Lecture Flashcards: The Chemical Basis of Life (Biomolecules, Bonds, Water, and Origin of Life)

Scientific investigation- a plan for asking questions and testing possible answers.

What is science?- Science is the careful study of the natural world, to understand how things work. The steps to study the natural world go through observation, experimentation, and analysis.

The goal of science is to learn and explain how nature works.

Steps to a scientific investigation (scientific method):

  1. Purpose- what are we researching, scientific question

  2. Research- sources from internet, books, etc.

  3. Hypothesis- if and then statement

  4. Experiment- test out this if and then statement

  5. Analysis- analyze whether or not the hypothesis was correct by showing data

  6. Conclusion- sharing the results with others, summarize experiment, communicate results to other scientists

Last step is to report and evaluate findings by sharing your investigation with others.

Make sure to make observations before asking the scientific questions

The point of an experiment is to prove the statement made in a hypothesis

Making observations and inferences:

A scientific investigation typically begins with observations. These observations then turn into inferences, which is a guess that is made based on your observations.

Example: Picture of a moth;

  1. Moth has spots on wings

  2. Spots look like eyes

    Inferences- The eye spots make the moth look like the face of an owl, therefore, the moth uses these spots to protect themselves from predators

The question can then be formed: Why does the moth have owl-like eye spots?

Then, a hypothesis must be formed, but has to be based on your scientific knowledge. Previous knowledge for example can be known that there are birds that are afraid of animals, so they will avoid owls and try to eat moths.

Hypothesis: If a moth has owl eyes, then prey will avoid eating them

Now we have to test the hypothesis. We need to conduct a controlled experiment, but need to consider the variables:

  1. Independent variables

  2. Dependent Variables

  3. Constants

  4. Control groups

  5. Experimental groups

These variables will insure the most accurate experiment to be conducted.

Time to draw conclusions.

  • Does the evidence agree with your prediction and support hypothesis?

  • Does the evidence always prove that your hypothesis is true (necessarily)

  • Evidence from an experiment can support a hypothesis, but not always prove it.

Last step is to communicate the results

Attending seminars or being included in discussions in order to share your investigation will open the investigation up to new perspectives and new opinions.

New opinions can be made by researchers, for example, Whatif a researcher concluded that the hypothesis is not true, because maybe the experiment was done wrong. Whatif the birds were scared away because of the presence of the experimenter?

Variables

A variable is a thing that can change in an experiment

  • Dependent variables: The characteristics or attributes that you measure during your experiment

  • Independent variables: The variable that affects the dependent variable

Constants

In the experiment, some other factors that might affect the dependent variable must not change; known as constants

Control group and Experimental group

These are used to be able to compare a group that is not being experimented on to a group that is being experimented on, the group that the independent variables is applied to during the experiment. The control group does not receive any treatment or variables, solely for comparison.

Other types of scientific investigations-

  • A scientist who is studying the extinction of a species, they cannot do a controlled experiment, because it is based on the past.

  • Natural studies such as plant studies make it hard to control sunlight or water, which makes it har to know which affects plant growth most. In this case, statistics can be used instead since variables cannot be controlled.

  • You can also make a model to create a scientific investigations, this can make more complex investigations easier to understand if you can actually see the process.

Difference between Scientific theory and Scientific law

Scientific theory-

  • result of several works that tested a hypothesis

  • Supported b a great deal of evidence

  • Can be questioned or rejected in the future

Scientific Law-

  • statements based on repeated experiments or observations that describe a consistent natural phenomenon

  • Evidence that cannot be questioned and will always be true in the future

Bio-Inspiration (biomimicry or biomimetics)

  • Scientists often mimic natures ideas to solve human problems

  • For example, aircraft’s was created based on the way birds wings are structured

Page 1 – Atoms, Molecules and Water

  • Unit 1: The Chemical Basis of Life – Atoms, molecules and water

  • All life forms are composed of matter

    • Matter: anything that has mass or occupies space

    • In living organisms, matter may exit in 3 forms: solid, liquid, gas

  • Atom: the smallest functional unit of matter that builds all chemical substances and ultimately all organisms

    • Atom consists of: nucleus, protons, neutrons, and electrons

    • Electron is equal in magnitude to the proton (charge balance)

    • Nucleus is composed of protons and neutrons

    • The simplest atom in the world is hydrogen

  • What is a chemical element?

