Biochemistry 1st Quarter 1st Year PDF

BIOCHEMISTRY 1ST QUARTER | 1ST SEMESTER | 1ST YEAR groups present, PROTEINS LINKS hydrogen-bonding ability, and chemical reactivity PP...

BIOCHEMISTRY 1ST QUARTER | 1ST SEMESTER | 1ST YEAR groups present, PROTEINS LINKS hydrogen-bonding ability, and chemical reactivity PPT LECTURE LINK: >700 amino acids are known https://drive.google.com/file/d/1UeUpOGPBFB TGRX4lXgb4NF25VesDHqv9/view ARTICLE 1 LINK: https://drive.google.com/file/d/1spTZu2cFKoPJ 5atBaM8c8Bgit8GTHQGv/view?usp=drive_lin k STANDARD AMINO ACIDS ARTICLE 2 LINK: 20 α-amino acids normally found in https://drive.google.com/file/d/1-jAw1vko7riIod proteins ro5ps_7P4e5Om38l16/view?usp=drive_link Divided based on the properties of PROTEINS R-groups CHARACTERISTICS OF PROTEINS Nonpolar amino acids: Contain one amino group, one carboxyl PROTEIN group, and a nonpolar side Naturally-occurring, unbranched chain polymer in which the monomer units ❖ Hydrophobic - Not are amino acids attracted to water Most abundant substance in cells after molecules water ❖ Found in the interior of Account for about 15% of a cell’s proteins, where there is overall mass no polarity Elemental composition - Carbon(C), Polar amino acids: Hydrophilic hydrogen (H), nitrogen (N), oxygen (O), ❖ Types - Polar neutral, and sulfur (S) polar acidic, and polar Average nitrogen content is basic 15.4% by mass POLAR AMINO ACIDS Contain iron(Fe), phosphorus(P), and Polar neutral: Contain polar but other metals in certain specialized neutral side chains proteins Six amino acids belong to this AMINO ACIDS: THE BUILDING BLOCKS FOR category PROTEINS Polar acidic: Contain a carboxyl group AMINO ACIDS apart of the side chains Containbothanamino(—NH2) and a Two amino acids belong to this carboxyl (—COOH) group category α-amino acids: Amino acids in which Polar basic: Contain an amino group the amino group and the carboxyl apart of the side chain group are attached to the - carbon Three amino acids belong to this atom category Side chains (R) - Vary in size, shape, charge, acidity, functional BIOCHEMISTRY 1ST QUARTER | 1ST SEMESTER | 1ST YEAR NOMENCLATURE Three-letter abbreviations are used for naming standard amino acids Abbreviations are the first three letters of the amino acid’s name ❖ Exceptions: Isoleucine (Ile), tryptophan (Trp), ESSENTIAL AMINO ACIDS asparagine (Asn), and Standard amino acids needed for glutamine (Gln) protein synthesis and must be One-letter symbols - Used for obtained from dietary sources comparing amino acid Types of dietary proteins - sequences of proteins Complete, incomplete, and ❖ Usually the first letter of complementary the name ❖ When more than one amino acid has the same letter, the most abundant amino acid gets the 1st letter 20 STANDARD AMINO ACIDS CHIRALITY AND AMINO ACIDS Four different groups are attached to the α-carbon atom in all of the standard amino acids Exception: In glycine, the R-group is hydrogen 19 of the 20 standard amino acids contain chiral center Molecules with chiral centers exhibit enantiomerism (left- and right-handed forms) Amino acids found in nature and in proteins are ʟ isomers Exceptions: Some bacteria BIOCHEMISTRY 1ST QUARTER | 1ST SEMESTER | 1ST YEAR Monosaccharides prefer ᴅ Equilibrium shifts with change isomers in pH Rules for drawing Fischer projection formulas for amino acid structures —COOH group is placed at the top of the projection formula R group is placed at the bottom, positions the carbon chain vertically —NH2 groupisplacedina horizontal position NH2 ontheleft-ʟ isomer ISOELECTRIC POINT (pl) NH2 ontheright-ᴅ isomer pH at which an amino acid exists in its zwitterion form - Carries zero net charge Different amino acids have different isoelectric points ACID-BASE PROPERTIES OF AMINO ACIDS CYSTEINE: A CHEMICALLY UNIQUE AMINO In pure form, amino acids are white ACID crystalline solids Standard amino acid that has a side Decompose before they melt chain that contains a sulfhydryl group Not very soluble in water (—SH group) α-amino acids exist as zwitterions in Sulfhydryl group imparts solution and in solid state cysteine a unique chemical Zwitterions: Molecules with property positive charge on one atom Cysteine, in the presence of mild and negative charge on another, oxidizing agents, dimerizes to form a but have no net charge cystine molecule ❖ Carboxyl groups give up Cystine contains two cysteine protons to produce a residues linked via a covalent negatively charged disulfide bond species ❖ Amino groups accept protons to produce a positively charged species Amino acid forms in solution Zwitterions, positive ion, and negative ion BIOCHEMISTRY 