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Semester 3: Molecular Biology
Genomes: organization, chromatin structure, repetitive sequences
Genomes: organization, chromatin structure, repetitive sequences
Genome Organization
Genomes are organized in a hierarchical manner where DNA is compacted into chromatin. In eukaryotes, DNA is wrapped around histone proteins to form nucleosomes, which further coil and fold to create higher-order structures. This organization allows for efficient packaging of genetic material within the nucleus and facilitates regulation of gene expression.
Chromatin Structure
Chromatin exists in two forms: euchromatin, which is loosely packed and transcriptionally active, and heterochromatin, which is tightly packed and transcriptionally inactive. The structure of chromatin is dynamic, influenced by various factors including histone modifications, DNA methylation, and the binding of non-coding RNAs. These modifications play a critical role in regulating gene expression and maintaining genome integrity.
Repetitive Sequences
Repetitive sequences are segments of DNA that occur in multiple copies within the genome. They can be categorized into tandem repeats, such as satellite DNA, and interspersed repeats, including transposable elements. Repetitive sequences contribute to genome architecture and stability but can also be implicated in genomic disorders and evolution by facilitating genetic variability.
DNA replication, repair mechanisms, mutations
DNA replication, repair mechanisms, mutations
DNA Replication
DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. It occurs in the S phase of the cell cycle and is essential for cell division. The process involves initiation, elongation, and termination phases. Key enzymes include helicase, which unwinds the DNA, DNA polymerase, which synthesizes the new strand, and ligase, which joins Okazaki fragments on the lagging strand.
Repair Mechanisms
DNA repair mechanisms are vital for maintaining genomic integrity. They correct damage caused by environmental factors or replication errors. Major repair pathways include base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR), and double-strand break repair (DSBR). Each mechanism involves recognition of the damage, excision of the damaged section, and replacement with the correct nucleotides.
Mutations
Mutations are alterations in the DNA sequence that can affect genetic information. They can be classified as point mutations, insertions, deletions, or duplications. Mutations can arise spontaneously or due to external factors such as radiation and chemicals. While some mutations are neutral or beneficial, others can lead to diseases such as cancer. Understanding mutations is crucial for advances in genetics and medicine.
Transcription in prokaryotes and eukaryotes
Transcription in prokaryotes and eukaryotes
Overview of Transcription
Transcription is the process of synthesizing RNA from a DNA template. It is the first step of gene expression and occurs in both prokaryotes and eukaryotes.
Transcription in Prokaryotes
In prokaryotes, transcription occurs in the cytoplasm. RNA polymerase binds to the promoter region of the gene. There is no mRNA processing; the mRNA is produced, then translated simultaneously.
RNA Polymerase in Prokaryotes
Prokaryotic RNA polymerase is a single enzyme with multiple subunits. It recognizes the promoter sequence and initiates transcription without the need for transcription factors.
Termination of Transcription in Prokaryotes
Termination can occur via two mechanisms: Rho-dependent and Rho-independent. Rho-dependent termination involves a protein factor Rho, while Rho-independent relies on the formation of a hairpin structure in the RNA.
Transcription in Eukaryotes
In eukaryotes, transcription occurs in the nucleus. Pre-mRNA must undergo processing before becoming mature mRNA. This includes capping, polyadenylation, and splicing.
RNA Polymerases in Eukaryotes
Eukaryotes have three main types of RNA polymerases: RNA polymerase I (rRNA), RNA polymerase II (mRNA), and RNA polymerase III (tRNA and other small RNAs). Each has distinct functions and properties.
Transcription Factors in Eukaryotes
Eukaryotic transcription requires transcription factors, which help RNA polymerase bind to promoter regions. These factors can be general or specific.
Termination of Transcription in Eukaryotes
Eukaryotic transcription termination involves cleavage of the pre-mRNA and the addition of a poly-A tail. The precise mechanisms may vary depending on the RNA polymerase.
Comparative Aspects of Transcription
Key differences include the location of transcription, the necessity for processing in eukaryotes, the number of RNA polymerases, and the involvement of transcription factors in eukaryotes.
Translation and regulation of gene expression
Translation and regulation of gene expression
Mechanisms of Translation
Translation is the process by which ribosomes synthesize proteins using mRNA as a template. It involves three main stages: initiation, elongation, and termination. Ribosomes, composed of rRNA and proteins, read the codons in mRNA and facilitate the binding of tRNA, which carries specific amino acids.
