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Mod. 3 - Proteins
Biochemistry Module 3
| Question | Answer |
|---|---|
| _________________ do all the work in living cells; making them the most important macromolecules | PROTEINS do all the work |
| (t/f) proteins are an amazing molecule because they are all functionally diverse even though they all have the same structure. | FALSE: Proteins are functionally divers and have a multitude of DIVERSE structures |
| list the five main functional categories of proteins | 1) transport 2) hormones 3) catalysts 4) structural 5) Protection |
| transport proteins help with what? | moving molecules |
| what are the functions of hormone proteins | communication between cells and organs. |
| what are catalysts (what is another name for this type of protein)? | enzymes, they speed up the rate of reactions without being changed in the process |
| what is the function of structural proteins | provide strength to tissues, cells, and organelles |
| what is the functions of protection proteins | to protect the cell/organism against foreign invaders |
| Antibodies are in what class of protein | protection proteins |
| protease is an enzyme. therefore, it fits in which type of protein | catalyst protein |
| what class of proteins would collagen fit into | structural proteins |
| relaxin fits into which class of proteins | hormone proteins |
| hemoglobin is in what class of proteins | transport proteins |
| what is the function of relaxin | relax the pelvic ligaments during childbirth |
| what is the function of protease (it also has an "industrial" use, what is it) | BIOLOGICAL USE: breaks down proteins in the cell for recycling amino acids INDUSTRIAL USE: in laundry detergents, added to help with removal of blood/food stains |
| where in the body can collagen be found | skin, tendons, and cartilage |
| what is the function of an antibody? | to help white blood cells fight against invaders |
| this group of amino acids are the simplest, they are relatively small, the side chains are straight, they are often found in the interior of the protein (away from polar water) and they are nestled with amino acids of this group | non-polar aliphatic group |
| what is the three letter and one letter abbreviation of the following amino acid. Also name the group that it belongs to GLYCINE | - Gly - G - Non-Polar Aliphatic Group |
| draw a glycine molecule | see drawing |
| Gly | GLY - Glycine |
| G | G - Glycine |
| what is the three letter and one letter abbreviation of the following amino acid. Also name the group that it belongs to ALANINE | - Ala - A - Non-polar Aliphatic Group |
| draw an alanine molecule | see drawing |
| Ala | ALA - Alanine |
| A | A - Alanine |
| what is the three letter and one letter abbreviation of the following amino acid. Also name the group that it belongs to VALINE | - Val - V - Non-Polar Aliphatic Group |
| Val | VAL - Valine |
| V | V - Valine |
| draw a Valine Molecule | see drawing |
| the Proline amino acid deviates from the general structure of most members of the group _________________; this structure is important because | NON-POLAR ALIPHATIC GROUP; this structure is not as flexible as the other members of this group |
| what is the three letter and one letter abbreviation of the following amino acid. Also name the group that it belongs to PROLINE | - Pro - P - Non-Polar Aliphatic Group |
| Pro | PRO - Proline |
| P | P - Proline |
| draw a the proline structure | see drawing |
| what is the three letter and one letter abbreviation of the following amino acid. Also name the group that it belongs to LUECINE | - Lue - L - Non-Polar Aliphatic Group |
| draw a Leucine molecule | see drawing |
| Leu | LEU - Leucine |
| L | L - Leucine |
| what is the three letter and one letter abbreviation of the following amino acid. Also name the group that it belongs to Isoeucine | - Ile - I - Non-Polar Aliphatic Group |
| draw an Isoeucine molecule | see drawing |
| Ile | ILE - Isoeucine |
| I | I - Isoeucine |
| what is the three letter and one letter abbreviation of the following amino acid. Also name the group that it belongs to METHIONINE | - Met - M - Non-Polar Aliphatic group |
| Met | MET - Methionine |
| M | M - Methionine |
| draw a Methionine molecule | see drawing |
| this group of amino acids is non-polar, has a ring of carbons, they are slightly larger and more rigid than Aliphatic amino acids | Non-Polar Aromatic Group |
| Name all the amino acids in the Non-polar aliphatic group (there should be 7) | - glycine - alanine - valine - proline - leucine - isoeucine - methionine |
| name all the amino acids in the non-polar aromatic group | - phenylalanine - tryptophan - tyrosine |
| what is the three letter and one letter abbreviation of the following amino acid. Also name the group that it belongs to PHENYLALANINE | - Phe - F - Non-polar Aromatic Group |
| draw a phenylalanine molecule | see drawing |
| F | F - phenylalanine |
| Phe | PHE - phenylalanine |
