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What is Life?

• There are varying definitions; homeostatic metabolism + development + growth + reproduction.
• According to (Abel, 2002). Life can also be defined as thermodynamic disequilibrium + low-entropy state + information encoding and transformation.
• Yet another definition, according to (Schulze-Makuch and Irwin, 2004) is evolution + reproduction + metabolism.
• However, for this course, the latter will be used.
  • (National Research Council, USA, 2007).

Defining Life

• Scientists propose definitions for life
• Those definitions are in peer-reviewed publications.
• The scientific community then decides on "working definitions" to use as guideline.
• Definitions are dynamic and always a work in progress.

Zika Virus

• The question "is a virus alive" is proposed
• Zika is a single-stranded RNA virus and is used as example
• Virus = Nucleic acids + protein coat.
• Viruses can be surrounded by a membrane.
• Viruses can only reproduce only in a host cell.
• SARS-CoV 2 also Infects human cells following complex processes.
• Viruses can evolve, through drug resistance or by creating new variants.
• Reproduction occurs, but only with the help of a host cell.
• No metabolic capabilities; use host cell's metabolism

Properties of Life

• Order
• Energy processing
• Evolutionary adaptation
• Regulation
• Reproduction
• Response to the environment
• Growth and development

Flower Mantids

• Camouflage is an example of evolutionary adaptation.
• Variations occur in offspring during natural selection.
• Some individuals will be slightly more camouflaged.
• The differential reproductive success dictates that Less visible individuals to prey and predators produce >more offspring
• Over generations, gradual changes take place.

Flu Vaccines

• There are 2 main types:
  • Attenuated (weakened) vaccines use a nasal spray.
  • Killed (damaged by heat, chemicals) vaccines use an injection.
• Virus applied to foreign host (e.g. chicken egg) is used to make attenuated vaccines.
• Variation occurs as some viruses have mutations to infect this new host.
• Those "lucky" viruses can replicate in the chicken egg.
• After a few months, accumulated mutations improve replication in chicken eggs.
• Eventually the virus will not replicate well in a human host.
• That end product leads to ->attenuated vaccine.

Evolution

• Charles Darwin proposed evolution can explain unity and diversity of life.
• All known life forms on earth share:
  • DNA as genetic material
  • A nearly identical genetic code
  • Ribosomes to translate proteins
  • Cell membranes
  • Similar basic metabolism
• Evolution can also explain the diversity of life.

Chemical Context of Life

• Elements, atoms, isotopes and molecules are key concepts.
• It is important to be able to distinguish covalent bonds, ionic bonds and weak bonds.
• Matter is anything that takes space, that turns into Elements and Atoms
• There are 118 known elements.
• Elements and atoms cannot be broken down to other substances by chemical reactions.

Periodic Table

• Important aspects of the periodic table include:
  • Atomic number
  • Symbol
  • Name
  • Atomic mass
• Atomic number = number of protons
• Mass number = sum of protons plus neutrons
• Isotopes differ only in the number of Neutrons.
• Radioactive isotopes decay spontaneously.
• This yields particles and energy.
• Radioactive decay is used in radiometric dating, to calculate age of items.
• Carbon dating uses radioactive 14C, which has a half-life time of 5700 years.
• Half-life time of 5700 years
• For dating is up to about 60,000 years.
• In 2010, scientists discovered a new kind of human: "Denisovan”, used to date bones.
• Knowing the ratio of 14C allows to identify bones in skeletons.
• Radiocarbon dating helped reveal whisky fraud, showing a "whiskey from 1863" was really made ~2010.

Atoms In the Human Body

• Key atoms include:
  • C
  • H
  • N
  • O
  • P
  • K
  • S
  • Cl
  • Na
  • Ca
  • Mg
• Key percentages include 96.3% (O, C, H, N) 3.7% (everything else), plus trace elements.
• For each element, it is also important to know the valences.