    • Each specific type of atom, such as nitrogen, hydrogen, oxygen, etc., is called an element

  • Parts of an atom

    • Electrons (e−): outside the nucleus, negatively charged

    • Proton (p+): positively charged

    • Neutrons (N0): particles with no charge

  • Note: Some minor typos in the transcript (e.g., proton vs. protein). The intended meaning is protons; atomic number equals the number of protons.

Page 2 – Atomic Structure and Electron Arrangement

  • An orbital (cloud-like shape) is the region where an electron is most likely found

  • Electrons occupy orbitals around an atom’s nucleus

    • Each orbital has a maximum capacity of 2 electrons

  • Electron shell concept:

    • Electrons have kinetic energy; the outer electron has higher energy

  • Each chemical element has a unique number of protons (atomic number, Z)

    • Example corrections from transcript: Hydrogen (H) has atomic number 1; typically 1 electron shell in its simplest form; atomic mass (average) ≈ 1.008 for hydrogen

  • Atomic number (Z) equals number of protons; Atomic mass is the mass of the nucleus (sum of protons and neutrons)

Page 3 – Periodic Table and Basic Atomic Facts

  • Periods (rows) in the periodic table indicate the number of electron shells (and correlate with atomic number)

  • Each element is located in a specific cell according to its atomic number (electrons)

  • Atoms have a small but measurable mass

  • Atomic mass is the mass of the atom’s nucleus (composed of neutrons and protons)

  • Atoms are the basic building blocks of matter and are incredibly small

  • They do have mass

  • Molecule: 2 or more atoms bonded together

  • Compound: a molecule composed of two or more different elements

    • Example: Pure sodium (Na) is a soft silvery-white metal

    • When sodium forms a compound with chlorine (Cl), NaCl is a white, relatively hard crystal that dissolves in water

    • This demonstrates that properties of a compound can be dramatically different from the properties of the constituent elements

  • Types of bonds (intro)

    • Single bond: two atoms share a pair of electrons (e.g., H–H)

    • Double bond: two atoms share two pairs of electrons

    • Triple bond: two atoms share three pairs of electrons (e.g., N≡N)

Page 4 – Electronegativity, Polar Covalent Bonds, and Polarity

  • Electronegativity: the ability of an atom to attract electrons in a bond with another atom

  • If two atoms with different electronegativities form a covalent bond, shared electrons are more likely to be closer to the nucleus of the more electronegative atom

    • Such bonds are polar covalent bonds

  • Example: Water (H2O) – oxygen is more electronegative than hydrogen

    • Shared electrons are drawn closer to the oxygen nucleus

    • Oxygen develops a partial negative charge; hydrogen atoms acquire partial positive charges

  • Unequal sharing of electrons gives the molecule polar attributes

  • Polar vs. nonpolar molecules – key distinctions: 1) Electronegativity difference

    • Polar molecules have uneven electron density; one end is more electronegative, creating partial charges (δ− and δ+)
      2) Solubility

    • Polar molecules tend to be soluble in polar solvents; nonpolar molecules tend to be soluble in nonpolar solvents
      3) Boiling and melting points

    • Polar molecules generally have higher boiling/melting points than nonpolar molecules of similar size due to stronger intermolecular forces
      4) [Transcript ends this section with an incomplete numeric point 4; the concept is covered above]

Page 5 – Hydrogen Bonding, Ionic Bonds, and Reactions

  • Hydrogen bonds (in water):

    • Oxygen is more electronegative than hydrogen, attracting electrons more strongly

