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Cells are “Alive”

But the molecules that make up cells are not static; they are in constant motion, interacting and undergoing various processes that sustain life.

Diversity of Eukaryotic and Prokaryotic Cells

• Prokaryotes, despite their simplicity, showcase incredible biochemical diversity due to their various methods of energy acquisition and adaptation to different environments.

• Procaryote (procaryotic)—as old as “life”

  • Includes the eubacteria and the archaea has a “simple genome

  • Single circular DNA molecule drifts within the cytosol procaryotic—circular stranded

    • rod or circle shape

  • all are unicellular, and no true multicellular forms

  • all have cell wall; none have organelles

    • Tough cell walls

      • The tough cell wall in prokaryotes provides protection from osmotic pressure, structural support, and defense against environmental threats and immune responses

  • extremely diverse, most cells are prokaryotic

  • Procaryotes—limited control:

    • In prokaryotes, transcription is relatively simple and typically occurs as soon as the DNA is accessible.

    • Regulatory control is more straightforward, often involving operons (clusters of genes regulated together), where a single promoter controls the transcription of multiple genes.

    • There's less complexity in regulating transcription, with fewer layers of control.

  • Horizontal gene transfer is a major evolutionary mechanism in prokaryotes, allowing them to rapidly acquire new traits like antibiotic resistance.

• Eukaryotic cells are characterized by their larger sizes and complex structures compared to prokaryotic cells. This complexity often arises from a symbiotic relationship among early unicellular organisms.

• Eucaryote (eucaryotic)—evolutionarily young

  • multiple DNA molecules

    • leads to other important differences

  • eucaryotic—linear stranded

  • contained within a nucleus

  • “complex” genome

  • network of internal membranes (organelles)

  • unicellular and multicellular forms

  • cell wall only in plants

    • HGT is less common in eukaryotes, it does happen in plant and fungi

  • limited diversity, some cells are eucaryotic.

  • Eucaryotes—extensive control:

    • Eukaryotic cells have more intricate transcription regulation due to their complexity and the need for fine-tuned gene expression.

    • Transcription is regulated at multiple levels, including enhancers, silencers, promoters, and the involvement of various transcription factors.

    • This extensive regulation allows for more precise control over when, where, and how genes are expressed in different tissues and stages of development.

  • Eucaryotes characteristics

    • The nuclear envelope allowed the genome to increase

      – larger genome = more proteins = more machines, more switches, more structures

      – cell got larger

      – cytoskeleton evolved

      – cell wall was lost (reacquired in plants)

      • Allowed flexibility and cell interactions, facilitating multicellular organization. (Plants reacquired a cell wall later for structural support.)

    • Not all of larger genome codes for protein

      – much of the eucaryotic genome is non-coding

      – many of these regions function in regulation

    • Controlled and selective expression of genes

      – allows the development of multi-cellular organism

  • Eucaryotes also transcribe– pre-mRNA, siRNA, snoRNA, snRNA, plus others (RNA process)

• Additional Information

  • Humans have more prokaryotic cells than eukaryotic cells; if you are sick, there is a disbalance of cells. It's about the balance between harmful and beneficial bacteria (prokaryotes) and how they interact with your eukaryotic cells.

  • All cells are caryotic; most are P, and a small amount are E

  • Plant and Fungi: 10-20 cell types

    • Secret enzyme to digest its food fungi

  • Animals: 100-200 cell types

Pre-RNA, SiRNA, SnoRNA, snRNA

During translations, these types are not translated into protein but instead have functional roles in the cell

• Pre-RNA (Precursor RNA):

  • The initial RNA transcript synthesized from DNA during transcription.

  • It undergoes processing (e.g., splicing, capping, polyadenylation) to become mature RNA (e.g., mRNA, rRNA, tRNA).

• siRNA (Small Interfering RNA):

  • Short double-stranded RNA molecules.

  • Involved in gene silencing by degrading specific mRNA, preventing translation.

• snoRNA (Small Nucleolar RNA):

  • Found in the nucleolus.

  • Guides chemical modifications (e.g., methylation, pseudouridylation) of rRNA, tRNA, and snRNA.

• snRNA (Small Nuclear RNA):

  • Found in the nucleus.

  • Plays a role in RNA splicing as part of the spliceosome complex

DNA vs RNA

All cells store their hereditary information in deoxyribonucleic acid (DNA)

• DNA

  • Long polymer of nucleotides

    • nucleotides consist of sugar-phosphate “backbone”

    • nitrogenous “base” attached to sugar

    • double-stranded

    • The reason it's double, is because evolution chose that shape because it requires less energy as opposed to any other shape or structure.

    • The way in which new DNA is synthesized ensures that the

      new molecules are identical to the old

    • The parent strand of DNA serves as a template “daughter” strand is complementary to a template

    • Each new DNA molecule

      • one “old” template strand, one new “complementary” daughter strand

      • DNA replication is therefore “semi-conservative”

• RNA

  • is a single-stranded molecule involved in various biological roles, primarily related to protein synthesis and gene regulation.

  • The most important difference—RNA molecules are usually

    single-stranded, fold onto itself into unique 3-D shapes

  • less stable than DNA

  • mRNA (messenger RNA): Carries genetic information from DNA to ribosomes for protein synthesis.

