Week 4 Notes
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Date Created: 09/08/16
Week 4 Chapter 4: Tuesday, September 6, 2016 12:21 PM Amino acids consist of a central carbon atom called the α (alpha) carbon, connected by covalent bonds to four different chemical groups: an amino group , a carboxyl group and a variable side chain or R group. The amino group gains a proton to become -NH and 3 carboxyl group loses a proton to become -COO . - The amino acid forms a tetrahedron. The R groups of amino acids differ from one amino acid to the next distinguishing one from the other. Hydrophobic amino acids do not readily interact with water or form hydrogen bond. Hydrophobic R groups tend to aggregate together, which is stabilized by weak van der Waals forces. R groups of basic and acidic amino acids are strongly polar. Basic amino acids are positive and acidic amino acids are negatively charged. Glycine increases flexibility of the polypeptide backbone, which is important in the folding of the protein. Proline creates a kink in the polypeptide chain and restricts the rotation of the C-N bond, which imposes constraints on protein folding in its vicinity. When two cysteine side chains come into proximity they can react to form an S-S disulfide bond, which covalently joins the side chains and are much stronger than ionic interactions of other pairs of amino acid and form cross-bridges to connect different parts of the same protein or different proteins. Successive amino acids in proteins are connected by peptide bonds. The bond formed between two amino acids is a peptide bond In forming the peptide bond, the carboxyl group of one amino acid reacts with the amino group of the next amino acid in line and a molecule of water is released. The C=O group is known as the carbonyl group and the N-H group is known as the amide group. Electrons are more attracted to the C=O group. The peptide bond is shorter than a single bond, it is not free to rotate like a single bond. Polymers of amino acids share a chemical feature common to individual amino acids, the ends are chemically distinct from each other. One end has a free amino group; the amino end and the other has a free carboxyl; the carboxyl end. A polymer of amino acids connected by peptide bonds is known as a polypeptide. The term protein is synonymous to polypeptide. Amino acids that are incorporated into a protein are often referred to as amino acid residues. The sequence of amino acids dictates protein folding, which determines function. The sequence of amino acids in a protein is its primary structure. The sequence of amino acids ultimately determines how a protein folds. Interactions between stretches of amino acids in a protein form local secondary structures. Longer- range interactions between these secondary structures in turn support the overall three- Bio 281 Lecture Page 1 ultimately determines how a protein folds. Interactions between stretches of amino acids in a protein form local secondary structures. Longer- range interactions between these secondary structures in turn support the overall three- dimensional shape of the polypeptide, which is its tertiary structure. Some proteins are made up of several individual polypeptides that interact with each other, and the resulting ensemble is the quaternary structure. When fully folded, some proteins contain pockets with positively or negatively charged side chains at just the right positions to trap small molecules; others have surfaces that can bind another protein or a sequence of nucleotides in DNA or RNA; some form rigid rods for structural support; and still others keep their hydrophobic side chains away from water molecules by inserting into the cell membrane. Secondary structures result from hydrogen bonding in the polypeptide backbone. Localized folding due to the hydrogen bonds between the carbonyl group and the amide group in two peptide bonds is a major contributor to the secondary structure of the protein. American structural biologists, Linus Pauling and Robert Corey studied crystals of highly purified proteins and discovered the two types of secondary structure are found in many different proteins. The α (alpha) helix and the β (beta) sheet. Both are stabilized by hydrogen bonding along the polypeptide backbone. In α helices, the polypeptide backbone is twisted tightly in a right-handed coil 3.6 amino acids per complete turn. The helix is stabilized by hydrogen bonds that form between each amino acid's carbonyl group and the amide group four residues ahead in the sequence. (indicated by the dashed lines) R groups project outward form the α helix. The chemical properties of the projecting R groups largely determine where the α helix is positioned in the folding protein and how it might interact with other molecules. The other secondary structure, the β sheet, polypeptide