BIOMG 1350 Notes Week 3
BIOMG 1350 Notes Week 3 BIOMG 1350
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This 6 page Class Notes was uploaded by genehan on Saturday September 3, 2016. The Class Notes belongs to BIOMG 1350 at Cornell University taught by Garcia-Garcia, M; Huffaker, T in Fall 2015. Since its upload, it has received 5 views. For similar materials see Introductory Biology: Cell and Developmental Biology in Molecular Biology and Genetics at Cornell University.
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Date Created: 09/03/16
BIOMG 1350 Professor Bretscher & GarciaGarcia Spring 2016 Week 3: Lecture 1 of 2 Monday, Feb 8, 2016 Lecture Title: Protein Structure Lecture Keywords: amino acids, sidechain (R) groups, peptide bonds, codon, methionine AUG, stop codons, Open Reading Frame, Genetic Code, tRNA adaptors, tRNA, tRNA synthetases, translation, Esite, Psite, Asite, noncovalent bonds, alpha helices, betasheets, coiledcoil I. Iclicker question: Which of the following statements is false? a. The RNA nucleotide CGA has a higher molecular weight than the DNA nucleotide CGA (True, each nucleotide of RNA has an additional oxygen.) b. In DNA, the amount of C and G is the same as A and T (False, there is an equal amount of C + T and G + A.) c. CG pairs are stronger than AT base pairs (True, CG pairs have 3 hydrogen bonds and AT pairs have 2 bonds.) d. DNA is a negatively charged molecule. (True, there is a phosphate in the backbone.) e. Base pairing is involved in determining the structure of RNAs. (True) II. There are different functional classes of proteins. a. Every reaction is catalyzed by an enzyme and there is usually one specific enzyme that catalyzes a reaction. b. Structural proteins help keep the cell shape. c. Transporters carry small molecules such as ions, sugars, and amino acids. d. Motor proteins use energy to undergo mechanical work. e. Signaling proteins are important for communication. f. Receptor proteins are useful for cells to know what environment they are in and for chemical signals III. Proteins are made of subunits called amino acids. a. Every amino acid has a positively charged amino group, a negatively charged carboxyl group and an alpha carbon atom. b. The sidechain (R) group distinguishes one amino acid from another. c. The polar amino acids that have an unbalanced charge in them are hydrophilic. d. The nonpolar amino acids do not have a charge and are hydrophobic. e. Basic groups have a positive charge and acidic groups have a negative charge. IV. Amino acids are linked by peptide bonds through a condensation reaction to form a polypeptide chain. a. The N terminus (amino group) is on the left and the C terminus (carboxyl group) is on the right when writing a polypeptide sequence. V. Protein synthesis is directed by genetic information. a. The 4 base code in DNA is transcribed into a 4 base code in mRNA and then is translated into the sequence using 20 amino acids. b. Each codon specifies a certain protein and there are 64 different possible codons. c. Using the genetic code, the nucleotide sequence of RNA is translated into the amino acid sequence of a protein. d. The start sequence is always the first methionine code AUG in the messenger RNA. i. AUG can be read as simply methionine if it is in the middle of a sequence. e. There are 3 stop codons: UAA, UAG and UGA. f. The Open Reading Frame ORF is the portion of the sequence that is translated. Therefore, there is a 5’ untranslated sequence and a 3’ untranslated sequence. VI. The Genetic Code was built up by chemical and genetic methods over the years. a. A synthetic mRNA is placed in a cellfree translation system with radioactive amino acids and what results is the synthesis of a radioactive polypeptide. VII. The base sequence in mRNA is translated into the amino acid sequence of a protein. a. You need tRNA adaptors to transfer the RNA code into the protein code and to bring in the appropriate amino acids. b. You also need a machine that will align the mRNA sequence with the adaptors and then stitch the polypeptide chain using amino acids. VIII. Cloverleaf shaped tRNAs link amino acids to codons. a. On the 3’ end, an amino acid is attached and the anticodon loop is where the anticodon will basepair with the sequence in mRNA. b. tRNAs have lots of chemical modifications and the base pairing within tRNA gives it a specific structure, IX. There are tRNA synthetases to attach amino acids to tRNAs . a. Through the tRNA, the