Valence Electrons

• Valence electrons are electrons in the outermost shell which determine chemical behavior.
• Elements with full valence shell are chemically inert, for instance noble gasses.

Electrons and Energy

• Energy is the capacity to cause change.
• An electron's state of potential energy is called its energy level, or electron shell.
• Electrons can absorb and loose energy.

Building Molecules

• Covalent bonds mean atoms with incomplete valence shells can share valence electrons.
• Covalent Bonds can be polar or non-polar.
• More electronegative elements pull electrons toward them.
• Atoms sometimes strip electrons from their bonding partners.
• This creates positive cations and negative anions, joined under ionic bonds.
• Compounds formed by ionic bonds are called ionic compounds, or salts.
• Weak bonds means stronger bongs in organisms are covalent.
• Weak bonds hold biological molecules in their functional form.
• The reversibility of weak bonds can be an advantage
  • Allows for conformational change in proteins and opening of DNA

Weak Chemical Interactions

• Most of the strongest bonds in organisms are covalent bonds.
• Covalent bonds form a cell's molecules
• Reversibility of weak bonds advantage
• Weak bonds conformational change in proteins
• Weak bonds opening DNA double strands
• Types of Weak Chemical Interactions
  • Hydrogen bonds
  • Van der Waals interactions

Hydrogen Bonds

• Form when a hydrogen of a molecule is attracted to another electronegative atom (O, N).
• Hydrogen Bonds = H2O (Water) plus NH3 (Ammonia)
• Valentces refer to the number of bonds an atom can form and determines molecular structure.
  • 1 = Hydrogen
  • 2 = Oxygen
  • 3 = Nitrogen
  • 4 = Carbon

Properties of Water

• Cohesion - It Sticks together due to hydrogen bonds which also explains surface tension
• Moderates temperature
• Expansion upon freezing.
• Good solvent.
• Has strong cohesive abilities.

High Specific Heat of Water

• High specific heat keeps temperatures at the coast moderate.
• Specific heat - a substance is the amount of heat that must be absorbed
• For 1 g to change its temperature by 1°C -The specific heat of water is 1 cal/(g• °C)
• A calorie (cal) is the amount of heat required to raise the temperature of 1 g of water by 1°C
• The "Calories" on food packages are actually kilocalories (kcal)
• 1 kcal = 1,000 cal

Cooling

• Evaporation - water is able to cool things down
• Evaporative Cooling because Heat of vaporization is the heat liquid should have
• Liquid must absorb for 1 g to be converted to gas
• Ice floats because water is less dense as a solid than as a liquid.
• When freezing - hydrogen bonds in ice keep molecules farther apart than in liquid water.
• In liquid water hydrogen bonds are very close

Water as a Solvent

• Solvent is Water, also versatile due to its polarity. Has the ability to dissolve both ionic compounds & polar molecules
• ionic compound is dissolved in water
• Each ionis surrounded by a sphere of water moleculeds called ydrarion shell.
• Some molecules don't dissilve in water = is non polar

Carbon and Life

• 140A, class 4 studies Carbon and Life and its chemical bonding.
• Carbon has the chemical bonds needed for life to form.
• It's worth understanding what makes carbon so important for life on earth
• The 7 most important functional groups of organic molecules and isomers are also explored.

The Importance of Carbon

• Carbon is the main component of organic chemistry.
• Organic compounds contain carbon and have C-H bonds.
• Carbon has the ability to form up to 4 bonds so organic compounds range from simple molecules to massive ones.
• Valency of 4 bonds.

