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Test 1
Biochem Test 1
| Term | Definition |
|---|---|
| How many naturally occurring elements are there? | 90 elements |
| How many of the 90 naturally occurring elements comprise 98% of the cell mass? | 3 (Hydrogen, Oxygen, and Carbon) -- mostly due to the fact that the body is comprised of a lot of water |
| What is the goldilox zone? | The distance from the sun that gives the right temperature to have liquid water |
| Why can't you have silicon based life? | Because the product of Si6H12O6 is SO2, which is ROCK. |
| What do elements + bonds create? | Molecules |
| What are polymeric molecules? | Similar molecules joined in chains |
| What are some examples of polymeric molecules? | Proteins (Amino Acids) and RNA&DNA (nucleotides) |
| What is something that macromolecules can form? | Organelles |
| What is the most important organelle? | Cell membrane |
| What is the cytoskeleton important? | Helps cells without walls maintain their shape |
| What are the functions of proteins? | Make enzymes, transport, provide structure, recognition |
| What are the functions of nucleic acids? | Genetics, structural ribosomes, make enzymes |
| What are three types of lipids? | Fats/Oils, Steroids, and Waxes |
| What did Pasteur realize about decomposition? | Decomposition is a biological and chemical action |
| What did the Buchner Brothers do? | Made a nutritional supplement known as a "Tonic" |
| How did the Buchner Brothers make the tonic? | Ground up yeast (from a brewery) -- preserved in high sugar (sugar was tastier) -- bottles exploded (proved that yeast were not dead) -- reground the yeast -- no growth on plates but bottles still exploded -- isolated enzymes |
| What are proteins that work without cells called? | Enzymes |
| What does the word "enzyme" mean? | In yeast |
| When a peptide bond forms, what is the product that is taken out? | Water (H2O) |
| Where do peptide bonds form? | Between the carboxy and amino terminal |
| In a stereochemical projection, what is the line that comes at you and what is the line that goes away from you (dashed or solid)? | Solid is coming at you, Dashed is going away from you |
| What is another word for the alpha carbon? | Tetrahedral carbon, central C atom |
| What does it mean to be chiral? | Have 2 mirror image forms (L and D) |
| What does the L chiral form stand for? | Levo |
| What does the D chiral form stand for? | Dextro |
| Where are L chiral forms found? | Found in biologically encoded proteins (genetic) |
| Where are D chiral forms found? | not genetically encoded -- found in bacterial cell walls |
| At a neutral pH, free amino acids exist as what? | Dipolar ions (Zwitterions) |
| A positive charge means that an element is (protonated/deprotonated)? | Protonated |
| A negative charge means that an element is (protonated/deprotonated)? | Deprotonated |
| As pH increases, COOH or NH3 is first to give up its proton? | COOH |
| At what pH will the dipolar form exist until? | pH = 9.0 |
| At waht pH does the amine group become deprotonated? | 9.0 |
| What is the physiological pH range? What does this mean about most amino acids? | 6.5-7.5 -- most amino acids will exist in the dipolar form |
| How many side chains are there for amino acids? | 20 side chains (R-groups) |
| What are 4 classifications of Amino Acids? | 1) Hydrophobic Amino Acids have mainly hydrogen R groups, 2) Neutral overall, 3) positively charged amino acids, 4) negatively charged amino acids |
| What do side chains consist of in hydrophobic amino acids that mainly have hydrogen R groups? | Hydrogens and Carbons |
| What amino acids are part of the hydrophobic amino acid group? 9 of them | Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline, Phenylalanine, Tryptophan |
| What is special about glycine? | It is the only achiral amino acid |
| What type of R group do neutral overall amino acids have? | Contains an electronegative atom that hoards electrons |
| What amino acids are part of the neutral overall group? 6 of them | Serine, Threonine, Tyrosine, Cysteine, Asparagine, Glutamine |
| What do serine, threonine, and tyrosine all have in common? | All have -OH groups -- O hoards the electrons from the H's |
| How is cysteine different than serine? | Cysteine has an HS group instead of an OH group |
| What linkages may 2 molecules of cysteine form? Are these bonds strong or weak? | Disulfide linkage (cystine) -- very strong (covalent) |
| What are similar between asparagine and glutamine? | Contain a terminal carboxamide |
| What are the positively charged amino acids? 3 of them | Lysine, Arginine, Histadine |
| What do lysine and arginine have in common? | long side chains that terminate in "+" charged group -- Lysine has an amino group and arginine has a Guanidium group |
| What type of group does histadine have? | Imidizole group (aromatic ring that can be "+" |
| Where is histadine usually found? | At the active site of enzymes -- where it can bind and release protons during the course of the enzymatic reaction |
| What are the 2 negatively charged amino acids? | Aspartic Acid (Aspartate) and Glutamic Acid (Glumamate) |
| What are unique about the negatively charged amino acid side chains? | They have acid side chains |
