Protein Structure

Peptide bond A peptide bond is formed through the reaction of the blank group of an amino acid with the blank group of another to form anblank linkage. A linear chain of amino acids, (thus called blank), can be formed by a series of such peptide bonds linking together several amino acid residues. By convention, peptide chain amino acid sequences are always written with the blank end (N-) on the left, and cblank end (C-) on the right Large side chain groups (side chains branched at the beta carbon) will result in very restricted set of available conformations. Small side chain groups will result in a much larger set of available conformations

Carboxylic, amino, amide Polypeptide amino, carboxylic

Structures of polypeptides Hierarchically analyzed structures: Primary Secondary Tertiary Quaternary structures All biological structure is dependent upon the environment - water (aqueous) or nonpolar, hydrophobic interior of membranes All structures are dynamic blank structure refers to the active, functional structure

Primary, Secondary, Tertiary, quaternary, native

Non-essential amino acids Most are made from blank or blank Cycle intermediates, plus an blank group Some non-essential amino acids require essential a.a. (BLANK AND BLANK) for their synthesis: a. Phe Tyr - OH (Reaction defective in PhenylKetonUria (PKU)) (Phe is an essential a.a.; Tyr thus becomes an essential a.a. in a PKU patients) b. Methionine (Sulfur) + Serine-OH Cysteine-SH

glycotic, citric acid, amino phe and MET

Secondary structure: motif Motif: combining secondary structural elements and producing specific geometric patterns. For example: helix turn blank in blank binding proteins, blank binding proteins

helix turn helix, calcium, dna

Deficiency of a single essential amino acid results in a negative nitrogen balance: can't make proteins with one amino acid missing!! 1. blank protein provides the best balance of essential amino acids. (2) blank are frequently low in one or more essential amino acids; vegetarians must get a proper balance of amino acids through variety of foods, nuts. (Long term vegan diet may also require supplementation with Vit. blank because it is made by microorganisms) Essential amino acids* of human: Know them! Human cannot synthesize the carbon skeletons PVT TIM HALL *: All are branched or aromatic a.a. except blank which provides Sulfur for biosynthesis, and Lys. **blank: a plentiful amino acid; hard to show a dietary requirement but humans can't synthesize it. ***blank-conditional essential: essential for growing blank, because they need so much, but not for adults because adults can make enough Arg in kidney and gut (please see the Amino Acid Metabolism II: Urea Cycle lecture).

Deficiency of a single essential amino acid results in a negative nitrogen balance: can't make proteins with one amino acid missing!! 1. Animal protein provides the best balance of essential amino acids. (2) Vegetables are frequently low in one or more essential amino acids; vegetarians must get a proper balance of amino acids through variety of foods, nuts. (Long term vegan diet may also require supplementation with Vit. B12 because it is made by microorganisms) Essential amino acids* of human: Know them! Human cannot synthesize the carbon skeletons PVT TIM HALL (Phe, Val, Thr, Trp, Ile, Met, **His, ***Arg, Leu, Lys) *: All are branched or aromatic a.a. except Met, which provides Sulfur for biosynthesis, and Lys. **His: a plentiful amino acid; hard to show a dietary requirement but humans can't synthesize it. ***Arg-conditional essential: essential for growing children, because they need so much, but not for adults because adults can make enough Arg in kidney and gut (please see the Amino Acid Metabolism II: Urea Cycle lecture).

1st Protein-Energy Malnutrition (PEM): Kwashiorkor (KW) (High carb but low protein diet) Kwashiorkor indicates an Edema due to deficient serum blank (Hypoalbuminemia) and other serum proteins. Muscle wasting: caused by lack of essential a.a., thus cannot efficiently synthesize new proteins Other symptoms include: anemia, stunted growth, skin lesions, depigmented hair, anorexia, enlarged fatty liver.

Kwashiorkor indicates an associated protein deficiency, but may have enough carbohydrates (thus enough calories serum albumin

Structure properties of Amino Acid (a.a.) L vs D Chirality of amino acid: the alpha carbon of each amino acid (except glycine) is attached to four different chemical group and thus is called a chiral or optically active carbon atom. D- and L-amino acid: when the carboxyl group is on top and the side chain is on the bottom, if the amino group is on the right, the amino acid is called D-amino acid; conversely, if the amino group is on the left, the amino acid is called L-amino acid. D- and L- of the same amino acid are mirrored images of each other. All amino acids found in mammalian proteins are Blank-amino acids.

