Biochem PART III Flashcards
(16 cards)
QUESTION 33: How do the base pairs in DNA crystal structures differ from those introduced in the Watson-Crick mode?
-DNA crystal structures show variation in what? This includes shifts in what?
-These structures reveal greater ____ and ____ in DNA compared to the ____ Watson-Crick model
-base pair positioning
-base-pair steps or inclination angles
-flexibilty; variations; rigid
QUESTION 34: How does base sequence affect local DNA structure?
-What two things does it influence?
-Some sequences adopt ___-like or ___-like forms, leading to what?
-orientation and displacement of base pairs
-A; C
-local deformations that affect the overall helix shape
QUESTION 35: Why do short stretches of A- or C-like DNA introduce wedges in the classical B-DNA helix?
-This is because they have different helical ____ and ___ compared to B-DNA
-A-DNA has an ____ ___-___ structure, causing what?
-radii and pitch
-inclined base-pair
-local distortions and curvature
QUESTION 36: What is a palindrome? In the case of DNA, how might a palindrome affect the double helix?
-A palindrome is a sequence of ______ that reads what?
-It can form what two things that are involved in genetic processes like recombination
-bases; the same forwards and backwards
-branches structures & four-way junctions
QUESTION 37: How does a G:G:G:G quartet differ from a G4 quadruplex?
-What is a G:G:G:G quartet formed by? How do they interact?
-How is a G4 quadruplex formed? What is it stabilized by?
-four guanine bases; hydrogen bonding
-by stacking multiple G:G:G:G quartets; a central cation
QUESTION 38: What is the approximate length, in base pairsm of the human genome?
-What is it?
-They are distributed across ___ different chromosomes
-3.3 billion base pairs
-23
QUESTION 39: What is a histone?
-They are ____ charged proteins that bind to what?
-What do they help do?
-They provide electrostatic interactions that are necessary for what to occur?
-Histones occur in what?
-positively; DNA
-package DNA within the nucleus
-DNA folding
-in pairs
QUESTION 40: What chemical features of histones are important to their interaction with DNA?
-They are ___ charged amino acids
-These charges interact with the ___ charged ____ ____ of DNA
-What does this help to do?
-positively
-negativitly; phosphate backbone
-organize and stablize the nucleosome
QUESTION 41: What is an α-helix?
-It is a _____-handed secondary structure in ____
-What is it formed by?
-right; proteins
-hydrogen bonds between carbonyl oxygen & amide hydrogens
QUESTION 42: Where are the side groups located in a classic right-handed a-helix?
On the outside of the structure
QUESTION 43: Why is an a-helix usually right-handed? What type of amino acid might accommate a left-handed a-helix?
-Due to the properties of the ____ ____ & arrangement of the ____ ____
-Amino acids that do what could accomodate a left-handed a-helix
-peptide bond; amino acids
-restrict rotation due to their ring structure
QUESTION 44: What chemical variables determine the structure of a polypeptide?
-What are the 4 things?
- Bond lengths
- Torsion angles
- Side-chain properties
- The sequence of amino acids
QUESTION 45: What chemical features stabilize an a-helix?
-_____ bonds between what?
-hydrogen bonds between carbonyl oxygen of one amino acid and amide hydrogen of another
QUESTION 46: What type of conformations does the backbone of a histone assume?
-It adopts what structures in the cental regions?
-How would you describe the ends (tails)?
-a-helical structures
-they are disordered & extended
QUESTION 47: What is ment by 3.6 residues per turn?
-In a typical ____-____, there are ____ amino acid residues in each what?
-a-helix
-3.6
-complete helical turn
QUESTION 48: Why do α-helices pack at angles with respect to one another?
-They do this to minimize what?
-They do this to optimize what?
-What does this allow for?
-steric clashes
-interactions between side chains
-a stable, compact structure