Hydrocarbons

• The structure variation of carbon "skeletons" vary in Branching Structure
• Hydrocarbons consists of only carbon and hydrogen
• Hydrocarbons can release large amounts of energy

Isomers

• Isomers are compounds with the same molecular formula but different structures.
• Structural isomers have different bonds
• Geometric isomers, such as Cis-trans isomers, have different rotation
• Enantiomers have mirror images of each other

Functions of Molecules and Functional Groups

• Enantiomers are important in the pharmaceutical industry.
• Two enantiomers of a drugs may have different effects.
• Usually, only one enantiomer is biologically active
• Several such as L Dopa are important

Functional Groups

• A few chemical groups dictate molecular function.
• Estradiol and Testosterone give an overview of chemical compounds.
• The 7 functional groups that exist in life as:
  • Hydroxal
  • Carbonal
  • Carboxyl
  • Amino
  • Sulfhydral
  • Phosphate
  • Methyl

Building Blocks

• Building blocks include hydrocarbons and hydrocarbons. Can also use carbon, oxygen & hydrogen such as is carbohydrates.

Organic Molecule Origins

• Before life evolved , where did organic molecules come from?

  • It can be from Extraterrestrial Sources of Organic Compounds?
  • Carbon compounds are common in meteorites that landed on Earth
  • The Miller Urey experiment attempts to mimic the pre-evolution creation of organic molecules. - It combines the most basic resources such as water and then uses electrical stimulation to create amino acids and other molecules.

• Organic Molecules and the Origin of Life are possibly:

  • The Atmosphere
  • Deep sea vents
  • Extraterrestrial

Macromolecules

• Macromolecules are explored in class. These building blocks include DNA, RNA ,proteins, polysaccharides and lipids.
• DNA, RNA ,proteins, Polysaccharides are true polymers of micromolecules.
• Polymerization is the process that creates these. Polymerization occurs through Dehydration.
  • A polymer is a long molecule of consisting of many monomers, such as the sequence Arg Gly Met.

Macromolecules

• Small organic molecules build macromolecules.
• Common Macromolecules include:
  • DNA, RNA
  • Proteins
  • Polysaccharides
  • Lipids

Polymers

• DNA, RNA, proteins, and polysaccharides are true polymers (made by adding monomers).
• Polymers get created via polymerization to macromolecules:
  • A polymer is a long molecule consisting of many similar building blocks (monomers).
    • DNA, polysaccharide, proteins
• Polymers get synthesized via dehydration.
• Polymers get broken down via Hydrolysis.

Carbohydrates

• Carbohydrates consist of simple carbohydrates (sugars - monosaccharides and disaccharides).
• Carbohydrate macromolecules are polysaccharides (polymers composed of many sugar building blocks)

Sugars

• Usually multiples of CH₂O
• Glucose (C6H12O6) is the most common monosaccharide
• Monosaccharides are classified by the:
  • Location of carbonyl group (aldose or ketose)
  • Number of carbons in the carbon skeleton
• Various types of isomers include:
  • Geometric
  • Structure
• In solutions many monosaccharides form rings
• It has linear and in ring form

Formation of Disaccharides & Polysacharides

• Polysachharides are polymers of sugars
• Formation of Disaccharides has been explored, for instance; Maltose & Sucrose
• Amylose
• Amylopectin

Sugars

• Starch: Is a linkage of a glucose
• Cellulos, has a linkage of β glucose.
• It can digest starch with amylases.
• Unable to digest cellulose ("fiber").
• Because body lacks the enzyme cellulase.
• Grass-eating mammals have cellulase, because use of Microorganisms.
• The functional differences between starch, cellulose, and glycogen are:
  • Energy storage in plants
  • Cell wall in plants
  • Energy storage in muscles

Health Impacts

• Processed carbohydrates should be avoided like starch & sugar, but little fiber (cellulose), increase risk of Type 2 Diabetes.
• Digestion follows this process:
  • Starch is digested by amylase -> to form Maltose ->which gets reduced by maltase -> to form glucose.

Types of Diabetes

• Diabetes follows:
  1. Healthy - Insulin receptor is all good
  2. Type 1 - Pancreas failure to produce insulin as well.
  3. Type 2 - Cells fail to respond to insulin properly.