| What is muctase? | The widget of molecular biology --- no such thing --- just a theoretical idea |
| What is unique about proline in a sequence? | The sequence cannot translate past proline -- it just stops -- can't skip over it, just stops |
| What is an essential amino acid? | Dietary requirement, because humans cannot synthesize them because the pathways are broken -- obtained from ingested food |
| What are the essential amino acids? | Histadine, Isoleucine, Leucine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine, Lysine |
| What are the non-essential amino acids? | Alanine, Arginine, Asparagine, Aspartate, Cysteine, Glutamate, Glutamine, Glycine, Proline, Serine, Tyrosine |
| What is a nutritional disorder lacking proteins? | Kwashiokor's |
| What is a primary structure of an amino acid? | Order of amino acids on protein "chain" -- determined usually by gene sequence -- held together by peptide bonds |
| How many amino acids does a dipeptide have? How many peptide bonds? | 2 amino acids -- 1 peptide bond |
| What is an oligopeptide? | Small stretch of amino acids -- less than 20 |
| What is a polypeptide? | Large stretch of amino acids -- can be 1000s (often used as synonym for protein) |
| How do you read an amino acid sequence? (amino to carboxy or carboxy to amino)? | Amino to Carboxy |
| Why do some species rely on metabolic water? Where does metabolic water come from? | Some species rely on it because they don't consume water. It comes from the peptide bond formation (precipitates one water for each bond formed) |
| Do peptide bonds wnat to break or form? | Break |
| Is energy required to form or is it released when a peptide bond is formed? | It is required to form |
| How is the stability of a peptide bond once it is made? | Is it realtively stable -- in a sterile tube with H20, it takes about 1000 years to break apart (if no catalyst is present) |
| What 2 parts does a polypeptide chain consist of? | The main chain or backbone and a variable part (R group) |
| Is a carbonyl group a hydrogen acceptor or donor? | Acceptor |
| Is an amino group a hydrogen acceptor or donor? | Donor |
| Which amino group is not a good hydrogen donor? | Proline |
| How many amino acids does a naturally occurring polypeptide contain? | Between 50 and 2000 amino acids |
| What is the largest biological protein? | Titin = 27000 amino acids (found in muscles) |
| What is the mean molecular weight of an amino acid? | 110 g/mol = 110 AMU |
| What is the molecular weight of most proteins? | Between 5500 and 22000 Daltons |
| How many hydrogen atoms is 1 Dalton equal to? | 1 Hydrogen |
| What link most commonly cross-links linear polypeptide chains? | Disulfide bonds |
| What did Frederick Sanger do? In what year? | In 1953 -- determined the amino acid sequence of insulin -- showed biologically derived proteins had a precisely defined aa sequence -- determined that only L-form aa's found in polypeptides (not D-form) -- everything was also connected with peptide bonds |
| How do proteins move through the polyacrylamine gel electrophoresis? | Based on size -- smaller move faster due to less resistance |
| How are polypeptide chains flexible yet restricted conformationally? 3 ways | 1) Peptide bonds are essentially planar, 2) Peptide bonds exhibit considerable double bond character due to the resonance of electrons involved (between single and double bond), 3) peptide bonds are uncharged |
| What is the C-N distance in a peptide bond? How does this compare to double and single bonds? | 1.32 A -- single bonds are 1.27 and doubles are 1.45 -- falls right in the middle |
| Why is it significant that peptide bonds are uncharged? | would affect how close proteins can come together within a 3D structure because AA are joined by peptide bonds and same charges repell -- can form compact globular structures that wouldnt be possible otherwise with charge repulsion |
| What are 2 possible configurations for planar peptide bonds? | Trans and Cis |
| Almost all peptide bonds in proteins are cis or trans? | TRANS |
| What are most peptide bonds in proteins trans? | Steric clashes can occur between R groups in cis arrangement but not in trans |
| What is different about the peptide bonds and the bonds between the amino group and alpha carbon and between alpha carbon and carbonyl group? What does this allow for? | Those bonds are just plain old single bonds and can rotate freely? This allows for complex 3D folding |
| What are the angles of rotations expressed as for bonds between N and alpha Carbon and alpha Carbon and carbonyl? | Phi for N and alpha carbon -- Psi for Alpha carbon and carbonyl bond |
| What are Ramachandran plots? | Involve Psi and Phi bonds -- allows you to plot these angles and view conformations |
| Who discovered the secondary structure? When? | Linus Pauling -- 1951 |
| Linus Pauling proposed that certain polypeptide chains have the ability to fold into TWO periodic structures. What are they? | Alpha Helix and Beta Pleated Sheet |
| What are two structures besides alpha helix and beta pleated sheet that have now been identified? | Turns and Loops |
| How is a secondary structure formed? What does this have to do with R groups? | Hydrogen bonding occurs between the NH and CO groups of peptide-bonded amino acids -- nothing to do with R groups |