| what is the three letter and one letter abbreviation of the following amino acid. Also name the group that it belongs to TRYPTOPHAN | - Trp - W - Non-Polar Aromatic Group |
| draw a tryptophan molecule | see drawing |
| W | W - Tryptophan |
| Trp | TRP - Tryptophan |
| what is the three letter and one letter abbreviation of the following amino acid. Also name the group that it belongs to TYROSINE | - Tyr - Y - Non-Polar Aromatic Group |
| Tyr | TYR - Tyrosine |
| Y | Y - Tyrosine |
| draw a tyrosine molecule | see drawing |
| describe the Polar but Neutral group of Amino Acids | they have a side chain with a dipole that can hydrogen bond, it interacts strongly with water and is usually found on the outside of the protein molecule |
| name the five amino acids in the Polar but Neutral group | 1) Serine 2) Threonine 3) Cysteine 4) Asparagine 5) Glutamine |
| what is the three letter and one letter abbreviation of the following amino acid. Also name the group that it belongs to SERINE | - Ser - S - Polar but Neutral |
| Ser | SER - Serine |
| S | S - Serine |
| draw a serine molecule | see drawing |
| what is the three letter and one letter abbreviation of the following amino acid. Also name the group that it belongs to THREONINE | - Thr - T - Polar but Neutral |
| draw a Threonine molecule | see drawing |
| Thr | THR - Threonine |
| T | T - Threonine |
| what is the three letter and one letter abbreviation of the following amino acid. Also name the group that it belongs to CYSTEINE | - Cys - C -Polar but Neutral |
| draw a cysteine molecule | see drawing |
| Cys | CYS - Cysteine |
| C | C - Cysteine |
| what is the three letter and one letter abbreviation of the following amino acid. Also name the group that it belongs to ASPARAGINE | - Asn - N - Polar but Neutral |
| draw an Asparagine molecule | see drawing |
| Asn | ASN - Asparagine |
| N | N - Asparagine |
| what is the three letter and one letter abbreviation of the following amino acid. Also name the group that it belongs to GLUTAMINE | - Gln - Q - Polar but Neutral |
| Gln | GLN - Glutamine |
| G | G - Glutamine |
| draw a glutamine molecule | see drawing |
| name the acidic amino acids | 1) aspartic acid 2) Glutamic Acid |
| what is the three letter and one letter abbreviation of the following amino acid. Also name the group that it belongs to ASPARTIC ACID | - Asp - D -Acidic Amino Acid |
| what are some properties of Acidic Amino Acids | chains with a pKa that is less than 7 and loose their protons in lower pH ranges; usually it is found in contact with water, anf found close to basic amino acids. |
| Asp | ASP - Aspartic Acid |
| D | D - Aspartic Acid |
| draw an aspartic acid molecule | see drawning |
| what is the three letter and one letter abbreviation of the following amino acid. Also name the group that it belongs to GLUTAMIC ACID | - Glu - E - Acidic Amino Acids |
| Glu | GLU - Glutamic Acid |
| D | D - Glutamic Acid |
| draw a glutamic acid molecule | see drawning |
| name the amino acids that are in the basic amino acids | 1) Arginine 2) Lysine 3) Histidine |
| what are some of the properties of basic amino acids | chains with pKa values that are greater than 7, these chains are normally positively charged, often found intact with water and near acidic acids |
| what is the three letter and one letter abbreviation of the following amino acid. Also name the group that it belongs to ARGININE | - Arg - R - Basic Amino Acids |
| Arg | ARG - Arginine |
| R | R - Arginine |
| draw arginine molecule | see drawning |
| what is the three letter and one letter abbreviation of the following amino acid. Also name the group that it belongs to LYSINE | - Lys - K - Basic amino acid |
| Lys | LYS - Lysine |
| K | K - Lysine |
| draw a lysine molecule | see drawing |
| what is the three letter and one letter abbreviation of the following amino acid. Also name the group that it belongs to HISTIDINE | - His - H -Basic Amino Acid |
| His | HIS - Histidine |
| H | H - Histidine |
| draw a histidine molecule | see drawing |
| what is an important/unique property of the Histidine | - does not have a charged group, it appears differently in slightly lower pH, the pKa of the new H3N+ is 6.00 |
| what important functional group does cysteine have? | Thiol (SH) |
| this particular amino acid can react with itself to from a disulfide bond | cysteine |
| what is a disulfide bond | when the sulfa in a cysteine amino acid reacts to the sulfa in another cysteine amino acid |
| what is the importance of the disulfide bonds | stabilizes the protein and is commonly found in proteins that exist outside the body (keratin - Hair, skin and nails) |
| (not a question) proteins from from condensation of amino acids | (not an answer) polypeptides are amino acids linked together |
| what are proteins | large, macromolecules, their shape is dictated by an amino acid (which is dictated by DNA) |
| what is the site of polypeptide formation | ribosomes |
| how are amino acids formed in ribosomes | synthesis reactions are bond amino acids bond to each other covalently |