Lipids

• Lipids are a diverse group of hydrophobic molecules, not true polymers.
• They are mostly consist of hydrocarbons, fats, triglycerides, phospholipids, or steroids
• Fats or triglycerides contain glycerol: 3-carbon alcohol with 3 OH-groups
• And has fatty acid attached to long carbon skeleton. Ester Linkage will be explored which helps with understanding (between carboxyl and OH group)
• Triglycerides form with dehydration. Then the fatty acid side chains are formed with single bond (saturated) or with cis.
• A saturated bond makes chains straight.
• What are fats so calorific? It is because lots of energy stored in the hydrocarbon bonds, with no double bonds in fatty acd chains.

Health

• Unsaturared fatty acid side chains contains double bonds. Double bonding causes binding for fats,
• Trans fats are bad , the intake associated with heart disease, where cis-fatty acids are good
• It's important to know the difference, some artificial, some artificial. Trans fats are made artificially from unsaturated vegetable oil.
• Major Function of fats is energy storage due to hydrocarbon chains
• Humans and other mammals store their long-term food reserves in adipose cells
• Adipose tissue also cushions vital organs and insulates the body

Phospholipids

• They Contains: both hydrophillic and hydrophobic components
• Glycerol
• 2 fatty acids
• hydrophobic
• 1 phosphate group
• hydrophilic When you mix phospholipids in water and is able to self assemble into layers

Lipids & Steroids

• Steroids: Are lipids characterized by a Carbon skeleton.

• The skeleton consists of 4 fused rings -Cholesterol : component in animal cell membranes.

  • Regulates fluidity and has a precursor from which other steroids are synthesized. What is the issue with cholesterol, though?
    • is there good and bad cholesterol?

• It can transported by different lipoproteins (low-density and high density)

• There are two main cell categories:

  • Prokaryotic
  • Eukaryotic

Proteins

• Protein Structures and Roles:

  • There are many functions do exists for it that are knowable and is an aspect of focus.
  • It is one or more polypeptide chains. Consists of Polypeptides, polymers. - It forms the amino acids through Peptide bond

• Key parts of the structure includes: Side Chain

• H3N+-C- C- o-

• H O - C- alpha

• Glycine , which is nonpolar and hydrophobic

• Side Chains non polar :hydrophobic

Protein Folding

• Amino Acid polymer is known as polypeptides
• The polypeptide chain can have:
• Amino End The carboyxl Chain
• Protein structure has four categories :
• • Primary which consist of it's amino acid sequence
• • Secondary results from hydrogen bonds - Can be in different states: Alpha Helix & Beta pleated Sheet
• Beta sheets can form aggregates which is when hydrogen bonds are formed
  • Teritary Structure
  • Is made up of : Hydrophobic interactions , Hydrogen Bond , ionic bond and Disulfide Birdges
• Quaternary is a result of Polypeptide Chain Subinits come together. It Is made up of: Multiple polypeptide chains form

Diseased Protein

• There are several diseases that impact protein structure.
• A key example is the sickled cells and the blood disorder they cause.
• Caused by the aggregation of polypeptide chains.
• The change is minor but impactful:
  • Has side-chain switch - Polar v non polar
  • Then it is a Electrically Charged Sidechain

Amino Switch

• The side-chain results in Glutamate turning into Valine. Making it hydrophobic
• Polar / charges switch is the root issue of it. This was an addition from polar/ charged which leads to hydrophobic

Human Cells

• In primary structure - and and tertiary form red blood cells.
• Secondary and tertiary changes due to chain reactions.
• But ultimately function is limited due to cell shape.
• However , gene therapy is now improving treatment for this issue in this area.
• Has proven promising with a 1 letter difference.

