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Protein Structure and Folding, Exams of Nursing

University of OxfordNursing

A comprehensive overview of the various aspects of protein structure and folding. It covers the fundamental concepts of hydrocarbons, functional groups, chemical interactions, and the different levels of protein structure, including primary, secondary, tertiary, and quaternary structures. The document delves into the characteristics and stabilizing forces of these structural elements, as well as the dynamics of protein folding and the models that describe this process. Additionally, it discusses the importance of disulfide bridges, reducing agents, and denaturing agents in protein structure and stability. This detailed information can be valuable for students studying biochemistry, molecular biology, or related fields, as it provides a solid foundation for understanding the complex and intricate nature of protein structure and its implications in biological processes.

Typology: Exams

2023/2024

Available from 10/12/2024

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BCH 351 Exam 1
Hydrocarbons are ... - correct answer ✔✔nonpolar, hydrophobic
5 Functional Groups - correct answer ✔✔amino, hydroxyl, sulfhydryl, phosphoryl, carboxyl, methyl
Amines - correct answer ✔✔nitrogen joined to at least one alkyl group
amide - correct answer ✔✔have a carbonyl group between the nitrogen and R group
functional group characteristics - correct answer ✔✔- contain electronegative atoms (O,N,S)
- usually electrically charged or polar
- make organic molecule amphiphathic
- create multifunctional molecules that increase functional diversity
- provide sights for intra and inter molecular interactions such as hydrogen bonding and ionic
interactions
types of chemical interactions - correct answer ✔✔covalent, ionic, hydrogen bonds, van der Waal,
hydrophobic effects
covalent bonds - correct answer ✔✔formed by atoms sharing valence electrons and fill each atoms
outer shell.
can be polar or nonpolar depending on if atoms are shared equally or not
polar covalent bond - correct answer ✔✔electrons are shared unequally. electronegativity >0.5
nonpolar covalent bond - correct answer ✔✔electrons are shared equally. electronegativity <0.5
common polar covalent bonds - correct answer ✔✔C-O, O-H, N-H
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Download Protein Structure and Folding and more Exams Nursing in PDF only on Docsity!

BCH 351 Exam 1

Hydrocarbons are ... - correct answer ✔✔nonpolar, hydrophobic 5 Functional Groups - correct answer ✔✔amino, hydroxyl, sulfhydryl, phosphoryl, carboxyl, methyl Amines - correct answer ✔✔nitrogen joined to at least one alkyl group amide - correct answer ✔✔have a carbonyl group between the nitrogen and R group functional group characteristics - correct answer ✔✔- contain electronegative atoms (O,N,S)

  • usually electrically charged or polar
  • make organic molecule amphiphathic
  • create multifunctional molecules that increase functional diversity
  • provide sights for intra and inter molecular interactions such as hydrogen bonding and ionic interactions types of chemical interactions - correct answer ✔✔covalent, ionic, hydrogen bonds, van der Waal, hydrophobic effects covalent bonds - correct answer ✔✔formed by atoms sharing valence electrons and fill each atoms outer shell. can be polar or nonpolar depending on if atoms are shared equally or not polar covalent bond - correct answer ✔✔electrons are shared unequally. electronegativity >0. nonpolar covalent bond - correct answer ✔✔electrons are shared equally. electronegativity <0. common polar covalent bonds - correct answer ✔✔C-O, O-H, N-H

ionic interactions - correct answer ✔✔also called charge-charge interactions or salt bridges. Occur betwen opposite charged atoms or groups. Ex: Na+ and Cl-. Electronegativity >2.0 (usually between most and least electronegative) hydrogen bonds - correct answer ✔✔form when a hydrogen that is covalently bonded to an electronegative atom is in proximity to another electronegative atom. Partial charges strong hydrogen bond - correct answer ✔✔linear weak hydrogen bond - correct answer ✔✔angled van der Waals interactions - correct answer ✔✔occur between neutral molecules/atoms by temporary dipole moments because of fluctuation in electron clouds. Temporary polarization Where does van der Waals interactions occur - correct answer ✔✔maximum attraction occurs at a distance slightly greater than the sum of the van der Waals radii of the two atoms hydrophobic effects - correct answer ✔✔due to the tendency of nonpolar molecules to pack close together away from water. Main factor behind protein folding, protein-protein association, formation of lipid micelles, and enzyme-substrate complex formation structure and chemistry of water - correct answer ✔✔unequal electron distribution, O is more electronegative than H. Angle of H-O-H bonds is 104.5. H2O exhibits permanent dipole moments hydrogen bond between water molecules - correct answer ✔✔each water molecule can form up to 4 hydrogen bonds 2 H donor sites 2 H acceptor sites