| where does do amino acids bond to each other. Draw the amino acid back bone showing this. | amine binds to the carboxylic acid |
| what is released as a by product after amino acids are joined together | a water molecule |
| since water is released as a byproduct of polypeptide formation, the reaction of amino acid bonding is called _____________ and the amino acids that are left are called ________________ | condensation reaction; residues |
| what is a dipeptide | two amino acids that are attached to one another |
| what is a peptide bond | the result of two amino acids joining together |
| what is an oligopeptide | a ***short*** chain of amino acids (usually 2-20 but there is no strict limmit) |
| normally when you write down the a string of polypeptides. it goes from the _______________ terminal end to the _______________ terminal end | Left to right (N-Terminal end (or Amine Group) to the C-Terminal end (Carboxyl Group)) |
| what is a protein back bone | it is the peptide bonds that are formed by all amino acids linked together, the R group points away from this. |
| what are residues | residues (are essentially the amino acids) and reflect the remaining amino molecule after a condensation reaction |
| a four residue molecule would indicate | that the molecule has four amino acids. |
| what the cut off point between a polypeptide and a protein? | Polypeptide is 99 molecules or less, and a protein is 100 molecules or more |
| what is the importance of a ribbon diagram | it highlights the protein backbone |
| a ribbon diagram does not show | the side chains (or r groups) |
| how are proteins measured | by weight in Daltons (Da) |
| convert 15 kDa to g/mol | 15000 g/mol |
| what are some examples of human hormones that are oligopeptides/polypeptides | oxytocin and relaxin |
| is albumin a peptide or a protein | albumin is a protein |
| Daltons measures _______________________ | mass |
| what is supramolecular chemistry | supramolecules are large molecules that can have 2 or three proteins combined. DNA is a supramolecular compound |
| what is protein conformation | the 3-D shape that amino acids take who they are folded into their protein structure. |
| name the two main types of protein confirmation | 1) fibrous proteins (usually long/extended structures) 2) globular (functional) proteins |
| (t/f) each protein adopts one and only one type of confirmation | FALSE: protein can adopt *at least* one confirmation. The protein can have more than one structure. |
| portions of proteins have a random confirmation are considered | intrinsically disordered |
| (t/f) generally speaking, only a small portion of intrinsically disordered proteins are considered functional | true: most intrinsically disordered proteins are not functional |
| (t/f) there is no specificity among proteins when it comes to structure and functions | FALSE: structure and function are highly specified among proteins and structure is VITAL to protein function |
| what are the standard levels of protein structure | - Primary - secondary - tertiary - quaternary |
| what is the primary structure of proteins | a polypeptide chain, the order of amino acids that are covalently bonded |
| (t/f) the primary structure of an amino acid includes disulfide bonds | TRUE: disulfide bonds are included in primary structures of amino acids |
| why might using one letter abbreviations of amino acids useful when writing out polypeptide chains | it helps determine polar and non-polar stretches in the protein, it can also be used to compare and contrast the proteins of other organisms or other proteins to look for similarities (this is usually done by a computer) |
| what is the secondary structure of a protein | the *local* 3-D structure of amino acid residues in close proximity to one another |
| what are the three types of secondary structures | 1) alpha-helices 2) beta-sheets 3) beta turns |
| what is the shape of an alpha helices | coiled, the backbone of the atoms form hydrogen bonds to stabilized the structure, the r-groups of the amino acid face out and the backbone is on the inside of the coil |
| about how many acids are in one rotation of the alpha-helix | 3.6 amino acids |
| how many angstroms exist per turn in an alpha helix | 5.4 anstroms per turn |
| what is an angstrom | 1 * 10^-10 m |
| name the three amino acids that you would be most likely to see in a alpha helix turn | alanine, arginine, and leucine |
| name two amino acids you would be less likely to see in a helix turn | proline, glycine |
| this type of amino acid model would give the viewer the sense of a protein's bulk (highlighting the lack of space) | space-filling model |
| in an alpha-helix, the side chains face out, what do they do (what is their purpose) | they interact and form non-covalent bonds with other side chains, water or other chemicals |
| what are beta sheets | they are the sheet-like structure or an extended structure of amino acids, creates a zig-zag orientation, with adjacent side chains that are as far apart as possible |
| what are beta sheets made out of | individual beta strands that are interacting with each other using hydrogen bonds |