    • In H2O, electrons in O–H covalent bonds are pulled toward oxygen

    • Oxygen in a water molecule bears a partial negative charge; hydrogens bear partial positive charges

  • Ionic bonds: attraction between positive and negative ions

    • Atoms are electrically neutral when they contain equal numbers of electrons and protons

    • Gaining or losing electrons creates ions with net electric charge

    • Ionic bonds form between two atoms when there is a transfer of electrons (typically between a metal and a nonmetal)

  • Transcript note: An isolated line mentions “An ionic bond occurs when a carbon binds to an ion,” which is technically inaccurate; ionic bonds form between ions, not specifically carbon-bound ions. The general concept is transferred here.

  • Covalent and Ionic bond (Lecture #3):

    • Covalent bond: electrons are shared between two nonmetals

    • Ionic bond: electrons are transferred from a metal to a nonmetal

  • Covalent vs. Ionic bonds summary (via transcript): Covalent = shared electrons; Ionic = transferred electrons, creation of ions

Page 6 – Chemical Reactions, Water, and Solutions

  • What happens in a chemical reaction?

    • Substances change into new substances by breaking and forming bonds

    • Step-by-step: breakup of starting substances, atom rearrangement, formation of new bonds

  • Properties of water (H2O):

    • Water is a liquid at standard conditions

    • Water has key roles in life processes (solvent, reactant, coolant, etc.)

  • Water as solvent: ionic and polar molecules dissolve readily in water; substances dissolved in a liquid are solutes; the liquid is the solvent

  • Aqueous solutions: solutions made with water

  • How a substance dissolves in water:

    • Covalent bonds in water are polar; oxygen is slightly negative, hydrogens slightly positive

    • A substance to dissolve must be electrically attracted to water molecules

  • Example: When NaCl is placed in water:

    • Water’s negative oxygen is attracted to Na+; the positive hydrogen is attracted to Cl−

  • NOTE: Generally, molecules with ionic and/or polar covalent bonds dissolve in water (hydrophilic). Nonpolar molecules (e.g., hydrocarbons) tend to be insoluble in water (hydrophobic). Lipids and oils are hydrophobic.

  • Hydrophilic vs. hydrophobic definitions and implications for solubility

  • Water performs many important tasks in living organisms (short list):

    • Participates in chemical reactions

    • Serves as a lubricant in saliva and feeding processes

    • Enables elimination of soluble wastes

    • Provides support

    • Evaporation helps animals cool down

Page 7 – Biomolecules (Biomolecules) and Basic Biology

  • Four major types of Biological Molecules (Biomolecules):

    • Carbohydrates

    • Amino acids (proteins)

    • Lipids

    • Nucleotides (DNA and RNA)

  • All living things are made of these four biomolecule types

  • Biomolecules are organic molecules (contain carbon); they form the basis of biological systems

  • Small molecules vs macromolecules:

    • Small molecules: e.g., hormones; primary and secondary metabolites

    • Macromolecules: proteins, nucleic acids, carbohydrates, lipids

  • Elements in biological systems: abundant elements include H, C, O, N; trace elements exist in smaller amounts

  • Cells contain four major biomolecule types that make up the majority of cell mass: lipids, nucleic acids, carbohydrates, proteins

Page 8 – Functional Groups of Biomolecules (Part I)

  • Biomolecule functional groups (examples): 1) Hydroxyl group (-OH)

    • Present in alcohols and carbohydrates

    • Imparts solubility in water and ability to form hydrogen bonds
      2) Carbonyl group (C=O)

    • Found in carbohydrates, lipids, and proteins

    • Essential in reactions such as condensation and hydrolysis

  • Note: The transcript lists the carbonyl group as “C=0,” which is a typographical error; the correct form is C=O

Page 9 – Functional Groups of Biomolecules (Part II)

  • 3) Carboxyl group (-COOH)

    • Acts as an acid by donating protons

  • 4) Amino group (-NH2)

