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Molecular Biology

Study of nucleic acids and proteins, essential macromolecules for life.

Central Dogma

DNA makes RNA makes Proteins, depicting the flow of genetic information.

DNA Replication

Process where DNA makes a copy of itself, crucial for cell division and growth.

Heredity

Passing on genetic traits from one generation to another.

Chargaff’s Rule

Equal amounts of adenine-thymine and cytosine-guanine in DNA.

DNA Polymerase

Enzyme synthesizing new DNA strands during replication.

Telomerase

Enzyme adding repetitive DNA sequences to chromosome ends.

Mismatch Repair (MMR)

Mechanism correcting incorrect base pairings during DNA replication.

Nucleases

Enzymes cleaving phosphodiester backbone in nucleotide chains.

Rosalind Franklin

Scientist who contributed to the discovery of DNA's double helix structure.

DNA Polymerase II

Enzyme binding to the 3’ end to add the correct base during DNA replication

Ligase

Enzyme responsible for joining DNA fragments together during replication and repair processes

Replication Fork Collapse

Break in the DNA strand's phosphodiester backbone leading to replication disruption

Base Excision Repair (BER)

Mechanism to correct incorrect base pairings by removing the base and replacing it

Nucleotide Excision Repair (NER)

Process to fix bulky DNA adducts by removing whole nucleotides

Nonhomologous End Joining

Rapid repair method for double-stranded DNA breaks

Homologous Recombination

Accurate repair method for double-stranded DNA breaks using a sister chromatid

Gel Electrophoresis

Technique to separate DNA fragments based on size using an electric current

Polymerase Chain Reaction (PCR)

Method to amplify specific DNA sequences rapidly and efficiently

Sanger Sequencing

Technique for reading nucleotide sequences using chain-terminating ddNTPs

TFIIA

Associated with building connections between TBP/TFIID and stabilization.

TFIIB

Builds a bridge for TFIID and Polymerase II connection.

TFIID

Large complex consisting of TATA-box binding protein (TBP) and TAFs (TBP Associated Factors), identifies promoter and recruits additional transcription factors.

TFIIE

Involved in DNA melting by separating DNA.

TFIIF

Binds to Polymerase II for stabilization.

TFIIH

Complex with a DNA helicase and polymerase II CTD kinase function, involved in DNA separation and phosphorylation.

Electrophoretic Mobility Shift Assay (EMSA)

Detects protein-DNA interactions, using radioactivity for precise identification.

Cold Probe

DNA piece without radioactivity, competes with the labeled probe to prove specificity of binding.

DNA Footprinting

Analyzes the exact sequence a protein binds to on DNA.

RNA Polymerase I

Transcribes pre-rRNA for ribosomes, essential for ribosome function.

RNA Polymerase III

Transcribes tRNA for translation, relies on TFIIIA, TFIIIB, TFIIIC, does not require TATA Box Binding Protein (TBP).

mRNA Capping

Addition of 7-methylguanosine to the 5’ end of mRNA to prevent degradation and aid in ribosome identification.

Polyadenylation

Addition of a polyA tail to the 3’ end of mRNA to prevent degradation and assist in ribosome identification.

RNA Splicing

Removal of introns from pre-mRNA to produce mature mRNA, essential for proper protein synthesis.

Alternative Splicing

Process leading to multiple splicing pathways, increasing protein diversity and functionality.

Polyadenylation

The addition of a poly(A) tail to the 3' end of an mRNA molecule.

Export factors

Proteins that facilitate the transport of mRNA from the nucleus to the cytoplasm.

Rephosphorylation

The process of adding phosphate groups back to a molecule.

Translation

The process of synthesizing a protein from an mRNA template.

tRNA

Transfer RNA molecules that carry specific amino acids to the ribosome during translation.

Aminoacyl-tRNA Synthetase

Enzyme responsible for attaching the correct amino acid to its corresponding tRNA.

Ribosome

Cellular machinery responsible for protein synthesis.

