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Test 1

Biochem Test 1

TermDefinition
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
Created by: 1363731667