Name the nucleotides and Nucleic acids
Nucleotides:
* Energy currency (ATP)
* Signaling molecules (cAMP)
* Enzyme co-factors (NAD, FAD)
* Building blocks of nucleic acids
Nucleic acids:
* Genetic information (DNA, RNA)
* All stages of protein synthesis (DNA, mRNA, tRNA, rRNA)
Nucleotides are the building blocks of nucleic acids. T or F?
True
Nucleotides share three components:
- Ribose sugar (ribose or deoxyribose)
- Nitrogenous base (purine or pyrimidine)
- Phosphate(s)
What is the difference between ribose and deoxyribose?
Ribose contains a hydroxyl group at the second carbon. While Deoxyribose contains a single hydrogen at the second carbon.
Identify the purines and the pyrimidines:
Purines: Adenine, Guanine
Pyrimidines: Cytosine, Uracil, and Thymine
What is the difference between nucleotides and nucleosides?
Nucleotides and nucleosides differ in whether they are phosphorylated
at the C5’ position.
How to do the nomenclature for nucleotides and nucleosides?
1) Which nitrogenous base is present (base name).
2) Whether the sugar is ribose or deoxyribose (deoxy prefix).
3) Whether there are phosphoryl groups (suffix of osine from nucleosides; ylate for nucleotides).
Physiological roles of nucleotides?
-Energy Transfer
-Signal Transduction
Nucleotides form linear nucleic strands through 5’-3’ phosphodiester linkages. T or F?
True
RNA function
- Ribosomal RNA (rRNA) - an integral part of ribosomes, ~80% of RNA in cells.
- Transfer RNA (tRNA) - carry activated amino acids to ribosomes for protein synthesis (small molecules 73-95 nucleotides long).
- Messenger RNA (mRNA) - Code for proteins; contains triplet codons
that specify the amino acid sequence of a protein. - Micro RNA (miRNA) are short oligonucleotides (22-24 nts in length)
that function in transcriptional and post-transcriptional regulation of
gene expression.
Base pairing in double helices
- Adenine (A) base pairs with Thymine (T).
- Guanine (G) base pairs with Cytosine (C).
What are the weak forces that stabilize the double helix?
- Hydrophobic effects. Burying purine and
pyrimidine rings in the interior of the helix. - Stacking interactions. Stacked base pairs
form van der Waals contacts. - Hydrogen bonds. Hydrogen bonding
between base pairs. - Charge-charge interactions. Electrostatic
repulsion of negatively charged phosphate
groups is decreased by cations (e.g. Mg2+)
and cationic proteins.
A double helix has two grooves of unequal width called the major and minor grooves. What is the difference between major and minor groove sides?
What are restriction endonucleases and what do they do?
They are enzymes that have these roles:
- Restriction endonucleases recognize and cleave specific DNA sequences.
- Bacterial defense mechanism against viral invasion.
- Host cells protect their own DNA by covalent modification of bases at the restriction site (e.g.methylation).
Duplex DNA contains ___ _____________, _____-___________ _______.
Duplex DNA contains two complimentary, anti-parallel strands. Because the strands are complimentary, the sequence of one strand determines the sequence of the other strand.
What is the complimentary strand to:
5’ ATGCATCG 3’
3’ CGATGCAT 5’
What happens in the denaturation of DNA?
Complete separation of double-stranded DNA by heat or chemical agents.
Denaturation of DNA is a cooperative process. T or F?
True
Melting temperatures reflect sequence compositions; the higher the GC
content the ______ the Tm
Melting temperatures reflect sequence compositions; the higher the GC
content the higher the Tm.
In both DNA and RNA, nitrogenous bases are linked to which carbon of the sugar ring?
-4’
- 2’
-1’
-3’
-5’
1’
Which nitrogenous base is found within DNA but not RNA?
guanine
adenine
uracil
thymine
cytosine
Thymine
For a DNA strand of the sequence
5’-TCCTACA-3’ the complementary strand will be:
5’-TGTAGGA -3’
Which of the following is FALSE? In cellular duplex DNA:
-All of the answers are correct
-the two strands are anti-parallel.
-nitrogenous bases of opposing strands are connected by hydrogen bonds.
-deoxyribose units within each strand are connected by phosphodiester bonds.
-a purine always hydrogen bonds with a pyrimidine.
-All of them are correct
Telomeres are:
-repetitive sequences found at the end of eukaryotic genes.
-repetitive sequences found at the end of eukaryotic chromosomes.
-binding sites for histone proteins.
-non-coding regions within eukaryotic genes.
-sequences that are self-complementary about a point.
-Repetitive sequences found at the end of eukaryotic chromosome.