    • Found in amino acids; can act as a base by accepting protons

  • 5) Phosphate group (-PO4)

    • Crucial in nucleic acids (DNA, RNA) and in energy storage/transfer (e.g., ATP)

  • 6) Sulfhydryl group (-SH)

    • Stabilizes protein structures via disulfide bonds

  • 7) Methyl group (-CH3)

    • Found in various biomolecules, including DNA; plays a role in gene expression regulation

  • 8) Ester group (-COO-)

    • Present in lipids; involved in energy storage and membrane structure

  • 9) Amide group (-CONH2)

    • Found in proteins; links amino acids via peptide bonds; also present in nucleic acids

Page 10 – Carbon, Carbohydrates, and Monosaccharides

  • Carbon:

    • Has two electron shells: first shell holds 2 electrons; outer shell holds 4 electrons

    • Therefore carbon can form up to four covalent bonds with other atoms

    • The simplest organic carbon molecule: methane, CH4 (one carbon atom bonded to four hydrogens)

  • Carbohydrates:

    • Essential in diet; provide energy; diverse roles in organisms

    • General formula: (extCH<em>2extO)</em>n( ext{CH}<em>2 ext{O})</em>n where n is the number of carbon atoms

    • Carbon, hydrogen, and oxygen ratio: 1:2:1

    • Monosaccharides: simplest sugars; glucose is a key example

    • Mono = one; saccharide = sugar

    • Most monosaccharide names end with the suffix -ose

    • Typically have 3 (triose), 5 (pentose), or 6 (hexose) carbon atoms

    • Glucose is the most important energy source for many organisms

    • In aqueous solutions, monosaccharides often exist in ring form

    • Energy released from glucose is used to form ATP (adenosine triphosphate)

  • Disaccharides: formed from two monosaccharides via dehydration synthesis

    • Common disaccharides: lactose, maltose, sucrose

    • Mechanism: dehydration reaction forms a glycosidic bond and releases a molecule of water

    • Note: The dehydration reaction is a condensation reaction that links monosaccharides

Page 11 – Polysaccharides and Their Roles

  • Monosaccharide units link to form polysaccharides via glycosidic bonds

  • Polysaccharide: many (poly) monosaccharides linked by covalent bonds; can be hundreds to thousands of units

  • Structures may be branched or unbranched

  • Examples include starch, glycogen, cellulose, chitin, pectin, and hyaluronic acid

  • Types by structure:

    • Homopolysaccharide (homoglycans): monomeric units are the same (e.g., starch, cellulose – glucose as the monomer)

    • Heteropolysaccharides (heteroglycans): composed of more than one type of monosaccharide (e.g., pectin, hyaluronic acid)

  • Types by function:

    • Storage polysaccharides: used for energy storage (e.g., starch in plants; glycogen in animals)

    • Glycogen is mainly stored in liver and muscles; broken down into glucose as needed

    • Structural polysaccharides: contribute to the structural components of cells (e.g., cellulose in plants, hemicellulose, chitin in exoskeletons)

Page 12 – Amino Acids and Proteins

  • Amino acids: the building blocks of proteins

    • Core structure: central carbon (alpha carbon) bonded to a hydrogen, amino group (-NH2), carboxyl group (-COOH), and a variable R-group

    • Some amino acids contain sulfur (e.g., methionine, cysteine)

  • Essential amino acids: cannot be synthesized by the organism and must be supplied in the diet

    • Examples listed (corrected): Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tyrosine, Valine

  • Non-essential amino acids: can be synthesized by the organism

    • Examples listed (corrected): Alanine, Arginine, Asparagine, Aspartic acid, Cysteine, Glutamic acid, Glutamine, Glycine, Proline, Selenocysteine, Serine, Tyrosine

  • Proteins (example): Hemoglobin

    • Most important protein in the body for oxygen transport from lungs to tissues; also carries carbon dioxide from tissues back to lungs

Page 13 – Nucleotides and Nucleic Acids

  • Nucleotide = 3 components

    • A phosphate group (one of the functional groups of nucleotides)

