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Questions and Answers
What direction does DNA replication occur in?
What direction does DNA replication occur in?
What is the primary function of helicase during DNA replication?
What is the primary function of helicase during DNA replication?
In which organisms is DNA replication more complex?
In which organisms is DNA replication more complex?
What type of genetic code is found in all living organisms?
What type of genetic code is found in all living organisms?
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What is the role of single-stranded binding proteins during DNA replication?
What is the role of single-stranded binding proteins during DNA replication?
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What is the function of topoisomerases during DNA replication?
What is the function of topoisomerases during DNA replication?
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Where do the origins of replication commonly occur in the genome?
Where do the origins of replication commonly occur in the genome?
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What enzyme is primarily responsible for unwinding the DNA double helix during replication?
What enzyme is primarily responsible for unwinding the DNA double helix during replication?
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Which of the following is true regarding Okazaki fragments?
Which of the following is true regarding Okazaki fragments?
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Which component is essential for the synthesis of the leading strand during DNA replication?
Which component is essential for the synthesis of the leading strand during DNA replication?
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Which of the following best describes Okazaki fragments?
Which of the following best describes Okazaki fragments?
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What is the primary function of DNA ligase?
What is the primary function of DNA ligase?
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Which process is involved in repairing double-stranded DNA breaks?
Which process is involved in repairing double-stranded DNA breaks?
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What is the role of the primase in DNA replication?
What is the role of the primase in DNA replication?
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During DNA replication, what movement is associated with the replication fork?
During DNA replication, what movement is associated with the replication fork?
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Which strand of DNA undergoes discontinuous synthesis during replication?
Which strand of DNA undergoes discontinuous synthesis during replication?
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Which molecule stabilizes the unwound single strands of DNA during replication?
Which molecule stabilizes the unwound single strands of DNA during replication?
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What determines the direction of DNA strand synthesis?
What determines the direction of DNA strand synthesis?
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What type of reaction does a kinase catalyze?
What type of reaction does a kinase catalyze?
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Which enzyme is primarily involved in the rate-determining step of glycolysis?
Which enzyme is primarily involved in the rate-determining step of glycolysis?
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What is the function of a phosphorylase enzyme?
What is the function of a phosphorylase enzyme?
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Which compound stimulates glycolysis by activating PFK-1?
Which compound stimulates glycolysis by activating PFK-1?
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What does a mutase enzyme do?
What does a mutase enzyme do?
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Which enzyme is inhibited by high levels of NADH during the TCA cycle?
Which enzyme is inhibited by high levels of NADH during the TCA cycle?
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What is the role of carboxylases in metabolic reactions?
What is the role of carboxylases in metabolic reactions?
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Which enzyme is activated by insulin in fatty acid synthesis?
Which enzyme is activated by insulin in fatty acid synthesis?
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What inhibits glycogenolysis by affecting glycogen phosphorylase?
What inhibits glycogenolysis by affecting glycogen phosphorylase?
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What is the main consequence of unbalanced translocations?
What is the main consequence of unbalanced translocations?
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What syndrome is associated with a congenital deletion on the short arm of chromosome 5?
What syndrome is associated with a congenital deletion on the short arm of chromosome 5?
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What genetic characteristic is primarily found in Williams syndrome?
What genetic characteristic is primarily found in Williams syndrome?
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Which of the following is NOT a finding associated with Cri-du-chat syndrome?
Which of the following is NOT a finding associated with Cri-du-chat syndrome?
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Which statement correctly describes balanced translocations?
Which statement correctly describes balanced translocations?
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What physical characteristic is commonly observed in individuals with Williams syndrome?
What physical characteristic is commonly observed in individuals with Williams syndrome?
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What genetic process primarily leads to the formation of abnormal gametes in translocation situations?
What genetic process primarily leads to the formation of abnormal gametes in translocation situations?
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What is a common outcome of unbalanced translocations during reproduction?
What is a common outcome of unbalanced translocations during reproduction?
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What is the primary function of adenosine deaminase (ADA)?
What is the primary function of adenosine deaminase (ADA)?
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Which condition is primarily associated with a deficiency of hypoxanthine guanine phosphoribosyltransferase (HGPRT)?
Which condition is primarily associated with a deficiency of hypoxanthine guanine phosphoribosyltransferase (HGPRT)?
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What is a common finding in patients with Lesch-Nyhan syndrome?
What is a common finding in patients with Lesch-Nyhan syndrome?
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Which of the following statements about genetic code is correct?
Which of the following statements about genetic code is correct?
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What is the inheritance pattern of severe combined immune deficiency (SCID) associated with ADA deficiency?
What is the inheritance pattern of severe combined immune deficiency (SCID) associated with ADA deficiency?
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Which is a notable clinical feature of Lesch-Nyhan syndrome?
Which is a notable clinical feature of Lesch-Nyhan syndrome?
