Biochemistry VIBiochemistry VI

Proteins & EnzymesProteins & Enzymes

ProteinsProteins

Large, complex organic moleculesLarge, complex organic molecules

Made of smaller monomers: Amino AcidsMade of smaller monomers: Amino Acids

Categories of proteins:Categories of proteins:– Structural ProteinsStructural Proteins– Storage ProteinsStorage Proteins– Transport ProteinsTransport Proteins– Defensive ProteinsDefensive Proteins– EnzymesEnzymes

Structural ProteinsStructural Proteins

Used to provide structure and support for Used to provide structure and support for certain parts of organismscertain parts of organisms

Examples:Examples:– Keratin in hair/horns of animalsKeratin in hair/horns of animals– Collagen in connective tissuesCollagen in connective tissues– Silk in spider websSilk in spider webs

Storage ProteinsStorage Proteins

Used to store other molecules for later useUsed to store other molecules for later use

Examples:Examples:– Casein in milkCasein in milk– Ovalbumin in egg whitesOvalbumin in egg whites– Zein in corn seedsZein in corn seeds

Transport ProteinsTransport Proteins

Used to assist in the transport of Used to assist in the transport of molecules into and out of a cell or other molecules into and out of a cell or other membranemembrane

Examples:Examples:– Hemoglobin (OHemoglobin (O22 carrier) in red blood cells carrier) in red blood cells

– Integral membrane proteinsIntegral membrane proteins

Defensive ProteinsDefensive Proteins

Used to protect cells and organisms Used to protect cells and organisms against foreign substances or life formsagainst foreign substances or life forms

Examples:Examples:– AntibodiesAntibodies– Cell surface recognition proteinsCell surface recognition proteins– Poisons made by plants, insects, snakes, etc.Poisons made by plants, insects, snakes, etc.

EnzymesEnzymes

Regulate the rate of chemical reactionsRegulate the rate of chemical reactions

Examples:Examples:– DNA polymerase and helicaseDNA polymerase and helicase– LactaseLactase– PeroxidasePeroxidase– SucraseSucrase

Amino AcidsAmino Acids

The building blocks of proteinsThe building blocks of proteins20 total amino acids20 total amino acidsSome can be synthesized by humans, Some can be synthesized by humans, others must be consumedothers must be consumed

Carbon w/ 4 groups:Carbon w/ 4 groups:

AmineAmine

Carboxyl (acid)Carboxyl (acid)

HydrogenHydrogen

R group (varies)R group (varies)

Amino Acid R GroupsAmino Acid R Groups

R Groups determine the physical and R Groups determine the physical and chemical properties of the proteinchemical properties of the proteinThey can be polar, nonpolar, acidic, or They can be polar, nonpolar, acidic, or basic (importance?)basic (importance?)They can also be used for the attachment They can also be used for the attachment of other inorganic groups that are essential of other inorganic groups that are essential for the functioning of the proteinfor the functioning of the protein– Heme group on hemoglobin bonds to FeHeme group on hemoglobin bonds to Fe2+2+

– Other organic co-enzymes from our diet Other organic co-enzymes from our diet (vitamins)(vitamins)

Putting Amino Acids TogetherPutting Amino Acids Together

To build a protein, the amino acids must To build a protein, the amino acids must be connected by peptide bondsbe connected by peptide bondsPeptide bonds connect the amine group of Peptide bonds connect the amine group of one amino acid to the carboxyl group of one amino acid to the carboxyl group of the nextthe nextThis bond is caused by a dehydration This bond is caused by a dehydration reactionreactionA chain of connected amino acids is called A chain of connected amino acids is called a polypeptidea polypeptide

Where Do A.A.s Come From?Where Do A.A.s Come From?

