What makes a strong acid?HCL is a much stronger acid than acetic acid:

Ka = 107

MeCOOH Ka = 1.74 x 10-5

This is to do with the strength (stability) of the conjugate base, Cl- is not strong enough to deprotonate H3O+, but acetate is. In other words, the chloride ion is inherently more stable than the acetate ion.• An acid’s pKa depends on the stability of its conjugate base.- The stronger the acid HA, the weaker its conjugate base A-- The stronger the base A-, the weaker the conjugate acid HA.• For example:- HI with pKa of -10, is a strong enough acid to protonate most functional groups. It’s conjugate base, I- is not really basic.- Methyl lithium is a powerful base, which behaves as CH3-. The conjugate acid is CH4, which isn’t acidic with pKa = 48.Peptide Bond Formation•Condensation rxn• Between –NH2 of n residue and –COOH of n+1 residue. • Rigid, inflexible. • Loss of 1 water molecule.The peptide bond has a barrier to rotation. The resonance structure explains this, and bond length comparisons are consistent with partial double bond character. As a consequence, the atoms are all constrained to lie in the same plane. The peptide bond is planar. But the planar conformation can be accommodated in two alternate forms denoted as trans and cis. The more stable trans form. The cis form is less stable because of its greater steric repulsion between the Cα atoms and their attached groups. Peptides and Proteins• Peptides and protein made up from long chains of amino acids via peptide bonds.• There are two types of protein structures: fibrous (elongated proteins not soluble in water and providing structural support), and globular (spherical proteins soluble in water and have specific function in the immune system and metabolism).The structural proteinsPrimary Structure • The sequence of amino acids • The peptide bond is rigid and can not move due to its partial double bond character of C-N bond. • To write peptide and protein always from N-terminal to C-terminal.Secondary Structure • Regular elements such as α-helices and β- sheets, which are formed between relatively small parts of the protein sequence. • They are determined by the local conformation of the polypeptide backbone. α-helix • Most abundant; ~35% of residues in a protein • Repetitive secondary structure • 1.5 Å rise in 100 rotation • C=Oof i forms H bonds with N-H of residue i+4 • Intra-strand H bonding • C=O groups are parallel to the axis; side chains point away from the axis • Polar ends present at surfaces • Amphipathic • All N-H and CO are H-bonded, except first N-H and last COβ-sheet• Other major structural element • Basic unit is a β-strand • Usually 5-10 Residues • Can be parallel or anti-parallel based on the relative directions of interacting β-strands • “Pleated” appearanceAnother important interaction is the formation of hydrogen bonds between the carbonyl oxygen and amide hydrogens on adjacent regions of the peptide backbone:β-sheet (with primary structure)(a) antiparallel and (b) parallel β-sheet. Blue and white beads represent the positively charged (Arg) and hydrophobic residues, respectively, and the polar residue (Tyr) and Gly residues are denoted by green beads. Solid lines indicate the disulfide bonds between Cys residues, and dotted lines indicate the backbone hydrogen bond (H-bond).β-pleated sheetThe chains are folded so that they lie alongside each other. All that means is that next-door chains are heading in opposite directions. Given the way this particular folding happens, that would seem to be inevitable.Some of the amino acids have hydrophobic side chains; others have hydrophilic side chains. The different AA like to interact with each other, and the protein chain folds to maximize these interactions. Also one important way a protein folds is such that the hydrophobic AA will be in the interior of the folded protein, and the hydrophilic AA will be on the surface. In addition to the backbone hydrogen bonds that permit the formation of secondary structures, other interactions between the side chains of the various AA govern the overall the folded structure of the protein.

Tertiary Structure• Describe the complete three-dimensional structure of whole polypeptide chain. • Include the relationship of different domains formed by the proteins’ secondary structure and the interactions of the amino acid substituent R group.• The specific folding of a protein is only thermodynamically stable within a restricted range of environmental parameters, e.g., Temperature, pH, ionic strengthQuaternary Structure• Quaternary structure is the 3-Dimensional arrangement of multiple folded protein or coiling protein molecules in a multi-subunit complex by hydrogen bond, electrostatic attraction and sulfide bridge.When functional unit consist of two or more structural domains, we speak of the “quaternary structure” of the protein.It is the linear sequence of amino acids in a protein that determines the 3-dimensional folded structure of that protein.Another way to state this concept is to say that “proteins fold to their thermodynamically most stable state”; ie, each particular folded protein has maximized all its particular combinations of possible hydrogen bonds, electrostatic interactions, hydrophobic interactions, etc, in its final folded shape:

To demonstrated that the linear sequence of amino acids in a protein determines the folded structure of that protein. Using a chemical called urea, he unfolded a protein called Ribonuclease-A, and then reduced its internal disulfide bonds with mercaptoethanol. (Disulfide bonds stabilize the folded protein in its original shape.) When the urea and mercaptoethanol is removed, the ribonuclease “renatured” back, and regained full enzymatic activity. Based on experiments, the information for the complete, correct folding of a protein is in the linear AA sequence of that protein.One of the impt functions of proteins is to serve as catalysts for chemical reactions necessary for life. Proteins that functions as chemical catalysts are called “enzymes.” The complex surface of a folded protein creates crevices that can bind other molecules. The interior of these crevices is lined with the chemically reactive side chains of the various AA. Consequently, proteins are excellent and very specific chemical catalysts. By stablilizing the transition state of the reaction, enzymes lower the activation energy.Synthesis of proteins• Transcription • Translation • Post-translational modification: phosphorylation, acetylation, methylation, glycosylationPost-Translational ModificationsProteins are involved in cellular signaling and metabolic regulation. They are subject to biological modifications. Almost all protein sequences are post-translationally modified and 200 types of modifications of amino acid residues are known. The dynamic nature of the proteomeThe proteome of the cell is changing. Various extra-cellular, and other signals activate pathways of proteins. A key mechanism of protein activation is post-translational modification These pathways may lead to other genes being switched on or off MS is key to probing the proteome and detecting PTMSDegradation of Proteins• Proteins are hold tgt by H bonding, electrostatic attraction and sulfide bridges, which are very sensitive to its chemical and physical environment. • The change of temperature, pH or ionic strength disrupts these interactions, causing protein denaturation • Protein loses its activity once its normal shape is lost.