1ST QUARTER | 1ST SEMESTER | 1ST YEAR PEPTIDES -yl suffix replaces the -ine or -ic NATURE OF THE PEPTIDE BOND acid ending of the amino acid name, except for tryptophan, for Under proper conditions, amino acids which -yl is added to the name can bond together to produce a Amino acid naming sequence begins peptide chain at the N-terminal amino acid residue Peptide: Unbranched chain of Example: Ala-leu-gly has the IUPAC amino acids name of alanylleucylglycine ❖ Dipeptide - Compound containing two amino ISOMERIC PEPTIDES acids Peptides that contain the same amino ❖ Oligopeptide - Peptide acids but present in different order are with 10 to 20 amino acid different molecules (constitutional residues isomers) with different properties ❖ Polypeptide: Long For example, two different unbranched chain of dipeptides can be formed from amino acids – Reaction is one molecule of alanine and between the amino glycine group of one amino acid Number of possible isomeric peptides and the carboxyl group of increases rapidly as the length of the another amino acid peptide chain increases Length of the amino acid chain can vary from a few amino acids to BIOCHEMICALLY IMPORTANT SMALL hundreds of amino acids PEPTIDES Peptide bonds: Covalent bonds SMALL PEPTIDE HORMONES between amino acids in a Best-known peptide hormones - peptide Oxytocin and vasopressin Every peptide hasan N-terminal end Produced by the pituitary gland and a C- terminal end Hormones are nonapeptides (nine amino acid residues) ❖ Have six of the residues held in the form of a loop by a disulfide bond formed from the PEPTIDE NOMENCLATURE interaction of two C-terminal amino acid residue keeps cysteine residues its full amino acid name All of the other amino acid residues have names that end in -yl BIOCHEMISTRY 1ST QUARTER | 1ST SEMESTER | 1ST YEAR Specific definition - Peptide in which at least 40 amino acid residues are present The terms polypeptide and protein are used interchangeably to describe a SMALL PEPTIDE NEUROTRANSMITTERS protein Several proteins have >10,000 Enkephalins are polypeptides amino acid residues neurotransmitters produced by the Common proteins contain brain 400–500 amino acid residues Bind receptor sites in the brain Small proteins contain 40–100 to reduce pain amino acid residues Best-known enkephalins More than one polypeptide chain Met-enkephalin: maybe present in a protein Tyr–Gly–Gly–Phe–Met Monomeric: Protein which Leu-enkephalin: contains one polypeptide chain Tyr–Gly–Gly–Phe–Leu Multimeric: Protein which SMALL PEPTIDE ANTIOXIDANT contains two or more Glutathione(Glu–Cys–Gly)-Tripeptidepr polypeptide chains esentin high levels in most cells PROTEIN CLASSIFICATION BASED ON Regulates oxidation–reduction CHEMICAL COMPOSITION reactions Simple protein: Protein in which only Antioxidant that protects amino acid residues are present cellular contents from oxidizing - More than one protein subunit agents such as peroxides and may be present superoxides Conjugated protein: Protein that has Unusual structural feature - Glu one or more non-amino-acid entities is bonded to Cys through the (prosthetic groups) present in its side-chain carboxyl group structure One or more polypeptide chains may be present Non-amino-acid components may be organic or inorganic May be classified further based GENERAL STRUCTURAL CHARACTERISTICS on the nature of prosthetic OF PROTEINS group(s) present PROTEIN ❖ Lipoprotein contains lipid prosthetic groups General definition - Naturally - ❖ Glycoprotein contains occurring, unbranched polymer in carbohydrate groups which the monomer units are amino acids BIOCHEMISTRY 1ST QUARTER | 1ST SEMESTER | 1ST YEAR ❖ Metalloprotein contains a DIFFERENCES IN ANIMAL AND HUMAN specific metal as its INSULIN prosthetic group PRIMARY STRUCTURE OF PROTEINS Types of structures - Primary, secondary, tertiary, and quaternary Primary structure: Order in which amino acids are linked together in a Immunological reactions gradually protein increase over time because animal Every protein has its own unique insulin is foreign to the human body amino acid sequence Human insulin produced from Frederick Sanger sequenced genetically engineered bacteria is and determined the primary available structure for the first protein IMPORTANT POINTS REGARDING PEPTIDE (insulin) in 1953 BOND GEOMETRY Primary structure of a specific protein Peptide linkages are essentially planar the same within the organism For two amino acids linked Structures of certain proteins through a peptide bond, six are similar among different atoms lie in the same plane species of animals Planar peptide linkage structure ❖ Example: