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Study Guide: Molecular Biology Concepts and Processes
1. Transcription
Definition: Transcription is the process of using parts of the DNA sequence as a template to synthesize RNA. This process is essential for producing RNA molecules involved in various cellular functions, including proteins.
Key Points:
RNA Types:
rRNA, tRNA, snRNA: Involved in cellular processes like protein synthesis and splicing.
mRNA: Carries genetic information from DNA to ribosomes to make proteins.
Promoter: A specific DNA sequence where transcription starts. It determines which DNA strand is read and how many RNA copies are made.
Enzymes:
RNA polymerase: Main enzyme that synthesizes RNA.
General transcription factors: Required at every promoter for initiation.
Transcriptional activators: Specific to each gene, these increase transcription.
Building Blocks of RNA:
Ribonucleotides (A, C, G, U): Building blocks of RNA. Each provides the energy needed for its incorporation into the RNA strand.
RNA Synthesis: Occurs in the 5' to 3' direction.
Processing in Eukaryotes: Primary transcripts (pre-mRNAs) must be processed before leaving the nucleus.
7mG Cap: Added to the 5' end for protection and export.
Poly-A Tail: Added to the 3' end for stability and export.
Splicing: Introns are removed and exons are joined by the spliceosome, a catalytic RNA.
Alternative Splicing: Allows for different combinations of exons to form various proteins from the same gene.
2. Replication
Definition: Replication is the process of copying the entire DNA sequence before cell division.
Key Points:
Origin of Replication: The DNA sequence where replication begins. Two replication forks are formed at each origin.
Strands:
Leading Strand: Synthesized continuously.
Lagging Strand: Synthesized in fragments (Okazaki fragments).
Enzymes:
DNA polymerase: Adds nucleotides to the growing DNA strand.
Helicase: Unwinds the DNA double helix.
Sliding clamp: Keeps DNA polymerase attached to the DNA.
SSBPs (Single-Strand Binding Proteins): Stabilize the unwound DNA.
Ligase: Joins DNA fragments.
Deoxyribonucleotides: (A, C, G, T) are the building blocks, and each provides the energy for its incorporation.
Mistakes During Replication:
Proofreading by DNA polymerase: Corrects errors during replication.
Mismatch repair: Occurs immediately after replication to correct any mistakes not caught during proofreading.
Telomeres: Protect the ends of chromosomes and help with replication.
3. Translation
Definition: Translation is the process by which ribosomes use mRNA to synthesize proteins.
Key Points:
Start Codon: The sequence where translation begins.
Eukaryotes: First AUG codon.
Prokaryotes: AUG preceded by a Shine-Dalgarno sequence due to polycistronic mRNAs.
Enzymes:
Ribosomes: The molecular machines that carry out translation.
tRNAs: Transfer amino acids to the ribosome.
Initiation, elongation, and release factors: Facilitate translation steps.
Amino Acids: The building blocks of proteins. Each tRNA carries a specific amino acid.
Protein Synthesis: Occurs from the N-terminus to C-terminus of the protein.
Location: Translation occurs in the cytoplasm (free ribosomes or rough ER).
Protein Folding: Proper folding is crucial for function, assisted by chaperones. Misfolded proteins are degraded.
4. Electron Transport Chain (ETC) vs. Photosynthesis
Electron Transport Chain (ETC) in Mitochondria:
Electron Donors: NADH (from glycolysis, pyruvate processing, and TCA cycle) and FADH₂.
Final Electron Acceptor: Oxygen, forming water (H₂O).
Proton Gradient: Used by ATP synthase to generate ATP.
Photosynthesis in Chloroplasts:
Electron Donors: Water (H₂O).
Final Electron Acceptor: NADP⁺, forming NADPH.
Proton Gradient: Used by ATP synthase to make ATP.
Calvin Cycle: Uses ATP and NADPH to produce carbohydrates.
5. DNA Repair Mechanisms
Mismatch Repair: Fixes mistakes made by DNA polymerase immediately after replication.