• Cystic fibrosis. A defect in the cystic fibrosis transmembrane conductance regulator (CFTR) gene causes cystic fibrosis (CF). A protein made by this gene controls the movement of the water and salt in and out of the body's cells. Genes in ppl with CF incorrectly code proteins. This causes thick, sticky mucus and salty sweat.• Neurofibromatosis. Neurofibromatosis is caused by point mutations in the Neurofibromin 1 or 2 gene.•Sickle-cell anemia. is caused by a point mutation in the β-globin chain of haemoglobin, causing the hydrophilic amino acid glutamic acid to b replaced with the hydrophobic amino acid valine at the 6th position.Disease Caused by Mutation• Cancer. Point mutations in multiple tumor suppressor proteins cause cancer. • A novel assay, Fast parallel proteolysis (FASTpp), might help swift screening of specific stability defects of specific proteins in individual cancer patients. • FASTpp measures the quantity of protein that resists digestion under various conditions.• A thermostable protease is used, which cleaves specifically atexposed hydrophobic residues.•The FASTpp assay combines the thermal unfolding, specificity of a thermostable protease for the unfolded fraction with the separation power of SDS-PAGE.• Due to this combination, FASTpp can detect changes in the fraction folded over a large physico-chemical range of conditions including temperatures up to 85°C, pH 6-9, presence or absence of the whole cytosolic proteome.Specific diseases caused by insertions/deletions• Tay-Sachs Disease. Tay-Sachs Disease is a fatal disease affecting the central nervous system. • Symptoms do not appear until approximately 6 months of age. The child becomes blind, deaf, unable to swallow, atrophied, and paralytic.• Mutations in the β-hexosaminidase A (Hex A) gene are known to affect the onset of Tay-Sachs.•CancerInsertion/deletion mutations cause colorectal cancer and other cancers with microsatellite instability.• While environmental factors contribute to the progression of prostate cancer, genetic component also will.• There are over 500 mutations on chromosome 17 that seem to play a role in the development of breast and ovarian cancer in the BRCA1 gene, many of which are Insertion/deletion.SNP and DISEASE• One study even identified two genes in which particular variants can slow the onset of AIDS, demonstrating the potential of this approach for understanding why people vary in their susceptibility to infectious diseases.• New technologies that are slashing the costs of sequencing and genome analyses will make possible the simultaneous genome-wide search for SNPs and other DNA alterations in individuals.Proteomics• Proteomics is the large-scale study of proteins, particularly their structures and functions.• Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells.• The proteome consists of the entire complement of proteins, including the modifications made to a particular set of proteins, produced by an organism or system.• This will vary with time and distinct requirements, or stresses, that a cell or organism undergoes.Number of Proteins in Human• Analyzing genome sequences alone will not lead to new therapies to fight human diseases.• Whereas the human genome has approximately 35,000 genes and theoretically the ability to encode up to 35,000 corresponding proteins.• The occurrence of alternative RNA splicing and posttranslational modifications (PTM), such as phosphorylations, acetylations, and glycosylations, or protein cleavages may increase the expression of proteins to 500,000–1,000,000.• The proteins reflect more accurately the intrinsic genetic mechanisms of the cell and their impact on the microenvironment, since they are the effectors and characterizeProteomics in Biomedical Research• Biomarkers are biomolecules that is associated with an increased risk of the disease and serve as indicators of biological and pathological processes or physiological and pharmacological responses to a drug.•Proteins that are impt indicators of physiological or pathological states may contribute to the early diagnosis of disease, which may provide a basis for identifying the underlying mechanism of disease development.• These differentially expressed proteins in serum have become an impt in monitoring the state for disease.• Comprehensive proteome of human serum fluid with high accuracy and availability has the potential to open new doors for disease biomarker discovery and for disease diagnostics.Proteomics in Cancer Diagnostics• Allied to genomics, proteomics technologies is valuable for identifying new markers that improve screening, early diagnosis, prognosis and prediction of therapeutic response or toxicity, as well as the identification of new therapeutic targets.• Studies on the proteome in cancer have used tissue samples and biological fluids including serum, plasma, saliva, and cerebrospinal fluid in search for the detection of diagnostic, predictive, and prognostic biomarkers.• Among the proteomics tools, mass spectrometry (MS) is one of the most used techniques for identifying unknown proteins. The mass spectrometer is an analytic instrument capable of converting neutral molecules into gaseous ions and separating them according to their mass-to-charge (m/z) ratio by using an electromagnetic field.Tandem mass spectrometry (MS/MS) offers information about specific ions. In this approach, distinct ions are selected based on their m/z from the first round of MS and are fragmented by a number of methods of dissociation, such as colliding the ions with a stream of inert gas, as in collision-induced dissociation or higher energy collision dissociation. Other methods of ion fragmentation include electron-transfer dissociation and electron-capture dissociation . These fragments are then separated based on their individual m/z ratios in another round of MS. MS/MS is commonly used to sequence proteins and oligonucleotides, as the fragments can be used to match predicted peptide or nucleic acid sequences that are found in databases. These sequence fragments can then be organized in silico into full-length sequence predictions.A sample is injected into the mass spectrometer, ionized and accelerated and then analyzed by mass spectrometry (MS1). Ions from the MS1 spectra are then selectively fragmented and analyzed by mass spectrometry (MS2) to give the spectra for the ion fragments.Sugars, amino acids and nucleotides can polymerize to form macromolecules called polysaccharides, proteins and nucleic acids. When sugars, amino acids and nucleotides polymerize, water is released. In the process of hydrolysis, a water molecule reacts with the bond linking the monomers. A monomer is broken off, resulting in a shorter polymer. Sugars are defined by the presence of an carbonyl group and multiple hydroxyl groups. Sugars like glucose can exist in both linear and ring forms. Like many organic molecules, sugars are “chiral” molecules- they can exist as right-handed (“D”) or left handed (L”) isomers. Right-handed (‘D’) forms predominate in cells.

When glucose forms a ring, the hydroxyl group attached to the number 1 carbon is locked into one of two alternate positions: either below the plane of the ring, or above it. These two ring forms of glucose are called alpha (α) (down) and beta (β) (up), respectively:Examples of sugar polymers: Starch is polymerized glucose, in which α-glucose monomers are polymerized via a 1-4 linkage. Cellulose, on the other hand, is polymerized glucose, in which β-glucose monomers are polymerized via a 1-4 linkage. (Animals don’t have enzymes to catalyze the hydrolysis of the β-glycosidic link in cellulose!)Starch Structure: Starch is made from chains of α-glucose