  • tRNA (transfer RNA): Delivers amino acids to ribosomes during translation.

    • Reason we have so many codon: The variety of codons arises from the fact that there are 64 possible combinations of three nucleotides (codons), but only 20 amino acids.

  • rRNA (ribosomal RNA): Forms the core of ribosomes, where proteins are made.

  • Regulatory RNAs (e.g., siRNA, miRNA): Control gene expression

• Mechanism

  • portion of single-stranded DNA (genes) serves as a template for the synthesis of an RNA molecule (transcript)

  • All cells transcribe mRNA, tRNA, rRNA

  • DNA : serves as the template for transcription and translation to produce proteins.

    • DNA is transcribed into messenger RNA (mRNA)→The mRNA is then translated into a protein through the help of ribosomes that read the mRNA in the set of three nucleotides (codons) and assemble amino acids to form a protein.

  • RNA: mRNA, transcribed from DNA, is the only RNA type that is translated into proteins. The translation process occurs in ribosomes, where the mRNA sequence determines the amino acid sequence of the resulting protein.

• Structure

• Ribose sugar instead of deoxyribose and oxygen was added

  • DNA bases are A, G, C, T Momoers

    • Nucleotides (monomers) → suger phosphate → DNA (polymer)

    • T instead of U in DNA

  • RNA bases are A, G, C, U Momoers

    • Nucleotides (monomers) → “:Ribose suger” phosphate→ RNA (polymer

  • Older RNA molecules tend to be less stable than DNA due to their single-stranded nature, making them more susceptible to degradation.

    • It's believed that uracil was the original base of early genetic molecules. Thymine likely evolved later in DNA to enhance stability and reduce errors in genetic information.

  • All cells also assemble ribonucleoprotein

    • combination of proteins and RNA molecules

    • function as machines and / or switches

    • ribosomes (all cells)

    • telomerase, spliceosome (eucaryotes only)

• Bonds

  • The bonds are held together by weak bonds. Why?

    • This allows the two DNA strands to be pulled apart without break-

      age of their backbones

      • A-T pairs have 2 hydrogen bonds.

      • C-G pairs have 3 hydrogen bonds.

  • The sugar phosphate are held by covalent bonds, How does this work?

    • The strong sugar-phosphate backbone ensures that the individual strands remain intact during these processes.

Transporters in the Plasma Membrane

Transporters play a crucial role in maintaining the homeostasis of cells by regulating the concentrations of various ions and molecules, thus influencing cellular pH. These transport proteins vary in mechanism and specificity.

• Selective barrier

  • retain nutrients and synthesized products in

  • exclude waste products

• Structural “scaffold”

  • attachment for proteins and other molecules

• Cell Wall

  • most bacteria and plant cells

  • very few animal cells

  • plasma membrane-all cells

Genomes

• Genomes

  • Gene Families

    • Homologous genes may result from:

      1. gene duplication: accidental copying (during

         replication) of the same sequence more than once

      2. intragenic mutation: errors during replication

         may result in slightly new sequences

      3. segment shuffling: accidental breaks in two or

         more gene regions are mis-repaired such that a

         new, hybrid gene sequence results

      4. horizontal transfer: the transfer of genetic

         material from one cell to another

         Viruses:

         1. affect procaryotic and eucaryotic cells

         2. FYI, viruses are NOT cells, are NOT alive

            they require a host, and they hijack the host to do their functional bidding; plus, they don’t have a nucleus, although their genetic material can have RNA OR DNA.

         3. Acquisition of environmental DNA almost exclusively prokaryotic

         4. Sexual reproduction

            1. primarily eucaryotic

            2. occasionally prokaryotic

  • Vertical transfer

    • – parent to offspring

    • – no “new” genetic material

• Free energy

  • Living cells need free energy to maintain their chemical processes, grow, and replicate. The transmission and propagation of genetic information also require energy. The amount of energy required to specify even a small bit of information can be calculated, but the basic concept is that life is inherently tied to the consumption and use of free energy. Without it, a cell would lose its ability to function and would decay toward equilibrium and death.

  • Conditions within cells are kept constant– but far from chemical equilibrium

  • Cells require large amounts of energy to maintain this homeostatic disequilibrium

    • For Plants (and other photosynthetic organisms): SUN,Photo

    • For Animals (and non-photosynthetic organisms): ATP, CRep.

    • For Certain Bacteria, chemosynthesis allows them to convert inorganic compounds into energy.

Mitochondria and Chloroplasts

• are thought to have evolved from free-living bacteria that were engulfed by an ancestral eukaryotic cell through phagocytosis.

  • Over time, these bacteria formed a symbiotic relationship with the host cell, eventually becoming the mitochondria (in animals and plants) and chloroplasts (in plants and algae) we see today.

  • Mito came first 1.5 to 2 billion years ago; the first euk cell likely had mito energy, then the ancestor of the chlor was believed to be cyanobacteria (photosynthetic bacteria) engulfed by the euk cell, which happened 1 billion years ago.

  • Evidence for this theory includes:

    • Their own genome (similar to bacterial DNA),

    • The ability to replicate by fission (like bacteria),

    • The presence of a double membrane (one from the bacteria and one from the host cell).