Biochemistry Exam #2 – Flashcards
85 test answers
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Alpha Helices are stabilized by what type of bond?
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Intra-helical Hydrogen Bonding
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What is the equation for pitch (p)?
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"n" (# residues per turn) x "h" (rise per residue)
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How many amino acid residues are apart and bonded during intra-helical H bonding in alpha helices?
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4
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In an alpha helix, the _____ Terminus is slightly negative and the ______ Terminus is slightly positive.
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C Terminus; N Terminus
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Inter-strand H Bonding occurs with which secondary structure?
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Beta Sheets
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Beta strands in the same direction is known as ?
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Parallel
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Beta strands in the opposite direction is known as?
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Antiparallel
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Complex structural motifs are constructed from repetitions of __________ motifs.
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Smaller
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Myoglobin, Neuraminidase, and Triosephosphate Isomerase (TIM) are examples of what?
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Supersecondary Structural Motifs
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The order in which secondary structures are placed is what domain category?
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Topology
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A protein that is mostly alpha helices, beta sheets or both is considered what domain category?
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Class
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An Alpha-Beta Barrel is known as what kind of domain category?
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Architecture
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In a tertiary structure, the hydrophilic side chain is located where in regards to a protein?
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Outside surface
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The hydrophobic side chain is located where in regards to a protein of tertiary structure?
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Inside
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Tertiary Structure is driven by the _______________?
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Hydrophobic Effect
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Tertiary Structure was proven by _____________?
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RNase A
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Urea and Guanidinium Ion are known as what?
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Chaotropic Agents
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True or False? Urea is NOT a strong hydrogen bonder?
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False, Urea is a very strong hydrogen bonder
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The unfolding of BPTI in the tertiary structure found that 3 disulfide bonds formed from side chains of 6 _________?
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Cysteines
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The higher the temperature such as Tm for a protein, the more _________ is needed to denature the protein.
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Energy
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Two or more proteins that come together to form a single biologically active protein is known as what?
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Quaternary Structure
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Silk Fibroin proteins are flexible because the interactions or bonding between the sheets involve what?
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Weak van der waals interactions
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Tertiary structures are slightly stable due to...?
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delta G = slightly negative (Gibbs Free Energy)
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The middle state between a native protein and denature protein is known as what?
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Intermediate State
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"Molten Globule" is known was what?
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Intermediate State
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What type of binding is required to stabilize a protein into a stable native halomyoglobin?
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Heme Binding
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Majority of protein foiling occurs in what type of landscape?
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Rugged
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Due to the rugged folding landscape, many proteins require ____________ to fold correctly.
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Chaperone
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What are the three components of a chperonin?
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GroES, Cis Ring and Trans Ring
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Please match the correct term on the left with the appropriate structural feature of proteins listed on the right.
1) primary structure A) the interaction between two separate protein strands
2) secondary structure B) the sequence of AA
3) tertiary structure C) small sections of organized protein structure, such as helices
4) quaternary structure D) the overall fold of a single protein strand, such as the globulin fold
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1. Primary Structure = the sequence of AA
2. Secondary Structure = small sections of organized protein structure, such as helices
3. Tertiary Structure = the overall fold of a single protein strand, such as the globulin fol
4. Quaternary Structure = the interaction between two separate protein strands
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Match the following characteristics to α helices, β sheets, or both.
1) 5.4Å/turn A) α helices
2) antiparallel arrangement B) β sheets
3) large dipole moment C) both
4) extensive H-bonding network
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1. 5.4Å/turn = α helices
2. Antiparallel Arrangement = β sheets
3. Large Dipole Moment = α helices
4. Extensive H-bonding network = both
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A ________ plot describes which structures in a polypeptide are sterically possible and which are not based on the angles of rotation about the backbone Namide -Cα and Cα-Ccarbonyl bonds.
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Ramachandran
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True or False? The amino acid side chain residues in an α helix point outwards away from the center of the helix.
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True
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Which statement correctly describes amphipathic (or amphiphilic) helices and sheets?
1. Amphipathic helices and sheets have hydrophilic and hydrophobic residues evenly distributed throughout their structure.
