (e.g. iron being present in hemoglobin to obtain oxygen and distribute to the system)
251
Temperature where enzymatic reactions occur the fastest
Optimum temp
252
What is the optimum temperature
37-45 degree C
253
What happens when enzymes deal with more substrate than the limit
Enzymes become SATURATED
254
Reaction rate________as substrate conncentration_______. (constant enzyme concentration)
increases, increases
255
256
part 4 (a and b) enzymes
257
Vitamin
258
259
260
261
262
263
-Are proteins that increase the rate of reaction by lowering the energy of activation
- they catalyze nearly all the chemical reactions taking place in the cells of the body
- not altered or consumed during reaction
-reusable
Enzymes
264
Enzyme molecules contain a special pocket or cleft called?
Active sites
265
- This explains enzyme specificity this explains the loss of activity when enzymes denature
- the active site has a rigid shape
-only substrate is a key that fits the lock of the active site
Lock-and-Key Model
266
An inactive and an enzyme without its non protein moiety
Apoenzyme
267
268
Is an active enzyme with its non protein component
Holoenzyme
269
Is a non-protein chemical compound that is bound to an enzyme and is required for catalysis
Cofactor
270
What is the 2 types of Cofactors
Coenzymes and Prosthetic groups
271
The non-protein component, loosely bound to apoenzyme by non-covalent bond
Coenzyme (Vitamins or compound derived from vitamins)
272
The non-protein component, tightly bound to the apoenzyme by covalent bonds
Prosthetic group
273
True or False:
Enzymes may recognize and catalyze:
- Group of substrate
- single similar substrate
- any type of bond
False:
Enzymes may recognize and catalyze:
- a single substrate
- a group of similar substrate
- particular type of bond
274
Type of Enzyme Specificity:
- catalyzes one type of reaction for a single substrate
- ex urease catalyzes only the hydrolysis of urea
Absolute
275
Type of Enzyme Specificity:
- catalyzes one type of reaction for similar substances
- ex Hexokinase adds a phosphate group to hexoses
Group
276
Type of Enzyme Specificity:
- Catalyze one type of reaction for a specific type of bond
- ex Chymotrypsin catalyzes the hydrolysis of peptide bonds
Linkage
277
- All chemical reaction require some amount of this to get them started
- it is first push to start reaction
Activation Energy or Energy of Activation
278
Mechanism of Action of Enzymes increases reaction rates by decreasing the Activation energy. Meaning they are ______
Inversely proportional
279
- the active site is flexible, not rigid
- the shape of the enzyme, active site, and substrate adjust to maximize the fit, which improves catalysis
- there is a greater range of substrate specificity
- this model is more consistent with a wider range of enzymes
Induced Fit Model
280
True or False:
Step by step of enzyme-substrate complex (reaction mechanism) is:
- Enzyme and Substrate combine to form complex
- a transition state will occur and an enzyme-product complex is formed
- the enzyme and product separate
True
281
Factor that affects Enzyme Activity including:
- extreme temperature are the most dangerous and may denature the enzyme
- pH 6-8
- substrate concentration
Environmental Conditions
282
Factor that affects Enzyme Activity including:
- inorganic substances are sometimes need for proper enzymatic activity
Cofactors and Coenzymes
283
The temp at which enzymatic reaction occur fastest
Optimum temperature (normal body temp at 37 )
284
True or False:
The rate of reaction increases as substrate concentration increases
True
285
True or False:
Maximum activity occurs when the enzyme is not saturated
False: Maximum activity occurs when the enzyme is not saturated
286
- has a structure like the substrate
- competes with the substrate for the active site
- has its effect reversed by increasing substrate concentration
Reversible Competitive inhibition
287
- has a structure different than the substrate
- distorts the shape of the enzyme, which alters the shape of the active site
-prevents the binding of the substrate
-cannot have its effect reversed by adding more substrate
Noncompetitive Inhibition
288
Six Functional Classes:
EC 1 -
EC 2 -
EC 3 -
EC 4 -
EC 5-
EC 6 -
EC 1 - Oxidoreductases
EC 2 - Transferases
EC 3 - Hydrolases
EC 4 - Lyases
EC 5- Isomerases
EC 6 - Ligases
289
Each enzyme has a classification number consisting of ___ digits
4
290
True or False
The name of an enzyme in many cases end in -ase and the name describes the function of the enzyme
True
291
(Not sure if correct pagkaintindi q dio) The four digits of classification number for enzymes consist of:
1st number -
2nd number -
3rd number -
4th number -
1st number - Class (Transferase)
2nd number - Subclass (Transfer of ___)
3rd number - Sub-sub class ( Acceptor)
4th number - Specific Name
292
