Lesson 2: Amino acids (Chapter 3)

Alanine

(Ala), [A] -hydrophobic side chains

Lipids

1. They do not dissolve in water, but organic substances 2. Have a hydrophilic head and a hydrophobic tail ^Liupid bilayer ex./ fatty acids have a hydrophilic head and hydrophobic tail

Over what pH range will glycine have charge between +0.5 and -0.5

AT the net charge of 0 which will have the pka of 6.1

Arginine

(Arg), [R] -charged side chains

Asparagine

(Asn), [N] -Polar (uncharged) side chains

Aspartate

(Asp), [D] -charged side chains

cysteine

(Cys), [C] -hydrophobic side chains

glutamine

(Gln), [Q] -Polar (uncharged) side chains

Glutamate

(Glu), [E] -charged side chains

Glycine

(Gly), [G] -hydrophobic side chains

isoleucine

(Ile), [I] -hydrophobic side chains

Leucine

(Leu), [L] -hydrophobic side chains

Lysine

(Lys), [K] -charged side chains

methionine

(Met), [M] -hydrophobic side chains

proline

(Pro), [P] -hydrophobic side chains

serine

(Ser), [S] -Polar (uncharged) side chains

Threonine

(Thr), [T] -Polar (uncharged) side chains

Tryptophan

(Trp), [W] -hydrophobic side chains

tyrosine

(Tyr), [Y] -hydrophobic side chains

Valine

(Val), [V] -hydrophobic side chains

Aromatic R groups

-Phenylalanine (Phe,F) -Tyrosine (Tyr, Y) -Tryptophan (Trp, W) 1. Phenylalanine has a hydrophobic benzyl side chain 2. Tyrosine is structurally similar to phenylalanine except that the para hydrogen of phenylalanine is replaced by the tyrosine by a hydroxyl group making tyrosiner a phenol -The hydroxyl group is ionizable by remains its hydrogen under normal physiological conditions

Chirality

1. 19 of 20 common amino acids the alpha carbon is chiral, or asymmetrical -glycine is the exception

What amino acids side chains are either acidic or basic?

1. Aspartate: exists as aspartic acid, which has a carboxylic acid group in its side chain -Water aspartic acid can react to produce aspartate 2. Glutamate: when it is a solid it exists as glutamic acid, which has a carboxylic acid group in its side chain. - In water, glutamic acid can react to produce glutamate 3. Lysine: As a solid, the side chain is uncharged -the side chain of lysine contains an amine group and since amine groups are basic, when lysine is dissolved in water, the amine group can react to produce a charges ammonium group 4. Arginine: when it is a solid, its side chain is uncharged *lysine and arginine have side chains that contain a basic group that can react with water to produce a cationic group 5. Histidine: when it is a solid, the side chain is uncharged -Like lysine and arginine, has a side chain that contains a basic group that can react with water to produce a cationic group ****The acidic and basic side chains of amino acids have their OWN pka values

Aliphatic R groups

1. Glycine (Gly,G): the smallest amino acid -Not chiral -Hydrophobic 2. Saturated (hydrophobic) amino acids -Leucine (Leu, L) -alanine (Ala, A) -valine (Val, V) -isoleucine (Ile, I) ^play an important role in establishing and maintaining the three dimensional structures of proteins because of their tendency to cluster away from water 3. Proline (cyclic) is also aliphatic but its ring structure makes it less hydrophobic (stacking ability)

Functions of Proteins

1. Many proteins function, the biochemical catalyst 2. Some proteins bind other molecules for storage and transport ex./ hemoglobin binds and transports O2 and CO2 in red blood cells and other proteins bind to fatty acids 3. Several types of proteins function as pore s and channels in membranes, allowing the passage of small, charges molecules 4. Some proteins, such as tubulin, actin, and collagen, provide support and shape to cells and hence to tissues and organs 5. Assemblies of proteins can do mechanical work ex./ movement with flagella -separation of chromosomes at moitisis -the constriction of muscles 6. Many proteins play a role in the cell -some are involved in translation whereas others play a role in regulation gene expression by binding to nucleic acids 7. some proteins are hormones, and regulate biochemical activities in target cells or tissues ^other proteins act as receptors of hormones 8. Proteins on the surface can act as receptors for various ligands and as modifiers of cell-cell interactions 9. Some proteins have highly specialized functions ex./ antibodies defend vertebrates against bacterial infections, and toxins produced by bacteria ^can kill larger organisms

Hydropathy

1. The ability to determine the hydrophobic or hydrophilic nature of an amino acid 2. Is important determinant of protein folding because hydrophobic side chains tend to be clustered in the interior of a protein and hydrophilic residues are usually found on the surface 3. hydropathy measurements of free amino acids can be successfully used to predict which segments of membrane-spanning proteins are likely to be embedded in a hydrophobic lipid bilayer

