Molecular Biology Overview

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Questions and Answers

Viruses are generally considered to be living beings by most scientists.

False (B)

The definition of life includes the ability to repair itself and to evolve.

True (A)

Life can be mathematically quantified with ease according to the discussed concepts.

False (B)

The cell is considered the fundamental unit of all living organisms on Earth.

<p>True (A)</p> Signup and view all the answers

Occam's razor suggests choosing the most complex solution to a problem.

<p>False (B)</p> Signup and view all the answers

Nucleic acids such as DNA and RNA are essential for life on our planet.

<p>True (A)</p> Signup and view all the answers

Semi-replicators can exist in certain environmental situations if sufficient energy is provided.

<p>True (A)</p> Signup and view all the answers

Algorithms created in artificial environments are universally accepted as living beings.

<p>False (B)</p> Signup and view all the answers

Johann Gregor Mendel is known as the father of Molecular Biology.

<p>False (B)</p> Signup and view all the answers

Mendel first applied a mathematical model to describe hereditary transmission.

<p>True (A)</p> Signup and view all the answers

The genetic traits referred to as 'Mendelian' are numerous and varied.

<p>False (B)</p> Signup and view all the answers

Charles Darwin was familiar with Mendel's work during his lifetime.

<p>False (B)</p> Signup and view all the answers

The substance that transmits genetic characters was named 'gene' in 1909 by Wilhelm Johannsen.

<p>True (A)</p> Signup and view all the answers

Mendel died from complications related to heart disease.

<p>False (B)</p> Signup and view all the answers

Lucretius wrote about the transmission of phenotypic characters in the first century BC.

<p>True (A)</p> Signup and view all the answers

Every living unit, such as a cell, is capable of replicating and evolving.

<p>True (A)</p> Signup and view all the answers

DnaA is the protein that closes the two DNA strands during replication.

<p>False (B)</p> Signup and view all the answers

DNA polymerase III synthesizes new DNA strands in the 3' -> 5' direction.

<p>False (B)</p> Signup and view all the answers

The DnaB protein is part of the helicase family and plays a role in unwinding DNA strands.

<p>True (A)</p> Signup and view all the answers

The replication bubble forms as DnaB proteins move towards each other from opposite directions.

<p>False (B)</p> Signup and view all the answers

Single-stranded binding proteins (SSBs) help to rejoin the DNA strands after replication.

<p>False (B)</p> Signup and view all the answers

Replication in prokaryotes is called semiconservative because it creates new strands from old templates.

<p>True (A)</p> Signup and view all the answers

The polymerases move in the same direction as the replication fork.

<p>False (B)</p> Signup and view all the answers

Topoisomerase proteins are responsible for synthesizing the new strands of DNA.

<p>False (B)</p> Signup and view all the answers

Ribosomes are only found in eukaryotic cells and do not exist in prokaryotic cells.

<p>False (B)</p> Signup and view all the answers

The Rough Endoplasmic Reticulum is involved in lipid synthesis.

<p>False (B)</p> Signup and view all the answers

The Golgi apparatus is responsible for determining the three-dimensional structure of proteins.

<p>True (A)</p> Signup and view all the answers

Lysosomes are limited to digesting only harmful molecules in the cell.

<p>False (B)</p> Signup and view all the answers

Peroxisomes are involved in breaking down harmful molecules such as hydrogen peroxide.

<p>True (A)</p> Signup and view all the answers

Vacuoles in plant cells are primarily responsible for synthesizing proteins.

<p>False (B)</p> Signup and view all the answers

Centrioles create the mitotic spindle to assist in chromosome separation during cell division.

<p>True (A)</p> Signup and view all the answers

Proteosomes are primarily involved in the synthesis of complex proteins.

<p>False (B)</p> Signup and view all the answers

Archaea are considered the first prokaryotes to have appeared on Earth.

<p>True (A)</p> Signup and view all the answers

Eukaryotic cells have simpler structures compared to archaebacteria.

<p>False (B)</p> Signup and view all the answers

The plasma membrane of archaebacteria is formed by phospholipids with stronger chemical bonds.