amino acid is selected by its codon. b. There is at least one tRNA synthetase for each amino acid. X. mRNA is decoded on ribosomes through translation. a. There is a large ribosomal subunit that catalyzes peptide bond formation and a small ribosomal subunit that binds mRNA and matches tRNA to mRNA codons. b. There is an exit site (Esite), a peptidyl tRNA (Psite) and an aminoacyltRNA (Asite). XI. Translation on ribosomes. a. There is a growing polypeptide chain with linkages at the P and A site, and a peptide bond forms while it is still attached to the Asite, then the large subunit translocates and a new tRNA comes in and the cycle begins again. b. The ribosomes in prokaryotes and eukaryotes are different. XII. Iclicker question: Which of these tRNA anticodons will recognize the mRNA AGC codon? a. GCU XIII. Proteins come in a variety of shapes and sizes but will always fold into the same structure if it is the same sequence in order to do its function. a. The 3 dimensional structure of a protein at its minimum energy state is determined solely by its amino acid sequence. b. The three types of noncovalent bonds that help proteins fold are electrostatic attractions between positive and negative charges, hydrogen bonds between hydrogen and oxygen, and van der Waals attractions between closely associated atoms. i. Electrostatic attractions and hydrogen bond are hydrophilic interactions while van der Waals are hydrophobic effects. c. Hydrophobic forces help protein fold into compact conformations as the hydrophobic core region has nonpolar side chains and hydrogen bonds can be formed to polar side chains on the outside of the molecule. XIV. The two common forms of protein structure are the alphahelix and betasheets. a. The structure of an alpha helix is stabilized by hydrogen bonding between the backbone amino and the backbone carbonyl group 4 sequences apart. b. Two alpha helices can form a coiledcoil (keratin) to be intertwined so that the hydrophobic residues are more stable. c. The betasheet has hydrogen bonds between the backbones of parallel chains and do not involve side chains. BIOMG 1350 Professor Bretscher & GarciaGarcia Spring 2016 Week 3: Lecture 2 of 2 Wednesday, Feb 10, 2016 Lecture Title: Proteins in Action Lecture Keywords: primary, secondary, tertiary, and quaternary sequence, protein domain, cysteine, disulfide bonds, binding site, enzyme, reaction coupling, feedback inhibition, phosphorylation, kinase I. Iclicker question – Which of the following is true? a. In amino acids, the side chain is attached to the C of the C=O group. (False, the side chains are attached at the alpha Carbon.) b. There are more uncharged polar amino acids than nonpolar ones. (False, half the amino acids are nonpolar and 5 are uncharged polar.) c. Methionine is only found at the Nterminal end of proteins. (False, it is found elsewhere in proteins.) d. There are 20 different tRNAs. (False, there are more as many amino acids are encoded by several codons.) e. In an alpha helix, every backbone C=O is Hbonded to a backbone NH. II. Proteins have primary, secondary, tertiary, and quaternary structure. a. The primary structure is the amino acid sequence. b. The secondary structure is the alphacarbon chain backbone. (alpha helices and betasheets) c. The tertiary structure shows one protein with all the side chains. d. The quaternary structure is the subunit structure of a multisubunit protein. i. Example – hemoglobin has two alphaglobins and two betaglobins. ii. Mature proteins can have many individual polypeptide chains/subunits. e. Protein structures can be shown using a backbone, ribbon, wire, and spacefilling model. III. Proteins are usually composed of separate functional domains. a. A protein domain is a segment of the polypeptide chain that can fold independently into a compact stable structure. b. Each domain has a specific function, such as catalyzing a biochemical reaction, or binding certain molecules. c. Functionally related domains usually have a similar protein sequence so using bioinformatics can help identify functionally related domains. d. Recombining domains can create proteins with different functions. IV. The only amino acid that has a sulfhydryl group SH is cysteine. a. Disulfide bonds between cysteine residues help stabilize favorable protein conformations of secreted proteins. Such bonds can occur between chains or within chairs. i. When you perm your hair, they decrease the number of disulfide bonds in