Flashcards
Protein Structure (Biochem 153A)
Cards in this deck (41)
- 1Define PeptideA peptide consists of less than 40 amino acids together.
- 2Define PolpeptideA polypeptide chain is defined as more than 40 amino acids together.
- 3How many structures can proteins exist in? Describe each structure briefly.!) Primary Structure -- amino acid sequence
2) Secondary Structure -- alpha helices beta sheets and motifs
3) Tertiary Structure -- describes the 3D structure of the given protein, includes the various secondary structures and the foldings between them.
4) Quaternary Structure -- two or more polypeptide linked together through electrostatic interactions. - 4Give two examples, along with their structures, of reagants that maybe used as denaturants.1) Guanidinium Ion:
2) Urea - 5What does it mean to 'denature' a protein?Denaturing a protein means to change its conformation from its native state.
This causes the protein to become biologically inactive. - 6What happens if we react a protein with a reducing agent such as beta-mercapthanol?The reducing agent helps break the disulphide bonds which hold the protein domains together in a single protein subunit.
- 7True or False: Hydrophobic residues are densely packed in the exterior of proteins.False.
They are densely packed in the interior of proteins. - 8True or False: H-bonding is maximised in proteins.True.
- 9Why are peptied bonds deemed rigid?Peptide bonds exist between the terminal carboxylate ion on one amino acid and the amino group of the other.
Due to a small electric dipole involved int he formation of the bond, the bond as a partial pi bond character. This restricts rotation. - 10True or False: Rotation isn't permitted on the peptide bond or on the bonds that surround the alpha carbon.False.
Rotation is ONLY not permitted on the peptide bond. The bond angle surrounding the N-C(a) and C-C(a) allow for rotation. - 11What is the Ramachandran Plot and why is it useful?Ramachandran Plot is a computer program based on the possible bond angle combinations of the hypothetical tri-peptide made up of triple Alanine.
- 12Describe the Ramachandran Plot.1) The white portions show combinations that don't exist.
2) light blue are combinations that are possible and dark blue are the ones that actually exist. - 13List the forces that hold proteins together.1) Electrostatic interactions
2) H-bonding
3) Van Der Waals Interactions
4) Hydrophobic interactions.
5) Aromatic Stacking - 14What are the two simplest secondary structures a protein can assume?1) Alpha Helix
2) Beta Sheet - 15Fill in the blanks: Hydrogen bonding in alpha helix structures is _________ whereas it is ___________ in beta sheet structures.1) intrastrand
2) interstrand. - 16Briefly describe a few characteristics of alpha helix:1) 3.6 residues per turn.
2) Each turn is 5.4 A long.
3) H-bond exists between every 4 amino acid residues. - 17In what direction do the R groups point in for an alpha helix?R groups point outwards and are aligned perpendicular to the helical axis.
- 18What are the bond angles permissible for an alpha helix structure by the Ramachandran Plot?The angle between the N and C(a) is ~ -60 degrees.
The angle between the C and C(a) is between -45 and 50 degrees. - 19Which side chains destabilise the alpha helix structure, and why?1) Lysine, Arginine -- positively charged side chains, repel each other extensively.
2) Glu/ Asp -- negatively charged side chains, also repel each other extensively.
3) Serine/ Cysteine -- can't form due to bulk and shape
4) Glycine -- rarely seen because smallest side chain; has a different kind of conformational flexibility.
5) Proline -- the nitrogen in the ring structure is unable to rotate due to steric hinderance; can't take the alpha helix conformation.
ii) IMPORTANT: the nitrogen in the ring also lacks available hydrogens to participate in H-bonding with other amino acid residues. - 20True or False: Alpha helix structure is stabilised by hydrophobic interactions, and that's why largely consists of non-polar amino acid residues.True.
- 21How is the Beta Sheet different from the Alpha helix?1) In the Beta sheet conformation, the amino acids are arranged in a zig-zag manner rather than a helical structure.
2) In B sheets, the R groups are positioned in an alternating manner, and are parallel to the axis.
3) B sheets exist in two motifs: parallel and antiparallel. - 22Which is more stable: Paralell beta strand or anti-parallel beta strands? Explain why.Anti-parallel beta strands are more stable because the H-bonding patterns are more optimal.
- 23Which amino acid residues are found in abundance in beta sheets?Glycine and Alanine because they are the smallest and have greatest conformational flexibility.
- 24What is a beta turn? Describe its common charecteristics briefly.1) A beta turn comprises of 4 amino acid residues.
2) It is also a commonly found secondary structure.
3) H-bonding exists between the 1st and the 4th amino acid residue. The middle residues are devoid of any interaction. - 25Which amino acids side chains are abundant in beta turns?1) Glycine -- has the smallest side chain, and thus greatest conformational flexibility.
2) Proline -- the nitrogen in the ring is perfect to take cis configuration (needed for the beta turn) - 26What are the two types of Beta turns and what are their specifications?Type 1: The third C(a) can be anything, and the second C(a) has to be proline.
Type 2: The third C(a) has to be Glycine and the second C(a) has to proline. - 27Which of the types of beta turns are more common?Type 1 is twice as common as Type 2.
- 28Name the two quaternary structures we have studied.1) Fibrous Proteins
2) Globular Proteins - 29List the main characteristics of Fibrous proteins.1) A simple repetitive secondary structure (helix or sheet)
2) used for structural support
3) exists in the form of a-keratin, collagen and silk fibroin, - 30True or False: Fibrous proteins are soluble in water.False:
Fibrous proteins are insoluble in water because of high concentrations hydrophobic residues. - 31Describe the main characteristics of a-keratin1) Found in hair, nails etc.
2) is an example of a coiled coil protein as two helices (in parallel orientation) are wound against each other to form a right handed super helix.
3) Held together by covalent crosslinks such as disulfide bonds. - 32Give an example of coiled coil proteintropomyosin
- 33How is collagen different from a-keratin1) Collagen also exists in the form of a supercoiled protein but due to 3 alpha chains and NOT alpha helices.
2) The chains when wound against each other form a right handed helix.
3) Collagen is found in muscles, specifically fibrils. The fibrils are cross linked by the modified histone and lysine side chains.
4) Formed by a Pro-Gly-4 Hyp repeating unit. - 34Describe main characteristics of Silk Fibrion1 ) Composed of beta sheets.
2 ) Rich in glycine and alanine due to flexibility of side chains.
3) structure stabilised by extensive H-bonding between Beta strands and Van De Waals interactions between sheets.
4) Flexible in comparison to a-keratin as structure held together by weak forces and not disulfide bonds. - 35What are the factors that can potentially lead to denaturing a protein?1) high heat
2) low pH
3) high salt (electrostatic interactions are competing)
4) use of urea or guanidium ion. - 36Presence of heme is myoglobin is called _______________.prostatic group.
- 37True or False: In favourable conditions such as low pH, two protein subunits will dimerise.True.
- 38Fill in the Blanks: All amino acid residues naturally occur as _____________L-stereoisomers.
- 39Fill in the blanks: Amino acids when dissolved in water exist as _____________zwitterion.
- 40True or False: Each amino acid has a characteristic titration curve.True
- 41—
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- Flashcards on Protein Structure (Biochem 153A), created by Anahita Sehgal on 22/04/2018.
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- Anahita Sehgal
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