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Course Objectives Chapter 4

by: Lauren Maddox

Course Objectives Chapter 4 Bio 214

Marketplace > James Madison University > Biology > Bio 214 > Course Objectives Chapter 4
Lauren Maddox

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Course objectives for chapter 4 for Cell Molecular Biology
Molecular and Cell Biology
Dr. Doyle
Study Guide
Biology; Cell Molecular Biology; BIO 214
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This 5 page Study Guide was uploaded by Lauren Maddox on Wednesday March 16, 2016. The Study Guide belongs to Bio 214 at James Madison University taught by Dr. Doyle in Fall 2015. Since its upload, it has received 25 views. For similar materials see Molecular and Cell Biology in Biology at James Madison University.


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Date Created: 03/16/16
BIO214 Chapter 4 Objectives After completing chapter 4, you should be able to answer the following questions. 1. What are some potential functions of proteins in cells? They provide the cell with shape and structure, execute most myriad functions. Forms the pumps and channels that control the passage of nutrients and other small molecules into and out of the cell. They can carry messages from one another. Act as signal integrators, act as motors that propel organelles through the cytoplasm. 2. How does a condensation reaction occur? Two molecules, two amino acids being hooked together by the loss of water….. a covalent peptide bond forms when the carbon atom of the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid. Because a water molecule is eliminated, peptide bond formation is classified as a condensation reaction. 3. Where is the peptide bond in a short peptide chain? Between C and N 4. Where are the amino (N) terminus and the carboxyl (C) terminus on a polypeptide? N is on the left side, C is on the left side 5. How will the chemistry of a side chain affect where an amino acid is located in a protein? If it is polar- buried within the protein, they are usually hydrogen bonded to other polar amino acids or to the polypeptide backbone, or nonpolar- tend to cluster in the interior of the folded protein, they can avoid contact with the aqueous cytosol that surrounds them inside a cell. 6. What types of interactions stabilize the three dimensional structure of a protein. Are the interactions limited to the side chains of the amino acids? Disulfide bonds, they form between two cysteine amino acids, as proteins exported from the cell (in er). They are bonds within a single polypeptide or bonds between polypeptides in 4 degree structure. They are stable in oxidizing environment 7. Be familiar with protein folding. Which conformation of a protein is most stable? Polypeptide chains are folded up, held by non-covalent bonds and hydrophobic interactions. A protein generally folds into the shape in which its free energy is minimized. Protein folding inside a cell- assisted by molecular chaperones, they bind to partially folded proteins, which help with folding. They prevent incorrect interactions, they make the process efficient and reliable. Proteins have 3-d structure- determined by the order of amino acids. Generally the final conformation, where the free energy is minimized. Folding can be spontaneous- all info in 1 degree structure. Proteins have one stable conformation, shape often changes upon interactions with other molecules. Conformational changes 8. Are there consequences of having misfolded proteins? Shape is crucial to function, if shape is incorrect, protein may not function properly—targeted for degradation. Incorrectly folded proteins can have more severe consequences, rarely can form protein aggregates. Misfolded proteins can potentially cause correctly folded proteins to refold. Can be involved in human disease- CJD, and 1 Alzheimer’s disease. Abnormal protein cannot be broken down- accumulates and kills cells. 9. What are the various levels of structure of proteins -- primary, secondary, tertiary and quaternary -- can you predict these structures? Shape is determined by 1 degree structure. Protein sequencing, and DNA sequencing. 