CHAPTER 9 Flashcards
LEVELS OF STRUCTURES IN NUCLEIC ACIDS
Primary, Secondary, Tertiary & Quaternary
Order of bases in the polynucleotide sequence
Primary structure
3D conformation of the polynucleotide backbone
Secondary structure
Structure that uses Supercoiling of the molecule in nucleotide
Tertiary structure
Structure of nucleotide that has an Interaction with other classes of macromolecules
Quaternary structure
Has 3 units [Purine, pyrimidine or phosphate groups]
NUCLEOTIDES
Six-membered ring and Parent compounds of several nucleobases
Pyrimidine bases
Nitrogen-containing aromatic compounds that make up the coding portion of nucleic acids
Nucleic acid bases
five-membered ring and Parent compounds of adenine and guanine
Purine bases
common nucleobases in pyrimidine
Cytosine, Thymine and Uracil
common nucleobases in purine
Adenine and Guanine
Has longer name but shorter structures
Pyrimidine
Has shorter name but longer structures
Purine
Purine or pyrimidine base bonded to a sugar (ribose or deoxyribose)
NucleoSide
has 2 component and Lacks phosphate group
NucleoSide
Has Three components
NucleoTide
What are the components of NucleoTide
Sugar, Base and Phosphate group
How NucleoTide produces nucleic acids
By Polymerization
Forms the backbone of nucleic acids; esterified to the 3ʹ hydroxyl of one nucleoside and the 5ʹ hydroxyl of another nucleoside
3ʹ, 5ʹ-phosphodiester bond
Common system of notation uses only the single letters to show the order of the bases
DNA
5 amp signifies what?
5ʹ-adenosine monophosphate
3 amp signifies what?
3ʹ adenosine monophosphate
Where dG is part of?
DNA
G stands for? and part of?
Guanosine, RNA only
How sequence should be read?
5’ to 3’ sequence
Structure In DNA Sequence of bases along the pentose-phosphodiester
Primary Structure
DNA Ordered arrangement of nucleic acid strands
Secondary Structure
Fundamental structural motif of DNA
DNA DOUBLE HELIX
Who proposes DNA DOUBLE HELIX?
James Watson and Francis Crick in 1953
Based on what is DNA DOUBLE HELIX?
Based on X-ray crystallography
How does base pairing is identified?
By Hydrogen Bonding
A—T base pair has ______ hydrogen bonds?
2 hydrogen bonds
G—C base pair has ______ hydrogen bonds
3 hydrogen bonds
Larger of two empty spaces
Major groove
Smaller of two empty spaces
Minor groove
Considered the normal, physiological DNA form
B-DNA
Right-handed helix
B-DNA
Whats the Difference of B-DNA & A-DNA?
both are Right-handed helix but A-DNA is
thicker
Has 10 base pairs per turn of the helix
B-DNA
Has 11 base pairs per turn of the helix and not found in vivo techniques
A-DNA
Left-handed double helix
Z-DNA
plays in regulation of gene expression
Z-DNA
Has extra twists in closed circular DNA
DNA SUPERCOILS
Type of double-stranded DNA in which the 5ʹ and 3ʹ ends of each strand are joined by phosphodiester bonds
Circular DNA
DNA with fewer than normal number of turns of the helix
negative supercoils
DNA with more than normal number of turns of the helix
positive supercoils
Coil direction of Counterclockwise
Positive Supercoils
Coil direction of clockwise
Negative supercoils
Enzymes that relax supercoiling in closed circular DNA
TOPOISOMERASES
Cut the phosphodiester, pass the other end through, and reseal
Class I
Cut both strands, cut ends, and reseal
Class II
Bacterial topoisomerase that introduces negative supercoils
DNA gyrase
Complex of DNA and protein
Chromatin
Basic proteins found complexed to eukaryotic DNA
Histones
Main types of Histones
H1, H2A, H2B, H3 and H4
What are the basic amino acid residues in Histones
lysine and arginine
What is the structure-like of chromatin
beads on a string
Globular structure in which DNA is wrapped
around an aggregate of histone molecules
Nucleosome
String portions are called
spacer regions
This is when Energy must be added to a sample of DNA to break the hydrogen bonds and
to disrupt the stacking interactions
Denaturation of DNA
Denaturation should be carried out by? and also known as?
Heat denaturation; Melting
Bases absorb light in the what wavelength region?
260-nm-wavelength
Does Wavelength of Absorption does not change?
T or F
TRUE
If Wavelength of Absorption does not change, the Amount of light absorbed is?
Increases
Does Renaturation is possible? How?
Yes, by slow cooling
It is a single stranded helix
RNA
what is the Pentose unit?
Beta D-Ribose
Single-stranded polynucleotide chain between 73 and 94 nucleotide residues long
tRNA
what type of bonding occurs in tRNA?
Intrachain hydrogen bonding
tRNA carries amino acid on which end?
3’ end
Ribonucleic acid is found in?
Ribosomes
What is the site of protein synthesis
Ribosomes
Used to monitor the dissociation and reassociation of ribosomes
Analytical Untracentrifugation
This involves Transcription
mRNA
This is known as draft before to be a complete RNA
heterogeneous nuclear RNA (hnRNA)
This interrupts the messages and should be removed
Introns
Found in nucleus of eukaryotic cells and has About 100 to 200 nucleotides long
snRNA
Help with processing of the iniPal mRNA transcribed from DNA into a mature form
Small nuclear ribonucleoprotein Partcles (snRNPs)
snRNPs is Protein–RNA complexes found in the nucleus that aid in processing RNA molecules and exported to?
Cytosol
Who unwinds DNA double helix?
DNA HELICASE
What is the direction of movement of DNA helicase?
To the Direction of movement of replication fork
Who ensures correct base pairing
DNA POLYMERASE
What is the preferred direction of DNA polymerase on a forming daughter strand?
5’ to 3’
What is the preferred direction of DNA polymerase on a forming daughter strand?
5’ to 3’
Who seals nicks/gaps of okazaki fragments?
Ligase
Which strand grows in segments?
Lagging strand
Other term of lagging strand?
Okazaki fragments