L is the one found in all mammalian proteins

Secondary structure - alpha helix The alpha helix is a blank blank helix which places the peptide backbone in the BLANK of the spiral with the side chains radiating BLANK; every peptide -CO- group forms a BLANK bond with the -NH- group of the fourth peptide. Alpha helices are often disrupted by blank or blank blank residues usually break and introduce a bend in alpha helices The alpha helix is depicted as a cylinder in protein structure diagrams

The alpha helix is a right-handed helix which places the peptide backbone in the middle of the spiral with the side chains radiating outside; every peptide -CO- group forms a Hydrogen bond with the -NH- group of the fourth peptide. Alpha helices are often disrupted by Pro or Gly Proline residues usually break and introduce a bend in alpha helices The alpha helix is depicted as a cylinder in protein structure diagrams

Secondary structure The nearby, local, or short range blank organization of the blank chains The peptide chain backbone is always blank and has significant blank-Bonding possibilities ; backbone should be arranged to maximize the backbone blank bonds The neighboring side chains should be oriented so that blank and blank repulsions are minimized

The nearby, local, or short range conformational organization of the peptide chains The peptide chain backbone is always polar and has significant H-Bonding possibilities ; backbone should be arranged to maximize the backbone H bonds The neighboring side chains should be oriented so that steric and charge repulsions are minimized

Primary structure The BLANK BLANKsequence of a protein (or a polypeptide). Each polypeptide is a linear sequence of amino acids starting from the BLANK to the BLANK (C-terminus) Determination of the amino acid sequence: Edman degradation Mass spectrometry (Mass spec): based on the molecular mass of a.a. Sequencing the gene or the mRNA is another approach to obtain the primary structure

AA n C, Edman Degradation, (Cutting Specific Amino Acids after Labeling)

Native structure Refers to the blank/blank form of the proteins; may be a stable form or a metastable form Usually stable only within a blankrange of pH and temperature in blankenvironments blank: unfolding of a protein's secondary and tertiary structures blank the hydrolysis of peptide bonds. Denaturation of protein results the loss of blank structure and function/activity. Denaturing condition/agent (denaturant): blank, organic blank, strong acids or bases, detergents and heavy metal ions such as lead.

Active, Refers to the functional/active form of the proteins; may be a stable form or a metastable form Usually stable only within a narrow range of pH and temperature in aqueous environments Denaturation: unfolding of a protein's secondary and tertiary structures without the hydrolysis of peptide bonds. Denaturation of protein results the loss of native structure and function/activity. Denaturing condition/agent (denaturant): heat, organic solvents, strong acids or bases, detergents and heavy metal ions such as lead.

Secondary structure: beta Sheet An extended sheet like structure formed by blank or more polypeptide chains in a blank by blank orientation The -CO- groups of one strand H bond to the -NH- groups on the other strand Stretched conformation with the Cα alternately blank a little above and below the plane of the beta sheet - blank The blank blank also are alternately above and below the plane of the beta sheet The two chains forming the beta sheet may be blank or blank Antiparallel beta sheets have blank spaced and widely spaced blank bonds alternating with each other ; parallel beta sheets tend to have blankspaced H bonds. The polypeptide chains that form a beta sheet are depicted as arrows in protein structure diagrams

An extended sheet like structure formed by two or more polypeptide chains in a side by side orientation The -CO- groups of one strand H bond to the -NH- groups on the other strand Stretched conformation with the Cα alternately lying a little above and below the plane of the beta sheet - pleated The side chains also are alternately above and below the plane of the beta sheet The two chains forming the beta sheet may be 'Parallel' or 'Antiparallel' Antiparallel beta sheets have closely spaced and widely spaced H bonds alternating with each other; parallel beta sheets tend to have evenly spaced H bonds. The polypeptide chains that form a beta sheet are depicted as arrows in protein structure diagrams

Quaternary structure The relative blank in space of blank blank of multi-subunit proteins Dominated by specific blank blank interactions Hemoglobin structure: Four different subunits; Each subunit is a single polypeptide