Role of mRNA in Translation
mRNA serves as the genetic blueprint for protein synthesis. It is transcribed from DNA and contains codons, which are sequences of three nucleotides that correspond to specific amino acids. The stability and translation efficiency of mRNA are regulated by various factors including polyadenylation and the presence of regulatory elements.
Regulation of Translation
Translation is tightly regulated at multiple levels, including the availability of ribosomes, tRNA, and initiation factors. Regulatory proteins and microRNAs can modulate the translation of specific mRNAs, ensuring cellular responses to environmental changes.
Post-Translational Modifications
After translation, proteins often undergo post-translational modifications such as phosphorylation, glycosylation, and ubiquitination. These modifications can influence protein function, activity, stability, and localization, playing critical roles in the regulation of cellular processes.
Translational Control in Development and Disease
Translational regulation is crucial during development, influencing processes such as cell differentiation and growth. Dysregulation of translation can contribute to diseases, including cancer, where specific mRNA translations are upregulated or downregulated.
Post-transcriptional modifications and RNA processing
Post-transcriptional modifications and RNA processing
Overview of Post-transcriptional Modifications
Post-transcriptional modifications are essential processes that occur after the transcription of RNA from DNA. These modifications play crucial roles in the maturation and regulation of RNA. Common types include 5' capping, polyadenylation, and splicing.
5' Capping
5' capping is a modification where a methylated guanine nucleotide is added to the 5' end of the RNA transcript. This modification protects the RNA from degradation, aids in ribosome binding during translation, and is involved in RNA export from the nucleus.
Polyadenylation
Polyadenylation involves the addition of a poly(A) tail to the 3' end of the RNA molecule. This tail enhances RNA stability, facilitates nuclear export, and is important for translation efficiency.
RNA Splicing
RNA splicing is the process of removing introns (non-coding regions) and joining exons (coding regions) together. This process generates a mature mRNA molecule that can be translated into a protein. The splicing is catalyzed by the spliceosome, a complex of proteins and RNA.
Alternative Splicing
Alternative splicing allows a single gene to produce multiple mRNA isoforms by including or excluding specific exons. This increases the diversity of proteins that can be encoded by the genome and is essential for proper cellular function.
RNA Editing
RNA editing is a post-transcriptional process where the nucleotide sequence of the RNA is altered. This can result in changes in the amino acid sequence of proteins or affect RNA stability and translation.
Significance of Post-transcriptional Modifications
These modifications are crucial for gene regulation, the stability of RNA, and the efficiency of translation. They also play roles in responding to environmental signals and cellular stress.
Post-translational modifications and protein sorting
Post-translational modifications and protein sorting
Introduction to Post-translational Modifications
Post-translational modifications are chemical modifications made to a protein after its translation. These modifications can affect protein function, localization, and stability.
Types of Post-translational Modifications
Common types of post-translational modifications include phosphorylation, glycosylation, methylation, acetylation, ubiquitination, and lipidation. Each modification can have distinct effects on protein activity and interactions.
Phosphorylation
Phosphorylation involves the addition of phosphate groups, typically to serine, threonine, or tyrosine residues. It plays a crucial role in signal transduction pathways and can activate or deactivate enzymes.
Glycosylation
Glycosylation is the addition of carbohydrate moieties to proteins. This modification is important for cell-cell recognition, adhesion, and protein stability.
Ubiquitination
Ubiquitination involves the attachment of ubiquitin molecules to a protein, marking it for degradation by the proteasome. This process is essential for regulating protein turnover and cellular homeostasis.
Protein Sorting Mechanisms
Protein sorting refers to the mechanisms by which proteins are directed to their appropriate cellular destinations. Sorting is crucial for maintaining cellular organization and function.
Signal Sequences
Many proteins contain signal sequences that direct their transport to specific organelles or cellular compartments. These sequences are often located at the N-terminus and are recognized by sorting machinery.
Endoplasmic Reticulum and Golgi Apparatus
Proteins destined for secretion or membrane insertion often enter the endoplasmic reticulum after translation. From there, they are processed in the Golgi apparatus before being sent to their final destinations.
Conclusion
Understanding post-translational modifications and protein sorting is essential for comprehending cellular functions and the regulation of biological processes.
