Biochem test 1
26. What are the proteinogenic alpha-amino acids? What type are they?
Twenty amino acids are encoded by the standard genetic code and are called proteinogenic or standard amino acids. The are divided into three categories based on how essential they are to humans: Essential, Non-Essential, and conditionally essential.
3. What are the Minimum requirements for collecting test (experimental) information?
1. report test results with units. 2. all data manipulation such as transformations, an calculations must be described. 3. Statistical analysis must be preformed according to protocol. 4. a summary of the test results with a conclusion. 5. explain unusual test results. 6. record the start and finish date of the study. 7. all entries must be recorded directly on the lab notebook with pen and mistakes one lined and initialed.
14. Describe 8 general functions of proteins in and out of the cell - what roles does each type play?
1.Hormonal Hormones are protein-based chemicals secreted by the cells of the endocrine glands. Usually transported through the blood, hormones act as chemical messengers that transmit signals from one cell to another. An example of a hormonal protein is insulin, which is secreted by the pancreas to regulate the levels of blood sugar in your body. 2.Enzymatic Enzymatic proteins accelerate metabolic processes in your cells, including liver functions, stomach digestion, blood clotting and converting glycogen to glucose. An example is digestive enzymes that break down food into simpler forms that your body can easily absorb. 3.Structural Also known as fibrous proteins, structural proteins are necessary components of your body. They include collagen, keratin and elastin. Collagen forms the connective framework of your muscles, bones, tendons, skin and cartilage. Keratin is the main structural component in hair, nails, teeth and skin. 4.Defensive Antibodies, or immunoglobulin, are a core part of your immune system, keeping diseases at bay. Antibodies are formed in the white blood cells and attack bacteria, viruses and other harmful microorganisms, rendering them inactive. 5.Storage Storage proteins mainly store mineral ions such as potassium in your body. Ovalbumin and casein are storage proteins found in breast milk and egg whites, respectively, that play a huge role in embryonic development. 6.Transport Transport proteins carry vital materials to the cells. Hemoglobin, for example, carries oxygen to body tissues from the lungs. 7.Receptor Located on the outer part of the cells, receptor proteins control the substances that enter and leave the cells, including water and nutrients. 8.Contractile Also known as motor proteins, contractile proteins regulate the strength and speed of heart and muscle contractions. These proteins are actin and myosin.
15. Describe the 4 basic levels of protein structure and give an example of each.
1.Primary The primary structure of a protein is its linear sequence of specific amino acids. Peptide bonds hold the adjacent amino acids together in the polypeptide chain. Aspartame Asp-Phe-Och3 2.Secondary structure The localized, repetitive coiling or folding of a protein is it's secondary structure. The most common forms are alpha helix's and beta pleated sheets. (Myoglobin) 3.Tertiary Structure The tertiary structure of a protein refers to the actual three dimensional structure of the polypeptide chain. A number of forces act to hold the polypeptide chain in this final configuration: Polar/Nonpolar Interactions Hydrogen Bonds Van der Waals Forces Ionic Interactions Disulfide Bonds They are found in Secretory proteins which include many hormones, enzymes, toxins, and antimicrobial peptides. 4.Quaternary Structures Some proteins have a quaternary structure; that is, they are comprised of two or more polypeptide chains. Each polypeptide chain in such a protein is called a subunit.(Collagen).
16. What types of bonds are important in each level of protein structure?
1.Primary: Peptide bonds which hold the adjacent amino acids together in the polypeptide chain. 2.Secondary structure: Secondary structure is held together by many Hydrogen bonds, overall giving the shape great stability. 3.Tertiary Structure: Tertiary structure is held together by three bonds: Disulphide Bonds - Where two Cysteine amino acids are found together, a strong double bond (S=S) is formed between the Sulphur atoms within the Cysteine monomers. Ionic Bonds - If two oppositely charged 'R' groups (+ve and -ve) are found close to each other, and ionic bond forms between them. Hydrogen Bonds - Your typical everyday Hydrogen bonds. 4.Quaternary Structures: hydrogen bonds between polar groups; and disulfide bonds
19. Describe the structure and function of the alpha helix.
Alpha helix is a form of secondary protein structure, in which the polypeptide backbone curves in a right-handed helical path. This allows hydrogen bonds to form between the carbonyl oxygen (C=O) of one residue and the amide nitrogen (N-H) of the residue four places further up along the peptide chain. Many alpha helices found in proteins have hydrophobic side chains exposed on one side and polar side chains exposed on the opposite side. The hydrophilic side would be positioned on the outer side of protein (where it would be in contact with water) while the hydrophobic side of the alpha helix would be folded towards the core of protein. If an alpha helix breaks, it can cause other local proteins to unwind. Cellular functions and higher biological functions can be disrupted. The protein alpha helix serves as a structurally supporting component for DNA, and for cellular cytoskeletons on a larger scale. On larger biological dimensions, alpha helices are important in the construction of hair as well as wool and hooves. They also serve a role in the composition of other structures, such as the alpha helix beta sheet, in which two or more chains of amino acids sit in parallel.