Diseases

• Protein Folding and cell can results : -Diseases such as such alzeimer or mad cow -Can result into prions .
• It must have a normal to diseasing transformation.
• This forms across aggregates

DNA & RNA

• Nucleic acids are polymers of nucleotides.
• Nucleotides are linked together by phosphodiester bonds.
• There are two types of nucleic acids: . Deoxyribonucleic acid (DNA) . Ribonucleic acid (RNA)
• DNA or RNA sugar molecules that consist of nucleosides.
• DNA is a double helix shape of linked molecules.
• Nucleuotide and the Sugar molecule .
• The Sugar and phosphate has back bone.
• Sugar Phosphate back ones run in op directions to each other = Antiparticle

Comparisons Between DNA and RNA

    - DNA: Double Stranded and is a Double Helix, RNA on the other hand is a single Stranded and carries Various Secondary Structures , Sugar molecule a deoxyribose - RNA has a ribose

• What is different is, for instance, : If DNA : It will have GCAT. / In RNA It will have GCAU.
• If it is Same Cells/ The individual amount varies.
• For DNA it will be the same / for RNA with its depend on chain express
• RNA: localized base pairing wide variety of structures

The 3 Major Cells & Gene Expression

• Gene expression is the DNA to RNA cycle in the nucleus where the coding is translated. —1:Synthesis of mRNA
• 2: Movement
• 3:Protein
• It goes through a process transcription then out of cells in to then cytoplasma into ribosomes to go to translation and out.

Cell Dimensions

• Cells range in size from
  • 10 m to 0.1 nm
• Two types of : Light or electron microscopes. . Electron is more power ful
• Resolution- Can not be smaller than 1/ 2 light (200 mm)
• Super resolution- Microscopic allows distinguish small
  • Structures 10-20mm

Prokayrotic vs Eukaryotic

• To review there different areas cells
  • Prokaryotic is bacteria and Archea
• ProKayotic cells are Characterized lack by membrane-bound organelles,a Nucleous etc
• Eukaryotic- Contains membrane-Bound -Contains organelles, cell division and dna

Similarities

    - DNA for Genetic code
    - Ribosomal
    - Cytosol

Prokayrotic Cell Design

    - Ribosomes and more
        - Cell wall
        - Plasma layer
        - Nucleoid
        - and chromosomes

Eukaryotic Cells

• Contains
  • Plant Cells
• Has Central Vacuole
  • Cell walls
  • Plasmodesmata

Cell Components and Function

• It follows endomembrane system consists to follow
• Nucleur is the power house . Made out of RNA, DNA a d more
• Enpdsomic Rectium follow 2 types of structure is the transportation to Smooth and then with
• Goldi Apparatus for final form
• Vacles are storage of some sort that breaks down
• Lysomes are basically for garbage use and breakdown other organals for resource

Nucleus Details

• The endomembrane system regulates protein traffic and performs metabolic functions in the cell.
• It has two important components:
  • Nuclear envelope
  • Endoplasmic reticulum Then those are key parts of the parts to remember.

Cell Components and Function

• It will have 2 areas smooth and rough and
• Has different structures

Smooth : Smooth Is Synthesis. Metabolism

• Rough is for Protein transportation out and is there where you get out
• and produce from new member , you then must see it being out of cytoplasm The 3 things - the nuclear envelope
• Enoplasmic
• Goldi Appatatus
  • Lysosomes
  • Vacuoles -Plasma Membrane to to to the
• Mitochondria: Site of cellular respiration
  • Intermembrane space - Outer Membrane a is the DNA

It follows the model.

• That then has a large surface. Area to boost
• Inner memrane
• Cristat
• Matrix
• Theory of Ednosymbions Mitochondria in and Plastids Small prokayoutes living with larger Host/Cell And is 11, 15 years +

•   Has Duplex Membrane - CirculationDNA - Smallest Prokotese
  

  -Division can split Human with ~ genes - It also as :
• It takes to :22RNA + code

Mitochondriral Disease

• Genetic Disorder = 1:200

• • It has a large variations like it also has more systems like frequent miscarriages. One possibilitie the trasfer - or even nucleal**

• To understand how those factors play a row on how the disease can be used also

• 1 Possibility : trasfer of health mitochondria .. or nuclear trasfern from the same donors are placed in. In which is then followed by donor egg

  What is the opinion on the 3 way patent theory? Should It be Legalized and if why