<p>True (A)</p> Signup and view all the answers

Histones are proteins that assist in the regulation of DNA structure and activity in eukaryotic cells.

<p>True (A)</p> Signup and view all the answers

The cytoskeleton is absent in eukaryotic cells.

<p>False (B)</p> Signup and view all the answers

The nucleus is the smallest organelle within a eukaryotic cell.

<p>False (B)</p> Signup and view all the answers

Eukaryotic cells all have a wall formed by polysaccharides.

<p>False (B)</p> Signup and view all the answers

The outer membrane of the nucleus is in direct contact with the cytoplasm.

<p>True (A)</p> Signup and view all the answers

The E pocket is present in Eukaryotic ribosomes.

<p>False (B)</p> Signup and view all the answers

Methionine is the first amino acid in Eukaryotic translation.

<p>True (A)</p> Signup and view all the answers

Ribosomal proteins assist in the peptidyl-transferase activity in Eukaryotes.

<p>True (A)</p> Signup and view all the answers

EF-Tu is responsible for positioning aa-tRNAs on the ribosome in Eukaryotes.

<p>True (A)</p> Signup and view all the answers

The RER is where ribosomal subunits are synthesized.

<p>False (B)</p> Signup and view all the answers

The release factor eRF1 is involved in the recognition of stop codons in Eukaryotes.

<p>True (A)</p> Signup and view all the answers

Prokaryotes utilize a release factor similar to eRF1 for translation termination.

<p>False (B)</p> Signup and view all the answers

The Shine-Dalgarno sequence is found in Eukaryotic mRNA molecules.

<p>False (B)</p> Signup and view all the answers

Flashcards

Protein Synthesis

The process of translating mRNA into a sequence of amino acids to create proteins.

Endoplasmic Reticulum (ER)

A network of interconnected membranes in the cytoplasm. It's involved in the production and transportation of proteins and lipids.

Rough Endoplasmic Reticulum (RER)

A type of ER that contains ribosomes. Its main function is to synthesize and modify proteins.

Smooth Endoplasmic Reticulum (SER)

A type of ER that lacks ribosomes. It is involved in the synthesis and modification of lipids and steroids.

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Golgi Apparatus

A stack of membrane-bound sacs in the cytoplasm. It modifies, packages, and sorts proteins for transport.

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Lysosomes

Small, membrane-bound organelles found in the cytoplasm. They contain enzymes responsible for breaking down waste materials and harmful substances.

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Peroxisomes

Small, membrane-bound organelles found in the cytoplasm. They break down harmful molecules like hydrogen peroxide.

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Vacuoles

Organelles typically found in plant and fungal cells, as well as in some protozoa. They store water and waste products, regulate pH, and help maintain internal pressure.

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Genetics

The study of genes and their inheritance, focusing on how traits are passed from parents to offspring.

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Molecular Biology

The branch of biology that studies the molecular mechanisms of cellular processes.

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Phenotype

Observable characteristics of an organism, such as eye color or height.

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Gregor Mendel

The first person to develop a mathematical model of heredity, using pea plants.

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Genes

Units of heredity, responsible for passing traits from parents to offspring.

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Evolution by natural selection

The process by which organisms evolve over time, driven by natural selection.

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Heredity

The process by which organisms produce offspring.

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Genetic Trait

A characteristic that can be inherited from parents to offspring.

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What is cell biology?

The study of a cell's composition and how it functions, providing the foundation for understanding complex organisms.

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Why aren't viruses considered living?

They are not considered living because they cannot interact with their surroundings independently, relying on host cells for survival.

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What is a semi-replicator?

A physical system able to partially replicate itself, potentially emerging under specific conditions with sufficient energy.

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What is Occam's razor?

Applying the simplest explanation to a phenomenon, choosing the most straightforward interpretation.

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How is life described in terms of a physical system?

A physical system that is not in a state of balance, requiring constant energy input to maintain its organization.

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What is a common definition of life?

A physical entity is considered living if it can be born, grow, interact with its environment, repair itself evolve, reproduce, and eventually die.