Base Excision Repair: Repairs single base lesions (e.g., due to deamination).
Not linked to replication, happens throughout the cell cycle.
Nucleotide Excision Repair: Removes larger DNA segments, often caused by UV damage (e.g., thymine dimers).
6. Characteristics of Amino Acids
Acidic Amino Acids: Lose an H⁺ at physiological pH, resulting in a negatively charged side chain.
Basic Amino Acids: Gain an H⁺ at physiological pH, resulting in a positively charged side chain.
7. Cancer Cell Mechanism: Nanotubes and Mitochondria
Cancer cells use nanotubes to hijack mitochondria from immune cells (T-cells).
This process allows cancer cells to consume more oxygen and enhance their metabolic processes.
Ras signaling is involved in the formation of these nanotubes.
8. Microtubules vs. Microfilaments
Microtubules: Larger, composed of tubulin. They exhibit dynamic instability (growth and rapid depolymerization).
Microfilaments: Smaller, composed of actin. They are involved in cell movement and shape.
This study guide summarizes essential molecular processes like transcription, replication, and translation, while also covering specialized topics like electron transport and repair mechanisms. Use this guide to understand the flow of genetic information and cellular functions in eukaryotic cells!
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1. Transcription
Definition: Transcription is the process in which a segment of DNA is used as a template to synthesize RNA. This RNA can be a functional molecule (such as rRNA, tRNA, and snRNA) or can be translated into a protein (mRNA).
Key Points:
RNA Types:
rRNA (ribosomal RNA): Part of the structure of ribosomes and crucial for protein synthesis.
tRNA (transfer RNA): Carries amino acids to the ribosome for protein synthesis.
snRNA (small nuclear RNA): Involved in splicing pre-mRNA.
mRNA (messenger RNA): Carries the genetic code from DNA to the ribosome for protein synthesis.
Promoter:
A promoter is a specific DNA sequence where RNA polymerase binds to initiate transcription.
It determines which DNA strand will be read and how many RNA copies will be made.
Core promoter and enhancers can modulate the rate of transcription.
Enzymes:
RNA polymerase: The enzyme responsible for synthesizing RNA by adding ribonucleotides complementary to the DNA template strand.
General transcription factors: These factors are required by all promoters to initiate transcription. They bind to the promoter region and assist in RNA polymerase recruitment.
Transcriptional activators: These proteins bind to specific regions of DNA (enhancers) and increase the rate of transcription for particular genes.
Ribonucleotides:
The building blocks of RNA: Adenine (A), Cytosine (C), Guanine (G), and Uracil (U).
Each ribonucleotide provides the energy for its own incorporation into the growing RNA strand.
RNA Synthesis:
RNA is synthesized in the 5’ to 3’ direction, meaning that RNA polymerase adds nucleotides to the 3’ end of the growing RNA molecule.
Eukaryotic RNA Processing:
7-methylguanosine (7mG) cap: Added to the 5’ end of the RNA molecule to protect it from degradation and help with ribosome binding during translation.
Poly-A Tail: Added to the 3’ end of the mRNA to increase stability and help with nuclear export.
Splicing: Removal of non-coding sequences called introns, and joining of coding sequences called exons. The spliceosome, a complex of small nuclear RNA and proteins, performs this task. Catalytic RNA (ribozymes) within the spliceosome catalyzes the splicing reaction.
Alternative Splicing: Allows one gene to code for multiple proteins by varying the exons included in the final mRNA product.
2. Replication
Definition: DNA replication is the process of copying the entire DNA sequence to ensure that both daughter cells receive identical genetic information during cell division.
Key Points:
Origin of Replication:
Replication begins at specific DNA sequences known as origins of replication. Multiple origins of replication exist on each chromosome in eukaryotes.
At each origin, two replication forks are formed, and DNA is replicated bidirectionally.
Leading vs. Lagging Strand:
Leading strand: Synthesized continuously in the 5’ to 3’ direction.