molecules. These are linked by glycosidic bonds. Starch is found in many parts of a plant as starch grains.Why is starch a good molecule for storage in plants?It is insoluble, so doesn’t draw water into cells by osmosis. Wont easily diffuse out of cells because it is insoluble, It can be stored in a small space because the tight coils make it compact, Can be easily hydrolyzed to give α-glucose , which can be used in respiration, They are a reserve form of sugar for times when free sugar In diet is absent. Starches called amylose(an unbranched α-glucose polymer) and pectin(a branched polymer) are the storage polysaccharides found in plants.Significance of Starch•Green plants use starch as their energy store. An exception is the family Asteraceae, where starch is replace by fructan inulin. Photosynthesis, plants use light energy to produce glucose from CO2.Starch •The glucose is stored mainly in the form of starch granules, in plastids such as chloroplasts and especially amyloplasts.• Toward the end of the growing season, starch accumulates in twigs of trees near the buds.• Fruit, seeds, rhizomes, and tubers store starch to prepare for the next growing season. From Glucose to Starch• Glucose is soluble in water, binds with water and then takes up much space and is osmotically active.• Glucose in the form of starch, is not soluble, therefore osmotically inactive and can be stored much more compactly.•Glucose molecules are bound in starch by the easily hydrolyzed alpha bonds. The same type of bond is found in the animal reserve polysaccharide glycogen.• This is in contrast to many structural polysaccharides such as chitin, cellulose and peptidoglycan, which are bound by beta bonds and are much more resistant to hydrolysis.

Production of glucose 6-phosphate• Glucose 6-phosphate is produced by phosphorylation of glucose on the sixth carbon.• This is catalyzed by the enzyme hexokinase in most cells, and, in higher animals, glucokinase in certain cells, most notably liver cells. One molecule of ATP is consumed in this reaction.• The major reason for the immediate phosphorylation of glucose is to prevent diffusion out of the cell. The phosphorylation adds a charged phosphate grp so the glucose 6-phosphate cannot easily cross the cell membrane.Two Forms of StarchAround 30%, tightlypacked structure,more resistant toDigestion. Amylose can Exist in Helical Forms.

Around 70%,highlybranched structure,being formed of 2,000to 200,000 glucoseunits can be quicklydegradedAmylopectin on the other hand is a branched-chain polysaccharide where in addition to the α-1,4-glycosidic bonds there is the occasional α-1,6-glycosidic bonds. Branching occurs about every 24-30 glucose units. Helical structure of amylopectin is disrupted by branching.Glycogen• A multibranched polysaccharide of glucose that is a form of energy storage in animals and fungi.• In humans, glycogen is made and stored in the cells of the liver and the muscles, and functions as the secondary longterm energy storage (primary energy stores being fats).•Glycogen is the analogue of starch, having a similar structure to amylopectin, but more branched and compact.• Glycogen is found in the form of granules in the cytoplasm in many cell types, and plays an impt role in the glucose cycle.• Glycogen forms an energy reserve that can be quickly mobilized to meet the need for glucose, but is less compact than the energy reserves of triglycerides.Glycogen is a branched biopolymer consisting of linear chains of glucose residues with further chains branching off every 10 glucoses. Glucoses are linked together linearly by α(1→4) glycosidic bonds. Branches are linked to the chains and are branched off by α(1→6) glycosidic bonds.CelluloseMade of β-glucose. To form glycosidic links, each β-glucose molecule is rotated 180o compared to the one next to it. Has straight, unbranched chains that run parallel to one another. Hydrogen bond links the chains. The β-glycosidic link between glucose molecules in cellulose results in a polymer that forms a long linear strand. The hydroxyl groups of one cellulose molecule are free to H bond with the hydroxyls of adjacent molecules. In plants, the long strands of cellulose bundle together to form microfibrils. Bundles of microfibrils form plant cell walls.• So many hydrogen bonds help to strength cellulose• This makes cellulose a good structural material, hence its use in plant cell walls to aid rigidity• cellulose does this by grouping together to form microfibrils• Cellulose prevents cell bursting, so they are turgid when full with water. This helps support stemsOther important structural polysaccharides are chitin and peptidoglycanBoth composed of polymers of “amino sugars, such as N-acetyl-glucosamine (chitin) or [N-acetyl-glucosamine plus N-acetyl-muramic acid] (Peptidoglycan).A mesh of peptidoglycan chains, crosslinked by covalent bonds, make up the tough and flexible bacterial cell wall. (antibiotics poison the bacterial enzymes that synthesize cell wall)Chitin (mono monomer) (Parallel strands joined by hydrogen bonds)• Chitin is a long-chain polymer of a Nacetylglucosamine, a derivative of glucose.• The main component of the cell walls of fungi, the exoskeletons of arthropods such ascrustaceans and insects, the radulae of molluscs, and the beaks and internal shells of cephalopods.•The structure of chitin is comparable to the polysaccharide cellulose, forming crystallinenanofibrils. In terms of function, it may be compared to the protein keratin.•It form covalent β-1,4 linkages (similar linkages between glucose units forming cellulose).• Chitin is cellulose with one hydroxyl group replaced with an acetyl amine group.Peptidoglycan (Parallel strands joined by peptide bonds)• also known as murein, is a polymer consisting of sugars and amino acids that forms a mesh-like layer outside the plasma membrane of most bacteria, forming the cell wall.• The sugar component consists of alternating residues of β-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid. Attached to the N-acetylmuramic acid is a peptide chain of three to five amino acids. The peptide chain can be crosslinked to the peptide chain of another strand forming the 3D mesh-like layer.• Peptidoglycan serves a structural role in the bacterial cell wall, giving structural strength, as well as counteracting the osmotic pressure of the cytoplasm.• peptidoglycan helps maintain the structural strength of the cell.•Peptidoglycan is also involved in binary fission during bacterial cell reproduction.•The peptidoglycan layer is substantially thicker in Gram-positive bacteria than in Gram-negative bacteria, with the attachment of the S-layer.• Peptidoglycan forms around 90% of the dry weight of Gram-positive bacteria but only 10% of Gram-negative strains.Meso-diaminopimelic acid (DAP) for Gram Positive

