nucleic acids Flashcards
levels of structure in nucleic acids
- Primary structure
Order of bases in the polynucleotide sequence
Specifies the genetic code - Secondary structure
Three-dimensional conformation of the polynucleotide backbone - Tertiary structure
Supercoiling of the molecule - Quaternary structure
Interaction with other classes of macromolecules, such as proteins
what are the structure in nucleic acids and proteins
a nucleic acid:
5’ to 3’
a protein:
N terminal to C terminal
monomer of nucleic acid
nucleotides
structure of nucleic acids
nitrogenous base
phosphate group
pentose sugar
Nitrogen-containing aromatic compounds that make up the coding portion of nucleic acids
nucleic acid bases
5 membered ring, polysaccharides
pentose sugar
ribose vs deoxyribose
Ribose
* Present in RNA
* Contains -OH group at carbon
Deoxyribose
* Present in DNA
* Lacks -OH group at carbon 2
Purine or pyrimidine base bonded to a sugar (ribose or deoxyribose)
nucleoside
*lacks phosphate group
Formed when phosphoric acid is esterified with an —OH of the monosaccharide, most commonly either the 3′ —OH or the 5′ —OH
nucleotide
*base + sugar + phosphate
what reaction is a nucleoside formation and how is it formed
condensation reaction
The base is attached to C1′ position of the sugar (β- configuration, pataas)
Formed by the addition of a phosphate group to a nucleoside
nucleotide
*water is released when phosphate is attached to C5’
it is the bond between ribose/ deoxyribose and each base
b-glycosidic bond
DNA vs RNA
- Deoxyribonucleic acid (DNA)
– Found within the cell nucleus
– Stores and transfers genetic information
– Passed from existing cells to new cells during cell division - Ribonucleic Acid (RNA)
– Occurs in all parts of a cell
– Primary function is the synthesis of proteins
3′ —OH of one 2-deoxy-D-ribose is
joined to the 5′ —OH of the next 2-deoxy-D- ribose by a
phosphodiester bond
it consists of a backbone of alternating units of 2-deoxy-D-ribose and phosphate
biopolymer
what is the overall charge of the nucleotide
The nitrogenous base can contribute a +1 charge if it is protonated, and the phosphate groups typically contribute a -2 charge. Therefore, when you consider these charges together, the overall charge of a nucleotide is usually negative (approximately -1), especially when accounting for one phosphate group. If there are multiple phosphate groups (as in ATP, for example), the overall charge would be even more negative. So, in summary, the nucleotide’s typical charge is negative due to the phosphate groups outweighing any potential positive contribution from the nitrogenous base.
a nucleotide chain has directionality
5’ end: free phosphate group
3’ end: free hydroxyl group
Sequence of bases along the pentose-phosphodiester backbone of a DNA molecule
primary structure of DNA
Ordered arrangement of nucleic acid strands
secondary structure of DNA
Three-dimensional arrangement of all atoms of a nucleic acid
tertiary structure of DNA
*referred to as supercoiling
Two polynucleotide chains wrapped around each other
DNA double helix
proposed by James Watson and Francis Crick in 1953
based on X-ray crystallography
how are the base pairs are held together
by hydrogen bonds
- which keeps the 2 strands of DNA aligned
- stabilize the double helix
The two strands run in opposite directions
antiparallel
one from 3’ to 5’ and the other from 5’ to 3’
how does one know if the bases are the most stable or preferred pairs
through x-ray cystography
briefly explain the different types of DNA configurations
index card
how does bases interact w each other
bases are hydrophobic
hence via hydrophobic bonding
true or false:
In standard B-DNA, each base is rotated 32° with respect to the preceding one
true -
* Perfect for maximal base pairing but not optimal for maximum overlap of bases
* Bases that are exposed to the minor groove must come in contact with water
[This allows for good base pairing but isn’t perfect for base stacking.
Some bases are exposed to water in the DNA’s minor groove.]
why do many bases adopt a propeller twist
Base-pairing distances are less optimal
base stacking is more optimal
- water is eliminated from minor-
groove contacts with bases
[Bases often twist like propeller blades to improve their positioning.]
why do bases slide sideways
allow them to interact better w the bases abv and below them
*the twist and slide depend on which bases are present
prokaryotic DNA
circular and forms supercoils
Extra twists (over and above those of the double helix) in closed circular DNA
DNA supercoils
Type of double-stranded DNA in which the 5′ and 3′ ends of each strand are joined by phosphodiester bonds
circular DNA
briefly explain the negative and positive supercoiling in simple terms
- Negative supercoils: Circular
DNA with fewer than normal number of turns of the helix - Positive supercoils: Circular DNA with more than normal number of turns of the helix
Enzymes that relax supercoiling in closed circular DNA
Topoisomerases
Complex of DNA and protein found in eukaryotic nuclei
chromatin
- resembles beads on a string
Basic proteins found complexed to eukaryotic DNA
histones
(H1, H2A, H2B, H3, and H4)
*rich in lys and arg
Globular structure in which DNA is wrapped around an aggregate of histone molecules
nucleosome
the how to break the hydrogen bonds of DNA and to disrupt the stacking interactions
denaturation
energy must be added - heating
heat denaturation is called melting
bases absorbs light in the 260nm wavelength region
true or false:
the separated strands cannot reconnect
false - that renaturation, when cooled slowly, the separated DNA strands can reconnect
hyperchromicity
DNA strands separate, they absorb more light
why does G-C pairs has a higher melting temperature
because G-C pairs have three hydrogen bonds, while A-T pairs have only two.
Consists of long, unbranched chains of nucleotides joined by phosphodiester bonds between the 3′ —OH of one pentose and the 5′ —OH of the next
RNA
* pentose unit is b-D-ribose (It is B-deoxy-D-ribose in DNA)
Single-stranded polynucleotide chain between 73 and 94 nucleotide residues long
Transfer RNA, tRNA
- short-single stranded RNA
- has a specific aa attached at one end
- carries aa to ribosomes for protein building
Ribonucleic acid found in ribosomes, the site of protein synthesis
Ribosomal RNA, rRNA
- 60-65% weight of the ribosomes
-35-40% weight of the protein portion
- protein synthesis
how many subunits are there in a ribosomes
2 subunits
- 1 larger than the other
Initially formed as a larger precursor molecule
heterogeneous nuclear RNA (hnRNA)
Ribonucleic acid that carries coded genetic information from DNA to ribosomes for the synthesis of proteins
Messenger RNA, mRNA
- small amt and short lived in cells
- tells ribosomes what proteins to make, directly copied from DNA
Found in nucleus of eukaryotic cells and recently discovered
Small nuclear RNA (snRNA)
- helps process other RNA s, especially mRNA
- works w protein t form snRNPs
snRNA complexes with protein and forms
small nuclear ribonucleoprotein particles (snRNPs)
what is the difference between
tRNA:
rRNA:
mRNA:
snRNA:
(found in)
tRNA: Amino acid carrier (cytoplasm)
rRNA: Part of protein-making machinery (ribosomes- cytoplasm and ER)
mRNA: Genetic message carrier (cytoplasm)
snRNA: RNA processing helper (nucleus)
which RNA is the most short lived
mRNA
list the RNA in order from shortest to long
snRNA: Shortest
tRNA: Short
mRNA: Varies, can be long
rRNA: Long
list the abundance of the RNA from most to low abundance
rRNA: Most abundant
tRNA: Fairly abundant
mRNA: Least abundant
snRNA: Low abundance