A functional class that catalyze group transfer reactions
EC 2 - Transferases
293
A functional class that:
- catalyze the hydrolysis of various bonds and add water across a bond
- catalyze hydrolysis where water is the acceptor of the transferred group ( esterases. peptidases glycosidases)
EC 3 - Hydrolases
294
A functional class that:
- cleave various bonds by means other than hydrolysis and oxidation
- can be through addition of water, ammonia or carbon dioxide across double bonds, or remove these elements to produce double bonds
- ex fumarase, carbonic anhydrase
EC 4 - Lyases
295
A functional class that:
- catalyze isomerization changes within a single molecule
- carry out many kinds of isomerization ( L to D isomerization and mutase reactions)
EC - Isomerases
296
A functional class that:
- join two molecules with covalent bonds Catalyze reactions in which two chemical groups are joined with the use of energy from ATP
- Ex. Acetyl - CoA Carboxylase, Glutamine synthetase
EC - Ligases (synthetases)
297
- organic compounds
- human body can't synthesize in enough amounts
- needed in micro and milligram quantities
- Essential for proper functioning of the body
Vitamins
298
Identify the Vitamin:
- co-substrate in the formation of structural protein collagen
-involved in metabolism of certain amino acids
- 100 mg/ day saturates all body tissues
- is required in collagen synthesis, healing of wounds
Vitamin C
299
Identify the Vitamin:
- Include Thiamin, Riboflavin, Niacin, Folate, Pantothenic acid, Biotin
- Are components of coenzymes
Vitamin B
300
Identify the Vitamin: (4)
- Involved in plasma membrane processes
- More hydrocarbon like with fewer functional groups
Vitamin A, D, E, K
301
Identify the Vitamin:
- Has role in vision
- 3 forms are active in the body
- Derived from b-carotine
- needed in synthesis of RNA
Functions include:
- Vision
-Regulating cell differentiation
- Maintenance of the healthy epithelial tissues via epithelial tissue differentiation
- Reproduction and Growth
Vitamin A
302
Identify the Vitamin:
- two forms active in the body
- sunshine vitamin: synthesized by uv light from sun
- controls correct ratio of Ca and P for bone mineralization
- As a hormone it promotes Ca and P absorption in intestine
Vitamin D
303
Identify the Vitamin:
- Four forms of Vitamin
- Alpha - tocopherol is the most active biological active form of this vitamin
- peanut oils, green and leafy vegetables and whole grain products
- antioxidant
Vitamin E
304
Identify the Vitamin:
- two major forms
- 1 is found in dark green, leafy vegetables
- 2 is synthesized by bacteria that grow in colon
- active in the formation of proteins involved in regulating blood clotting
Vitamin K
305
Is an active enzyme that consists of only protein
Simple Enzyme
306
Many enzymes are active only when they combine with ______ such as metal ions or small molecules
Cofactor
307
Is a cofactor that is a small organic molecule such as a vitamin and prepares the active site for catalytic activity
Coenzyme
308
Identify the Vitamin:
- soluble in aqueous solutions
-cofactors for many enzymes
- not stored in the body
Water-soluble vitamins
309
Identify the Vitamin:
- Vitamins A, D, E, and K
- Soluble in lipids but not in aqueous solutions
- important in vision, bone formation, antioxidants, and blood clotting
- stored in the body
Fat-soluble Vitamins
310
Identify the Vitamin:
- was the first B vitamin identified
- is part of the coenzyme thiamin pyrophosphate
- is used to decarboxylate a -keto carboxylic acids
- sources are liver, yeast, whole grain, cereal, and milk
Thiamin (B1)
311
Identify the Vitamin:
- is found in the coenzymes flavin adenine dinucleotide and flavin mononucleotide
- is needed for good vision and healthy skin
sources are liver, chicken, eggs, green leafy vegetables, dairy foods
Riboflavin (B2)
312
Identify the Vitamin:
- is part of the coenzyme
nicotinamide adenine
dinucleotide involved in oxidation-reduction reactions
- Sources are brewer’s yeast,
chicken, beef, fish, liver, brown
rice, and whole grains
Niacin (B3)
313
Identify the Vitamin:
- Is part of coenzyme A needed for energy production as well as glucose and cholesterol synthesis
- Is found in salmon, meat, eggs, whole grains, and
vegetables
Pantothenic Acid (B5)
314
Identify the Vitamin:
- is required in the transamination of amino acids and
decarboxylation of carboxylic acids.
- Sources are meat, liver, fish, nuts, whole grains, spinach
Pyridoxine and pyridoxal (b6)
315
Identify the Vitamin:
- Consists of four pyrrole rings
with a Co2+.
- Is a coenzyme for enzymes
that transfer methyl groups
and produce red blood cells
Cobalamin (B12)
316
Identify the Vitamin:
- Consists of pyrimidine, p-aminobenzoic acid, and
glutamate
- used in the transfer of
methyl groups and the synthesis of nucleic acids
Folic Acid (Folate)
317
Nucleic
suko na q d2