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What is a cell?

The basic building block of all living beings present on Earth.

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Why are nucleic acids important for defining life?

They are essential molecules carrying genetic information, enabling replication and passing on traits.

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What are Archaebacteria?

Archaebacteria are single-celled organisms that thrive in extreme environments like hot springs or highly saline lakes. They are believed to be among the earliest life forms on Earth.

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What makes the cell membrane of Archaebacteria unique?

Archaea are characterized by having a cell membrane with unique lipids that are more stable in extreme environments, making them different from Bacteria.

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What are the defining characteristics of eukaryotic cells?

Eukaryotic cells are complex cells that possess a nucleus and other membrane-bound organelles, which are specialized compartments within the cytoplasm.

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What is the function of the nucleus in a eukaryotic cell?

The nucleus is the control center of a eukaryotic cell, containing the genetic material (DNA) in the form of chromosomes.

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What is the cytoskeleton and its role in eukaryotic cells?

The cytoskeleton is a network of protein fibers essential for maintaining cell shape, supporting the cell's structure, and facilitating the movement of molecules within the cytoplasm.

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What are organelles in eukaryotic cells?

Organelles are specialized structures within the cytoplasm of eukaryotic cells, each performing a specific function. Examples include the nucleus, mitochondria, and Golgi apparatus.

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What are histones and their function?

Histones are proteins that bind to DNA in the nucleus, helping to regulate DNA structure and control gene expression. They are crucial for processes like replication and transcription.

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What are lamin proteins and their role?

Lamin proteins are proteins that line the inner nuclear membrane, providing structural support and contributing to nuclear shape and function.

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oriC

A specific DNA sequence that serves as the starting point for DNA replication in prokaryotes.

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DnaA protein

A protein that binds to oriC and initiates the unwinding of the DNA double helix, marking the beginning of replication.

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DnaB protein

A protein that is essential for the unwinding of the DNA double helix, utilizing its helicase activity to separate the two strands.

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SSB protein

A protein responsible for stabilizing single-stranded DNA during replication, preventing their premature re-association.

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DNA polymerase III

A key enzyme in DNA replication responsible for synthesizing new DNA strands using an existing template strand. It adds nucleotides in the 5' to 3' direction.

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Replication bubble

A region where DNA replication is initiated and where the two DNA strands separate, creating a bubble.

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Semiconservative replication

The process of DNA replication in which each new DNA molecule consists of one original strand and one newly synthesized strand.

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5' to 3' direction

The direction of DNA strand elongation occurs from the 5' end to the 3' end.

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Peptidyl Transferase Activity in Eukaryotes

In eukaryotes, the large ribosomal subunit (60S) is responsible for peptide bond formation. This is accomplished by the 28S rRNA within the 60S subunit, aided by specific ribosomal proteins. This contrasts with prokaryotes where the peptidyl transferase activity resides within the 23S rRNA of the 50S subunit.

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Absence of E Site in Eukaryotes

Eukaryotic ribosomes do not have an E site (exit site) like prokaryotic ribosomes. This means that "unloaded" tRNAs, after delivering their amino acid, exit the ribosome differently in eukaryotes.

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Translocation in Eukaryotes

Similar to prokaryotes, eukaryotic ribosomes use the EF-G protein for translocation. Translocation is the movement of the mRNA and tRNA complex along the ribosome after a peptide bond has been formed.

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Translation Termination in Eukaryotes

In eukaryotes, translation termination is mediated by the release factors eRF1 and eRF2. eRF1 recognizes stop codons on the mRNA and releases the newly synthesized protein chain, while eRF2 assists in the process. This contrasts with prokaryotes that use release factor RF1 and RF2.

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Ribosome Synthesis and Localization in Eukaryotes

Eukaryotic ribosomes are synthesized in the nucleolus and then transported to the cytoplasm. Once in the cytoplasm, they can either remain free or become associated with the Rough Endoplasmic Reticulum (RER).