Knowing ionic states of side chains

1. The charged state influences protein folding and the three dimensional structure of proteins 2. Understanding the ionic properties of amino acids in the active site of an enzyme helps one understand enzyme mechanisms 3. The titration of alanine shows that is has two ionizable groups a. As more base is added to the solution of acid, the titration curve exhibits two pka values at pH 2.4 and pH 9.9 ^each pka value is associated with a buffering zone where the pH of the solution changes relatively little when more base is added

Titration of amino acids with basic and acidic side chains

1. Titration starts by cleaving the proton at the spot with the lowest pka -1.5+ net charge 2. Titration then cleaves the proton at the spot with the second lowest pka - 0.5+ net charge 3. Titration then cleaves the proton with the highest pka -0.5- net charge *isoelectric point is found by taking the average of the pkas of the 2 spots that give a combined net charge of 0 -DON'T calculate the average of all the combined pka values -DON'T average the 1st and last values ^isolelectric point will either be between the first 2 values or the last 2 values

Types of lipids

1. fatty acids 2. steroids: sex hormones, cholesterol 3. Waxes: waxes in plants and animals ex./ beeswax and wax in your ears

Ionization of Amino Acids

1. physical properties of amino acids influence the ionic states a. ionizable groups are associated with pKa and pH based on which the concentrations of protonated and unprotonated forms are equal 2. Every amino acid has at least 2 pka values corresponding to the ionization

Enzyme modified amino acids

1. several common amino acids are chemically modifies to produce biologically important amines -They are synthesized by an enzyme-catalyzed reaction that include decarboxylation and deamination ex./ histamine (constriction of certain blood vessels), Epineophrine (adrenaline in medulla of the brain), and Tyrosine (thyroid hormones go through biosynthesis)

At what pH will glycine have a net charge of -0.5

9.8

What is the pH value that corresponds to the halfway point between these two numbers?

9.8+ 2.4/2= 6.1

Lake Magadi in Kenya is an extreme environment. The water in Lake Magadi has a pH level of around 11, which is toxic to most living things. Even so, extremophile bacteria have been found living in the lake. Which structure would be expected to predominate in Lake Magadi?

Amino Acid anions would predominate in the lake because the lake is extremely basic. Amino acid anions predominate in basic solutions

If a bike is missing all of its parts except for the middle structure, how is it like an amino acid?

Amino acids are all the same when they are missing their most distinct and important parts, AKA the side chains

Amino Acids

Amino acids are the "building blocks" of proteins -The amino acids found in living things are molecules that contain both a carboxylic group as well as an amine functional group attached to the second carbon atom -All amino acids have the same backbone ^The backbone is a carboxylic acid group and an amine group -Are incorporated in any protein in any and every cell -The amine group of one amino acid and the carboxylate group of another amino acid are condensed during protein synthesis to form amide linkages

Amino acid anions

Amino acids with a negative charge on one end of the amino acid -predominates in highly basic solutions

Amino Acid Cation

Amino acids with a positive charge on one end of the amino acid -Predominate in highly acidic solutions -both the carboxylic acid and Amine are protonated, so the amine group becomes an ammonium group ^Since both groups are protonated , both groups become weak acids within titration

Which group or groups in an amino acid are charged at highly acidic pH levels?

Ammonium ion (A.A. cation)

Zwitterion

An amino acid with a negatively charged carboxylic acid group on one end and a positively charged ammonium group on the other end -When amino acids neutralize each others -In water, amino acids generally exist as zwitterions *An un-ionized form of an amino acid molecule is generally NOT present in an aqueous solution of an amino acid * amino acids usually exist as zwitterions in the solid state -Has properties of both an acid and a base *predominates at neutral pH levels

The stomach of a human has a pH between 1 and 2. Draw the structure of serine at the pH level you'd expect to find in the stomach

An amino cation because they predominate in highly acidic solutions

Amino acid stereoisomers

Are nonsuperimposible mirror images called enantiomers -Two of the 19 chiral amino acids, isoleucine and threonine, have two chiral carbon atoms *So, they can have 4 stereoisomers

Negatively charged side groups and their amide derivatives

Aspartate (Asp, D) and glutamate (Glu, E) are dicarboxylic amino acids and have negatively charged hydrophilic side chains at pH 7 1. Aspartate possesses a b-carboxyl group and glutamate possesses a g-carboxyl group 2. under most physiological conditions they are both found as conjugate bases -have suffix -ate 3. glutamate is MSG a food enhancer 4. They have uncharges polar highly polar side chains due to the amide groups

Based on the titration of glycine, over the pH range will glycine have a net charge greater than the magnitude of +0.5?