Many foods contain amino acids in the Many foods contain amino acids in the form of proteinform of protein

When we digest protein, we recycle the When we digest protein, we recycle the amino acids and re-assemble them into amino acids and re-assemble them into our proteinsour proteins

Types of Amino AcidsTypes of Amino Acids

Structure of a ProteinStructure of a Protein

The code in the DNA recipe is a sequence The code in the DNA recipe is a sequence of A’s, T’s, C’s and G’sof A’s, T’s, C’s and G’sThe corresponding RNA copy of the recipe The corresponding RNA copy of the recipe contains this code, which is read in 3’scontains this code, which is read in 3’s– AUG, GGC, CUA, AAU, GCC, etc…AUG, GGC, CUA, AAU, GCC, etc…

Every 3 letter combination translates into 1 Every 3 letter combination translates into 1 specific amino acidspecific amino acidThe chain of amino acids has a specific The chain of amino acids has a specific sequencesequence

Structure of ProteinStructure of Protein

Primary StructurePrimary Structure– A unique sequence of amino acids in a polypeptide A unique sequence of amino acids in a polypeptide

chainchain

Secondary StructureSecondary Structure– Repeated folds and coils of a polypeptide chainRepeated folds and coils of a polypeptide chain

Tertiary StructureTertiary Structure– Irregular contortions from bonding of the side chains Irregular contortions from bonding of the side chains

of the various amino acidsof the various amino acids

Quaternary StructureQuaternary Structure– overall protein structure that results from the overall protein structure that results from the

aggregation of tertiary subunits aggregation of tertiary subunits

Fibrous ProteinsFibrous Proteins

Found only in animalsFound only in animals

Rod or wire-like shapesRod or wire-like shapes

Usually structural/storageUsually structural/storage

Water insoluble (hydrophobic R-groups)Water insoluble (hydrophobic R-groups)

Common in connective tissues, tendons, Common in connective tissues, tendons, bone matrix, and muscle fiberbone matrix, and muscle fiber

Examples: keratins, collagens, elastinsExamples: keratins, collagens, elastins

Globular ProteinsGlobular Proteins

Soluble in aqueous solutions (water)Soluble in aqueous solutions (water)

Apolar amino acids are oriented toward Apolar amino acids are oriented toward the center of the globe-like structurethe center of the globe-like structure

Used as enzymes, messengers Used as enzymes, messengers (hormones), transporters(hormones), transporters

Examples: hemoglobin, Examples: hemoglobin,

immunoglobulins, insulinimmunoglobulins, insulin

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EnzymesEnzymes

Enzymes speed up metabolic reactions Enzymes speed up metabolic reactions

Enzymes: catalytic proteins Enzymes: catalytic proteins

Catalyst: reduces the activation energy Catalyst: reduces the activation energy

Activation energy (EActivation energy (Eaa): energy required to ): energy required to

start a reaction start a reaction

EnzymesEnzymesSubstrate: reactant an enzyme works on Substrate: reactant an enzyme works on Active site: pocket where substrate is Active site: pocket where substrate is worked on worked on Induced fit: brings chemical groups into Induced fit: brings chemical groups into positions that enhance their ability to work positions that enhance their ability to work between the enzyme and substrate between the enzyme and substrate Effects of temperature and pH: enzymes Effects of temperature and pH: enzymes have an optimal temperature and pH they have an optimal temperature and pH they work withinwork withinMetabolic pathways consist of chains or Metabolic pathways consist of chains or cycles of enzymescycles of enzymes

Induced-Fit ModelInduced-Fit Model

EnzymesEnzymes

Cofactors: helpers bound into active site Cofactors: helpers bound into active site

Coenzyme: an organic cofactor Coenzyme: an organic cofactor

Competitive inhibitors: block the active site Competitive inhibitors: block the active site

Non-competitive inhibitors: bind to another Non-competitive inhibitors: bind to another part of the enzyme, inhibiting work part of the enzyme, inhibiting work

Allosteric site: receptor site away from the Allosteric site: receptor site away from the active site, where other molecules regulate active site, where other molecules regulate activityactivity

EnzymesEnzymes

Feedback (end-product) Inhibition: Feedback (end-product) Inhibition: metabolic pathway is switched off by its metabolic pathway is switched off by its end productend product

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