7. Relate the pH scale to various compartments in the cell - i.e. do all compartments have the same pH? If not why?
All cellular compartments maintain a distinctive pH that is essential to their function. For example, lysosomes have pH ~ 5.0, in order to degrade harmful substances. The acidification of endosomes as they mature from early to late stages is required for the dissociation of receptors and ligands so that receptors can be recycled to the cell surface
23. What are the basic chemical moieties of an amino acid? How does each moiety function in protein structure? Diagram the generalized amino acid structure at pH 7.0.
Amino group, Carboxyl group, Alpha Carbon, hydrogen and an R group (side chain) that can be polar, non polar, acidic, basic etc. The R group (side chain) gives each amino acid its unique properties. α helix and β sheet result from hydrogen-bonding between the N-H and C=O groups in the polypeptide backbone, without involving the side chains of the amino acids. The hydrogen is important for rotation. The diagram at pH 7.0 is in slide 64
31. What are the essential amino acids? What amino acids are considered conditionally essential? Why are they considered conditionally essential?
An essential or indispensable amino acid, is an amino acid that cannot be synthesized de novo by the organism (i.e., from other available organic molecules), and therefore must be supplied in the diet. nutritional essentiality is characteristic of the species, not the nutrient. Nine amino acids are generally regarded as essential for humans. They are: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. Amino acids arginine, cysteine, glycine and tyrosine are considered conditionally essential, meaning not normally required in the diet, but must be supplied exogenously(externally) to specific populations that do not synthesize it in adequate amounts. For example Patients living with PKU must keep their intake of phenylalanine extremely low to prevent mental retardation and other metabolic complications. However, phenylalanine is the precursor for tyrosine synthesis. Without phenylalanine, tyrosine cannot be made and so tyrosine becomes essential in the diet of PKU patients.
13. Describe the pH effect on protein folding? Name 3 amino acids that are particularly subject to this effect. And tell me why.
As you slowly alter the pH you break hydrogen bonds. If the protein is subject to changes in pH, the internal interactions between the protein's amino acids can be altered, which in turn may alter the shape of the protein. Although the amino acid sequence (also known as the protein's primary structure) does not change, the protein's shape may change so much that it becomes dysfunctional, in which case the protein is considered denatured. Pepsin, the enzyme that breaks down protein in the stomach, only operates at a very low pH. At higher pHs pepsin's conformation, the way its polypeptide chain is folded up in three dimensions, begins to change. The stomach maintains a very low pH to ensure that pepsin continues to digest protein and does not denature. Trypsin is another enzyme that is effected by the pH in its environment. It breaks dietary proteins in the small intestine and requires alkaline environment around pH 8. Lipase is an enzyme that breaks down fats and is produced in the pancreas, mouth, and stomach. lipase optimum pH varies based on where it is produced for example in the ancreases 7.5-8.
34. How does Bond Rotation Determine protein folding? Be specific. How would a non-conservative substation alter structure? (like proline for anything but proline) answer in terms of rotation.
Bond rotation determines protein folding, 3D structure This is determined by the nature of the "R" group and it's surrounding "R" groups - the particular environment. steric interactions within the polypeptide severely limit plausible conformations. Steric Hindrance Interference to rotation caused by spatial arrangement of atoms within molecule. Atoms cannot overlap. Atom size defined by van der Waals radii• Electron clouds repel each other. Non-conservative substation changes the R group in that position and the nature of the R group determines bond rotation.
25. Describe how "R" groups function in protein folding- what is the role of Van Der Waal radii? ( not Van der Wall forces)
Bond rotation determines protein folding, 3D structure. This is determined by the nature of the "R" group and it's surrounding "R" groups - the particular environment Interference to rotation caused by spatial arrangement of atoms within molecule Atoms cannot overlap Atom size defined by van der Waals radii (The van der Waals radius, rw, of an atom is the radius of an imaginary hard sphere which can be used to model the atom for many purposes) Electron clouds repel each other
5. Describe chemical bonding from a biochemical point of view- include the types of bonds- their frequency in peptides and proteins, their roles in primary secondary and tertiary structures and their relative contributions to each level of protein organization
Chemical bonds are formed by joining two or more atoms. The combination has lower energy than the separate atoms. There are covenant bonds in which one or more pairs of electrons are shared by two atoms. Ionic bond in which one or more electrons from one atom are removed and attached to another atom. There are also metallic and hydrogen bonding. Primary-covalent bonds= peptide bonds linking amino acids Secondary- Hydrogen bonds conforming protein into beta pleated sheets or alpha helices Tertiary-hydrogen bonds, ionic bonds, van der waals forces, hydrophobic reactions, covalent bonds forming final shape. Quaternary-covalent bonds, ionic bonds or others linking domains.