At a pH less than 2.4

The pH levels in most regions of the body are slightly basic. In the body, do you think aspartic acid will exist mainly as unreacted aspartic acid molecules or as aspartate ions?

Because the body is basic, it would act as a buffer when ab acid is present so aspartate ion

Which group or groups in an amino acid are charged at highly basic pH levels?

Carboxylate ion (A.A. anion)

Titration

Cation-> zwitterion-> anion ^1+ net charge ^0 net charge ^-1 net charge *After the first titration, there is a solution with half cation form and half zwitterion form Then, the pka=pH and the net charge is +0.5 *After the second titration, there is a solution that is half anion and half zwitterion Then, the pka=pH and the net charge is -0.5 *Between the first and third titration, the zwitterion predominates and the net charge is 0 *When the pka=pH the concentrations are equal

The pka of the basic group in the side chain of the arginine molecule is 12.5. At physiological pH levels, will the side chain of arginine molecule exist mainly in the charged form or in the uncharged form?

Charged form because the acid will deprotonate in the basic environment

Nucleotides

Consist of: 1. a 5 carbon sugar 2. a heterocyclic nitrogenous base 3. at least one phosphate group -The nitrogenous bases of nucleotides belong to two families known as purines and pyrimidines ^The base is joined to c-1 of the sugar and the phosphate group is attached to one of the other sugar carbons (usually c-5)

ATP

Consists of Adenine moiety linked to ribosomes by a glycosidic bonds *The linkage between the ribose and the group is a phosphoester linkage because it includes a carbon and a phosphorus atom -IS the central carrier of energy in living things ^The potential energy associated with the hydrolysis of ATP can be used directly in biochemical reactions or coupled to a reaction in a less obvious way

Net charge

Depends on the proportions of the different forms of the amino acid that are present -The cationic form of an amino acid has a net charge of 1+ - The zwitterion form has a net charge of 0 ' -The anionic form has a net charge of -1 *if more than one form of the amino acid is present, the overall net charge depends on the proportions of the different forms present ^50% of the amino acids molecules in a solution and in the cationic form and 50% are in the zwitterion form; the net charge of the amino acid will be +0.5 ^If the amino acid molecule in a solution has 50% in the anionic form and 50% in the zwitterion form, the net charge of the amino acid will be -0.5

Positively charged R groups

Histidine (His, H), lysine (Lys, K) and arginine (Arg, R) have hydrophilic side chains that are nitrogenous 1. The side chain of histidine an imidazole ring substitute -The protonated form of the ring is called an imidazolium ion ion -At pH of 7 most histidines are neutral ^When there is a positive side chain present the pH does lower 2. Lysine: a diamino acid with both a and e amino groups -The e- amino group exists as an alkylammonium ion at a neutral pH and confers a positive charge in proteins 3. Arginine: the most basic of the 20 amino acids because its side chain guanidinium ion is protonated under all conditions normally found within a cell -Arginine side chains also contribute positive charges in proteins

The side carboxylic acid group of aspartate acid has a pka of 3.9 (acidic). When dissolved in a solution buffered to a pH of 7.0 (neutral), do you think this compound will exist mainly as unreacted aspartic acid molecules of aspartate ion?

It would exist as an ion because the side chain would deprotonate leaving the ion (charged) side chain

Stereochemical designation

L:laevus; left D: dextros; right -The 19 chiral amino acids used in the assembly of proteins are all of the L configuration, although a few of the D amino acids occur in nature *most living organisms do not select L amino acids from a mixture because only L amino acids are synthesized in sufficient quantities. ^The predominance of L amino acids in modern species is due to the evolution of metabolic pathways that produce L amino acids and NOT D amino acids

Polypeptides

Linear polypeptides fold into a distinct three-dimensional shape -This shape is determined largely by the sequence of its amino acid residues ^This sequence information is encoded in the gene for the protein ^This linear representation is called Fischer projection >Shows a ring like it is going off the page -A polypeptide chain is represented as a combination of wires, helical ribbons, and broad arrows Ring: Hawthorn projection -Rotated 90 degrees -The ring form is most commonly shown as a Hawthorn Projection ^This representation is a more accurate way of depicting the actual structure if the ribose *A change in the projections does not cause a break of covalent bonds. The two basic forms of carbohydrate structures, linear and ring forms, do require the breaking and forming of covalent bonds

of the amino acids aspartate, glutamate, lysine, arginine, and histidine, which will have charged side chains in the stomach?