Insulin from has considerable rigidity, pigs, cows, sheep, and therefore rotation of groups humans are similar but about the C—N bond is not identical hindered Amino acids are linked to each other ❖ Cis–trans isomerism is by peptide linkages possible about C—N bond ❖ Trans isomer is the preferred orientation PRIMARY STRUCTURE OF A HUMAN SECONDARY STRUCTURE OF PROTEINS MYOGLOBIN Arrangement in space adopted by the backbone portion of a protein Types - Alpha-helix (α helix) and beta- pleated sheet (β pleated sheet) Alpha-helix structure: A single protein chain adopts a shape that resembles a coiled spring (helix) Coil configuration maintained by hydrogen bonds Twist of the helix forms a right-handed, or clockwise, spiral BIOCHEMISTRY 1ST QUARTER | 1ST SEMESTER | 1ST YEAR Hydrogen bonds between C=O Types of stabilizing interactions and N—H entities are oriented observed parallel to the axis of the helix Covalent disulfide bonds All of the amino acid R groups Electrostatic attractions (salt extend outward from the spiral bridges) ❖ -There is not enough Hydrogen bonds room within the spiral Hydrophobic attractions TYPES OF STABILIZING INTERACTIONS Disulfide bonds - Covalent,strong,and involve two cysteine units Electrostatic interactions(salt bridges) - Involve the interaction between charged side chains of acidic and basic amino acids Hydrogen bonds - Can occur between amino acids with polar R groups Hydrophobic interactions - Occur when two nonpolar side chains are close to each other BETA-PLEATED SHEET STRUCTURE STABILIZING INFLUENCES THAT Two fully extended protein chain CONTRIBUTE TO THE TERTIARY segments in the same or different STRUCTURE molecules Held together by hydrogen bonds ❖ - H-bonding between chains - Inter and/or intramolecular QUATERNARY STRUCTURE OF PROTEINS Organization among the various TERTIARY STRUCTURE OF PROTEINS peptide subunits in a multimeric Overall three-dimensional shape of a protein protein Highest level of protein Results from the interactions between organization amino acid side chains (R groups) that Found in proteins that have two are widely separated from each other or more polypeptide chains (subunits) BIOCHEMISTRY 1ST QUARTER | 1ST SEMESTER | 1ST YEAR ❖ Subunitsareindependent Kills microorganisms by ofeachotherandnot denaturation of proteins covalently bonded to A fever above 106°F is dangerous each other Denatures and inactivates the Contain even number of body’s enzymes, which function subunits as catalysts PROTEIN HYDROLYSIS PROTEIN CLASSIFICATION BASED ON Reverseofpeptidebondformation SHAPE Results in the regeneration of an Fibrous proteins: Protein molecules amine and carboxylic acid with elongated shape functional groups One dimension is much longer Protein digestion - than the others Enzyme-catalyzed hydrolysis Generally insoluble in water ❖ Free amino acids Have a single type of secondary produced are absorbed structure into the bloodstream and Tend to have simple, regular, transported to the liver for and linear structures the synthesis of new Aggregate together to form proteins macromolecular structures Hydrolysis of cellular proteins to amino ❖ Example: Hair, nails, etc acids is an ongoing process, as the Globular proteins: Protein molecules body resynthesizes needed molecules with peptide chains folded into and tissue spherical or globular shapes PROTEIN DENATURATION Water soluble substances - Partial or complete disorganization of Hydrophobic amino acid proteins characteristic residues are in the protein core three-dimensional shape Membrane proteins: Occurs due to disruption of its Proteinsassociatedwith cell secondary, tertiary, and membranes quaternary structural Insoluble in water - Hydrophobic interactions amino acid residues are on the Coagulation - Precipitation out of surface biochemical solution of denatured FIBROUS PROTEINS: α-KERATIN protein Provide protective coating for Example: Egg white is a organisms concentrated solution of protein Majorproteinconstituentofhair,feather, albumin, which forms a jelly nails, horns, and turtle shells when heated Mainly made of hydrophobic amino Cooking denatures proteins acid residues Makes it easy for enzymes in our Individualmoleculesarealmostwhollyhe body to hydrolyze/digest protein lical BIOCHEMISTRY 1ST QUARTER | 1ST SEMESTER | 1ST YEAR Pairs of these helices twine PROTEIN CLASSIFICATION BASED ON about one another to produce a FUNCTION coiled coil Proteins play crucial roles in Coiling at higher levels produces biochemical processes the strength associated with Diversity of functions exhibited by -keratin-containing proteins proteins exceeds the role of