Arrangement, Polypeptide Chains, subunit-subunit

Ionization properties of a.a-II Physiological pH=7.4. (But in stomach, pH= 2.0 to 4.) Amino group is positively charged in the protonated form (pH well below pK2); neutral in the deprotonated form (pH well above pK2) Carboxylic group is neutral in the protonated form (pH well below pK1) and negatively charged in the deprotonated form ( pH well above pK1) Amino acids become positively charged at low pH and negatively charged at high pH at near neutral pH, the carboxylic group may be negatively charged and the amino group may be positively charged , with the net charge = 0; called the zwitterionic form pH at which the net charge on the molecule is zero is called isoelectric point or pI

Faze Sentido Ja sei isso Depronate starting with the mais acidio parti. (Quandando Mudando pra um area mais basico) Zwitterionic

Identification of amino acids Amino acids react with blankto produce blue / black colored derivatives; this is used as a common detection method for proteins Amino acids can be separated and identified by blank (paper chromatography or high performance liquid chromatography, HPLC). Large polypeptides may be hydrolyzed by proteases before their amino acid compositions are identified through chromatography blank blank (MS): a.a. can be identified based on its molecular mass.

Ninhydrin Chromatography, Mass Spectrometry

Dietary proteins and protein energy malnutrition (PEM) Nitrogen (mainly from proteins) Balance: (nitrogen intake minus nitrogen losses (Nin - Nout)) blank N balance (intake > losses): growing child; pregnant woman; body builders blank (intake = losses): adult needs 0.8 g/kg/day of high quality proteins blank N balance (intake < losses): Illness, trauma, surgery, stress (stress hormones: epinephrine, cortisol) Dietary protein or essential amino acid deficiency: (1) Kwashiorkor (KW, kwä-shē-ˈȯr-kər): protein but not calorie deficient (edema) (2) Marasmus: both protein and calorie deficient (muscle wasting) (3) Anorexia nervosa: psychological eating disorder (4) Fasting, starvation (muscle protein degradation for gluconeogenesis) (5) Deficiency of a single essential amino acid

Nitrogen (mainly from proteins) Balance: (nitrogen intake minus nitrogen losses (Nin - Nout)) Positive N balance (intake > losses): growing child; pregnant woman; body builders Balanced (intake = losses): adult needs 0.8 g/kg/day of high quality proteins Negative N balance (intake < losses): Illness, trauma, surgery, stress (stress hormones: epinephrine, cortisol) Dietary protein or essential amino acid deficiency: (1) Kwashiorkor (KW, kwä-shē-ˈȯr-kər): protein but not calorie deficient (edema) (2) Marasmus: both protein and calorie deficient (muscle wasting) (3) Anorexia nervosa: psychological eating disorder (4) Fasting, starvation (muscle protein degradation for gluconeogenesis) (5) Deficiency of a single essential amino acid

Protein misfolding and related diseases blank blank blank(PCDs): are a group of diseases, in which the blank protein conformations result in cell toxicity and functional deficiency, or lead to dominant negative effects. Alzheimer's disease (AD) Huntington disease (HD) Parkinson disease (PD) Transmissible spongiform encephalopathies (TSEs) Creutzfeldt-Jacob disease in humans scrapie in sheep mad cow disease (or bovine spongiform encephalopathy) in cattle. blank: accumulation of the iblank, spontaneously aggregating proteins. Amyloids are often resistant to blank, accumulates as deposits in the cells and causes tissue/organ damage. (may contribute to the pathology of AD, HD, PD) Theblank protein can, sometimes , blank the misfolding of normal protein (Prion protein, PrP). PrP may be the causes of TSEs.

Protein misfolding and related diseases Protein Conformational Disorders (PCDs): are a group of diseases, in which the altered protein conformations result in cell toxicity and functional deficiency, or lead to dominant negative effects. Alzheimer's disease (AD) Huntington disease (HD) Parkinson disease (PD) Transmissible spongiform encephalopathies (TSEs) Creutzfeldt-Jacob disease in humans scrapie in sheep mad cow disease (or bovine spongiform encephalopathy) in cattle. Amyloids: accumulation of the insoluble, spontaneously aggregating proteins. Amyloids are often resistant to degradation, accumulates as deposits in the cells and causes tissue/organ damage. (may contribute to the pathology of AD, HD, PD) The misfolded protein can, sometimes , catalyze the misfolding of normal protein (Prion protein, PrP). PrP may be the causes of TSEs.