Lagging strand: Synthesized discontinuously as Okazaki fragments in the 5’ to 3’ direction, but overall direction of replication is 3’ to 5’ relative to the DNA template.
Enzymes:
DNA polymerase: Adds nucleotides to the growing strand, ensuring base-pairing with the template strand.
Helicase: Unwinds the DNA double helix ahead of the replication fork.
Sliding clamp: Helps hold DNA polymerase onto the DNA template.
Single-strand binding proteins (SSBPs): Bind to and stabilize single-stranded DNA regions to prevent reannealing or degradation.
Ligase: Joins Okazaki fragments on the lagging strand by sealing the sugar-phosphate backbone.
Deoxyribonucleotides:
The building blocks of DNA: Adenine (A), Cytosine (C), Guanine (G), and Thymine (T). Each provides the energy for its incorporation into the DNA strand.
Mistakes and Repair:
Proofreading by DNA polymerase: DNA polymerase has a 3’ to 5’ exonuclease activity that allows it to correct errors during replication.
Mismatch Repair: A mechanism that fixes errors not corrected by proofreading during replication. It occurs immediately after DNA replication and involves removing the incorrect base and replacing it with the correct one.
Telomeres:
The telomeres are repetitive DNA sequences at the ends of chromosomes that protect the DNA from degradation and loss during replication.
Telomerase: An enzyme that extends telomeres by adding repetitive nucleotide sequences to the ends of chromosomes, counteracting the shortening of chromosomes during DNA replication.
3. Translation
Definition: Translation is the process by which the information encoded in mRNA is used to assemble amino acids into proteins at the ribosome.
Key Points:
Start Codon:
The start codon is the first codon of the mRNA that signals the beginning of translation. It codes for the amino acid methionine (AUG) in eukaryotes and prokaryotes.
Eukaryotic mRNAs are monocistronic (one mRNA codes for one protein), so translation begins at the first AUG codon.
Prokaryotic mRNAs are polycistronic (one mRNA codes for multiple proteins), and translation can begin at multiple AUGs, each preceded by a Shine-Dalgarno sequence.
Enzymes:
Ribosomes: The molecular machines that carry out protein synthesis. Ribosomes consist of two subunits (large and small) that facilitate the binding of tRNA and mRNA.
tRNAs: Transfer amino acids to the ribosome. Each tRNA carries a specific amino acid and has an anticodon that pairs with the mRNA codon.
Initiation, elongation, and release factors: Proteins that facilitate the various stages of translation.
Amino Acids:
The building blocks of proteins. There are 20 different amino acids, each with a unique side chain (R group).
Translation Steps:
Initiation: The ribosome assembles around the mRNA and the first tRNA, which carries methionine, binds to the start codon.
Elongation: The ribosome moves along the mRNA, matching each codon with the appropriate tRNA, and catalyzing the formation of peptide bonds between amino acids.
Termination: When a stop codon is reached, release factors cause the ribosome to dissociate, releasing the newly synthesized protein.
Protein Folding: Proper protein folding is essential for function. Misfolded proteins are often assisted by chaperones, and misfolded proteins that cannot be repaired are degraded by the proteasome.
4. Electron Transport Chain (ETC) vs. Photosynthesis
Electron Transport Chain (ETC) in Mitochondria:
Electron Donors: NADH and FADH₂, produced during glycolysis, pyruvate processing, and the TCA cycle.
Final Electron Acceptor: Oxygen (O₂), which combines with electrons to form water (H₂O).
Proton Gradient: Electrons are passed through protein complexes in the inner mitochondrial membrane, pumping protons (H⁺) into the intermembrane space. This creates a proton gradient.
ATP Synthase: Utilizes the proton gradient to drive ATP synthesis.
Photosynthesis in Chloroplasts:
Electron Donors: Water (H₂O), which is split to release oxygen (O₂).
Final Electron Acceptor: NADP⁺, which is reduced to NADPH.