folds back and forth on itself, forming a pleated sheet that is stabilized by hydrogen bonds between carbonyl groups in one chain and amide groups in the other chain across the way (dashed lines). R groups project alternately above and below the plane of the β sheet. Β sheets consist of 4 to 10 polypeptide chains aligned side by side, with the amides hydrogen-bonded to the carbonyls on either side. Β sheets are denoted by broad arrows, where the direction of the arrow runs from the amino end of the polypeptide segment to the carboxyl end. Polypeptide chains are antiparallel. Tertiary structures result from interactions between amino acid side chains The three-dimensional conformation of a single polypeptide chain, usually made up of several secondary structure elements. The shape is largely defined by interactions between the amino acid R groups. By contrast, the formation of secondary structures relies on interactions in the polypeptide backbone. Tertiary structure is determined by the spatial distribution of hydrophilic and hydrophobic R groups along the molecule. Some amino acids can be far apart in the polypeptide chain, but can end up near each other in the folded protein. Primary structure determines the secondary and tertiary structures. Tertiary structure determines function because it is the three-dimensional shape of the molecule-the contours and distributions of charges on the outside of the molecule and the presence of pockets that might bind with smaller molecules on the inside -- that enables the protein to serve as structural support, membrane channel, enzyme or signaling molecule. Certain R groups can form hydrogen bonds with a specific small molecule and hold it in place in a pocket in the center of a bacterial protein. Most proteins can be unfolded, or denatured, by chemical treatment or high temperature that disrupts that hydrogen and ionic bonds holding the tertiary structure together. Under these conditions, the proteins lose their functional activity. Mutant proteins containing an amino acid that prevents proper folding are often inactive or don't function properly. Polypeptide subunits can come together to form quaternary structures Some proteins are composed of two or more polypeptide chains or subunits with a tertiary structure that come together to form a higher-order quaternary structure. In a protein with a quaternary structure, the polypeptide subunits may be identical or different. Fig 4.10a shows a protein produced by HIV that consists of two identical polypeptide subunits. Some proteins, such as hemoglobin are composed of different subunits. When one subunit binds to oxygen, a slight change of structure is transmitted to other subunits, making Bio 281 Lecture Page 2 When one subunit binds to oxygen, a slight change of structure is transmitted to other subunits, making it easier for them to take up oxygen. Chaperones help some proteins fold properly Most proteins fold within milliseconds as it is being synthesized. However, some are folded more slowly which is dangerous for the molecule because in its denatured state, the hydrophobic groups are exposed to other macromolecules in the crowded cytoplasm. With the hydrophobic effect and van der Waals interactions, the improper aggregation of hydrophobic groups may prevent proper folding. Some proteins can denature due to elevated temperature. Cells have proteins called chaperones that help protect slow-folding or denatured proteins. Chaperones bind to hydrophobic groups and nonpolar R groups to shield them from inappropriate aggregation, in cycles of binding and release they give the protein time to find its shape. 4.2 Translation: How proteins are synthesized In translation, the sequence of bases in an RNA molecules known as messenger RNA (mRNA) is used to specify the order in which successive amino acids are added to a newly synthesized polypeptide chain. Translation needs many components. First, a cell needs ribosomes, which are complex structures of RNA and protein that bind with mRNA and are the site of translation. In prokaryotes, translation occurs as soon as the mRNA comes off the DNA template. In eukaryotes, the processes of transcription and translated a physically separated: transcription in the nucleus and translation in the cytoplasm. Ribosomes consist of a small subunit and a large subunit. The large subunit includes three binding sites for molecules of transfer RNA, which are called the A (aminoacyl) site, P (peptidyl) site and E (exit) site. A major role of the ribosome is to ensure the mRNA is in the place on the ribosome, the sequence in the mRNA coding for amino acids is read in successive, non-overlapping groups of three nucleotides. Each non-overlapping group of three adjacent nucleotides constitutes a codon and each codon in the mRNA codes for a single amino acid in the