other FIBROUS PROTEINS: COLLAGEN biochemical molecules Most abundant protein in humans(30% Functional versatility of proteins stems of total body protein) from their ability to: Major structural material in tendons, Bind small molecules ligaments, blood vessels, and skin specifically and strongly Organic component of bones and Bind other proteins and form teeth fiber-like structures Predominant structure- Triple-helix Integrate into cell membranes Glycine and proline help Catalytic proteins are known for their maintain the structure of the role as catalysts triple-helix Almost every chemical reaction GLOBULAR PROTEINS: HEMOGLOBIN in the body is driven by an An oxygen-carrier molecule in blood enzyme Transports oxygen from lungs to Defense proteins are central tissues functioning of the body’s immune Tetramer(four polypeptide chains) system Each subunit contains a heme Known as immunoglobulins or group antibodies ❖ One molecule can Transport proteins bind to small transport up to four biomolecules, transport them to other oxygen molecules at time locations in the body, and release them ❖ Iron atom in heme as needed interacts with oxygen Messenger proteins transmit signals to GLOBULAR PROTEINS: MYOGLOBIN coordinate biochemical processes between different cells, tissues, and Oxygen-storage molecule in muscles organs Monomer Examples: Insulin, glucagon, and Consists of a single peptide human growth hormone chain and one heme unit Contractile proteins are necessary for One molecule carries one O2 all forms of movement molecule Examples: Actin and myosin Has a higher affinity for oxygen than Human reproduction depends hemoglobin on the movement of sperm, Oxygen stored in myoglobin molecules which is possible because of serves as a reserve source for working contractile proteins muscles when oxygen demand exceeds its supply BIOCHEMISTRY 1ST QUARTER | 1ST SEMESTER | 1ST YEAR Structural proteins confer stiffness and Buffer proteins are part of the system rigidity by which the acid–base balance within Collagen is a component of body fluids is maintained cartilage Fluid-balance proteins maintain fluid α-keratin gives mechanical balance between blood and strength and protective surrounding tissue covering to hair, nails, feathers, GLYCOPROTEINS and hooves Contain carbohydrates or carbohydrate Transmembrane proteins control derivatives in addition to amino acids movement of small molecules and Examples: Proteins in cell ions through the cell membrane membrane and blood group Have channels to help markers of the ABO system molecules enter and exit the cell Collagen Selective, allow passage of only Structural feature - one type of molecule or ion 4-hydroxyproline (5%) and 5- Storage proteins bind(and store) small hydroxylysine (1%) molecules Carbohydrate units are attached Ferritin - Iron-storage protein by glycosidic linkages to which saves iron for use in the collagen at its 5-hydroxylysine biosynthesis of new hemoglobin residues molecules ❖ Direct the assembly of Myoglobin - Oxygen-storage collagen triple helices protein present in muscle into collagen fibrils Regulatory proteins are found IMMUNOGLOBULINS embedded in the exterior surface of Produced as a protective response to cell membranes the invasion of microorganisms or Act as sites for receptor foreign molecules molecules Serve as antibodies combat invasion of Bind to enzymes (catalytic the body by antigens proteins) and control enzymatic Antigen: Foreign substance, action such as a bacterium or virus, Nutrient proteins are important in the that invades the human body early stages of life, from embryo to Antibody: Biochemical infant molecule that counteracts a Examples: Casein (found in milk) specific antigen and ovalbumin (found in egg Bonding of an antigen to variable white) regions of immunoglobulins occurs ❖ Milk provides through hydrophobic interactions, immunological dipole–dipole interactions, and protection for hydrogen bonds mammalian young BIOCHEMISTRY 1ST QUARTER | 1ST SEMESTER | 1ST YEAR LIPOPROTEINS Conjugated proteins that contain lipids and amino acids Help suspend lipids and transports them through the bloodstream Classes of plasma lipoproteins Chylomicrons - Transport dietary triacylglycerols from intestine to the liver and to adipose tissue Very-low-density lipoproteins (VLDL) - Transport triacylglycerols synthesized in the liver to adipose tissue Low-density lipoproteins (LDL) - Transport cholesterol synthesized in the liver to cells throughout the body High-density lipoproteins (HDL) - Collect excess cholesterol from body tissues and transport it back to the liver for degradation to bile acids