| what are the two different variations of beta sheets | 1) anti parallel beta sheets 2) parallel beta sheets |
| describe the structure of the anti-parallel beta sheets | one beta strand will end and then the amino acid sequence turns on itself and the next beta strand goes the opposite direction |
| about how many angstroms are in one anti-parallel beta sheet | 7.0 angstrom |
| describe the parallel beta sheets | the beta strands go in the same direction |
| how many angstroms are in one parallel beta strand | 6.5 angstroms |
| what is the difference between the parallel and the anti-parallel sheets | the hydrogen bonding partners are different and the distances are different for each repeat |
| what is the purpose of beta turns | they permit amino acids to form secondary structures that are immediately next to eachother |
| beta turns are most commonly: | - 4 unit residues - 180 degree turns - completely different from beta sheets - can form both alpha -helixes and beta sheets |
| what is a motif | a collection of stable groups of secondary structures |
| give an example of a motif | beta-meander (a beta sheet that meanders kind of like a stream) |
| (not a question0 variety of motifs are found in a variety of proteins in diverse organisms | (not an answer) occupy a position between secondary and tertiary structures but not one of the four levels |
| what are tertiary structures | they are the 3-D structure of the protein *as a whole," this includes all the secondary structures |
| how are tertiary structures maintained | disulfide bonds and non-covalent bonds |
| myoglobin contains a heme ring. this heme ring is called a _____________________ | prosthetic group |
| what is a prosthetic group | the non-amino acid portion of a molecule, that is necessary for the structure and function of the protein, |
| (t/f) all proteins have prosthetic groups | FALSE: NOT all proteins have prosthetic groups |
| what class of proteins does myoglobin fit into | myoglobin is a functional (globular) protein |
| compare and contrast the force of a whole protein to that of a covalent bond | Whole Protein: 20-65 kJ/mol Covalent Bond: 400kJ/mol |
| what is the function of a protease inhibitor | inhibit protease from degrading other protiens |
| give examples of fibrous proteins | keratin, collagen, (generally long and extended structures made almost entirely of alpha-helices |
| what is the function of a beta barrel conformation | to create pores across a plasma membrane (integral proteins) have hollow centers and permits ion and molecule passage |
| what makes beta barrels | beta sheets wrapped around themselves |
| what is the quaternary structure | the description of a macromolecule, it contains two (or more) independent polypeptide chains that are associated with one another. |
| how are the different polypeptide chains in a quaternary structure described | by number and orientation |
| a staphylokinase is considered to be a dimer because | it has two identical polypeptide chains |
| what is a dimer | two tertiary structures brought together to make a quaternary structure |
| a hemoglobin is considered a tetramer becase it has | four tertiary structures that have been brought together |
| name the subunits in hemoglobin | there are two alpha subunits and two beta subunits |
| there is a protein in an earth worm that has up to 180 sub units. the name of this protein is | lumbricus erythrocruorin |
| proteins that end in -"in" | are not enzymes |
| proteins that end in "-ase" | are enzymes |
| what are enzymes | they are globular (functional) proteins that accelerate the speed (by about 1 thousand times) of chemical reactions, enzymes are highly specific and highly specialized, they are critical to every biological process |
| in order for a reaction to occur, what must happen first | the reactant must first bind to the enzyme |
| Fumerase is an enzyme used in the __________________ cycle | citric acid cycle |
| the citric acid cycle is considered a ____________________ reaction, because it adds water to double bonds | hydration reaction |
| write the chemical reaction that takes place with Fumarate | Fumarate + Water => Malate -OOCCH + H2O => -OOCCH2CH(OH)COO- |
| the hydration reaction of fumarate.... | helps produce energy for a cell |
| what is the generalized reaction of an enzyme | E+S => ES => E+P |
| what is a substrate | a chemical species that binds to the enzyme |
| what is an ES complex | an Enzyme substrate complex is a substrate that is bound to the enzyme but it is not converted yet |
| what is the actual function of Fumarase | breaks the double bond of Fumarate by adding water |
| lyase enzymes | a molecule that creates/breaks a double bond by adding water |
| according to the Internations Union of Biochemistry and Molecular Biology there are 6 classes of enzymes, what are they | 1) oxidorecuductase 2) transferals 3) hhydrolase 4) isomerases 5) ligases 6) lyase |
| oxidoreductase enzymes | perform oxidation and reduction reactions |