your hair keratin, curl your hair, and then restrengthen the bonds to keep your hair in that shape. b. Insulin was the first protein sequenced using protein sequencing technology and insulin is stabilized by disulfide bonds. V. Some macromolecular complexes contain proteins and RNA. Ribosomes contain 4 RNAs and 82 different proteins. a. RNA can have catalytic activity, similarly to enzymes. b. People believe that the origin of life began with RNA when proteins didn’t exist. VI. Proteins have a binding site to do selective binding of protein to a ligand (a small molecule that binds) using weak noncovalent interactions. a. The binding sites allow a protein to interact with specific ligands, often thought of as the lock and key method. VII. Enzymes catalyze chemical reactions without being used up themselves. a. Enzyme binds a substrate A molecule, undergoes a chemical reaction, and releases a molecule B as product. The enzyme remains unchanged and can be used again. b. The reaction must be energetically favorable in order for an enzyme to catalyze. Enzymes are needed to lower the activation energy barrier. i. Without the activation energy barrier, the reaction would spontaneously happen. (example, gasoline would spontaneously combust) c. For an energetically unfavorable reaction, reaction coupling is used by pairing an energetically favorable reaction with one that is unfavorable so that the two together become an energetically favorable reaction. i. ATP is the energy source in the cell and cycles between ATP and ADP in the cell. ii. ATP becomes ADP and an inorganic phosphate. iii. ATP hydrolysis can drive an energetically unfavorable reaction. 1. Condensation reactions are energetically unfavorable. Instead, break down reactions to get two energetically favorable sub reactions. 2. The activation step proceeds by attaching a phosphate onto molecule B from ATP and the condensation step happens when molecule HA reacts with POB and results in AB, phosphate, and water. VIII. Iclicker question – Which of the following is true? a. Specific interactions between proteins employ electrostatic interactions and hydrogen bonds, but do not involve hydrophobic interactions. (False, hydrophobic interactions can be important in proteinprotein interactions, as well as found in the core of the proteins.) b. RNAs are information or structural molecules and cannot catalyze chemical reactions. (False, Many chemical reactions are based on RNA.) c. Disulfide bonds are used to stabilize many cytosolic proteins. (False, the cytosol is a reducing environment, so disulfide bonds are generally not found in cytosolic proteins) d. Protein domains that have similar functions generally have related primary and secondary structures. (True) e. Proteins almost never contain more than four subunits. (False, they can have many subunits.) IX. Protein activity is regulated by the control of protein amount (efficiency and rate of mRNA) and protein activity (inhibition or activation by ligands). X. Feedback inhibition occurs in metabolic pathways to regulate reactions. a. Product F can inhibit enzyme 1 so enzyme 1 is changed in its shape so that the reaction cannot take place. XI. Phosphorylation, adding a phosphate to a specific side group on a protein, is mediated by a specific enzyme called a kinase. a. Kinases place phosphates onto a molecule whereas phosphatases remove phosphates. b. Phosphorylation can either turn on or turn off a certain molecule. c. Serine, threonine, and tyrosine are the three side chains recognized by kinases. d. We have 518 kinases, which represent only 2% of our proteome. XII. The cancer protein Src causes sarcomas and is controlled by phosphorylation. a. SH2 binds phosphotyrosine, kinase phosphorylates specific tyrosines, and has a critical tyrosine on the Cterminus. b. When the critical tyrosine is phosphorylated, the kinase is inactive. c. When phosphatase removes the phosphate, the structure loosens and becomes partially active. d. The partially active kinase autophosphorylates itself and then becomes a fully active kinase and this results in enhanced cell growth. e. Then, to turn this pathway off, a phosphatase removes the activating phosphate and another regulatory kinase phosphorylates the critical tyrosine and inactivates csrc. f. The critical tyrosine was mutated in vsrc which means you can’t have turn it off because it cannot be phosphorylated and it remains active.
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