BIOM 121 1st Edition Lecture 1 Outline of Current Lecture I. Protein Structure and FunctionA. PrimaryB. SecondaryC. TertiaryII. Structural MotifsIII. Protein Binding and Enzyme CatalysisIV. Regulating Protein FunctionV. Noncovalent modification to regulate protein functionCurrent LectureChapter 3 – Protein Structure and Function- Proteins are polymer amino acids linked together thru peptide bonds- It’s the composition of amino acids that give it its unique function- Structure- cytoskeleton- Regulation- ways we turn proteins on and of- Enzymes- proteins that make or break covalent bonds- Transport- ions and small molecules1. Primary Structure of Proteins- Know characteristics of Amino Acids and what makes it diferent from another- Alpha carbons, carboxyl group, and Amine group make up the backbone- R groups are what vary between each Amino Acid- Know charges of each type of AA; acidic- negative, basic- positive, polar- no charge- Glycine is the smallest AA and can fit in places that other AA’s can’t2. Secondary Structure (alpha helix and beta sheet)- Starting to form a 3D structure- R groups DO NOT play a role, the helix is held in place by bonds in the backbone - One amino group is bonded to carboxyl group of another AA3. Tertiary Structure- Overall 3D shapeThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.- R groups come in to play and stabilize the tertiary structure by bonds: hydrophobic, ionic bonds, or polar bonds- Not permanent, gives flexibilityStructural motifs – are particular combinations of secondary and tertiary structure. 1. Leucine zippers or coiled-coils –- used for transcription factor dimerization  (Protein that binds to DNA to make RNA)- Two transcription factor proteins that bind together (dimer)- Leucine zipper makes up the area where they bind together- 2 alpha helixes, 1 in each proteins, are hydrophobic AA (Leucine and Valine) bind to each other like a zipper!- Always used to mediate binding to a protein- Combo of secondary and tertiary structuresOther structural motifs:2. EF hand – - Alpha helix – loop- alpa helix- In loop have polar (-) charge- Charged AA bind to Ca2+3. Zinc finger – - Found in transcription factors- Allows it to fit/bind to major groove of DNA- Alpha helix adjacent to a loop- Coordination of Zinc (Cystine and histidine_ acts to stabilize alpha helixDomains – distinct regions of tertiary structure. Larger than a motif, building block of proteins. Like a lego, doesn’t change size or function. Doesn’t matter what protein you plug them into, it always does the same thing. 2 types of domains are:Functional domains- characteristic Topological domains- transmembrane, particular location 3.3 Protein Binding and Enzyme Catalysis• The functions of many proteins are based upon their ability to bind to a ligand. • Specificity – that a protein prefers one substrate over another• Affinity – how tight that binding is, the strength of the bond– Is the inverse of the binding reaction; smaller the number = higher affinity• Active site - specific AAs that bind and catalyze reactionVmax or maximum velocity:– How much product an enzyme can make in 1 second– Maximum velocity– Directly proportional to how much enzyme there is– Point where it doesn’t matter how much substrate is added bc the enzyme can only work so fastKm (Michaelis constant):– Measure of affinity between substrate and enzyme– Km= ½ vmax– Substrate conc. at ½ vmax= Km– If substrate doesn’t bind as well,• Takes longer time to make product– Low Km= high affinityRegulating protein function:• 1. Can increase/decrease level of protein by altering rate of synthesis or degradation• 2. Can change location or concentration of the substrate or cofactor• 3. Can regulate the intrinsic activity – affinity of substrate bindingAltering Protein DegradationLife span of proteins– Some may only last minutes (might only be used for division and then degraded)– Misfolded proteins– Mutated proteins– Lysosome- organelle that’s used for beaking down proteins but usually used for proteins brought into the cellProteasome– normal cytosolic proteins– Really large protein complex in cell– 3 subunits- 20s catalytic core– B subunits break peptide bonds– 19s cap linearizes a particular protein– Ubiquitination used to destroy proteins (Tag proteins so they are recognized by the proteasome)– Ub. Is 76 AA peptide that binds to lysine groups on the protein to be destroyed– Need at least 4 Ub on protein so that protease catalyzes itNoncovalent modification to regulate protein function• 1) Binding of Ca: low levels in cytoplasm– Gets stored in mitochondria, ER, or pumped out to outside cell– 10,000x Ca forms gradient across cell membrane– Upon a stimulus, Ca goes into cytoplasm– Ca binds to loop in EF hands (motif), when Ca binds, the loops cross over each other and massive confirmation change à dictates if proteins bind to each other– Calmodulin has 4 EF hands, starts linear and then with Ca it wraps around on itself, this regulates binding to another protein. Turns on protein #2.– After this, Ca gets pumped out real quick.• 2) GTPase superfamily:. Proteins that can bind to GTP; either active (on) state when bound to GTP– have intrinsic ability to hydrolize GTP to GDP– This turns it of– GAP protein – inactivator protein; GTPase accelerating protein, speeds up removal of terminal Phosphate– GDP (of) is the normal state– GEF- guanine exchange factor, pull of GDP from protein. But the affinity of this active site is so high, that if any GTP is floating around in cell it will automatically