  • ionization state of these weak acids regulates not only their function but also their interaction with other biological molecules
  • structure and function of these molecules is often regulated by pH of the solution Henderson-Hasselbalch equation - correct answer ✔✔shows the direct relationship between pH of a solution and the ratio of deprotonated form [A-] to the protonated form [HA] of some ionizable group Titration curve of weak acids - correct answer ✔✔used to determine the amount of weak acid that is being deprotonated at different pH conditions biological buffering system - correct answer ✔✔carbonic acid (H2CO3) and bicarbonate (HCO3-) buffering system is used to maintain physiological pH acidosis - correct answer ✔✔when blood pH falls below 7. alkalosis - correct answer ✔✔when blood pH rises above 7. amino acids - correct answer ✔✔proteins are linear heteropolymers of a-amino acids properties of amino acids - correct answer ✔✔- Capacity to polymerize
  • Useful acid-base properties
  • Varied physical properties
  • Varied chemical functionality Amino acid general structure - correct answer ✔✔4 different groups covalently bonded to the carbon. L&D forms of amino acids - correct answer ✔✔- naturally occuring proteins contain nearly all L amino acids except glycine which contains an asymmetric a-carbon stereoisomers - correct answer ✔✔molecules with the same chemical formula but differ in their arrangement or configuration of atoms in space

enantiomer - correct answer ✔✔Non-superimposable mirror image (L and D forms) amino acid classification - correct answer ✔✔Grouped based on R-group Nonpolar (hydrophobic)

  • mostly linear or branched hydrocarbons (7)
  • aromatic (3) Polar (Hydrophilic)
  • uncharged (5)
  • positively charged (3)
  • negatively charged (2) Folded polypeptide chain - correct answer ✔✔polar/hydrophilic amino acids
  • on the protein surface
  • forming H-bonds with water Nonpolar/Hydrophobic amino acids
  • cluster in the interior
  • minimizing interaction with water Glycine, Gly - correct answer ✔✔ Alanine, Ala - correct answer ✔✔ Valine, Val - correct answer ✔✔ Leucine, Leu - correct answer ✔✔ Isoleucine, Ile - correct answer ✔✔

ionization of amino acids - correct answer ✔✔- the ionic state influences the protein folding therefore the 3D structure of the proteins

  • the ionic state influences the activity of the proteins
  • each ionizable group has a pKa value
  • as the pH of the solution increases, different ionizable groups become deprotonated Zwitterion (dipolar ion) - correct answer ✔✔a molecule carrying both positive and negative charges with a net charge of zero isoelectric point (pI) - correct answer ✔✔- a point on the pH range where the average charge on the molecule sums to exactly zero
  • the average of the two pKas between the zwitterion peptide bond formation - correct answer ✔✔N terminus to C terminus. can only be added to C terminus COO- and NH3+ create peptide bond and H2O. add in trans formation resonance structure of the peptide bond - correct answer ✔✔- electrons are delocalizaed over the carbonyl oxygen and the carbonyl carbone and the amide nitrogen
  • carbonyl caron has partial negative charge --> hydrogen bond acceptor
  • amide nitrogen has partial positive charge --> hydrogen bond donor planar peptide groups in a polypeptide chain - correct answer ✔✔the partial double bond of the peptide bond restricts the rotation around the peptide bond psi bond - correct answer ✔✔bond between alpha carbon and the carbonyl carbon of an amino acid phi bond - correct answer ✔✔between the N of amino group and alpha carbon

configuration of peptide bonds - correct answer ✔✔trans because cis is sterically hindered and therefore unfavorable Ramachandran plot - correct answer ✔✔- shows the allowable combination of phi and psi angles for any two amino acid residues on the basis of steric hindrance

