Nucleic acids: DNA and RNA overview

Nucleotides
The monomers from which the polymers DNA and RNA are made

ATP, energy-rich molecule==> provides energy for biochemical reactions;
Cyclic AMP & cyclic GMP=> intracellular signals;
Substrates for kinases (an enzyme that adds a phosphate group to a protein);
Enzyme cofactors
What are some functions of nucleotides?

DNA (deoxyribonucleic acid)
RNA (ribonucleic acid)
What are the 2 classes of nucleic acids?

D-ribose;
2-deoxyribose (in nucleotides used to make DNA)
Nucleotides contain either the aldopentose , or _.

The Cs in ribose are given the ‘ (“prime”) symbol
How do you distinguish b/w the numbering of C atoms in the sugar and in the base?

5
Linked to ribose is a phosphate in an ester bond at C _.

Nitrogenous base derived from purine or pyrimidine
Also linked to ribose, in a B-N-glycosidic bond at C 1, is a _____.

Adenine & Guanine
What are the purines?

Cytosine, Uracil, & Thymine
What are the pyrimidines?

Ribose or 2-deoxyribose linked to a base
What is a nucleoside?

Nucleosides joined to one or more phosphoryl groups
What is a nucleotide?

Nucleotides linked by phosphodiester bonds b/w the 5′ phosohate group of one nucleotide and the 3′ hydroxyl group of another
How are nucleic acids (DNA/RNA) formed?

Nucleic acids
Genetic information is contained in the _.

Genetic information
The information required for synthesis of polypeptides w/ specific amino acid sequences

Genome
All of the genetic material

DNA
The genome of cells is __.

RNA
Some viruses have __ genomes.

DNA ==> RNA ==> Protein
Information flow of genetic material:

Transcription
Copying of the DNA sequence information into RNA

Translation
This happens to information in RNA molecules during polypeptide chain synthesis:

Alternating sugar and phosphate units;
The information in a DNA or RNA molecule is in the sequence of the bases attached to this backbone
What does the backbone of a polynucleotide contain?

Write the sequence of the bases in the nucleotides, w/ 5′ to 3′ direction written left to right;
Sequences are one-directional (ACG is not the same as GCA)
What is a common shorthand way to designate the sequence of a nucleic acid molecule?

Adenine (A), thymine (T), guanine (G), and cytosine (C);
The sugar is deoxyribose
What residues does DNA contain and what is the sugar?

Adenine (A), uracil (U), guanine (G), and cytosine (C);
The sugar is ribose
What residues does RNA contain and what is the sugar?

DNA occurs in cells as a double-stranded helix;
RNA is single-stranded
What is the difference in DNA and RNA structures?

Hydrogen bonds
In a DNA double helix, pairs of nucleotides in opposite strands are linked by _.

Purine; pyrimidine
A _ always pairs with a _.

T;
C;
(this means the amounts of these pairs in a DNA sample are always equal)
A is always paired w/ . G is always paired w/ .

TRUE
This happens b/c G-C pairs form 3 H-bonds, whereas A-T pairs form 2 H-bonds.
T or F
G-C pairs are always more stable than A-T pairs.

Complementary
Two DNA strands must be _ in sequence in order for the correct base pairing to occur.

FALSE.
They are antiparallel (opposite);
The 5′ end of one strand is near the 3′ end of the other strand.
T or F
The two DNA strands in a double helix run in the same direction.

The B-DNA consists of 2 polynucleotide strands that wind about a common axis to form a double helix;
The 2 strands are antiparallel;
The planes of the bases are nearly perpendicular to the helix axis;
Each base is H-bonded to a base on the opposite strand to form a planar base pair;
The “ideal” B-DNA helix has 10 base pairs per turn;
B-DNA has 2 deep exterior grooves that wind b/w its sugar-phosphate chains;
These grooves are of unequal size and are called “the major groove” and “the minor groove”;
These grooves make binding sites for proteins
What is the B-DNA helix?

Semiconservative, meaning a new copy contains one strand from the old molecule and one strand that has been newly synthesized
DNA replication is __.

Yes; they can be separated by physical treatments that disrupt H-bonding (heat, pH, etc.)
Is it possible for the two strands of a double helix to be unwound? If so, how?

Melting
The separation of DNA strands

Denatured
The single stranded DNA that resulted from melting a double helix

Melting temperature
Tm;
Temperature at which 1/2 of the double stranded structure is lost;
Usually b/w 70 and 90 degrees C

B/c G-C pairs have more H-bonds and are more stable than A-T pairs;
AT-rich regions of a DNA molecule will melt first
Why does a higher GC content lead to a higher Tm?

Annealing
The process of heating and cooling denatured DNA strands, which result in the base pairs reforming and the double stranded structure being regained

Renatured
When the double stranded structure of DNA is regained after annealing

The nucleus
Where is DNA found in eukaryotic cells?

Histones
Nuclear DNA is associated w/ a number of these proteins;
Small proteins w/ large numbers of Arg and Lys residues;
Basic side chains are involved in iconic interactions w/ negatively charged phosphates in DNA;

Chromatin
DNA-protein complex

Nucleosome
An organized structure formed when DNA folds around a group of 8 histones;
Regularly spaced about every 200 base pairs along a DNA molecule

Ribosomal RNA (rRNA)
An integral part of ribosomes;
Accounts for ~80% of RNA in cells

Transfer RNA (tRNA)
Carry activated amino acids to ribosomes for polypeptide synthesis;
Small molecules, 73-95 nucleotides long

Messenger RNA (mRNA)
Carry sequence information to the translation complex

microRNA
Noncoding RNAs ~21 nucleotides long that help to regulate gene expression post-transcription

DNA is the molecule that stores genetic information in living things. It consists of two strands that are antiparallel and complementary to each other.

The full name for DNA is Deoxyribose Nucleic Acid. ‘Deoxy’ comes from the fact that the second carbon atom of the sugar molecule in DNA is deoxygenated.

• Nitrogenous bases – Adenine, Thymine, Guanine, and Cytosine.
• 5 atom carbon sugar molecule – deoxyribose
• Phosphate group.

The nitrogenous base is joined to the sugar molecule by a hydrogen bond attached to the first carbon atom. The phosphate group is joined to the sugar molecule by a phosphodiester bond on the third carbon atom.

RNA (Ribonucleic acid)

Ribonucleic acid (RNA) is a polymeric molecule whose function is coding, decoding, regulation and expression of genes in living things.

RNA has nitrogenous bases (Adenine, Guanine, Cytosine, and Uracil), the phosphate group and the 5 carbon atom sugar molecule (ribose).

DNA is mostly found inside the cell nucleus while RNA is mostly found in the cytoplasm as well as in the nucleolus.

Transcription is the process by which the cell synthesizes RNA from the DNA template, which is carried out by RNA polymerase

Base pairing

DNA

• Adenine pairs with Thymine
• Guanine pairs with Cytosine

RNA

•  Adenine pairs with Uracil
• Guanine pairs with Cytosine

Differences between DNA and RNA

DNA is mostly found within the nucleus while RNA is mostly found in the cytoplasm

DNA has a deoxyribose sugar whose second carbon is deoxygenated while RNA contains a ribose sugar whose second carbon is oxygenated.

DNA contains Adenine, Thymine, Guanine, and Cytosine as the nitrogenous bases while RNA contains Adenine, Uracil, Guanine, and Cytosine as nitrogenous bases.

DNA is usually double-stranded while RNA is single-stranded unless during hybridization of RNA to double-stranded DNA through the formation of R-loops.