24. Describe Chirality and Enantiomers in terms of amino acid and protein structure. Which forms do we usually use?
Chiral molecules have a unique three-dimensional shape and as a result a chiral molecule and its mirror image are not completely identical. Enantiomers are chiral molecules that are mirror images of one another but they are not super-imposable. Common amino acids are stereo isomers meaning they have a chiral α carbon center. Amino acids can exist in either the D or L configuration however, all chiral amino acids in proteins have the L configuration.
27. Name 2 Nonstandard amino acids and describe their functions.
Examples of nonstandard amino acids include the sulfur-containing taurine and 1-Aminocyclopropane Taurine Works on Glycine receptors in the brain- the same receptor that strychnine works on. 1-Aminocyclopropane is a small disubstituted cyclic amino acid and a key intermediate in the production of the plant hormone ethylene
17. How did the globin family arise? And why do we need different types of globins? (function)
Globins are haem-containing proteins involved in binding and/or transporting oxygen. Globins have evolved from a common ancestor and can be divided into three groups: single-domain globins, and two types of chimeric globins, flavohaemoglobins and globin-coupled sensors. Several functionally different haemoglobins can coexist in the same species. The major types of globins include: Haemoglobin (Hb): tetramer of two alpha and two beta chains. Hb transports oxygen from lungs to other tissues in vertebrates. Myoglobin (Mb): monomeric protein responsible for oxygen storage in vertebrate muscle. Neuroglobin: a myoglobin-like haemprotein expressed in vertebrate brain and retina, where it is involved in neuroprotection from damage due to hypoxia or ischemia. Cytoglobin: an oxygen sensor expressed in multiple tissues.
32. What makes glycine and proline different from the majority of proteinogenic amino acids?
Glycine is unique among proteinogenic amino acids in that it is not chiral. It can fit into both hydrophilic and hydrophobic environments because of its single hydrogen atom side chain. Proline is an α-Amino acid. The distinctive cyclic structure of the proline side chain gives the prolin an exceptional confrontational rigidity. Glycin and proline help stabilize the triple helix.
22. Describe the formation, growth and chemical modification of hair.
Hair keratin consists of many protein alpha-helices. Three alpha-helices are interwoven into a left-handed coil called a protofibril. Eleven protofibrils are bonded and coiled together to make a microfibril. Hundreds of these microfibrils are cemented into an irregular bundle called a macrofibril. These in turn are mixed with dead and living cells to make a complete strand of hair. , in order for hair to grow 6 inches in one year, 9-1/2 turns of a -helix must be produced every second.
9. Describe how you put togther a double helix in DNA- explain the role of all bond types and of water.
Hundereds of nucleotides are linked togther to form a DNA strand by joining phosphate and suger sides. A long strand of nucleotides is called polynucleotide. These nucleotides are connected by phosphodiester bonds. After DNA strands are formed they join togther to form a double helix. The double helix is stablized by hydrogen bonds and hydrophopic interactions between the bases resulting in the exposure of more polar surfaces to water. histones are highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes. They are the chief protein components of chromatin, acting as spools around which DNA winds, and play a role in gene regulation. Phospate efffect how tightly wrapped the DNA around the histone which effect the degree of expression.
6. Describe the role and formation of hydrogen bonds in DNA and in protein.
Hydrogen bonds hold complementary strands of DNA together, and they are responsible for determining the three-dimensional structure of folded proteins including enzymes and antibodies. Protein structure is partially determined by hydrogen bonding. Hydrogen bonds can occur between a hydrogen on an amine and an electronegative element, such as oxygen on another residue. As a protein folds into place, a series of hydrogen bond "zips" the molecule together, holding it in a specific three-dimensional form that gives the protein its particular function. Hydrogen bonds hold complementary strands of DNA together. Nucleotides pair precisely based on the position of available hydrogen bond donors (available, slightly positive hydrogens) and hydrogen bond acceptors (electronegative oxygens). The nucleotide thymine has one donor and one acceptor site that pairs perfectly with the nucleotide adenine's complementary acceptor and donor site. Cytosine pairs perfectly with guanine through three hydrogen bonds.