| What is the alpha-helix? | Rod-like structure with a tightly coiled backbone -- R groups extend outward from the backbone |
| How is the alpha-helix stabilized? | With Hydrogen bonding between NH and CO groups of the main chain |
| Why do we coil? | Otherwise the amino acids would be too far apart to bind together -- this brings them closer together |
| Each amino acid is related to its neighbor by a rise of ____ Angsroms along the helical axis and a rotation of ____ degrees. | 1.5 A and 100 degrees |
| What is the Angstrom of a DNA helix? How does this compare to an alpha helix? Does this mean alpha helix is more sparse or denser than DNA? | DNA = 3.4 A, Alpha Helix is 1.5 A -- Alpha helix is denser than DNA |
| How many amino acids are there in a turn of an alpha helix? | 3.6 Amino Acids |
| Amino acids spaced apart by how many in a primary structure are close together in a helix? | Spaced apart by 3 or 4 amino acids (residues) |
| What will amino acids spaced apart by 2 be in relation to each other in the helix? | Opposite sides -- unlikely to make contact |
| What is the "pitch" of a helix? | Full revolution of the helix |
| How is the size of the pitch of helix measured? | 1.5 A (rise) multiplied by number of amino acids per turn (3.6 per turn) = 5.4 A |
| Are most helices right handed turns or left handed turns? Clockwise or counterclockwise? Why? | Right handed clockwise -- More energetically favored because there would be fewer collisions (steric clashes) between R groups |
| How are helices represented when drawn? | In ribbons or cylinders |
| Which 3 amino acids tend to destabilize helices due to branching? | Valine, Threonine, Isoleucine |
| Which 3 amino acids tend to disrupt because their side chains contain H-bond donors or acceptors in close proximity to main chain and therefore compete for H bonding with CO and NH groups? | Serine, Aspartic Acid, Asparagine |
| Which amino acid is a helix breaker? Why? | Proline -- because of its lack of NH group and because ring structure prevents it from assuming a Psi value to fit into an alpha helix |
| What % of soluble proteins are composed by alpha helices? | 25% |
| How is a beta sheet formed? How does this differ from a helix? | Requires multiple lines of proteins -- Helices come from single linear protein |
| Is a B-sheet coiled or fully extended? | Fully extended |
| What size (Angstroms) is a Beta sheet compared to a Helix? | Beta sheet is 3.5 A and a helix is 1.5 A |
| Do parallel beta sheets hydrogen bond at an angle or straight up and down? | At an angle |
| Do anti-parallel sheets bond at an angle or straight up and down? | Straight up and down |
| How many beta strands must be present to form a beta sheet? | 2 or more |
| In a 2-D picture are beta strands on top of each other or in one line? | Adjacent (in one line) -------O------O----O----- |
| What is the typical number of stands that interact to form a sheet? | 4 or 5 typically but can be as few as 2 or as many as 10+ |
| What is the shape that can denote a B-sheet? Where does the point point towards? | An arrow -- the arrow tip points to the direction of the carboxy terminus |
| Do beta sheets form planar structures or globular structures? | Flat, planar -- slightly twisted |
| Why are turns and loops important? | Allow polypeptide chains to change directions by making reverse turns and loops -- brings about compactness (globular shape) |
| Where are turns and loops most often found? What is a function that this location can aid in? | On the surface of globular proteins -- often participate in interaction of the protein with the environment and other molecules |
| Loops exposed to aqueous environments are usually composed of: | Hydrophilic amino acids (charged + or -) |
| What are two examples of fibrous proteins? | Collagen and keratin |
| Where is alpha keratin found? What is is composed of? | Wool and hair -- two right handed helices intertwined to form a left handed super helix (coiled coil) |
| What does the function of a coiled coil protein depend on? | Secondary structure rather than tertiary |
| How many coiled coil proteins do humans contain? | About 60 |
| Where are human coiled coil proteins found? | In cytoskeleton -- myosin and tropomyosin |
| What are the two alpha keratin chains linked by? | van der Waals forces and some ionic interactions |
| What is the most abundant mammalian protein? | Collagen |
| What is collagen the main component of? | Skin, bone, cartilage, tendons, teeth |
| How many helical polypeptide chains is collagen made of? How many amino acids is each chain made of? What interlocks between the 3 fibers? | 3 chains -- 1000 AAs each (prolines interlock between the 3 fibers) |
| What is a tertiary structure? | Most important structural level in terms of protein function -- 100% based on primary sequence of AAs. -- Deals with R-group interactions |
| Where is myoglobin found? | Cardiac and Skeletal muscle |
| Myoglobin is ___ amino acids long. It folds a little/a lot? | 153 -- a lot! 1/10 the length of primary sequence |
| What % of myoglobin is an alpha helix? How many helices are there? | 70% myoglobin molecule is alpha helices -- there are 8 of them |