1 structure- the order of the amino acids 2ndstructure- a-helices and b-sheets 3 structure- 3d conformation of the entire chain- includes helices, sheets, coils, loops, fold, etc. how the structures come together in space. The entire polypeptide 4 structure- complex of more than one polypeptide chain. Multiple subunits come together tertiary and quaternary structure- hydrophobic, van der Waals, hydrogen, ionic, and disulfide bonds structure begins with its amino acid sequence-primary structure then includes a helices and b sheets that form within certain segments of the polypeptide chain-secondary structure full, 3d conformation formed by an entire polypeptide chain- a helices, b sheets, random coils- tertiary structure protein molecule is formed as a complex of more than one polypeptide chain- quaternary structure 10.What are two types of secondary structure? How are these structures stabilized? B-sheet and B-pleated sheet. They result from hydrogen bonds forming in the polypeptide backbone. Backbone-backbone h-bonds. a-helix, H-bonds between C=O and N-H of the peptide backbone. No R-groups involved. Weak attractions are what is stabilizing these structures. A-helices can be right or left handed. Hydrogen bond between every 4 peptide bond. There is a bond between c=O and n=h, regular helix with a turn every 3.6 amino acids. A- helices abundant in cell membranes. transmembrane domains- membrane core is hydrophobic. In a-helix, hydrophilic peptide backbone is hydrogen-bonded. Hydrophobic side chains protrude out. Amphipathic helix. Hydrophobic amino acids interact. Common motif, found in keratin, myosin. Two common folding patterns: a helix and b sheet. A helix-keratin-skin, hair, nails. B-sheet- silk. They result from hydrogen bonds that form between the N-H and C=O groups in the polypeptide backbone. Amino acid side chains are not involved, so they can be generated by many different amino acid sequences. Helix- regular structure that resembles a spiral staircase- generated by placing many similar subunits next to each other- right handed or left handed. A-helix is generated when a single polypeptide chain turns around itself to form a structurally rigid cylinder. Hydrogen bonds are formed between every fourth amino acid. B-sheet- formed when hydrogen bonds form between segments of a polypeptide chain that lie side by side. Form the core of many proteins. Stabilized by B 2 sheets that stack together tightly, with their amino acid chains interdigitated like the teeth of a zipper. B-sheet, or b-pleated sheet. H-bonds between c=o and n-h of backbone. No r- groups involved. Two strands are zipped up because of the hydrogen bonds between the strand. In beta sheets, you have side chains either up or down. Two varieties of B-sheet- anti-parallel and parallel. B sheet can provide tensile strength. Look at slide 31 for this diagram. B-sheet forms a flat surface in anti- freeze proteins. They prevent crystals from growing. Stacking of B-sheets can allow misfolded proteins to aggregate. 11.Define the terms motif, domain and protein family. Domains- discrete modules within tertiary structure. Domains fold independently, function independently. Each domain can have its own activity. Secondary structures form domains. Motif- a recurring substructure. Motif doesn’t necessarily function independently. Protein families- related structures, and related but not identical functions. Each family member has an amino acid sequence and a 3d conformation that closely resemble those of the other family members 12.What are Molecular Chaperones and what is their role in the cell in helping proteins to fold? Assist with protein folding inside a cell. Bind to partially folded proteins. Prevent incorrect interactions, make process efficient and reliable. Slide 15 13.What is a disulfide bond? What amino acid(s) is involved? They help stabilize a 3-d structure. They form between 2 cysteine amino acids- as proteins exported from the cell (in ER). Bonds within a single polypeptide or bonds between polypeptides in 4 structure. Formed before an enzyme in endoplasmic reticulum secretes a protein that links together two –SH groups from cysteine side chains that are adjacent in the folded protein. Act as a sort of atomic staple to reinforce the protein’s most favored conformation. These linkages can either tie together 2 amino acids in the same polypeptide chain or join together many polypeptide chains in a large protein complex. 14.What levels of protein structure are stabilized by disulfide bonds? Are disulfide bonds found in all proteins, regardless of location in the cell? Extracellular proteins- protein molecules that are either attached to the outside of a cell’s plasma membrane or secreted as part of the extracellular matrix. They are not in the cytosol. 15.How do enzymes function? How does the structure of an active site favors the formation of product? Enzymes lower activation energy by orienting two molecules to favor reactions, create partial negative and positive charges in the substrate that favor a reaction, and strain the substrate molecule, forcing it to a transition state. They have non-protein components: cofactors and coenzymes. Cofactors are inorganic compounds. Coenzymes are organic components. Enzyme activity is regulated, the cell generated only molecules needed at that particular moment. They don’t deplete energy reserves, they don’t have molecules it doesn’t need, and it does not deplete stockpiles of critical substrates. 