Demonyo Flashcards
- 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
Amino Acid
The amino acids commonly dealt with are?
a- amino acids
The name amino acid suggests that these structures have what?
Amine and Acid group ( amino acid and carboxylic acid group)
How many different groups are attached to the central carbon of amino acids have and what type of carbon is it?
4 different groups and chiral carbon
What arrangement does amino acid have?
Tetrahedral arrangement
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?
2 unique spatial arrangements and 2 possible isomers
The position of the carbon atom in amino acids is? And what are attached to this carbon atom?
Alpha (a), NH2 and -COOH group
Amino acids have _______ structure that vary in size, shape, charge, activity, functional groups present, hydrogen-bonding ability, and chemical reactivity
R = side chain
How many amino acids are known?
More than 700
Based on common “R” groups, there are how many standard amino acids?
20 (The Mighty Twenty)
Nearly all amino acids in biochemistry are of the ______ -form which is the opposite of _______ which nearly always occur as the D-isomer
L-form ( L for Life), sugars
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
True
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.
Fischer’s convention
True or False:
The non-ionic form occurs in significant amounts in aqueous solutions
False: The non-ionic form does not occur in significant amounts in aqueous solutions
The zwitterionic form predominates at normal pH of what?
pH= 7.4
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
True
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
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
The amino acid residues in protein molecules are exclusively what?
L-isomers
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 _______.
L-isomers, stereospecific
The 20 common amino acids are a-amino acids they have a ______ group and _____ group
Carboxyl group, amino group
The 20 common amino acids differ from each other in their ______ or ______
Side chain or R groups
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.
residues, constituents
What are the uncommon amino acids?
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
Uncommon amino acids are _____ not found in proteins
Derivatives
( L-Chloramphenicol, Epinephrine, Histamine, Ornithine, Citrulline, Serotonin, gamma Aminobutyric acid (GABA) , b-Alanine)
What are the Biologically Active Amino Acid Derivatives
gamma Aminobutyric acid (GABA), Histamine, Dopamine, Thyroxine
Uncommon Amino Acid function as a derivative of Proline, found in plant cell wall proteins
4-hydroxyproline
Uncommon Amino Acid function found in collagen, a fibrous protein in connective tissues
5-hydroxylsine
Uncommon Amino Acid function is a constituent of myosin, a contractile of muscles
6-N0 methyllysine
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
Uncommon Amino Acid function as a derivative of four Lysine residue, which is found in the fibrous protein elastin
Desmosine
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
Uncommon Amino Acid function as key intermediates (metabolites) in the biosynthesis of arganine and in the urea cycle
Ornithine and Citrulline
All amino acids show optical activity except for ______
Glycine (no chiral carbon)
This isomer has the ability to rotate the plane of polarized light to the right
Dextrorotatory (+)
This isomer has the ability to rotate the plane of polarized light to the left
Levorotatory (-)
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.
When an amino acid is dissolved in water it exist in solution as a ______ or _______
Dipolar ion or Zwitterion
Zwitterion is German for
Hybrid Ion
Zwitterion can act as an ____ as a _____ and an ____ as a _____
acid, proton donor, base, proton acceptor
Substances like Zwitterion having dual nature are amphoteric and are often called what?
Ampholytes
Titration has a plot that has 2 distinct stages corresponding to?
Deprotonation pf two different groups on glycine
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
Convenient notations for proton concentration and the equilibrium constant for ionization, respectively
pH and pK
Measure of the tendency of a group to give up a proton
pK
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
What are the nonpolar, all phatic R groups in the Mighty 20?
Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine
What are the Aromatic R groups in the Mighty 20?
Phenylalanine, Tyrosine, Tryptophan
What are the Positively charged R groups in the Mighty 20?
Lysine, Arginine, Histidine
What are the polar, uncharged R groups in the Mighty 20?
Serine, Threonine, Cysteine, Asparagine, Glutamine
What are the negatively charged R groups in the Mighty 20?
Aspartate, Glutamate
In chemical reactions most often the amino acid will be drawn with the carboxyl group as?
-COOH
In chemical reactions most often the amino acid will be drawn with the amine group as?
NH2
Appearance of molecules at what physiological pH?
pH= 7.4
What is considered the more correct form to draw amino acids?
