Molecular Biology DNA and RNA Quiz

Nucleic Acids

• Nucleic acids are the energy-rich compounds that are the monomers of nucleic acids.
• They provide energy for metabolic processes.
• They are part of enzyme cofactors, such as NAD (nicotinamide adenine dinucleotide) and FAD (flavin adenine dinucleotide).
• They act as secondary chemical messengers in response to hormones.
• A nucleotide consists of three portions: a nitrogenous base, a sugar (deoxyribose or ribose), and one or more phosphate groups.

Nucleotides

• Common purine bases are adenine and guanine.
• Common pyrimidine bases are cytosine, uracil, and thymine.
• Some common nucleotides include ATP (adenosine triphosphate), ADP (adenosine diphosphate), AMP (adenosine monophosphate), GTP (guanosine triphosphate), UTP (uridine triphosphate), and CTP (cytidine triphosphate).

Nucleosides

• A nucleoside consists of a nitrogenous base covalently attached to a sugar (ribose or deoxyribose) but without the phosphate group.
• When a nucleoside is phosphorylated, a nucleotide is formed.
• Purine nucleosides end in "-sine" (e.g., adenosine, guanosine).
• Pyrimidine nucleosides end in "-dine" (e.g., cytidine, uridine, deoxythymidine).

Nucleic Acids - DNA

• DNA is found in the chromatin of the cell's nucleus and also in mitochondria and chloroplasts.
• It contains genetic information in segments called genes.
• It provides information for constructing other cell components.
• DNA is made of nucleotide monomers and has a double helix structure.
• The double helix is also called B-form DNA or B-DNA and is very stable.
• DNA exists in other variations such as A-DNA and Z-DNA which are converted into B-DNA at normal physiological conditions.
• The backbone of DNA is comprised of deoxyribose sugar linked by phosphodiester bridges.
• The 3' hydroxyl group of one sugar is linked to the 5' hydroxyl group of another sugar by a phosphodiester bond
• The strands run antiparallel to each other (one strand runs 3' to 5', and the other runs 5' to 3').
• The nitrogenous bases are adenine (A), thymine (T), cytosine (C), and guanine (G).
• Adenine pairs with thymine (A=T) via two hydrogen bonds.
• Guanine pairs with cytosine (G≡C) via three hydrogen bonds.
• The GC pair is held together more strongly than the AT pair due to the stronger triple bonds.
• The pairing of bases is called complementary base pairing and the sequences are complementary but not identical.
• The DNA helix can be bent or supercoiled due to flexibility. This allows the DNA to be wrapped around proteins, compacting DNA into smaller volumes.

Nucleic Acids - RNA

• RNA is found in the cell's cytoplasm and nucleolus.
• It is formed from DNA by a process called transcription.
• RNA consists of a phosphate group, a nitrogenous base (adenine (A), uracil (U), cytosine (C), and guanine (G)), and a sugar (ribose).
• RNA is similar to DNA, the nitrogenous bases carry genetic information and the sugar-phosphate serves to maintain the structure.
• RNA structure is single stranded and runs in the 5' to 3' direction.
• Base pairing can occur, thus the molecule can fold on itself in the form of a hairpin structure which does not require equal amounts of complementary base pairs.

Types of RNA

• Ribosomal RNA (rRNA) makes up 80% of RNA in cells and is the most abundant and stable form.

• rRNA has a higher GC content than AU content.

• In the cytoplasm, rRNA combines with proteins to form ribosomes.

• Transfer RNA (tRNA) occupies 15% of the total RNA in the cell and is the smallest polymeric form.

• tRNA functions as a carrier of activated amino acids to a growing polypeptide chain in protein synthesis.

• tRNA binds to specific amino acids and has a three-fold clover leaf configuration.

• The 3' end of tRNA contains the CCA sequence. Amino acids bind to this end via esterification.

• The anticodon region base pairs to the corresponding codon region on the mRNA molecule. Each tRNA molecule has a specific anticodon triplet.

• Messenger RNA (mRNA) comprises 5% of RNA in the cell and is otherwise called template RNA.

• It is synthesized on the surface of the DNA template and carries genetic information from nuclear DNA to the cytosol.

• mRNA is used as a template for protein synthesis.

• monocistronic mRNA carries the code for a single protein.

• polycistronic mRNA carries the code for more than one kind of protein.

Genetic Code

• The sequence of bases that encodes a functional protein is called a gene
• The relationship between the base sequence and the amino acid sequence of a particular protein is called the genetic code
• A codon consists of 3 nucleotides.
• There is a table of these codons and their corresponding amino acids.

Consequences of Altering the Nucleotide Sequence

• Silent mutation: A change in the nucleotide sequence that doesn't alter the amino acid or protein function.
• Nonsense mutation: A change in an mRNA codon that encodes a STOP codon, thus prematurely stopping the protein translation process.
• Missense mutation: A change in an mRNA codon that results in substituting one amino acid for another in the polypeptide chain.