polypeptide chain. Different ways of parsing the string into three-letter words are known as reading frames. mRNA can only be translated into the correct protein if it is translated in the proper reading frame. When the ribosome establishes the correct reading frame, translation of each codon in the mRNA into one amino acid is carried out by means of transfer (tRNA) Each has a characteristic self-pairing structure that can be drawn as a cloverleaf, in which the letters indicate the bases common to all tRNA molecules, but the actual structure is more like figure 4.13b. Three bases in the anticodon loop make up the anticodon; these are the three nucleotides that undergo base pairing with the corresponding codon. Each tRNA has the nucleotide sequence CCA at its 3' end, and the 3' hydroxyl of the A is the attachment site for the amino acid corresponding to the anticodon. Enzymes called aminoacyl tRNA synthetases connect specific amino acids to specific tRNA molecules. These enzymes directly translate the codon sequence in a nucleic acid to a specific amino acid in a polypeptide chain. The enzyme binds to multiple sites on any tRNA that has an anticodon corresponding to the amino acid, and it catalyzes formation of the covalent bond between the amino acid and tRNA. A tRNA that has no amino acid is said to be uncharged and one with its amino acid is said to be charged. Anticodon and codon interactions are the result from base pairing and their anti-parallel nature. The genetic code shows the correspondence between codons and amino acids Most codons specify an amino acid according to a genetic code. AUG is the initiation codon which specifies met. Met is mostly cleaved off by an enzyme after synthesis is complete. Any codons prior to Met isn't coded, after met, codons are translated until the stop codon is Bio 281 Lecture Page 3 AUG is the initiation codon which specifies met. Met is mostly cleaved off by an enzyme after synthesis is complete. Any codons prior to Met isn't coded, after met, codons are translated until the stop codon is encountered: UAA, UAG or UGA. The chemical basis of these patterns results from two features of translation. In many tRNA anticodons, the 5' base that pairs with the 3' (third) base in the codon is chemically modified to form a pair with two or more bases at the third position. In the ribosome, there is less than perfect alignment between the third position of the codon and the base that pairs with it in the anticodon, so the requirements for base pairing are relaxed; this feature is of the codon-anticodon interaction is referred to as wobble. Translation consists of initiation, elongation and termination Initiation, where the AUG codon is recognized and Met is established as the first amino acid. Elongation, successive nucleotides are added one by one to the growing chain. Termination, the addition of amino acids stops and the completed polypeptide chain is released. Initiation requires a number of protein initiation factors that bind to the mRNA. In eukaryotes, one group of initiation factors binds to the 5' cap that is added to the mRNA during processing. These recruit the small subunit of the ribosome, other factors bring up tRNA with Met. The complex scans mRNA until it encounters the first AUG triplet. After AUG is encountered, the large ribosomal subunit joins the complex and the initiation factors are released, and the next tRNA joins the ribosome at the A site. A bond connects Met to the tRNA which is then transferred to the amino group, forming a peptide bond. After this the uncharged tRNA shifts to the E site and is released into the cytoplasm. Ribosome movement along mRNA and formation of peptide bonds require energy from proteins called elongation factors. Elongation continues until a stop codon is reached, then a protein release factor binds to the A site of the ribosome. This causes the bond connecting the protein to the tRNA to break, creating the carboxyl terminus and completing the chain. Once finished, the small and large ribosomal units disassociate from the mRNA and each other. In eukaryotes, initiation complex forms at the 5' cap and scans until AUG is encountered. In prokaryotes, there is no 5' cap therefore the initiation complex is formed at one or more internal sequences present in mRNA known as the Shine-Dalgarno sequence. It is followed by an AUG codon eight nucleotides downstream that serves as the initiation. Prokaryotic mRNAs code for more than one protein and this mRNA is known as a polycistronic mRNA. A polycistronic mRNA results from transcription of a group of functionally related genes located in tandem along the DNA and transcribed as a single unit from one promoter. This type of gene organization is known as an operon. Bio 281 Lecture Page 4 Bio 281 Lecture Page 5
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