  • specific regions in this plot reflect specific secondary structures
  • the map can be used to predict whether a sequence of amino acids can form which types of secondard structures secondary protein structure - correct answer ✔✔regular repetitve arrangement of local regions of the polypeptide backbone examples
  • alpha helix
  • loops
  • beta strand
  • beta turn alpha-helix - correct answer ✔✔- almost always right handed helix
  • h-bonds between carbonyl O (n) and residue of the (n+4) amide
  • 3.6 amino acids per turn
  • side chain (r group) pointing outward, do not participate in h-bonding resonance structure of peptide bonds - correct answer ✔✔- to stabilize the helix, negatively charged amino acids are often found on the N-terminus whereas positively charged amino acids are often located on the C-terminus
  • the N and C termini tend to be located on protein surface where the charge can be neutralized by interaction with H2O or charged ions folded protein in aqueous solution - correct answer ✔✔hydrophobic residues facing inward, hydrophilic residues facing outward

type 1 beta turn - correct answer ✔✔carbonyl oxygen oriented inward type 2 beta turn - correct answer ✔✔carbonyl oxygen oriented outward tertiary protein structure - correct answer ✔✔refers to the spatial arrangement of the secondary structural elements in the polypeptide chain

  • short range secondary structures located distrantly from each other are often brought together in the folded tertiary structure stabilizing forces in tertiary protein structure - correct answer ✔✔- noncovalent interactions between amino acid side chains -- hydrophobic effect is the major stabilizing force
  • disulfide bonds between two nearby Cys residues
  • metal ions -- iron and zinc major classes of tertiary protein structure - correct answer ✔✔fibrous proteins globular proteins fibrous proteins - correct answer ✔✔structural function globular proteins - correct answer ✔✔chemical function domain - correct answer ✔✔defined structures that globular proteins fold into Protein Domain - correct answer ✔✔- a compact, independently folded region of tertiary structure
  • size varies from 25/30 to several hundred amino acids
  • larger proteins often contain two or more distinct domains
  • a domain frequently posses some defined function

Types of major secondary structure - correct answer ✔✔- alpha helix

  • predominantly beta strand
  • alpha/beta (intermingled)
  • alpha + beta (not intermingled) motif - correct answer ✔✔super secondary structures
  • combination of alpha helices, beta strands, and loops forming distinct structures
  • associated with particular functions alpha-alpha corner and beta-alpha-beta loop - correct answer ✔✔most common motifs provides two layers of secondary structure helix bundle - correct answer ✔✔- contains 4 or more alpha helices
  • provides hydrophobic pockets or hydrophilic channels beta barrel - correct answer ✔✔- contains multiple twisted beta strands forming a beta sheet in a barrel structure
  • provides channels for polar molecules greek key fold - correct answer ✔✔- consists of 4 or more beta strands linked together to form a beta sheet structure Rossmann fold - correct answer ✔✔- complex protein fold in which there are alternating alpha helices and beta strands
  • found in proteins that bind nucleotides TIM barrel - correct answer ✔✔- consists of alternating alpha helix/beta strand barrel
  • found in a large number of metabolic enzymes

Disulfide Bridge - correct answer ✔✔- does not drive protein folding

  • can prevent protein unfolding beta-mercaptoethanol (BME) - correct answer ✔✔reducing agent Urea - correct answer ✔✔denaturing agent what determines the native conformation - correct answer ✔✔the amino acid sequence dynamics of protein folding - correct answer ✔✔denatured or unfolded state --> intermediate state (may be several) --> native or folded state Intermediate states - correct answer ✔✔a compact partially folded state that has native-like secondary structure and folding topology but lacks the defined tertiary structure iteractions hydrophobic collapse model - correct answer ✔✔hydrophobic residues first form the interior and then form the secondary and tertiary structures framework model - correct answer ✔✔local secondary structures form independently and then leads to tertiary structures nucleation model - correct answer ✔✔localized tertiary structures lead to other secondary and tertiary structures Gibbs free energy (ΔG) - correct answer ✔✔the difference between folded (native) and unfolded (denatured) state must be favorable (ΔG<0) in order to drive the folding process Enthalpy (ΔH) - correct answer ✔✔the heat content of a system
  • favorable because more interactions (noncovalent interactions or disulfide bonds) in the folded state than in the unfolded state. ΔH<

