Central Dogma and Gene Regulation

These flashcards cover key terms and concepts related to the Central Dogma of Molecular Biology and gene regulation.

Central Dogma of Molecular Biology

The process of transferring genetic information from DNA to RNA to proteins.

Nucleotide

The basic building block of nucleic acids, consisting of a sugar, a phosphate group, and a nitrogenous base.

Phosphodiester linkage

The bond formed between the phosphate group of one nucleotide and the hydroxyl group of the sugar of another nucleotide.

Transcription

The process of synthesizing RNA from a DNA template.

Translation

The process of synthesizing proteins from mRNA.

Antiparallel strands

The orientation of the two strands of DNA where one strand runs in the 5' to 3' direction and the other runs in the 3' to 5' direction.

RNA polymerase

The enzyme responsible for synthesizing RNA from a DNA template during transcription.

Gene regulation

The process of turning genes on and off, affecting the production of specific proteins.

Hydrogen bonds

The weak bonds that hold complementary base pairs together in nucleic acids.

Activated nucleotide

A nucleotide that has been modified to carry additional phosphate groups, increasing energy potential.

Amino acid

The building blocks of proteins that combine to form polypeptides.

Peptide bond

The covalent bond formed between two amino acids during protein synthesis.

Eukaryotic transcription

The process of transcription in eukaryotic cells, which includes the involvement of multiple RNA polymerases and additional transcription factors.

Hairpin loop

A secondary structure formed in RNA when complementary sequences base pair within the same strand.

Phenotype

The observable physical or biochemical characteristics of an organism, determined by its genotype.

Genotype

The genetic constitution of an individual, represented by the specific DNA sequence.

Explain the sequential flow of genetic information as described by the Central Dogma of Molecular Biology, detailing the key processes involved in converting genetic information from DNA into functional proteins.

The Central Dogma describes the flow: DNA → RNA → Protein. It begins with transcription, where genetic information from a DNA template is synthesized into RNA by RNA polymerase. This RNA, specifically messenger RNA (mRNA), then undergoes translation, where its sequence is used to synthesize a polypeptide chain (protein) on ribosomes. This process ensures the accurate expression and manifestation of genetic traits.

Describe the structural components of a nucleotide and elaborate on how these components are assembled to form a nucleic acid polymer, focusing on the role of phosphodiester linkages.

A nucleotide consists of three parts: a pentose sugar, a phosphate group, and a nitrogenous base. Nucleic acid polymers (DNA or RNA) are formed when the phosphate group of one nucleotide forms a phosphodiester linkage with the hydroxyl group of the sugar of an adjacent nucleotide. This covalent bond creates the sugar-phosphate backbone, giving the nucleic acid its structural integrity and directionality (5' to 3').

Distinguish between transcription and translation, identifying the primary template and product of each process, and the cellular location where they predominantly occur in eukaryotic cells.

-   **Transcription**: Uses a DNA template to synthesize RNA (mRNA, tRNA, rRNA). It occurs in the nucleus of eukaryotic cells. The primary enzyme is RNA polymerase.
-   **Translation**: Uses an mRNA template to synthesize proteins (polypeptide chains). It occurs on ribosomes in the cytoplasm of eukaryotic cells (or on the rough endoplasmic reticulum). Key components include mRNA, tRNA, and ribosomal RNA.

Explain the significance of the antiparallel orientation of DNA strands in the context of molecular processes like replication and transcription. How does this structural feature influence enzyme activity?

The antiparallel strands of DNA mean one strand runs 5' to 3' and the other runs 3' to 5'. This orientation is crucial for replication and transcription because DNA polymerases and RNA polymerases can only synthesize new strands in the 5' to 3' direction. The antiparallel nature allows both template strands to be read correctly, albeit with different mechanisms (e.g., leading vs. lagging strand in replication, or different mechanisms for initiation by RNA polymerase). It also ensures the correct pairing of complementary bases and the stability of the double helix.

Discuss the various roles of hydrogen bonds in the structure and function of nucleic acids, specifically referencing their contribution to the double helix and processes requiring strand separation.

Hydrogen bonds are weak, non-covalent bonds that form between complementary nitrogenous bases (A-T/U, G-C) in nucleic acids. In DNA, they are critical for holding the two antiparallel strands together to form the stable double helix structure. Their weakness is essential as it allows the strands to be readily separated (unwound) by enzymes like helicase during DNA replication and transcription, enabling access to the genetic information stored in the sequence.

Elaborate on the concept of an 'activated nucleotide' and explain its importance in the energetics of nucleic acid synthesis.

An activated nucleotide is a nucleotide that has been modified by the addition of two extra phosphate groups, forming a nucleoside triphosphate (e.g., ATP, GTP, CTP, UTP for RNA; dATP, dGTP, dCTP, dTTP for DNA). The hydrolysis of the terminal pyrophosphate bonds releases a significant amount of free energy. This energy release makes the phosphodiester bond formation (polymerization) energetically favorable and serves as a crucial driving force for the synthesis of nucleic acid polymers.

Describe the process of eukaryotic transcription, highlighting at least two key features that differentiate it from prokaryotic transcription, such as the involvement of specific enzymes or regulatory elements.

Eukaryotic transcription is the synthesis of RNA from a DNA template in eukaryotic cells. Key differentiating features include:
1. Multiple RNA Polymerases: Eukaryotes have three main RNA polymerases (Pol I, Pol II, Pol III), each transcribing different types of RNA (e.g., Pol II transcribes mRNA). Prokaryotes typically have one RNA polymerase.
2. Transcription Factors: Eukaryotic RNA polymerases require numerous transcription factors to bind to the promoter and initiate transcription. These can include general transcription factors and specific regulatory factors (enhancers, silencers) that modulate gene expression over long distances.
3. RNA Processing: Eukaryotic primary RNA transcripts (pre-mRNA) undergo extensive processing (5' capping, 3' polyadenylation, splicing) before becoming mature mRNA, which is absent in prokaryotes.

Define genotype and phenotype, and explain how the Central Dogma of Molecular Biology provides the mechanistic link between them.

Genotype refers to the specific genetic makeup of an individual, represented by their DNA sequence. Phenotype refers to the observable physical, biochemical, or behavioral characteristics of an organism. The Central Dogma (DNA → RNA → Protein) provides the mechanistic link: the DNA genotype is transcribed into RNA, which is then translated into proteins. These proteins perform the functions that determine the ultimate observable phenotype of the organism. Environmental factors can also influence how a genotype is expressed as a phenotype.

Explain how gene regulation contributes to cell differentiation and the vast diversity of cell types within a multicellular organism, despite all cells containing the same genetic information.

Gene regulation, the process of turning genes on and off, is fundamental to cell differentiation and the diversity of cell types. All somatic cells in a multicellular organism generally contain the same DNA (genotype). However, during development, different sets of genes are selectively activated or repressed in different cell types. For example, muscle cells express actin and myosin, while nerve cells express neurotransmitter receptors. This selective expression, or differential gene regulation, leads to cells developing specialized structures and functions, ultimately giving rise to the various tissues and organs that constitute a complex organism.