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Translation Initiation in Eukaryotes

In eukaryotes, the initiation of translation starts with the binding of the 40S ribosomal subunit along with other proteins to form the 43S complex. This complex then interacts with the mRNA, forming the 48S complex. This complex scans the mRNA to find the start codon, 'AUG', where translation will begin.

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First Amino Acid in Eukaryotic Translation

In eukaryotic translation, the first amino acid incorporated into a polypeptide chain is always methionine (Met). This is different from prokaryotes where the first amino acid is formylmethionine (fMet).

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Absence of Shine-Dalgarno Sequence in Eukaryotes

Eukaryotes lack the Shine-Dalgarno sequence, a key element in prokaryotic translation for ribosome binding to mRNA. This sequence is replaced by other mechanisms in eukaryotic translation initiation.

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Study Notes

NutriGenΩics Overview

  • Nutrigenomics is a valuable tool for introduction to the subject, presented in a concise format.
  • The book is divided into three parts: Cellular Biology, Genomics, and Nutrigenomics.
  • The material is designed for students with little to no prior experience in Cellular Biology and Genomics.
  • Genomics is important for understanding the relationship between food and human/animal diseases.
  • The bibliography is comprehensive to encourage further reading.

Table of Contents Details

  • Contains a detailed list of topics covered in the book, including page numbers for each section.
  • Topics span Cellular Biology (life, prokaryotes/eukaryotes, evolution), Genomics (DNA, RNA, genome size mechanisms), Molecular Biology (replication in prokaryotes/eukaryotes, transcription, translation, microRNA, transposons, epigenetics), and Nutrigenomics (nutrigenomics, origin of humans, diet evolution in humans, breeding, grain consumption and autoimmune conditions)
  • Covers the technologies commonly used in genomics (PCR, RT-PCR, etc.)

Cellular Biology Details

  • Discusses the basics of cells, prokaryotic and eukaryotic cells with their differences.
  • Explains the structure of prokaryotic cells (Figure 1) and eukaryotic cells (Figure 4) and their components (Figure 5).
  • Describes prokaryotic and eukaryotic flagella (Figure 6) and mitochondria (Figure 7), and ribosomes (Figure 8).
  • Covers the endoplasmic reticulum (Figure 9) and Golgi apparatus (Figure 10).
  • Discusses the function of vacuoles, peroxisomes, centrioles, and their roles in the cell (Figure 11).
  • Includes a description of the cell wall in Gram positive and Gram negative bacteria (Figure 2).

Genomics Details

  • Defines genomics as the study of the genome (DNA and RNA).
  • Expands on the structure and variations of DNA (Figure 2.2).
  • Covers RNA and discusses how it's synthesized from DNA.
  • Details different types of RNA—including mRNA, rRNA, tRNA, and how these function in protein synthesis—explaining their role and differences from DNA.
  • Describes the significance of gene duplication and expansion in genomic variations.
  • Covers the mechanisms associated with altering genome-size.

Molecular Biology Details

  • Explores replication in prokaryotic (Figure 18) and eukaryotic cells (Figure 20) in detail, including the key enzymes and steps involved in DNA replication, highlighting the difference between leading and lagging strands.

Nutrigenomics Details

  • Defines Nutrigenomics and how it connects genomics to nutrition, studying the impact of food on human and animal populations (Figure 1)
  • Explains the origin of humans, tracing their dietary evolution (meat eating and consumption of plants and seeds, the development of agriculture)
  • Looks into the evolution of humans, from our earliest ancestors to how early humans' dietary habits influenced their genotypes/phenotypes (Figure 3).

ADH, AMY1, and LCT Mutations

  • Details the roles of ADH, AMY1, and LCT genes in human evolution.
  • Discusses the positive selection of mutations in these genes that have occurred in different human populations.
  • Links the variations of these genetic factors to the frequency of consumption of particular nutrients, such as milk or grains.

Technologies in Genomics

  • Discusses the techniques for studying genes and genomes, including Polymerase Chain Reaction (PCR), Reverse Transcription PCR (RT-PCR), Microarray technology, and Next-Generation Sequencing (NGS).
  • Describes each technique and its advantages in detail.

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