Entropy (ΔS) - correct answer ✔✔the degree of freedom of a system

  • unfavorable from protein folding (ΔS<0) however it is hightly favorable with surrounding water (ΔS>>>0)
  • overall ΔS> characteristics of protein folding - correct answer ✔✔- amino acid sequence alone determines native conformation
  • extremely rapid
  • takes place through a series of partially structured intermediate states
  • follow the laws of thermodynamics --> folded proteins reach a low energy state --> more stable
  • cooperative and sequential process --> the formation of one part of a structure leads to the formation of the remaining parts of the structure
  • different domains fold independently --> more efficient
  • some protein folding is assisted by chaperon proteins chaperon proteins - correct answer ✔✔- prevent protein aggregation
  • protect or repair damaged protein caused by temperature increases (also called heat shock proteins)
  • bind to misfolded proteins and use ATP hydrolysis to facilitate correct folding Clamp Chaperon Protein - correct answer ✔✔- ATP binding induces conformational change that allows unfolded proteins to bind
  • ATP hydrolysis induces another conformational change that fold and release the protein Chamber Chaperon Protein - correct answer ✔✔GroES is the cap GroEL is upper and lower chamber misfolded proteins - correct answer ✔✔degrades: reduces the level of functional protein (loss of function) aggregated: interfere with cellular processes (gain of function)
  • hydrophobic tail can penetrate into the protein interior and disrupt the hydrophobic effects among the nonpolar amino acids chaotropic agents - correct answer ✔✔- urea and guanidinium chloride are excellent hydrogen bond formers three types of fibrous proteins - correct answer ✔✔keratin collagen fibroin keratin - correct answer ✔✔- dominant protein of hair, nails, outer skin, claws, quill, horns, and hooves
  • a homodimer of two helical peptides that wrapping around each other to form a coiled coil structure
  • individual keratin helix is right handed
  • coiled coil dimer is left handed
  • insoluble because of long sequences (300+ residues) stabilizing forces for keratin - correct answer ✔✔within individual helix: hydrogen bonds between amide H and carbonyl O, just like an alpha helix within coiled coil dimer: hydrophobic effects, every 3-4 amino acid is hydrophobic and forms a hydrophobic interface between two helices between coiled coil dimers: disulfide bonds between Cysteine residues. more disulfide bonds = stronger keratin structure collagen - correct answer ✔✔- most abundant protein in the mammals
  • dominant protein of skin, bone, teeth, tendon, and cartilage basic structure of collagen - correct answer ✔✔triple helix fiber
  • 3 left handed helices form a right handed triple helix fiber
  • each helix has a distinctive amino acid sequence (Gly - X - Y) where X is usually Pro and Y is often 4- hydroxyproline
  • Gly lies near the center of the triple helix stabilization within triple helix fiber - correct answer ✔✔- no H bonds within individual helix
  • hydrophobic effects and H bonds stabilized between the individual helix -- between amide H (Gly) in one chain and carbonyl O (Pro) -- OH group in 4-hydroxyproline can also be used stabilization between triple helix fiber - correct answer ✔✔- prolines can be substituted by hydroxylated lysine
  • hydroxylated lysine cross-links stabilized between triple helix fibers Scurvy: Lack of Vitamin C - correct answer ✔✔- the enzyme prolyl hydroxylase is used to hydroxylate prolines during collagen synthesis
  • this enzyme requires the cofactors vitamin C
  • no vitamin C leads to enzyme inactivation causing no proline hydroxylation meaning less hydrogen bonds and weaker triple helix fiber which results in skin lesions and poor wound healing fibroin - correct answer ✔✔- the silk protein of insects
  • beta sheet structure
  • every other amino acids is Gly Stabilizing forces in Fibroin - correct answer ✔✔within beta sheet:
  • antiparallel beta strands stabilized H bonds between separate strands
  • H bonds form between backbone NH and CO groups on separate strands between beta sheets:
  • van der Waals interaction between separate sheets
  • form between the side chains of the beta sheets