Nucleotides and Nucleic Acids Flashcards
(22 cards)
What are the two main types of nucleic acids?
- DNA (deoxyribonucleic acid)
- RNA (ribonucleic acid)
What are the monomers of nucleic acids called?
Nucleotides
What is the structure of a DNA nucleotide?
- A ribose sugar without oxygen on its carbon two (deoxyribose) forms the central part of the nucleotide
- A phosphate (PO₄²⁻) group is bonded to the ribose on its carbon five
- A nitrogenous base is bonded to the ribose on its carbon one
The phosphate group will be an ion unless hydrogens have bonded to the two oxygen anions
What is the structure of an RNA nucleotide?
- It is mostly the same as an DNA nucleotide, with two key differences
- The sugar will be ribose instead of deoxyribose, meaning carbon two will have a hydroxyl group attached to it instead of just hydrogen
- The nitrogenous base will be uracil whenever the equivalent base on a DNA nucleotide is thymine (RNA cannot have thymine, and DNA cannot have uracil)
How are polynucleotides (nucleic acids) formed?
- A hydroxyl group on the phosphate group in one nucelotide interacts with the hydroxyl group on carbon three on the pentose sugar of another nucleotide
- A molecule of water is produced, so the linkage is a condensation reaction
- The bond formed is called a phosphodiester bond as two form per nucelotide
- Nucleotides can be separated via hydrolysis reactions upon the introduction of water molecules
- This process is the same for the formation of DNA and RNA strands
What is the structure of ATP (adenosine triphosphate)?
- Central ribose sugar
- Three phosphate groups (same as the ones in DNA and RNA nucleotides and attached as shown below) bonded to carbon five of the ribose sugar
- Adenine (and always adenine) bonded to carbon one of the ribose sugar
ATP is a single nucleotide and cannot form polynucleotides. Therefore, it is not a nucleic acid
How does ATP release energy?
- The end phosphate group is cleaved in a hydrolysis reaction, requiring a small amount of energy
- This forms ADP (adenosine diphospate), ATP with one fewer phosphate groups, and a phosphate ion
- The liberated phosphate ion proceeds to form bonds, releasing large amounts of energy
- ATP is only used as a form of short-term energy storage due to the instability of the phosphate bonds
- However, it is the universal energy currency as the energy released by the respiration of any molecule (carbohydrates, lipids, etc.) produces ATP
ATP is rapidly produced by reattaching a phosphate group to ADP; this is a condensation reaction called phosphorylation
What are the four bases found on DNA?
- Thymine
- Cytosine
- Adenine
- Guanine
Uracil is found on RNA in place of thymine
What two categories can the four bases found on DNA be separated into and which bases belong to which categories?
- Pyrimidines - the smaller bases with single carbon rings
- Thymine and cytosine are pyrimidines
- Purines - the larger bases with two carbon rings
- Adenine and guanine are purines
Uracil is a pyrimidine like thymine
What is the structure of a DNA molecule?
Exclude details about the individual nucleotides
- It is a nucleic acid that can have a few to a million nucleotides
- It consists of two strands of polynucleotides that twist around each other; this is called a double-helix
- The nitrogenous bases in the nucleotides form hydrogen bonds with nitrogenous bases in the nucleotides on the other strand
- The two strands run in the opposite direction, so are considered antiparallel
- One strand, called the 5’ to 3’ strand is oriented such that the bond on the carbon five comes before the bond on the carbon three when moving downwards on the strand on any particular nucleotide; the other, called the 3’ to 5’ strand, is orientated in the opposite direction
The structure of the individual strands has been discussed already
Which bases bond to which bases in a DNA molecule?
- Cytosine bonds with guanine, forming three hydrogen bonds
- Adenine bonds with thymine, forming two hydrogen bonds
- This is called complementary base pairing
- A pyrimidine bonds to a purine and vice versa
What are the steps to obtain purified DNA by precipitation?