| transferals enzymes | transfer a group from one molecule to another |
| hydrolase enzymes | break bonds through hydrolysis |
| isomerase enzymes | rearrange a molecule |
| ligases enzymes | join two molecules or join to parts of a molecule |
| what is luciferase | an enzyme in a lightning bug |
| what type of enzyme is a luciferase (consider this: the reactions that make luciferin are triggered by the presence of oxygen) | oxidoreductase |
| cofactors and coenzymes are a form of | cofactors and coenzymes are forms of prosthetic groups |
| what is a cofactor | a non-protein of an enzyme and is only present in some enzymes |
| what are some examples of cofactors | - metal ions - have positive charge density - trace metals |
| what are coenzymes | cofactors that are also organic compounds |
| what are some examples of cofactors | - vitamin c - nniacin |
| what is the function of co enzymes | they assist in the transfer of chemical groups |
| the lack of coenzymes can make enzymes non functional, leading to the cause of | some medical conditions |
| what is an apoenzyme | an enzyme with out a cofactor (inactive) |
| what is a holoenzyme | an enzyme with a cofactor added (active) |
| comparing the activity of the apoenzyme with the activity of the holoenzyme helps with what | determine the role of the cofactor/coenzyme |
| define activity | the enzymes ability to turn reactants into products |
| define activation | an enzyme activity is initiated/increased ability to generated products; this can occur with addition of cofactor, increase activity, and can occur with some other changes |
| what are active sites | spot on enzyme where catalyzes takes place |
| about how many amino acids help define the enzymes active sites | 10 amino acid residues define the space |
| who does the active site work | the amino acid residues form non-covalent bonds with substrates and generated favorable energy needed for chemical reaction, provides energy to initiate reaction |
| what gives the enzyme specificity | the active site |
| what is an induced fit | when the shape of the enzyme changes to accommodate the substrate; small movements of amino acids to bind a substrate |
| draw a graph that shows how an enzyme lowers the gibbs free energy of a reaction | see picture |
| what is the transition state | the enzyme changing during conformation to match substrate shape, the structure of the molecule as it transitions to a new molecule |
| in the transition state, the Potential Energy is (high/low) | in the transition state the potential energy of the enzyme is HIGH |
| what is the most unstable part of a reaction when the enzyme is involved | the transition stage, because it is most difficult for molecule to adopt this state |
| name three factors that varies the rate of the reaction | 1) increased/decreased substrate concentration 2) pH of the solution 3) Temperature |
| how does substrate concentration play a role in reaction rate | with increase substrate concentration then there is an increased rate of substrates running into each other |
| at what point does substrate concentration no longer work | when all enzyme active sites are full |
| how does pH affect the rate of the reaction | the enzymes only function at certain pH levels, if the pH is too high or low, then the enzyme degrades |
| (t/f) various enzymes can exist at different pH levels | TRUE, some cells live in locations with high or low pH and have enzymes that can also live at pH's of that level. also the enzymes in lysosomes exist at pH levels of 5.0 |
| uncatalyzed, with the increase in temp. what happens to the reaction | rates increase and for each 10 degrees C the rate increases two times |
| why does increased temp help increase reaction rate | gives molecule more energy and permits more collision |
| for enzymes what happens with increased temperature | leads to and"unfolding" of the protiens and renders the enzyme innert. therefore the organism needs to be at optimal temps (37 degrees of C). |
| what are inhibitors | they stop enzymes from working, or at least slows them down |
| how do inhibitors work | they bind to the enzyme to prevent a reaction |
| how do inhibitors bind to enzymes | non-covalent integrations |
| name the three types of inhibitors | 1) competitive 2) uncompetitive 3) mixed |
| how do competitive inhibitors work | they compete with the substrate for the active site on an enzymes and the best one creates a strong bond at the active site |
| how does an uncompetitive inhibitor work | this is seen in enzymes that have more than one active site; these enzymes bind to the enzyme substrate complex instead of the active site. This prevents catalysis |
| how do mixed inhibitors work | these can work in enzymes that have two or more active sites. these inhibitors can bind to either an enzymes active site OR the enzymes substrate complex |
| how are artificial inhibitors used | in poisons or medication drugs |
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kandriot
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