2. Sheets are typically hydrophilic on one surface, whereas helices usually have both hydrophilic and hydrophobic residues evenly distributed throughout their structure.
3. Amphipathic helices and sheets have predominantly hydrophilic (or hydrophobic) residues on one face.
4. Helices are typically hydrophilic on one surface, whereas sheets usually have both hydrophilic and hydrophobic residues evenly distributed throughout their structure.
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3. Amphipathic helices and sheets have predominantly hydrophilic (or hydrophobic) residues on one face.
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Which of the following statements about globular proteins are true?
1) The protein folds to make itself as compact as possible.
2) The packing of the protein is such that hydrophilic residues appear on the surface where they can interact with an aqueous environment.
3) Irregularities of the protein's surface allow for the formation of clefts, which are often where the protein promotes a chemical transformation.
4) Regions of secondary structures folding on one another are examples of the protein's tertiary structure.
A. 1,2 and 3
B. 2, 3 and 4
C. 1, 2 and 4
D. All of the listed statements are correct
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D. All of the listed statements are correct
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Which statements about β and γ turns are correct?
1) Their purpose is to reverse the direction of the polypeptide chain.
2) There are two types, I and II, which differ mainly in the conformation about the i+1 and i+2 residue amide bond.
3) They typically contain large, hydrophobic residues.
4) Their conformation is held in place through H bonds.
A.Only statements 1, 2, and 3 are correct.
B. Statements 1, 2, and 4 are correct.
C. Only statements 2, 3, and 4 are correct.
D. All of the listed statements are correct.
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B. Statements 1, 2, and 4 are correct.
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Where in a globular protein is the amino acid glycine likely to be located?
A. the hydrophilic interior
B. the hydrophobic interior
C. the hydrophilic exterior
D. the hydrophobic exterior
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B. the hydrophobic interior
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Which of the following statements regarding Anfinsen's denaturing experiments with ribonuclease A are valid?
1) Exposing the denatured protein to air oxidation and then dialysis to remove urea restored the protein to its original functionality.
2) Removing urea by dialysis and then allowing air oxidation of the denatured protein restored the protein to its original functionality.
3) Denaturing the protein with both urea and β-mercaptoethanol yielded an inactive protein.
4) Protein folding is determined by its primary sequence.
A. Statements 1, 2, and 4 are valid.
B. Only statements 2, 3, and 4 are valid.
C. Statements 1, 2, and 4 are valid.
D. All of the listed statements are valid.
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B. Only statements 2, 3, and 4 are valid.
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Which of the following statements regarding the folding of proteins is NOT true?
A. Salt bridges stabilize the fold.
B. Hydrophobic residues pack together because the side chains are attracted to each other through weak Van der Waals interactions.
C. Internal H bonds stabilize the fold.
D. Van der Waals interactions have a stabilizing, cumulative effect.
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B. Hydrophobic residues pack together because the side chains are attracted to each other through weak Van der Waals interactions.
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Which of the following statements is NOT true?
A. A prosthetic group is usually a small organic molecule required for activity by a protein.
B. A cofactor usually refers to a metal ion required for activity by a protein.
C. An intact protein, complete with its cofactor or metal ion, is known as a holoprotein.
D. A protein stripped of its cofactor or metal ion is known as a holoprotein.
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D. A protein stripped of its cofactor or metal ion is known as a holoprotein.
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Tertiary structure is NOT directly dependent on _____.
A. peptide bonds
B. hydrogen bonds
C. hydrophobic interactions
D. bonds between sulfur atoms
E. ionic bonds
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A. peptide bonds
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The secondary structure of a protein results from _____.
A. ionic bonds
B. bonds between sulfur atoms
C. hydrogen bonds
D. hydrophobic interactions
E. peptide bonds
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C. hydrogen bonds
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What type of bond joins the monomers in a protein's primary structure?
A. ionic
B. S - S
C. peptide
D. hydrophobic
E. hydrogen
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C. peptide
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Proteins are polymers of _____.
A. amino acids
B. nucleotides
C. hydrocarbons
D. glycerol
E. CH2O units
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A. amino acids
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Which of the following statements about protein quaternary structure are correct?