Nucleic Acids• Two classes of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)• Cells use DNA to determine and control the synthesis of proteins with the help of mRNA.• mRNA dictates the synthesis of protein from amino acids delivered by transfer RNA.• Made up from three components: nucleobases, sugars and phosphoric acid.If U were used in DNA, then when the C in a G:C base pair deaminated to become U, the G:C base pair would become a G:U base pair. A G:U base pair is detected by the ongoing DNA-repair enzymes. Since U is not used in DNA, any U formed can be recognized as illegitimate and have to come from mutated a C; it is cut out by repair enzymes and replaced with C.The nucleotide (Base + sugar + phosphate)Note: to distinguish between sugar and base, positions in the sugar are designated with a prime ( ’)

A strand of DNA is made by attaching one nucleotide onto a second one, and then a third one on the second one, etc. DNA is synthesize in beginning at the 5’ end and progressing towards the 3’ end. Consequently, the convention when writing out the nucleotide sequence of a nucleic acid is to begin with the 5’ nucleotide on the left and end with the 3’ nucleotide on the right

Other shorthand notation for DNA sequence: 5’- TCA – 3’Two ‘complementart strands of DNA can specifically pair with each other, beacuse the bases form specific hydrogen bond.Double helix structureDNA contains major and minor grooves and many DNA-binding, gene regulatory proteins prefer to bind nucleotides located in the major groove.1. DNA molecule consists of two polynucleotide chains in a double helix configuration.2. The two strands are anti-parallel.3. The sugar-phosphate backbone is on the outside of the helix, bases are on the inside.4. A always pairs with T; G always pairs with C. The sequence of one strand (5’ → 3’) dictates thesequence of the other strand.5’ GCATGCAATGCCGAATG 3’3’ CGTACGTTACGGCTTAC 5’5. 2nm wide diameter: perfect for purine-pyrimidine bond.6. Base pairs are 3.4 Å apart: a complete 360º turn of the helix is 34 Å, which equals 10 base pairs.7. The helix has a major groove and a minor groove.8. When heated or when deviating from physiological conditions, hydrogen bonds between the two DNA strands are cleaved and the strands are separated from each other to form single string DNA (ssDNA).RNAThe structure of RNA is similar to that of DNA except:1. The nucleotide subunits have ribose, rather than deoxyribose as the sugar2. Uridine is substituted for thymidine3. RNA is generally found as a single-stranded molecule in cells.3-D structure of RNA• GCAU instead of GCAT• Due to the additional –OH group on the ribose sugar, steric hindrance is too great to allow for the formation of a double strand. So, RNA exists as a single stranded molecule.• RNA can loop back to form internal self base-paired structures, called “stem-loop structures”Transfer RNA Contains a Modified Base Ψ from UridineIt is found in tRNA, found with thymidine and cytosine in the TΨC arm and is one of the invariant regions of tRNA. It is expected to play a role in association with aminoacyl transferases during their interaction with tRNA, and hence in the initiation of translation. Recent studies suggest it may offer protection from radiation.RNA molecules can form complex structures with pockets and clefts on their surface. Also the purine and pyrimidine nitrogenous bases contain chemically reactive functional groups that can catalyze chemical reactions.Proteins Proteins are synthesized beginning with the ‘amino terminal’ amino acid and finishing with the ‘carboxy terminal’ amino acid. And when writing out the amino acid sequence of a protein, the convention is the amino terminus on the left , the carboxy terminus on the right.