Lysine, arginine, and histidine will be charged because they will protonate in the acidic environment

R side groups containing sulfur

Methionine (Met,M) and cytosine (Cys, C) are the two amino acids 1. Mehtionine contains a nonpolar methyl thioether group in its side chain and this makes it one of the more hydrophobic amino acids -Plays a special role in protein synthesis because it is almost always the first amino acid in a growing polypeptide chain 2. Cysteine: The structure of cysteine resembles alanine with a hydrogen replacing the sulfhydryl group -Although the side chain is quite hydrophobic, it is also very reactive (forms weak hydrogen bonds with oxygen and nitrogen via the sulfhydryl group) -The two cysteine side chains must be adjacent in three dimensional space in order to form the disulfide bond bu they don't have to be close together in the amino acid sequence of the polypeptide chain

For a proline cation, the pka of the carboxylic acid group is 2.0, while the pka of the ammonium group is 10.6. What is the isoelectric point of proline?

PI=10.6+2.0/2= 6.3 *you just find the average!

Phenylalanine

Phe, F, nonpolar

Henderson-Hasselbalch Equation

Tells the relationship between the pH of a solution, the pka of a solution, and the proportions of deprotonated to protonated acid molecules in the solution

R

The R within a structure stands for the "rest" of the molecule -It determines properties of different amino acids AKA side chain -Side chains effect water solubility *H2O will NOT react with a hydrophobic side chain

At a pH level far above the isoelectric point of a given amino acid, which d you think would predominate, the cationic form or the anionic form?

The anion

At a pH level far below the isoelectric point of a given amino acid, which do you think would predominate, the cationic form of the amino acid or the anionic form?

The cation

Peptide bond

The combination of a carbon atom of an amino residue and the nitrogen atom of another

Metabolism

The degradation and synthesis of organic compounds to produce energy to be extracted, stores, and used

Cathode

The electrode with the negative charge - cations are attracted to cathodes

Anode

The electrode with the positive charge -Anions are attracted to anodes

Suppose the aqueous solution of glycine at the pH=11 is placed in the electric field (similar to that of an electrolytic cell). To which electrode (the cathode or the anode) would the amino acid molecule move?

The glycine molecule would move toward the anode

Suppose an aqueous solution of glycine at pH= 3 is placed in an electric field (similar to that in the electrolytic cell). To which electrode would the amino acid molecules move?

The glycine molecule would move toward the cathode

Suppose the aqueous solution of glycine at the isoelectric point is placed in the electric field (similar to that of an electrolytic cell). To which electrode (the cathode or the anode) would the amino acid molecule move?

The glycine molecule would not move toward either electrode

Purines

The major purines are: 1. Adenine (A) 2. guanine (G)

Pyrimidines

The major pyrimidines are: 1. cytosine (C) 2. Thymine (T) 3. uracil (U)

Isoelectric point

The point at which the net charge of the amino acid is 0 (zwitterion) -AT this point the zwitterion form of the amino acid predominates -At this point the cationic and anionic forms of the amino acid will have equal concentrations (neutral) - The isoelectric point is halfway between the pka value of the carboxylic acid group of the amino acid and the pka value of the amine group ' ^Since different amino acids have different pka values for these groups, different amino acids also have different isoelectric points

Glycine

The simplest amino acid -has a side chain or R group with a hydrogen atom

Fatty acids

The simplest forms of lipids 1. Carboxylate at one end attached to a long carbon tail -part of larger molecules (glycerophospholipids)

Ribonucleotides

The sugar is ribose -in deoxyribonucleotides, it is a derivative of deoxyribose

What form of glycine would you expect to predominate at the 6.1 pH level?

The zwitterion

RNA

There are 3 kinds of RNA molecules: 1. Messanger RNA (mRNA): involved directly in the transfer of info from DNA to protein 2. Transfer RNA (tRNA): smaller molecule required for protein synthesis 3. rRNA: ribosomal RNA: major component of RNA

Bio-genetics

a branch of thermodynamics that deal with energy change

Which group or groups in an amino acid are charged when the amino acid is in its zwitterionic form?

ammonium ion and carboxylate ion

At what pH level will glycine have a net charge of +0.5?

at exactly 2.4

Stereoisomers

compounds that have: 1. The same molecular formula 2. different arrangement, or configuration, in space

The pH of blood in a healthy person is 7.4 Of the amino acids aspartate, glutamate, lysine, arginine, and histidine which will have charged side chains in the blood stream.

glutamate, lysine, and arginine because they are basic and would protonate in a slightly acidic environment

Over what pH range will glycine have a net charge greater than -0.5?

greater than 9.8

What is the isoelectric point of glycine?

pH= 6.1 because the charge is 0

What would be the net charge of glycine at this pH level>

the net charge would be 0 at the zwitterion form of glycine with the pH of 6.1

Given that amines are weak based which of the following do you think ammonium ions (such as methylammonium ion) would be?

weak acids (conjugate acid)

Given that carboxylic acids are weak acids, which of the following do you think carboxylate ions (such as the acetate ion) would be?

weak bases (conjugate base)