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What treatment is effective in managing hyperuricemia in Lesch-Nyhan syndrome?
What treatment is effective in managing hyperuricemia in Lesch-Nyhan syndrome?
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Which of the following correctly describes the concept of codon degeneracy?
Which of the following correctly describes the concept of codon degeneracy?
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What is a requirement for homologous recombination to occur?
What is a requirement for homologous recombination to occur?
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Which condition is associated with nonhomologous end joining dysfunction?
Which condition is associated with nonhomologous end joining dysfunction?
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How does nonhomologous end joining generally affect the DNA?
How does nonhomologous end joining generally affect the DNA?
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What is a possible outcome when homologous recombination is defective?
What is a possible outcome when homologous recombination is defective?
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What happens to a double strand break during homologous recombination?
What happens to a double strand break during homologous recombination?
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What role do BRCA1 and BRCA2 play in DNA repair mechanisms?
What role do BRCA1 and BRCA2 play in DNA repair mechanisms?
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What distinguishes nonhomologous end joining from homologous recombination?
What distinguishes nonhomologous end joining from homologous recombination?
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In which type of DNA repair is the loss of nucleotides typically minimal?
In which type of DNA repair is the loss of nucleotides typically minimal?
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Study Notes
High-Yield Principles in Biochemistry
- Biochemistry is the study of carbon compounds.
- Fundamental building blocks of life are made in collapsing stars.
- The power to control genetics is awesome and terrifying.
- Studying metabolic pathways, enzyme deficiencies and regulatory steps are important for high yield.
- This study material includes topics in molecular biology, genetics, cell biology, metabolic principles (vitamins, cofactors, minerals, single-enzyme deficiency diseases).
- Don't spend time learning details about organic, physical, and chemical mechanisms or structures.
- Understanding biochemical techniques such as ELISA, immunoelectrophoresis, Southern blotting, and PCR is important.
- Integrating biochemistry with pharmacology and genetics is valuable.
Chromatin Structure
- DNA exists in chromatin form to fit into the nucleus.
- DNA loops around a histone octamer to form a nucleosome.
- Hl binds to nucleosomes and linker DNA, which stabilizes the chromatin fiber.
- DNA has a negative charge, whereas histones are positive.
- In mitosis, DNA condenses into chromosomes.
- DNA and histone synthesis occurs during S phase.
- Mitochondria have circular DNA without histones.
Nucleotides
- Nucleoside = base + sugar (ribose/deoxyribose)
- Nucleotide = base + sugar (ribose/deoxyribose) + phosphate, linked by 3'-5' phosphodiester bonds.
- Purines (adenine, guanine) have two rings.
- Pyrimidines (cytosine, uracil, thymine) have one ring.
- Uracil is in RNA, and thymine is in DNA.
- Methylation of uracil forms thymine.
- The 5' end of a nucleotide has a triphosphate group that is the energy source.
De Novo Pyrimidine and Purine Synthesis
- Various drugs (e.g., immunosuppressants, antineoplastics, antibiotics) work by interfering with nucleotide synthesis.
- Examples of drugs that interfere are 6-MP, MTX, Azathioprine, Mycophenolate, and Ribavirin.
- Leflunomide inhibits dihydroorotate dehydrogenase.
Purine Salvage Deficiencies
- Adenosine deaminase (ADA) deficiency affects the degradation of adenosine and deoxyadenosine.
- This leads to increased dATP, which inhibits ribonucleotide reductase activity and DNA precursors in cells. Decreases lymphocytes.
- Defective purine salvage (absent HGPRT) results in increased uric acid production
- Lesch-Nyhan syndrome is an X-linked recessive trait caused by deficient HGPRT activity.
- Characterized by intellectual disability, self-mutilation, aggression, hyperuricemia (↑ uric acid), gout and dystonia.
- Treatment involves allopurinol and febuxostat.
DNA Replication
- DNA replication occurs in a 5' to 3' direction.
- It is semiconservative (each new DNA molecule contains one original strand and one new strand).
- Starts at origins of replication.
- Helicase unwinds DNA at the replication fork.
- Single-stranded binding proteins (SSBs) prevent strands from reannealing.
- Topoisomerases relieve DNA supercoiling.
- Primase synthesizes RNA primers.
- DNA polymerase III elongates the leading and lagging strands.
- DNA polymerase I removes RNA primers and replaces them with DNA.
- DNA ligase joins Okazaki fragments.
- Telomerase adds repetitive sequences to telomeres to prevent loss of genetic material during replication.
DNA Repair
- Double-strand breaks repaired by nonhomologous end joining (NHEJ) or homologous recombination.
- Nucleotide excision repair: removes bulky helix-distorting lesions (e.g., pyrimidine dimers).
- Base excision repair: removes altered bases and apurinic/apyrimidinic (AP) sites.