Proton Gradient: Like in mitochondria, protons are pumped across the thylakoid membrane to create a proton gradient.
ATP Synthase: Uses the proton gradient to generate ATP.
Calvin Cycle: Uses the ATP and NADPH produced in the light reactions to convert carbon dioxide (CO₂) into glucose.
5. DNA Repair Mechanisms
Mismatch Repair:
Occurs immediately after DNA replication. The repair system detects mismatched base pairs, removes a portion of the newly synthesized strand containing the error, and resynthesizes the correct sequence.
Base Excision Repair:
Repairs single base lesions, such as those caused by deamination (the loss of an amino group).
Occurs throughout the cell cycle and is not linked to replication.
Nucleotide Excision Repair:
Repairs bulky DNA lesions, like thymine dimers caused by UV light, by removing a segment of the DNA strand containing the damage and then filling the gap with correct nucleotides.
6. Characteristics of Amino Acids
Acidic Amino Acids: Have a carboxyl group (-COOH) in their side chains that loses an H⁺ at physiological pH, making them negatively charged. Example: Aspartic acid and glutamic acid.
Basic Amino Acids: Have an amino group (-NH₂) in their side chains that can gain an H⁺ at physiological pH, making them positively charged. Example: Lysine, Arginine, and Histidine.
7. Cancer Cell Mechanism: Nanotubes and Mitochondria
Nanotubes are tubular structures that cancer cells can form to transfer mitochondria from immune cells (such as T-cells).
By stealing mitochondria, cancer cells can enhance their metabolic activity and gain a growth advantage.
This mechanism supports Ras signaling, which drives cellular processes like growth and survival.
8. Microtubules vs. Microfilaments
Microtubules:
Structure: Hollow tubes made of tubulin subunits.
Function: Provide structural support, facilitate intracellular transport (e.g., vesicle trafficking), and are involved in cell division (spindle formation).
Dynamic Instability: Microtubules can grow and shrink rapidly by adding or removing tubulin dimers from their ends.
Microfilaments:
Structure: Thin filaments composed of actin subunits.
Function: Play a major role in cell shape, motility, and muscle contraction. They are also involved in cell division (cytokinesis).
Exam Notes
Energy and Reactions
Phosphate groups breaking:
Negative charges repel each other.
Feedback inhibition:
Example of allosteric regulation.
Uncatalyzed reaction:
Does not have a higher ∆G.
Tip: Relearn how to calculate when given percentages (e.g., C = 40%, what is A?).
Spontaneous and exergonic reactions:
Characterized by a negative change in free energy (∆G).
Negative overall ∆G.
DNA and Transcription
Helicase:
Breaks hydrogen bonds during DNA replication.
Histones:
Act as "spools" around which DNA binds.
Alternative splicing:
Allows for different proteins to be made from a single gene.
Loosely packaged DNA has higher levels of gene expression.
During transcription, both strands are not used as templates for RNA.
Water and Bonds
Unique properties of water:
Polarity.
Hydrogen bonds.
Hydrogen bonds in ice:
Keep water molecules of ice further apart than those in liquid water.
Polarity and electronegativity:
Uneven sharing of electrons in covalent bonds leads to polarity.
Macromolecules
Types:
Polymers and monomers.
Experiments and Principles
Miller-Urey experiment:
Demonstrated the abiotic synthesis of organic molecules.
Chargaff's rule:
Nucleotide pairing (A-T and G-C).
Watson, Crick, Franklin, Wilkins:
Discovered the double helix structure of DNA.
DNA Replication and Processes
PCR (Polymerase Chain Reaction):
Amplifies targeted DNA regions.
Requires energy and incoming nucleotides.
Telomeres:
Extend DNA by adding repetitive nucleotide sequences.
DNA polymerase proofreading:
Ensures the correct sequence is synthesized.
Key Enzymes:
Helicase: Unwinds DNA.
Primase: Synthesizes primers.
DNA polymerase: Adds nucleotides.
Ligase: Seals gaps in DNA.