DNA Replication

• DNA replication is the duplication of genetic material.
• During replication the hydrogen bonds between nitrogenous bases are broken separating the strands.
• Each separated strand serves as a template for the synthesis of a new strand that is complementary to the parent strand.
• The enzyme DNA polymerase moves along each template strand and reads the nucleotide.
• The enzyme ligase joins the complementary nucleotide in the new strand.
• DNA polymerase moves in the 3' to 5' direction.
• Other proteins are needed for unwinding the helix, separating the strands, and joining segments into a continuous strand.
• DNA replication is semi-conservative, meaning each new DNA molecule contains one original strand and one new strand.

DNA Replication

• DNA polymerase is a remarkable enzyme that minimizes mistakes during base pairing.
• It contains two active sites: one for polymerization and one for proofreading.
• If a wrong nucleotide is inserted, the proofreading site recognizes the error and removes it.
• If not recognized, the change results in a permanent alteration; a genetic mutation.

Transcription

• This is the process by which RNA is formed from DNA.
• The information in the DNA molecule is carried by the mRNA molecule.
• During transcription, the double helix of the DNA temporarily separates.
• A complementary strand of mRNA (anti-sense strand) assembles on one DNA strand.
• The process is catalyzed by RNA polymerase in a 5' to 3' direction.
• mRNA then leaves the DNA template and carries the information to the ribosomes for polypeptide synthesis.

Translation

• In translation every three consecutive nucleotides on the mRNA is called a codon.
• Each codon codes for a particular amino acid.
• mRNA determines the sequence of amino acids in a protein, which occurs in the translation process.
• Translation is the process that requires numerous enzymes, ribosomes, amino acids, mRNA, tRNA, and energy (ATP and GTP).
• One of the tRNA folds has a specific triplet codon to which an amino acid is attached.
• The amino acid binds covalently to this region, and at least one kind of tRNA is present for each of the 20 amino acids.
• Some amino acids have more than one tRNA molecule.
• There is a triplet codon called an anticodon located at another folded end of the tRNA molecule.
• The anticodon is the complementary code for the attached amino acid.
• When an amino acid is linked to the tRNA molecule, base pairing can occur between the anticodon region of the tRNA and the mRNA molecule.
• Translation involves three major steps (initiation, elongation, and termination).

Translation- Initiation

• During initiation, the small subunit of the ribosome binds at the start codon (AUG) near the 5' end of the mRNA strand.
• The large subunit of the ribosome joins with a special initiator tRNA molecule (which codes for methionine).
• If the reading is at the wrong nucleotide, the remaining triplets will be incorrectly read.
• Incorrect amino acids will be inserted producing a useless polypeptide.

Translation- Elongation

• A tRNA with the amino acid, bonded to it, then base pairs with the mRNA molecule.
• This process requires energy.
• The preceding amino acid is linked to the incoming amino acid by a peptide bond.
• The initiator tRNA to which methionine was attached is then released.

Translation- Termination

• Translation ends when the ribosome reaches a stop codon (UAA, UAG, or UGA).
• No tRNA molecules have anticodons to stop codons, so no amino acids are assigned to these codons.
• Release factors recognize stop codons and release the polypeptide chain from the ribosome.
• The process needs energy.
• The ribosome then splits into subunits and can be reassembled for another round of protein synthesis.
• Many mRNA molecules can be translated simultaneously.

Biotechnology

• Biotechnology encompasses fields like forensic science, DNA profiling, genetically modified foods, and various applications.
• Applications include genetically modified plants, micro-propagation, bio-fertilizers/bio-pesticides for agriculture; stem cells, monoclonal antibodies, and vaccines for health care; industrial enzymes for fermentation processes; biofuels and in bioinformatics/bio-mining.

Genetic Diagnosis

• Methods like PCR (polymerase chain reaction) are used to detect genetic variations related to diseases such as haemophilia, HIV, cystic fibrosis, sickle-cell anemia, phenylketonuria, multiple sclerosis, Tay-Sachs disease, and Alzheimer's disease, along with metabolic diseases like lactose intolerance.

Genetic Diseases

• A small change in the genetic code can lead to significant differences in the resulting protein, impacting the protein's function, which may cause major malfunction or disease.

Other Applications

• Proteins made by genes in bacteria, such as insulin or tissue plasminogen activator (TPA) to dissolve blood clots.
• Genetically modified crops like soybeans, maize, tomatoes, rice, and sweet potatoes.

Genetically Modified Foods

• Genetically modified organisms (GMOs) are primarily used for food production.
• Examples include soybean, corn and canola that are herbicide-resistant.
• Bt corn and cotton provide resistance to insect pests.
• Also papaya resistant to a virus, and rice/sugar cane improvements.