- Mismatch repair fixes mismatched nucleotides in the new strand.
Mutations in DNA
- Single nucleotide substitutions include transitions (purine to purine or pyrimidine to pyrimidine) and transversions (purine to pyrimidine or vice versa).
- Frameshift mutations result from insertions or deletions of nucleotides that are not multiples of 3.
- Splice site mutations lead to retained introns in mRNA, affecting protein function.
The Lac Operon
- The lac operon (in E. coli) regulates lactose metabolism.
- Low glucose → ↑ cAMP → activation of CAP protein → increased transcription.
- High lactose → repressor protein detaches from operator (gene) site → increased transcription
Functional Organization of a Eukaryotic Gene
- A gene contains coding regions (exons) and non-coding regions (introns).
- Promoters are regions where RNA polymerase binds and initiates transcription.
- Enhancers and silencers affect gene expression.
RNA Processing (Eukaryotes)
- Initial transcript (hnRNA) is modified to become mRNA.
- Capping of the 5' end, polyadenylation of the 3' end, and splicing of introns.
- Mature mRNA is transported to the cytoplasm to be translated.
- Quality control of mRNA occurs in processing bodies (P-bodies).
Introns vs exons
- Exons contain the code for proteins or functional RNA.
- Introns are non-coding sequences, important for gene regulation.
- Alternative splicing combines different exons to produce multiple proteins from a single gene.
tRNA Structure and Charging
- tRNA is cloverleaf-shaped (75-90 nucleotides) with a CCA 3' end
- Aminoacyl-tRNA synthetases are enzymes responsible for attaching the correct amino acid to a tRNA
- Anticodon loop recognizes a codon.
- There are unique enzymes (1 per amino acid) to pair a specific amino acid with its tRNA.
Protein Synthesis
- Protein synthesis occurs in the cytoplasm/ribosomes.
- Initiation factors help attach the 40S ribosomal subunit to the mRNA.
- Elongation factors add amino acids to the growing polypeptide chain.
- Termination factors stop polypeptide synthesis when a stop codon is reached.
- Post-translational modifications alter the protein structure (eg. trimming, covalent alteration, or chaperone proteins.)
Cell Cycle Phases
- Checkpoints regulate the progression through the cell cycle (G1, S, G2, M)
- Cyclins and cyclin-dependent kinases (CDKs) regulate the cell cycle progression.
- Tumor suppressors (eg. p53, Rb) play a role in regulating cell cycle progression.
Rough and Smooth Endoplasmic Reticulum
- Rough ER (RER) synthesizes secretory proteins and adds N-linked oligosaccharides to lysosomal proteins.
- RER location is inside the cytoplasm of cells; ribosomes embedded on the outer membrane.
- Smooth ER (SER) synthesizes steroid hormones and helps detoxify drugs and poisons.
- SER location is inside the cytoplasm of cells; free ribosomes are not attached to the membrane.
Cell Trafficking
- Golgi apparatus sorts and modifies proteins and lipids from the ER.
- Endosomes sort material from the exterior and Golgi to lysosomes or back to the membrane/Golgi
- I-cell disease is a lysosomal storage disorder caused by a defect in N-acetylglucosaminyl-1-phosphotransferase.
Cytoskeletal Elements
- Microfilaments (made of actin): cell contraction.
- Intermediate filaments: maintain cell structure (eg. vimentin.)
- Microtubules: essential for cell division, transport, and cilia/flagella.
- Molecular motors (dyneins and kinesins): transport to different directions/ends on a microtubule track
Peroxisome
- Membrane-enclosed organelle involved in ß-oxidation of very long-chain fatty acids, a-oxidation of branched-chain fatty acids.
- Catabolism of amino acids and ethanol.
- Synthesis of bile acids and plasmalogens (important membrane lipids, especially in white matter).
Proteasome
- Barrel-shaped protein complex involved in degrading polyubiquitin-tagged proteins.
- Many cellular processes depend on the proteasome such as the immune response, neurodegenerative disorders.
DNA Repair
- Non-homologous end joining (NHEJ)- two damaged ends are joined.
- Homologous recombination- a damaged strand is repaired using a complementary strand.
- Nucleotide excision repair- removes pyrimidine dimers formed by UV damage.
- Base excision repair- removes altered bases or apurinic/apyrimidinic sites.
- Mismatch repair- corrects errors missed during DNA replication
DNA Repair mechanisms
- Cells use various mechanisms to repair damaged DNA, ensuring genetic integrity.
- NHEJ repairs double-strand breaks.
- Homologous recombination ensures accuracy in DNA strand repair.
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Description
Test your knowledge on the intricacies of DNA replication with this quiz. Discover the roles of various enzymes and processes involved, from helicase to Okazaki fragments. Challenge yourself and see how well you understand the mechanics of genetic duplication.