Tertiary structure Refers to the blank of the domains and to the final arrangement of blank in the polypeptide. Results in the overall shape of globular proteins or other shapes Stabilized by blankbonding, electrostatic blank, blank bonds Usually results in a blank interior and blankexterior in soluble proteins Often results in a blank exterior in membrane internal segments

Refers to the folding of the domains and to the final arrangement of domains in the polypeptide. Results in the overall shape of globular proteins or other shapes Stabilized by hydrogen bonding, electrostatic interactions, disulfide bonds Usually results in a hydrophobic interior and hydrophilic exterior in soluble proteins Often results in a hydrophobic exterior in membrane internal segments

Summary: interesting side chains blank blank and blank contain hydroxyl groups in their side chains; can form hydrogen bonds; may also accept phosphate groups or fatty acids to form esters blankcontains a thiol (or sulfhydryl) group which can dimmerize with another sulfhydryl to give disulfide bonds -SH + -SH -S---S- Cysteine thio may be used to bind to iron, copper or other metal ions blank and blank side chain carboxylates can bind to calcium ions blank imidazole nitrogen can bind to copper and iron Oppositely charged side chain groups such as aspartate and lysine can interact with each other through blank forces (or salt bridge) Large hydrophobic side chain groups such as leucine, isoleucine and valine can interact with each other through blank interactions Normal amino acids incorporated into proteins may be modified in the protein - for example, some lysine residues in protein may be converted to hydroxylysine; some proline residues in proteins may be converted to hydroxyproline (See Collagen Lecture).

Serine, threonine and tyrosine cystenine histidine aspartate lysine, electrostatic bridges, hydrophobic,

Stability and folding into the native structure Polypeptide chains seem to fold into the native structure even as they are being synthesized - blank folding Denaturation is rblanke under certain conditions for certain proteins (e.g., blank recovers significant activity if gently denatured and then the denaturants removed) Recovery of activity implies recovery of structure; since in the denatured condition only blank structure is present, primary structure is sufficient to fold the protein back to the native structure: blank structure often determines secondary, tertiary and quaternary structures. blank correct folding of some proteins require the help of other proteins - blank (e.g., heat shock proteins: Hsp70, Hsp90 etc).

Stability and folding into the native structure Polypeptide chains seem to fold into the native structure even as they are being synthesized - cotranslational folding Denaturation is reversible under certain conditions for certain proteins (e.g., ribonuclease recovers significant activity if gently denatured and then the denaturants removed) Recovery of activity implies recovery of structure; since in the denatured condition only primary structure is present, primary structure is sufficient to fold the protein back to the native structure: primary structure often determines secondary, tertiary and quaternary structures. Chaperons: correct folding of some proteins require the help of other proteins - chaperons (e.g., heat shock proteins: Hsp70, Hsp90 etc).

Proteins contain 20 common amino acids Nonpolar, aliphatic side chains: GAVLIMP Glaciers in Alaska Victoriously Locate Isolated Prowlers methodically Nonpolar, aromatic side chains: PT POOF TWYKES TyIRLERS Polar, uncharged side chains: STTCTAG Sticky tart ties cut tylers art gun Polar, charged side chains: Basic: ALH ANGRY LEMURS HIT HARD- Positively charged at physiological pH Acidic: ATTORNEY GENERAL - Negatively charged at physiological pH Selenocysteine is amino acid #21

onpolar, aliphatic side chains: Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline Nonpolar, aromatic side chains: Phenylalanine, Tryptophan Polar, uncharged side chains: Serine, Threonine, Tyrosine (Tyrosine is aromatic), Cysteine, Asparagine, Glutamine. Polar, charged side chains: Basic: Lysine, Arginine, Histidine - Positively charged at physiological pH Acidic: Aspartic acid, Glutamic acid - Negatively charged at physiological pH Selenocysteine is amino acid #21

Secondary structure: bends In all proteins, regions of α-helix and β-sheet structure are connected to each other through short sequences where the peptide conformation takes a turn or makes a bend These bends are usually near the blank of the proteins Many of the peptide residues within the bend may hydrogen bond to the blank rather than to other peptide residues The blank nature of the bend region and common lack of structure makes these regions susceptible to blank blank and blank are often found in the bends

surface, water, exposed, proteolysis, proline, glycine