29. How does Kwashiorkor occur? What exactly is it? Would it be possible to get Kwashiorkor if you got the wrong enantiomers of essential amino acids?
Kwashiorkor is a form of malnutrition caused by inadequate protein intake in the presence of fair to good energy (total calories) intake. You can get enough calories but if you don't get the essential amino acids our bodies can't make then you can't make proteins - so the calories are pretty much useless. Yes, if the person got the wrong enantiamer they would still get this. That is because your body can only use the L enamtiamer and if you get the wrong kind your body can not use it.
What are the Minimum requirements for collecting test (experimental) information?
Minimum requirements for collecting test information include entering test results with units.
30. Explain the role of Isomerism in diet and nutrition.
Most amino acids occur in two possible optical isomers, called D and L. The L-amino acids represent the vast majority of amino acids found in proteins. Exposure of food proteins to certain processing conditions induces racemization of all L-amino acids to D-isomers. Racemization of L-amino acids residues to their D-isomers in food and other proteins is pH-, time-, and temperature-dependent. The diet contains both processing-induced and naturally formed D-amino acids. The latter include those found in microorganisms, plants, and marine invertebrates. Racemization impairs digestibility and nutritional quality. The nutritional utilization of different D-amino acids varies widely in animals and humans. In addition, some D-amino acids may be both beneficial and deleterious. D-amino acids are abundant components of the proteoglycan cell walls of bacteria. this helps prevent many enzymes from recognizing the proteins in bacterial coats - it's a protective measure. In part this is how probiotics work.
33. Describe the formation and nature of the amino acid bond and peptide backbone.
Proteins are linear polymers formed by linking the α-carboxyl group of one amino acid to the α-amino group of another amino acid with a peptide bond (also called an amide bond). The formation of a dipeptide from two amino acids is accompanied by the loss of a water molecule. A series of amino acids joined by peptide bonds form a polypeptide chain, and each amino acid unit in a polypeptide is called a residue. A polypeptide chain consists of a regularly repeating part, called the main chain or backbone, and a variable part, comprising the distinctive side chains. The polypeptide backbone is rich in hydrogen-bonding potential.
21. How are Disulfide Bonds formed in proteins? Where are they found? How do we break them? How do they work in the process of making functional insulin?
Side chain of cysteine contains highly reactive thiol group. Two thiol groups form a disulfide bond. Disulfide bond formation generally occurs in the endoplasmic reticulum by oxidation. Therefore disulfide bonds are mostly found in extracellular, secreted and periplasmic proteins, although they can also be formed in cytoplasmic proteins under conditions of oxidative stress. Disulfide bonds can be broken by addition of reducing agents. The most common agents for this purpose are ß-mercaptoethanol (BME) or dithiothritol (DTT). Insulin is built from 51 amino acids and is one of the smallest proteins in the body. It is structured with two polypeptide chains linked by two disulfide bonds, connecting the amino acid Cysteine to Cysteine. There is also a third disulfide bond that connects these same amino acids within Chain A.
1. Describe Purpose and Objectives section as it applies to a lab notebook.
Statement or definition of experiment. Anticipated outcomes and plans to achieves outcomes.
28. What are the 4 major classes of proteinogenic alpha-amino acids?
The are Non-polar side chains, Polar side chains, Electrically charged side chains which are divided into Acidic and Basic and they differ by the nature of the R group (side chain). Proline is unique in that it is the only amino acid where the side chain is connected to the protein backbone twice, forming a five-membered nitrogen-containing ring. Strictly speaking, this makes Proline an imino acid. This difference is very important as it means that Proline is unable to occupy many of the main chain conformations easily adopted by all other amino acids. In this sense, it can be considered to be an opposite of Glycine, which can adopt many more main-chain conformations. For this reason, Proline can often be found in very tight turns in protein structures (i.e. where the polypeptide chain must change direction). It can also function to introduce kinks into alpha helices, since it is unable to adopt a normal helical conformation.
35. What are the Protein Conformation Framework constraints? How do backbone tortion angles work? Which angles are most important?
The constrains are steric hindrance due to arrangement of atoms within a molecule as atoms cannot overlap. This spatial arrangement is influence by atom size which is defined by Van der Waals radii. Additionally electron clouds repel each other. The two torsion angles of the polypeptide chain, also called Ramachandran angles describe the rotations of the polypeptide backbone around the bonds between N-Cα (called Phi, φ) and Cα-C (called Psi, ψ). The Ramachandran plot provides an easy way to view the distribution of torsion angles of a protein structure. It also provides an overview of allowed and disallowed regions of torsion angle values, serving as an important indicator of the quality of protein three-dimensional structures. Phi and Psi angles are the most important because they are not restricted from rotation by resonance.