| Is the interior of mygolobin glob hydrophobic or hydrophilic? | almost 100% hydrophobic -- only 2 polar amino acids on interior (both are hisitidine -- where Fe/O2 bind) |
| Is the exterior of myoglobin hydrophilic or hydrophobic? | Mix of both |
| Unpaired NH and CO act hydrophobically or hydrophilically? | Hydrophilically |
| What is the only way to embed a protein in a hydrophobic layer? How do you do this? | Need to pair all hydrogen bonds in NH and CO -- the only way to do this is by making a Beta Sheet |
| What are porins? | Pore proteins found in membranes |
| H20, glucose, and amines will only pass through a proin if it is _______. | Hydrophilic |
| What is a motif? | repeating structure found in different species of protein -- example -- helix, turn, helix, turn, helix, turn |
| What is a Quaternary structure? | optional structure -- arise from joining 2 or more separately made polypeptides into a single unit |
| What is the simplest quaternary structure? | Dimer |
| What is the difference between a homodimer and a heterodimer? | Homodimer is two identical structures -- heterodimer is two non-identical structures (2 diff sequences) |
| What is the poster child of quaternary structures? | HEMOGLOBIN |
| What subunits does hemoglobin have? | 2 alpha subunits and 2 beta subunits (not like beta sheet or alpha helix) -- these have to do with alpha and beta genes |
| What is the minimum number of genes required to make hemoglobin? | 2 (1 alpha and 1 beta gene) |
| What is Beta Thalassemia? | defect in Beta gene -- to have this gene, you would have to inherit a defective beta gene from BOTH parents (alpha are still normal) |
| Who proved experimentally the importance of the primary structure? | Christian Anfinsen (1950s) -- said that primary was more important than secondary |
| What were the components of the experiment that Christian Anfinsen did? | Worked with RNAse (124 amino acids) -- Chaotropic agents (things that disrupt higher structure -- ex is urea because it will break all non-covalent R group bonds in a protein) -- BME also disrupts sulfide linkages |
| What was the experiment that Christian Anfinsen did specifically? | Treated RNAse with urea and BME -- lost 100% of the activity (denatured) -- you get a primary structure when you remove these -- used dialysis to remove urea and BME -- it resumed tertiary structure then |
| What was Cyrus Levinthal's hypothesis? | protein folding is COMPLEX -- 100 amino acid protein, each aa can assume 3 different conformations (3^100 possibilities) -- If each conversion takes 10^-13 seconds, it would take 1.6 x 10^22 years to fold properly -- but his experiment happened in hours |
| Why did the Levinthal's Paradox happen? | Richard Dawkins - Idea of cumulative selection -- Monkey typewriter |
| What does it mean to be Intrinsically Unstructured Protein? | Does not have discrete 3-D structure -- meaning they will not always form or fold the same way |
| __% of Eurkaryotic proteins have at least 1 unstructured region of at least ___ amino acids | 50%; 30% |
| How do unstructured proteins get their structure? | When they interact with other proteins |
| What is the genome paradox? | How do we have so few genes? When one gene forms with another gene, one structure is formed. But if that one gene forms with a different gene, a different structure is formed. Can connect them differently to make different structures. |
| What are metamorphic proteins? | No real state at equilibrium -- exist in multiple forms -- structure influenced by what binds to them (PRIONS) |
| What are prions? | altered structure of a protein that naturally occurs in the nervous system -- misfolded protein causes other proteins to misfold -- can make all proteins assume the bad forms (lethal) |
| What must a person to do a protein in order to analyze? | Purify |
| What is the first step to purifying a protein? | Performing an Assay |
| What must be present and functional in an activity assay? | Enzymes |
| What is present in a color changing assay? | Alkaline Phosphatase |
| Enzyme + Chromogenic substrate = ____ | COLOR |
| What does it mean to "salt out" | Solubility separation based on solubility in water -- increase the concentration of salt, however, proteins begin to precipitate out (barely soluble proteins precipitate in low salt and very soluble proteins precipitate in high salt) |
| What is a MCWO filter in filtration? | When proteins are sorted out using a molecular weight cut-off -- let lower molecular weight pass thru -- then you do an assay on both sides to find your protein based on size |
| What is size exclusion chromotography? | column made of hollow sepharose beads with defined pore sizes -- small proteins can fit through the pores so they wander in and out SLOWLY making their way down the column --large proteins that dont fit thru the pores come straight thru the column QUICKLY |
| What is Ion Exchange Chromatography? | the beads don't have holes in them, but you can charge them -- proteins stick a specfic charge of beads -- protein is always the same charge as the one who rejects it -- |
| Very positive proteins need _____ salt to known them off the column | high |
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