- Grind a sample of plant tissue in a mortar and pestle to break down the cell walls
- Mix with detergent to break down the cell membrane and release the cell’s contents into solution
- Add salt to break the hydrogen bonds between the water molecules and DNA
- Add protease to help break down histones (proteins associated with DNA in chromosomes)
- Add a layer of ethanol to cause DNA to precipitate out of the solution
- Observe the DNA as white strands between the layer of ethanol and the rest of the solution and spool them onto a glass rod
The ethanol reduces the water concentration, causing DNA to precipitate out as nucleotides and nucleic acids are soluble in polar solvents like water but not non-polar solvents like ethanol as a result of their polarity
Why is DNA replication semi-conservative?
DNA molecules produced by replication consist of one strand from the template molecule and one newly-formed strand
What is the process of semi-conservative DNA replication?
- Helicase moves along the backbone of a DNA molecule, unwinding it and breaking the hydrogen bonds between bases
- Free nucleotides in the cytoplasm then pair with exposed complementary bases on each template strand and hydrogen bonds form between bases
- As this happens, phosphodiester bonds form between adjacent nucleotides on the newly-created strands; this process, and the previous process, is catalysed by DNA polymerase moving along the template strand
- In this way, two identical DNA molecules are produced
- The two template strands are antiparallel; one is the leading strand and one is the lagging strand
- This leads to differences in how DNA polymerase molecules act on them as the enzyme can only move in one direction
What are random, spontaneous errors in DNA replication called and what do they entail?
- Mutations
- They involve a change in the sequence of bases, either through an addition, deletion or substitution
What are the base pairs in a strand separated into and what do these divisions code for?
- Triplets, also called codons
- The three bases that form the triplet on a strand code for an amino acid in protein synthesis
Why is genetic code considered universal?
- All organisms have the same bases coding for the same amino acids
- However, the sequence and number of bases will be different in the genetic code each organism (with the exception of monozygotic twins)
What do all the bases in a single gene collectively code for?
A single polypeptide chain, so the primary structure of a protein
This is with the exception of genes that code for functional RNA molecules like rRNA
What does the non-overlapping nature of genetic code mean?
- Each base is part of only one codon and contributes to the code for only one amino acid
- This ensures DNA sequences are read in-frame
What is the degenerate nature of genetic code?
- Multiple combinations of base-pairs within triplets (multiple triplets) code for the same amino acid
- For example, the amino acid proline has four variations of codons that code for it
- The stop codon, which does not code for any amino acid, has three variations
This is a safeguard against mutations; it means changes in the sequence of bases do not necessarily entail a change in the sequence of amino acids in synthesised proteins
What is the process of transcription in protein synthesis?
- A DNA molecule is unwound by DNA helicase, breaking hydrogen bonds between bases
- RNA polymerase moves along the antisense (5’ to 3’) strand, adding RNA nucleotides with complementary bases to the DNA strand and forming phosphodiester bonds between these newly added bases
- This forms an mRNA molecule which is the same as the sense, or template (3’ to 5’) DNA strand, apart from the differences in DNA and RNA nucleotides
- This mRNA strand detaches from the antisense strand, exits the nucleus and heads for a ribosome
- The DNA molecule is reformed
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What is the process of translation in protein synthesis?
- The newly-synthesised mRNA molecule attaches to a specific site on the small subunit of a ribosome
- The anticodon loop on a free tRNA molecule—three exposed bases in a loop on the strand—will bind to a codon with complementary bases on the mRNA molecule (the first codon always codes for methionine, which every protein initially begins with)
- Each tRNA molecule has an amino acid corresponding to the anticodon on its other end
- Two tRNA molecules bind to adjacent codons simultaneously on the mRNA molecule and a peptide bond forms between the two amino acids on the ends of these tRNA molecules
- The ribosome moves along the mRNA strand, and the tRNA molecule on the first amino acid detaches, leaving the amino acid. The second tRNA molecule then becomes the first
- This process repeats, with only two tRNA molecule on the ribosome at one time, until a stop codon is reached on the mRNA molecule and the polypeptide is released
- A tRNA molecule can be up to 95 nucleotides long
- Multiple ribosomes can move along the same mRNA molecule to synthesise multiple identical polypeptides