12. Describe the role of hydrophobic effects on folding and stabilization in proteins. Of lipids?
The hydrophobic effect is the property that nonpolar molecules like to self-associate in the presence of aqueous solution. In the case of protein folding, it is used to explain why many proteins have a hydrophobic core which consists of hydrophobic amino acids, such as alanine, valine, leucine, isoleucine, phenylalanine, and methionine grouped together; often coiled-coil structures form around a central hydrophobic axis. When a protein has been folded in the correct way it usually exists with the hydrophobic core as a result of being hydrated by waters in the system around it which is important because it creates a charged core to the protein and can lead to the creation of channels within the protein.
11. Why is water such a good solvent under our environmental conditions? What specific attributes of water allow it to be a god solvent? Which might be a better solvent at -160c - water or methane? And why would it be better?
The polarity and hydrogen-bonding capability of water make it a highly interacting molecule. Water is an excellent solvent for polar molecules. The reason is that water greatly weakens electrostatic forces and hydrogen bonding between polar molecules by competing for their attractions. The existence of life on Earth depends critically on the capacity of water to dissolve a remarkable array of polar molecules that serve as fuels, building blocks, catalysts, and information carriers. High concentrations of these polar molecules can coexist in water, where they are free to diffuse and interact with one another. AT -160C water will be frozen and methane will be a liquid and in turn a better solvent.
Describe the role of shape in the function of a molecule
The shapes of some molecules cause them to have an unequal distribution of electron. This is called polarity. Polar molecules have more electrons around certain atoms, causing the molecule to have a slightly negative charge on one side and slightly positive charge on the other. Polar molecules are attracted to each other due to these opposing partial charges. Molecular shape is important to scientists because it is believed to be the basis for how most molecules of life recognize and respond to one another
20. Describe parallel and anti parallel beta pleated sheets. How can beta sheets orientate charge and hydrophobicity?
This structure occurs when two (or more, e.g. ψ-loop) segments of a polypeptide chain overlap one another and form a row of hydrogen bonds with each other. This can happen in a parallel arrangement or in anti-parallel arrangement. In anti-parallel arrangement, the C-terminus end of one segment is on the same side as the N-terminus end of the other segment. In parallel arrangement, the C-terminus end and the N-terminus end are on the same sides for both segments. The "pleat" occurs because of the alternating planes of the peptide bonds between amino acids; the aligned amino and carbonyl group of each opposite segment alternate their orientation from facing towards each other to facing opposite directions.
10. What exact properties of Van der Waals forces make these forces important in biological systems? And how do they work?
Van der Waals forces are also known as "dispersion forces" or "London dispersion forces." In every molecule, electrons are always moving between the different orbitals. Therefore, sometimes the electrons will be more concentrated on one side of the molecule than the other, creating polarity within the molecule, even if the molecule is not normally polar. Van der Waals forces are the weakest kind of bond, and are responsible for bonding between hydrocarbons. Van der Waals interactions are essential to the attractive forces felt between neutral H2O molecules. Without them, water could not go from a gas into its solid or liquid forms. These intermolecular forces also play a very important part in determining the properties of various molecular compounds, like melting and boiling points and crystal structures. In addition, these forces help form large molecules, like proteins and DNA into the shape required for them to function.
8. How would pH alter the structure of DNA? Of a protein? Mechanisms please!
majority of proteins are quite specific about which task they perform. Protein structure is what dictates this specificity, and the three-dimensional (tertiary) structure is particularly important. When this specific three-dimensional structure is disrupted, the protein loses its functionality and is said to have undergone denaturation. The interactions, such as hydrogen bonding , that dictate the tertiary structure of proteins are not as strong as covalent chemical bonds. Because these interactions are rather weak, they can be disrupted with relatively modest stresses. Changes in pH affect the chemistry of amino acid residues and can lead to denaturation. Hydrogen bonding often involves these side changes. Protonation of the amino acid residues changes whether or not they participate in hydrogen bonding, so a change in the pH can denature a protein. pH extremes can cause denaturation of DNA which is defined as the formation of single strands from double stranded DNA (as opposed to an irreversible loss of structure). pH extremes weaken H-bonds that normally hold together the base pairs of double helix.
2. What goes in the test (experimental) preparation section?
relevant test methods, equipment, and conditions must be described. All laboratory equipment must be identified by type, manufacturer, and model or tool number. It is important to verify that the calibration and preventive maintenance are current on all equipment. All test methods and test specifications must be described in detail.