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CORNELL BIOMG 1350 - Macromolecules: Protein

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I. Proteinsa. Enzymes: catalyze covalent bond formation or breakageb. Structural Proteins: Actin, tubulin, keratins, collagenc. Transporters: carry small molecules like ions, sugars, amino acids etc.d. Motor Proteins: use energy stored in ATP to do mechanical worke. Storage Proteins: ferritin in the liver stores ironf. Signal Proteins: carries signals from cell to cell and inside cellg. Receptor Proteins: detect and transmit chemical signalsh. Gene Regulatory Proteins: bind DNA to regulate transcriptioni. Many others…II. All proteins function by specific interactions with other molecules- a protein’s phsycial; interaction with other molecules determines its biological propertiesIII. Protein Components:a. Amino acids are the subunits of proteins: have a side chain group (R group), carboxyl group (negative charge), amino group (positive charge)b. 20 amino acids in nature- some are negative, some are positive, and some are neutral. Polar= hydrophilic, nonpolar= hydrophobicc. Different side chains determine propertiesi. Example: lysine: basic polar, aspartic acid: negative charge, serine: uncharged but polar because it likes water because there is a dipole and can make hydrogen bonds with water, leucine: nonpolarIV. Amino acids are linked together by peptide bonds.a. Condensation reaction: to create a peptide bond, water is release. Always have a free amino and carboxyl group.b. Can be assembled into long polypeptide.c. Genetic information directs the synthesis of proteinsIV Protein Synthesis:d. Transcription: DNA mRNA synthesise. Translation: mRNAprotein through reading codons on the mRNA and translating it into a specific amino acid via the genetic code.f. An RNA molecule has three possible reading frames.g. How to decide which code it reads first: start codon is always AUG; but AUG is not always a start codon (N-terminus).h. There are three stop codons: UGA, UAA, UAG (C-terminus).i. There is a 5’ and a 3’ end. It starts at the 5’ end.How was the genetic code determined?j. In in-vitro you can make a synthetic mRNA into a cell-free translation system to figure out amino acid sequence.How is the base sequined in mRNA translated into the amino acid sequence of a protein?k. You need:i. adaptors to translated the RNA code and bring in the right amino acids. The adapters are tRNAs.1. tRNAs are short RNAs. They attach an amino acid on the 3’ end and the 5’ end has an anticodon2. They contain some unusual cases produced by chemical modification.3. tRNAsynthetases attach amino acids to tRNAs.4. There is at least one tRnasynthetase for each amino acid .ii. A machine that will align the mRNA sequence with the adapters and stitch the amino acids together to form the polypeptide chain. It is called the ribosome1. Have large subunit and a small subunit. Small subunit bings mRNA and matches tRNA to mRNA codons. Large subunit builds polypeptide chain.2. E site: ejection of free tRNA3. Peptidyl: peptide bond formation4. AMinoacylr-tRNA site: new bound tRNA waiting to be coded into an amino acid.5. After this, the large subunit translates down the 5’3’ direction, followed by the small subunit.Proteins come in a variety of shapes and sizes:l. The structure of a protein is determined solely by its amino acid sequencem. Three types of non-covalent bonds help proteins fold:i. Hydrostatic (polar), Hydrogen (polar), Van Der Waals (nonpolar side chains attract each other)ii. Polar interaction: hydrophiliciii. Nonpolar interaction: hydrophobic, cannot form any bonds with water. They aggregate together.iv. Folded proteins enjoy water (hydrophobic core) while unfolded proteins do not like water.V. Protein Structure:a. A helix: side chain do not contribute to helical structure, side chains project outwardi. Two A helices can form a coiled-coil. Held together by hydrophobic interactions. Very strong.b. Beta sheet: hydrogen bonds between chains, do not involve side chains.i. Regular, rigid, flat.BIOMG 1350 1st Edition Lecture 4Outline of Last Lecture I. Basic concepts of macromoleculesOutline of Current Lecture II. ProteinsIII. Protein ComponentsIV. Protein SynthesisV. Protein StructureCurrent LectureI. Proteinsa. Enzymes: catalyze covalent bond formation or breakageb. Structural Proteins: Actin, tubulin, keratins, collagenc. Transporters: carry small molecules like ions, sugars, amino acids etc.d. Motor Proteins: use energy stored in ATP to do mechanical worke. Storage Proteins: ferritin in the liver stores ironf. Signal Proteins: carries signals from cell to cell and inside cellg. Receptor Proteins: detect and transmit chemical signalsh. Gene Regulatory Proteins: bind DNA to regulate transcriptioni. Many others…II. All proteins function by specific interactions with other molecules- a protein’s phsycial; interaction with other molecules determines its biological properties III.Protein Components:a. Amino acids are the subunits of proteins: have a side chain group (R group), carboxyl group (negative charge), amino group (positive charge)b. 20 amino acids in nature- some are negative, some are positive, and some are neutral. Polar= hydrophilic, nonpolar= hydrophobicThese 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.c. Different side chains determine propertiesi. Example: lysine: basic polar, aspartic acid: negative charge, serine: uncharged but polar because it likes water because there is a dipole and can make hydrogen bonds with water, leucine: nonpolarIV. Amino acids are linked together by peptide bonds.a. Condensation reaction: to create a peptide bond, water is release. Always have a free amino and carboxyl group.b. Can be assembled into long polypeptide. c. Genetic information directs the synthesis of proteins IV Protein Synthesis:d. Transcription: DNA mRNA synthesise. Translation: mRNAprotein through reading codons on the mRNA and translating it into a specific amino acid via the genetic code. f. An RNA molecule has three possible reading frames. g. How to decide which code it reads first: start codon is always AUG; but AUG is not always a start codon (N-terminus).h. There are three stop codons: UGA, UAA, UAG (C-terminus).i. There is a 5’ and a 3’ end. It starts at the 5’ end.How was the genetic code determined?j. In in-vitro you can make a synthetic mRNA into a cell-free translation system to figure out amino acid


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