Initiation

The beginning stage of translation where the ribosome assembles at the start codon.

Elongation

The stage of translation where amino acids are added to the growing polypeptide chain.

Termination

The final stage of translation where the ribosome reaches a stop codon and releases the polypeptide.

Enhancers vs

Enhancers can be located far from the promoter they regulate and are orientation distance independent, while proximal elements are located closer to the promoter and are often position and orientation dependent.

mRNA Degradation Pathways

Processes like deadenylation-dependent mRNA decay involve removing the polyA tail first, followed by degradation by a deadenylase enzyme complex, which is more efficient than a standard exonuclease.

Linker Scanning Experiment

Technique to identify crucial regions within a DNA sequence for transcriptional activity by comparing modifications at different DNA nucleotides and observing changes in transcription levels.

RNAi (RNA interference)

Involves the recognition and degradation of specific RNA sequences in the cytoplasm by the RISC complex, leading to inhibition of translation based on the degree of match between the RNA and the template.

Reporter Genes

Utilization of genes like GFP, luciferase, and LacZ to study gene expression patterns and protein localization in living cells, providing visual cues for gene activity.

Blotting Techniques

Methods such as northern blots and FISH used to detect and analyze specific RNA molecules within a sample, allowing visualization of gene expression patterns.

PCR-based Methods

Techniques like RT-PCR, qPCR, and RNA-Seq employed to detect and quantify gene expression levels, providing insights into gene activity and regulation.

Chromatin Structure

DNA packaging into chromatin involves nucleosomes, where DNA wraps around histone proteins, impacting gene expression based on the level of compaction, with looser packaging associated with active transcription.

Chromatin Immunoprecipitation (ChIP)

Process used to study protein-DNA interactions by immunoprecipitating specific chromatin regions, providing insights into gene regulation and chromatin structure.

Lysine Acetylation

Changing lysine from a positively charged state to a neutral state, resulting in weaker binding to negatively charged DNA.

Telomeres Packaging

Telomeres are tightly packaged structures at the ends of chromosomes to prevent fraying and degeneration throughout the life cycle.

Heterochromatin Spread

Heterochromatin can spread through the recruitment of proteins that deacetylate enzymes and promote further heterochromatin formation.

HP1 Function

HP1 (Histone 1) is a protein present in heterochromatin that binds to the ends of DNA wrapped around nucleosomes to prevent flexibility and maintain tight packaging.

Boundary Elements

Specific DNA sequences that block the spread of heterochromatin, maintaining distinct chromatin regions.

Transcription Factors

Proteins that regulate chromatin packing by recruiting enzymes like Histone Acetylase (HAT) to decondense chromatin for transcription or Histone Deacetylase (HDAC) for chromatin compaction.

ChIP (Chromatin Immunoprecipitation)

A technique using antibodies to study specific protein modifications on DNA, allowing the identification of markers on chromosomes.

Dsup Protein

Damage suppressor protein that shields DNA from radiation-induced damage, enhancing cell viability post-radiation exposure.

Next-Gen Sequencing

A high-throughput sequencing method that involves library preparation, bridge PCR, and modified Sanger sequencing for efficient genome analysis.

CRISPR-Cas9 System

A genome editing tool utilizing CRISPR sequences and Cas9 protein to induce targeted DNA breaks, enabling gene modifications with high precision.

Efficiency

DNA is least efficient, Protein is most efficient

Cost

DNA costs the less, Protein costs the most

Specificity

RNA and Protein have better specificity

CRISPR Variance

CRISPR technology has various applications and modifications

CRISPRi

CRISPR interference uses dCas to interfere with gene expression

CRISPRa

CRISPR activator spikes the expression of a gene

CRISPR in Humans

CRISPR technology applications in humans for treating genetic diseases

Cancer

Using CRISPR to modify T cells to target specific tumors in cancer treatment

Human Embryos

CRISPR applications in modifying human embryos to correct genetic mutations

Sickle Cell

Using CRISPR to correct genetic mutations in bone marrow for sickle cell disease