3 Enzymes bind to one or more ligands, called substrates, and convert them into chemically modified products. They speed up reactions, without ever being changed. Enzymes act as catalysts that permit cells to make or break covalent bonds at will. This catalysis of organized sets of chemical reactions by enzymes creates and maintains the cell, making life possible. They only catalyze a single type of reaction. They need an active site to create the enzyme-substrate complex. Bonds that need to be broken are inside the active site, and those reduce the activation energy. In reactions involving two or more substrates, the active site acts like a template or mold that brings the reactants together in the proper orientation for the reaction to occur. The enzymes contains positioned chemical groups that speed up the reaction by altering the distribution of electrons in the substrates. Many enzymes participate intimately in the reaction by briefly forming a covalent bond between the substrate and an amino acid side chain in the active site. 16.Define the term ‘regulation.’ Are enzymes in a cell always working? They are not always working. 17.Explain the difference between positive regulation and negative regulation. What are some common methods of regulation used by cells? Negative regulation- turns enzyme off-feedback inhibition. Positive regulation-turns enzyme on (or up!)-regulatory molecule will stimulate enzyme activity. In both positive and negative regulation, a second molecule binds to the protein and alters its activity. 18.What is feedback inhibition? What enzymes in a pathway are typically controlled by feedback inhibition? Feedback inhibition-product from end of pathway turns off enzyme at start of pathway. High concentrations of end product (z) will shut down flow through pathway. There are four different amino acid synthesis pathways. Products feedback to inhibit enzymes. Product will bind to earlier enzyme, shut it down! Works very rapidly, reversed rapidly when product level decreases. Inhibitory product often has a completely different shape from the substrate. Active site is very specific for substrate. Where is the inhibitor binding? Allostery- other site. Enzymes have more than one binding site, and the two sites must interact. Interaction between sites depends on a conformational change. Inhibitor binding causes the shape of the protein to change and this reduces activity. Feedback inhibition will trigger a conformational change- binding at one site causes a shift in the protein structure, in feedback inhibition, binding of the inhibitor causes the protein to shift. It doesn’t accommodate the substrate as well. Feedback inhibition- an enzyme acting early in a reaction pathway is inhibited by a late product of that pathway. Whenever large quantities of the final product begin to accumulate, the product binds to an earlier enzyme and slows down its catalytic action, limiting further entry of substrates into that reaction pathway. Feedback inhibition is a negative regulation- it prevents an enzyme from acting. Enzymes can be subject to positive regulation- enzyme’s activity is stimulated by a regulatory molecule rather than being suppressed. Positive regulation occurs when a product in one branch of the metabolic maze stimulates the activity of an enzyme in another pathway. 4 19.What is an allosteric protein? How does binding at an allosteric site regulate enzyme activity? Exist in two conformations. For the regulation of enzymes- for the negative regulation-turns enzyme off- feedback inhibition. Uses allostery- binding of a molecule at a second site. Positive regulation-turns enzyme on- regulatory molecule will stimulate enzyme activity- uses allostery-binding of a molecule at a second site. 20.What is protein phosphorylation? What are protein kinases and protein phosphatases? How do they control enzyme activity? Adding or removing phosphate groups will alter enzyme activity. Has both positive and negative regulation. Adding a phosphate group- serine, threonine, or tyrosine amino acids. Enzyme: a protein kinase. Dephosphorylation is catalyzed by a phosphatase- hundreds of different kinases in a particular cell-many phosphatases. Kinases add the phosphate groups, phosphatases remove the phosphate groups 5


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