The generalized structure of an amino acid: Amino acids are chiral molecules (can exist as right or left handed forms). But whereas in the case of sugar, the right-handed form predominates in cells, in the case of amino acids, it is the left-handed form that is found in cells.Amino Acids• Names for amino acids are abbreviated to either three symbol or a one symbol short form.• 20 amino acids found in living organisms.• Building blocks of peptide and protiens• Linear chain of amino acids forms peptide/protein.• Peptides - Small peptides with fewer than about ten amino acids are called oligopeptides• and peptides with more than ten amino acids are termed polypeptides.• Proteins – Chain of amino acids with molecular weights of more than 10,000 (50–100 amino acids) are usually termed proteins.• R group varies, thus, can be classified based on R-group.• Glycine is the simplest amino acid. Side chain R=H.• Unique because Gly α-carbon is achiral.Chiral: when a molecule is not superimposable on its mirror imageZwitterionic character, pK and pI• At the pH under physiological conditions (pH 6-7), the amino group (pK 8.7~10.7) is ionized to NH3+ and the carboxyl group (pK 1.8~2.5) is ionized to –COO-. So, at physiological pH,. amino acids are zwitterionic• pK is the dissociation constant for H+.• pI (isoelectric point) - It is a specific pH value at which aa exhibits no net charge.• It can be estimated via the Henderson- Hasselbalch equation pI = ½ (pKNH3++pKCOOH), where pKi and pKj are the dissociation constants of the ionization groups involved.• At its isoelectric point, amino acid remains stationary under an applied electric field.Acid-Base PropertiespH and pKa• The pH of a solution is a measure of the acidity of the solution. It is defined as Where ] is the concentration of hydronium ions in the solution.• Consequently, the pH of a solution depends on two things-The concentration of the solution – if we have two solutions of the same acid, the more concentrated solution will have more free H3O+ ions and therefore a lower pH.-The acid in question – if we have two equally concentrated solution of acid, the solution of a strong acid will have a lower pH than that of a weak acid, because it is fully dissociated and therefore produces more H3O+ ions. HCL for example, is completely dissociated.Therefore, we see that pH does not measure the strength of an acid, but the acidity of a given solution.• The pH of water is 7. This means that a solution of pure water has 10-7 mol/dm3 of hydronium ions. This can only happen through the autoprotolysis of water:

This mean that in water,• To be clearer about what a strong and weak acid is, we look at the reaction:

The position of the equilibrium is measured by the equilibrium constant Now, in dilute solutions of acid, stays roughly constant at about 56 mol/dm3. we therefore define a new equilibrium constant – the acidity constant This is also expressed in logarithmic form are as follows: Because of the minus sign, the lower the pKa the higher the Ka and the stronger the acid.• It turns out that the pKa of an acid is the pH at which it is exactly half-dissociated. This can be shown by re-arranging the expression for Ka:

Clearly, when [AH] = [A-], pH = pKa• This information is rather useful:o At a pH above the pKa, the acid exist as A- in water, and will therefore be fairly soluble.o At a pH below the pKa, the acid exists mostly as HA in water, and will probably be less soluble.

Amino Acids: Classification based on R group • Basic amino acids • Acidic amino acids • Aliphatic amino acids • Aromatic amino acids • Hydroxyl containing amino acids• Sulfur containing amino acids• Secondary amino acids

Level Description Stabilized by:Primary The sequence of amino acids Peptide bonds

Secondary Formation of a-helices and b-pleated sheets H-bonding between peptide groups along the peptide backboneTertiary Overall three-dimensional shape

of a polypeptideBonds and other interactions between R-groups, or between R-groups and the peptide backbone

Quaternary Shape produced by combination of polypeptides

Bonds and other interactions between R-groups, and between peptide backbones of different polypeptides