1) It involves a complex of two or more proteins interacting with each other.
2) The subunits of the structure can be either identical or different.
3) The interactions between subunits can give rise to indefinite growth of polymeric complexes.
4) Most assemblies of protein subunits have one or more defined axis of rotation.
A. Only statements 2, 3, and 4 are valid.
B. Only statements 1, 2, and 3 are valid.
C. Only statements 1, 3, and 4 are correct.
D. All of the listed statements are correct.
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D. All of the listed statements are correct.
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Another name for Cruzfeldt-Jacob Disease is known as ____________________?
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Mad Cow Disease
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What is the source of Cruzfeldt-Jacob Disease?
A. Virus
B. Bacteria
C. DNA
D. Protein
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D. Protein
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Cruzfeldt-Jacob Disease is resistant to ___________________, and can't be destroyed by __________________.
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Protease Action ; Heating
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What is the name of the protein responsible for this disease?
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Prion Protein aka "PrPc"
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PrPc is anchored to what?
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Cell Membrane
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What anchors this protein?
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GPI Anchor
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The tertiary structure of PrPc is stabilized by what bond?
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Disulfide Bond
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PrPc is:
A. Hydrophobic
B. Hydrophilic
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A. Hydrophilic due to being on the exterior surface which is aqueous soluble or (i.e. polar)
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At the end of the protein's life span, it is what?
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Endocytosed
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Name the two types of endosomes?
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Recylcing Endosome & Degradative Endosome
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Some PrPc will assume _____________ structure.
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PrPsc
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Match the description with the two terms below:
I. Terms:
1. PrPc
2. PrPscII. Description:
A. Hydrophilic
B.Hydrophobic
C. Beta Sheet
D. Alpha Helices
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PrPc = Hydrophilic and mostly Alpha Helices
&PrPsc = Hydrophobic and mostly Beta Sheets
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PrPc can aggregate to form rod-like clusters known as?
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Fibrils
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PrPc can form what on the cell surface?
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Plaque
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Alzheimer's disease comes from what type of protein?
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Beta Amyloid
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The normal structure of the beta amyloid protein is that is has ___________________ (alpha helices or beta sheets) and is also ________________ (hydrophilic or hydrophobic )
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alpha helices ; hydrophilic
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Misfolding of the beta amyloid via proteolysis leads to the protein to become what?
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Beta Sheets
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Osteogenesis Imperfecta involves what?
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Collagen
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Biologically active collagen contains ________ helices of collagen wrapped around eachother.
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3
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This 3 helices of collagen is known as ?
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Tropocollagen
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What is contained in the interior and exterior of tropocollagen?
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Interior = Proline
Exterior= Glycine
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A mutation in tropocollagen will most likely occur where?
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Glycine
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True or False? The substituion will be an amino acid with a much larger substituent group so tropocollagen will either not form or form weakly.
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True
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___________ is an enzyme that forms hydrogen bonds on outside of tropocollagen and stabilizes the helix.
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Hydroxylases
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A staggered pattern that forms collagen fibers is known was what?
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Striation
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The cross-link between tropocollagen helices results from the modified ___________ residues?
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Lysine (Lys)
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Collagen becomes weak and connective tissue deteriorates as a result of a disease known as _____________ which is due to a decrease in Vitamin ________.
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scurvy ; Vitamin C
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Vitamin _______is needed for the formation of bone matrix.
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Vitamin K
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Insufficient vitamin c will lead to an inactive form of ____________ and not be able to form stable tropocollagen helices.
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Hydroxylase
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What cell organelle is used to synthesize oxygen to give ATP?
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Mitochondria
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The shape of the curve tells us what about a protein?
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Binding Process
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Maximal Binding is what?
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The maximum binding capacity of a protein
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The concentration of ligan that gives 50% of binding is known as what?
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Kd
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Kd shows us that binding is what type of process?
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Equilibrium process
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The larger the Kd, it has ______________the affinity and the lower the Kd, it has _________________ the affinity.
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low affinity ; high affinity
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Which protein, either Myoglobin or Hemoglobin have the higher affinity for oxygen?
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Myoglobin due to a smaller Kd value
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