Molecular Biology and DNA Replication Quiz

DNA Structure

• DNA is a double-helix composed of repeating DNA nucleotides.
• Each nucleotide has three components: a phosphate group, a deoxyribose sugar, and an organic base.
• The two DNA strands in a double helix are antiparallel.
• The 3' end of the strand has a deoxyribose sugar, and the 5' end of the strand has a phosphate group.
• DNA nucleotides are joined together by strong chemical bonds between the phosphate group of one nucleotide and the deoxyribose sugar of another. This forms a sugar-phosphate backbone.
• The two strands are held together by complementary base pairing.
• Adenine pairs with Thymine (2 hydrogen bonds)
• Cytosine pairs with Guanine (3 hydrogen bonds)

DNA Organisation

• DNA is found in linear chromosomes within the eukaryotes' nucleus (e.g. plant, animal & fungi).
• DNA is found in circular chromosomes within prokaryotes' cytoplasm and in mitochondria and chloroplasts of eukaryotes.
• DNA is found in plasmids in the cytoplasm of prokaryotes and yeast cells.
• DNA is tightly coiled and packaged with associated histone proteins.

DNA Replication

• DNA is replicated by DNA polymerase prior to cell division.
• DNA polymerase requires primers to start replication.
• A primer is a short strand of nucleotides that binds to the 3' end of the template DNA.
• DNA polymerase adds DNA nucleotides using complementary base pairing to the deoxyribose (3') end of the new strand.
• DNA replication occurs in one direction on the leading strand and in fragments on the lagging strand.
• Fragments on the lagging strand are joined by ligase.

Polymerase Chain Reaction(PCR)

• PCR amplifies DNA using complementary primers targeting specific sequenced regions.
• Primers are short DNA sequences complementary to target sequences.
• Repeated heating and cooling cycles amplify the target DNA region.
• DNA is heated to 92-98°C to separate strands.
• Cooled to 50-65°C for primers to bind to target sequences.
• Heated to 70-80°C for heat-tolerant DNA polymerase to replicate the region.
• Each cycle doubles the amount of DNA.
• PCR needs a DNA template, nucleotides, primers, heat-tolerant polymerase, and pH buffer.
• PCR has practical applications in forensic science, paternity testing, and diagnosing genetic disorders.

Gene Expression

• Gene expression involves the transcription and translation of DNA sequences.
• Only a fraction of genes are expressed in a cell at any given time.
• Transcription and translation involve three types of RNA: mRNA, tRNA, and rRNA.
• RNA is single-stranded and composed of nucleotides with ribose sugar, phosphate, and one of four bases (Cytosine, Guanine, Adenine, and Uracil).
• mRNA carries a copy of DNA's code from the nucleus to the ribosome.
• tRNA carries the specific amino acid to the ribosome.
• rRNA and proteins form ribosomes.

Transcription

• RNA polymerase moves along DNA, unwinding it and breaking hydrogen bonds between bases.
• RNA polymerase synthesizes a primary mRNA transcript using RNA nucleotides via complementary base pairing.
• Uracil in RNA is complementary to Adenine.

RNA Splicing

• Some DNA transcribed is non-coding (introns) and must be removed.
• RNA splicing involves removing introns and joining coding regions (exons).
• The order of exons remains unchanged during splicing.
• Alternative splicing allows for multiple proteins to be expressed from one gene.

Translation

• tRNA is involved in translation of mRNA into a polypeptide at a ribosome.
• Translation starts at a start codon and ends at a stop codon.
• Anticodons bond to codons by complementary base pairing.
• Peptide bonds link amino acids together.
• tRNA leaves the ribosome as the polypeptide forms.

Protein Structure

• Amino acids are linked by peptide bonds to form polypeptides.
• Polypeptide chains fold to form a protein's three-dimensional shape held together by hydrogen bonds.
• Protein shape determines function.
• Phenotype is determined by the proteins produced as a result of gene expression.

Cellular Differentiation

• Cellular differentiation is where a cell expresses certain genes to produce proteins specific to its function.
• Stem cells are unspecialized cells that can divide and/or differentiate.
• Embryonic stem cells can differentiate into all cell types in the organism, and are therefore pluripotent.
• Tissue stem cells are involved in growth, repair, and renewal of tissues.
• They're multipotent, meaning they can differentiate into a limited range of cell types within a tissue.
• Therapeutic uses of stem cells involve repairing damaged or diseased organs or tissues.

Ethical Issues

• Use of embryonic stem cells raises ethical concerns, involving the destruction of potential life.

Genomic Sequencing

• Genomic sequencing determines the sequence of nucleotide bases in individual genes or entire genomes.
• Computer programs identify base sequences that are similar to known genes.
• Bioinformatics is essential for analyzing genomic data.
• Many genomes, particularly of disease-causing organisms, pest species, and model organisms, have been sequenced.
• Gene conservation across organisms has implications for understanding evolutionary relationships.

Phylogenetics

• Phylogenetics studies evolutionary history and relationships.
• Sequence data is used to determine relationships between species.
• Fossil evidence aids in mapping out evolutionary events, including the order in life's evolution, and the last universal ancestor.

Mutations

• Mutations are changes in DNA that alter or prevent protein synthesis.
• Single-gene mutations involve alterations in DNA nucleotide sequences.
• Substitution mutations: replacing one DNA nucleotide with another
• Insertion mutations involve inserting an extra DNA nucleotide.
• Deletion mutations involve removing a DNA nucleotide.
• Frame-shift mutations occur when insertions or deletions cause a change in the reading frame of the DNA sequence, which drastically alters protein structure.
• Splice-site mutations affect the process of RNA splicing by altering the recognition sequences.
• Nonsense mutations create premature stop codons, leading to shorter proteins.
• Missense mutations change an amino acid in the protein.

Speciation

• Speciation: Formation of new species.
• Isolation (geographic, behavioral, ecological) prevents gene flow between populations.
• Mutations create genetic variation within and between populations.
• Natural Selection favors more suitable mutations.
• Different reproductive isolation mechanisms create separate species.

Molecular Clocks

• DNA or protein sequences are used to estimate when species diverged during evolution.
• Differences in nucleotide/amino acid sequences reflect evolutionary time.
• Divergence rates must be assumed constant for reasonable estimates.

Pharmacogenetics and Personalised Medicine

• Pharmacogenetics uses genome information to choose appropriate drugs for diseases.
• Personalised medicine uses an individual's genome for selecting the most effective drugs and dosage.

Test your knowledge on key concepts of molecular biology, including DNA replication, phylogenetics, and PCR. This quiz covers the roles of various enzymes, the differences between leading and lagging strands, and the significance of molecular clocks in estimating divergence times. Perfect for students in biology classes or anyone interested in genetics!