Zwitterion
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)
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)
A change in a cell’s membrane potential that makes it more negative. Opposite of depolarization
Hyperpolarization
Glycine can be modified by addition of what?
A fatty acid (myristate - 14 carbons)
It is the most important amino acid to learn
Glutamate (E, Glu)
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
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)
Region of the brain which influences memory
Hippocampus
Asparagine can be converted into Aspartate by ________
Hydrolyzing the amide bond
The R groups of both Asparagine and Glutamine are quite______, having a slightly positive charge
polar
Relationship between the molecules and the sequence
Q END
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
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
True or False:
If the protein retains its function, then these amino acids are NOT critical for protein’s functions and vice versa
True
Ketone formation from amino acids and a very important reaction that some amino acid can undergo in the body is removal of ammonia
Deamination
The ___________ is formed when ammonia is removed from a-carbon and replaced with a ketone group
a- ketoglutaric acid
Removing _______ from Glutamate and replacing it with a _________, the carbon skeleton of Glutamate can be metabolized for energy
Ammonia, keto group
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)
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
- 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
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)
-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
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
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)
-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)
_____ 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
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
The enzyme responsible in the synthesis of Tyrosine from Phenylalanine is
Phenylalanine hydroxylase (PAH)
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
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
An enzyme in the synthesis of Catecholamines that added to the meta position to the benzene ring of Tyrosine
Hydroxyl group
An enzyme in the synthesis of Catecholamines that has O standing for OH
Dihydroxyphenylalanine (DOPA)
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
In the synthesis of Catecholamines the conversion of DOPA to Dopamine by?
decarboxylic DOPA
- The amine form of dihydroxyphenylalanine
- neurotransmitter in the brain
- controls the pressure of blood through the kidneys
Dopamine
Are used to stimulate Dopamine release to control attention deficit disorder - used for social purposes because they quickly create dependence and schizoid behavior
Amphetamines
Dopamine is converted to Noradrenaline by hydroxylating the _______
B-carbon
Another name for Noradrenaline is ________ and similarly Adrenaline is called _________
Norepinephrine , Epinephrine
- 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
Inner part of the adrenal gland, controls hormones that help a person cope with physical and emotional stress
Adrenal medulla
Noradrenaline is converted to Adrenaline by adding a ______ group to the _____ group of Noradrenaline
Methyl, Amine
Ethanol with an amine group and phenyl group
Ethanolamine
In forming Adrenaline, a methyl group is transferred to the ______
Nitrogen
Enzyme that describes the reaction, and the N indicates that the transfer was to the nitrogen group
Phenylethanolamine – N – methyl transferase (PNMT)
Identify the amino acid:
- similar to Tyrosine but you can see a W in its ring structure
Tryptophan (W, TRP)
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
- 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)
Is an inhibitor of serotonin receptors, The use of this substance causes vivid hallucinations
Lysergic acid diethylamine (LSD)
A drug which activates serotonin receptors in the brain, had been used to give people a sense of well being
Prozac
Glutamic acid is decarboxylated at the ________
a-carbon
CH3CH2CH2COOH
Butyric acid
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
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
Decarboxylation of glutamic acid by the enzyme ______ forms y-amino butyric acid (GABA)
Glutamic acid decarboxylase
-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
Enhances the action of GABA
Benzodiazapines (Valium)
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)
- 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
Identify the amino acid: (2)
- have hydroxyl group in their r-group
Serine (S, SER)
Threonine (T, THR)
Serine is _____ with a hydroxyl group attached to it. For Threonine, with a hydroxyl and methyl group added to it
Alanine
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
True or False:
In Glycosylation of Amino Acids ether bonds can be formed by condensing it with another hydroxyl group
True
When sugar, having multiple hydroxyl groups, can be attached to proteins at Serine or Threonine by what type of ether bond?
O-glycosidic bond
Beside Serine or Threonine, what is another amino acid to which sugars can attach is? Where n-glycosidic bond is formed
Asparagine
These 2 amino acids both contain sulfur
Cysteine (C, CYS) and Methionine (M, MET)
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)
What is removed when oxidation of 2 cysteine occurs
Removal of Hydrogen
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
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)
A rare deficiency when present, may lead to reduced growth rate, along with liver damage, muscle loss, edema, skin lesions, and lethargy
Methionine deficiency
