Midterm 1

• Molecules --> cells --> tissues --> organs --> organisms
• Cells: basic microscopic unit of all living beings
• Tissues: cells that aggregate to form a specific function
• Organ: a fully differentiated structural + functional unit in an animal that is specialized for some particular function
• Robert Hooke:

  • Termed the pores inside a cork "cells"
  • Based on cells inhabited by monks living in a monastary
  • Used a double lens microscope
• Anton Leewenhock:

  • Examined pond water under the microscope
  • Observed microscopic "animalcules" that moved
  • Used a single lens microscope
• Cell Theory:

  1. All organisms are composed of one or more cells
  2. The cell is the structural unit of life
  3. Cells can arise only by division from a pre-existing cell
• Basic Properties of Cells: Life

  • Most basic property
  • Smallest units to exhibit this property
• Basic Properties of Cells: Highly Complex + Organized

  • Organization is achieved through random processes
  • Stochastic
  • Cells from different species share similar:
  • Structure + composition
  • Metabolic features
  • Have been conserved throughout evolution
• Basic Properties of Cells: Possess a genetic program + the means to use it

  • Organisms are built according to information encoded in a collection of genes
  • Information is packaged into a set of chromosomes in the cell nucleus
  • All cells in an organism contain identical copies of DNA
  • Become differentiated via development from a single fertilized egg
  • Molecular structure of genes allows for changes in genetic information (mutations)
  • Variation among individuals (basis of biological evolution)
• Genes:

  • Store information
  • "Blueprints" for constructing all cellular structures
  • Directions for running cellular activities
  • Program for making more of themselves
• Basic Properties of Cells: Capable of reproducing

  • Mitosis + meiosis
  • Reproduce by division
  • Contents of a "mother" cell are distributed into 2 "daughter" cells
  • Prior to division, genetic material is duplicated
  • Each daughter cell receives a complete + equal share of genetic information
• Basic Properties of Cells: Acquire + utilize energy

  • Photosynthesis
  • Provides fuel for all living organisms
  • All energy comes from sunlight
  • Animal cells derive energy from the products of photosynthesis
  • Mainly in the form of glucose
  • Cells can convert glucose into ATP
• Basic Properties of Cells: Carry out a variety of chemical reactions

  • Sum total of chemical reactions in cells = metabolism
  • Function like miniaturized chemical plants
  • Bacterial cells are capable of hundreds of different chemical transformations
  • All chemical changes in cells require enzymes to increase the rate of the reaction
• Basic Properties of Cells: Engage in mechanical activities

  • Cells are very active
  • Transport materials
  • Assemble + disassemble structures
  • Move itself from one site to another
  • Activities are based on dynamic, mechanical changes within cells
  • Initiated by changes in the shape of "motor" proteins
  • Motor proteins: a type of molecular "machine" used for mechanical activities
• Basic Properties of Cells: Able to respond to stimuli

  • Have receptors that sense environment + initiate responses
  • Can move away from an object in its path or towards nutrients
  • Cells in plants + animals are covered with receptors that interact with substances in the environment
  • Hormones, growth factors, extracellular materials, + substances on the surfaces of other cells can interact with these receptors
  • May respond to stimuli by:
  • Altering their metabolism
  • Moving from one place to another
  • Committing suicide
• Basic Properties of Cells: Capable of self-regulation

  • Robust + protected from dangerous fluctuations on composition and behavior
  • Feedback circuits serve to return cells to their appropriate state
  • Maintaining a complex, ordered state requires constant regulation
  • Cellular factors function without the benefit of conscious direction
  • Each step is spontaneous BUT must occur in a way that the next is triggered automatically
  • Information in the DNA genome programs this spontaneous machine
• Basic Properties of Cells: Evolve

  • Origin of cells is unknown
  • All living organisms evolved from a single, common ancestral cell
  • Ancient cell is referred to a s the last universal common ancestor (LUCA)
• 2 Classes of cells, prokaryotic + eukaryotic

  • Similarities:
  • An identical genetic language
  • A common set of metabolic pathways
  • Many common structural features
• Eukaryotes:

  • Temporal (time) and spatial (space) arrangements of biochemical evens in the cell are critical for cell function
  • Large amounts of energy are put into maintaining membrane-bound domains to localize biochemical events
• Size limiting factors of a cell:

  • Need to maintain adequate local concentrations of substances required for necessary cellular functions
  • Need adequate surface area relative to volume
  • Rates at which molecules can diffuse
• Surface Area + Volume:

  • If a cell requires oxygen to produce energy , the surface area to intracellular volume must be large enough so that oxygen can easily diffuse into every part of the cell
  • As cell SA gets larger, the volume increases at a higher rate
  • SA is important because exchanges between the cell + its surroundings take place there
  • Volume determines the amount of exchange that is needed
  • Beyond a certain threshold, a large cell wouldn't have a large enough SA to allow for intake of enough nutrients + release of water
• Cytoplasm:

  • Volume of a cell, excluding the nucleus
  • Filled with organelles, cytoskeletal components, and cytosol
• Cytosol:

  • Semi-fluid liquid, Jello-like
  • Molecules move within the cytosol by:
  • Diffusion:
  • Unassisted motion that relies on concentration gradients
  • Active transport
  • Specialized machinery that can move molecules/vesicles along the cytoskeleton from one place to another
• Synthetic Biology:

  • Field oriented to create a living cell in the laboratory
  • Consider ethical implications
  • Uses nucleic acids, proteins, and lipids
• Good experimental species:

  • Widely studied
  • Well characterized
  • Easy to manipulate
  • Other advantages:
  • Relatively simple organisms
  • Fast generation time
  • Large number of offspring
  • Easy to manipulate in the lab
  • Inexpensive to breed
• Virus: an infectious agent that can only replicate inside a living cell
• Provirus: a virus genome that has been incorporated into the genome of its host
• Virion: a complete viral particle, which includes the genome, capsid, and in some cases, an envelope
• Viroid: an infectious agent that is composed solely of RNA (no coat proteins)
• Prion: an infectious protein that can transmit its folded shape to other native folded proteins
• Virus Particles (virions):

  • Consist of nucleic acids (RNA or DNA) enclosed in a protein coat
  • Can bind, enter, + replicate within a host cell
  • All viral genomes encode 3 types of proteins:
  • For replication
  • For packaging + delivering
  • For modification of host cell
• Coronavirus (COVID 19):

  • Zoonotic
  • Can be transmitted between animals + people
  • Binds to heparin sulfate proteoglycan and the ACE2 receptor
  • ACE2 receptor:
  • Angiotension converting enzyme 2
  • Prominent on lung alveolar epithelial cells
• Most abundant chemicals in life:

  • Hydrogen
  • Carbon
  • Nitrogen
  • Oxygen
• Covalent bonds:

  • Strong bonds formed by the sharing of electrons between adjacent atoms
  • # of bonds formed depends on # of electrons needed to fill its outer shell
• Polar + Non-polar molecules:

  • Electrons sharing unequally = polar covalent bond
  • Electronegativity: indication of an atom's ability to attract and electron
  • Greater electronegativity --> greater ability of an atom to attract an electron + form a polar covalent bond
• Polar molecules:

  • Asymmetric distribution of charge
  • Molecule has partial + and partial - regions
  • Polarity determines the molecules reactivity
• Non-polar Molecules:

  • Lack electronegative atoms + strongly polarized bonds
  • Relatively inert/non-reactive
• Ionization:

  • Very strongly electronegative --> can capture electrons from other atoms during a chemical reaction
• Negatively charged ions gain an electron --> anion