    • A nitrogenous base (adenine, cytosine, guanine, thymine [DNA], uracil [RNA])

    • A five-carbon sugar (pentose)

  • Purine bases: Adenine (A) and Guanine (G)

  • Pyrimidine bases: Cytosine (C), Thymine (T) [DNA], Uracil (U) [RNA]

  • Example nucleotide: Adenosine triphosphate (ATP) – energy-storage and energy-transfer molecule with 3 phosphate groups, a 5-carbon sugar, and an adenine base

  • Nucleic Acids

    • Polymers of nucleotides: Polynucleotides

    • DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)

    • Each nucleic acid is made from 4 nucleotides

    • Nucleotides are joined to form polymers (nucleic acids)

  • ATP is a key nucleotide used in energy transfer within cells

Page 14 – Fatty Acids and Lipids

  • Lipids: a fourth major group of biomolecules; hydrophobic

  • Fatty acids: long hydrocarbon chains with a terminal carboxyl group (-COOH); monomer of lipids

  • Types of fatty acids (as monomers): 1) Saturated fatty acids

    • No double bonds between carbon atoms

    • Typically solid at room temperature

    • Structure is linear (straight)

    • Example: butter
      2) Unsaturated fatty acids

    • One or more C=C double bonds

    • Typically liquid at room temperature

    • Double bonds create kinks/bends in the tails

    • Example: cholesterol-related fats; HDL (high-density lipids) often referred to as “good fat”

  • Lipids overview

    • Lipids are hydrophobic biomolecules that include fats, oils, and phospholipids

    • Roles: energy storage, structural components, signaling molecules in cells

    • They yield more than twice the energy per unit mass compared with carbohydrates

    • Major components of cell membranes; important in signaling

    • They participate in hormonal signaling and other cellular communications

Page 15 – Phospholipids and Cell Membranes

  • Phospholipids: key components of cell membranes

    • Hydrophilic (polar) head: glycerol + phosphate group (water-attracting)

    • Hydrophobic (non-polar) tails: two fatty acids (water-repelling)

    • Amphipathic nature: both hydrophobic and hydrophilic parts are essential for membrane formation

  • Phospholipids in membranes: phospholipid bilayer

    • Heads face outward toward water; tails face inward away from water

    • Forms the structural foundation of all biological membranes

  • Roles in membranes:

    • Fluidity: phospholipids allow movement and flexibility within the membrane

    • Selectivity: helps control what enters and exits the cell via bilayer and embedded proteins

Page 16 – Major Biological Polymers and Origin of Life (Overview)

  • Major kinds of biological polymers

    • Each molecule is formed from relatively few atoms, but organisms also contain macromolecules

    • Monomers and polymers:

    • Nucleic acids: nucleotide monomers; genetic activity and inheritance

    • Carbohydrates: monosaccharide monomers

    • Lipids: glycerol + fatty acids as monomers

    • Proteins: amino acids as monomers; structural roles, signaling, enzymes

  • Mammalian cells: proteins and lipids account for about 75% of dry mass

  • Origin of life on Earth – Objective (four overlapping stages)

    • Hypothesized to proceed via complex organic molecules assembling into life-like systems

  • Three important systems thought to be among the first to start life: proteins, RNA, DNA

    • Interactions among these systems contributed to the formation of living organisms

  • Four-stage hypothesis for the origin of life (as per transcript):

    • Step 1: Nucleotides and amino acids were produced before cells existed

    • Step 2: Nucleotides polymerized to form RNA and/or DNA; amino acids polymerized into proteins

    • Step 3: Polymers became enclosed in membranes

    • Step 4: Membrane-enclosed polymers acquired cellular properties

  • Stepwise outline in the transcript (summarized):

    • Abiotic synthesis of organic monomers first, followed by polymerization to form polymers and pre-cells

    • Formation of a membrane-enclosed compartment with self-replicating molecules

    • Subsequent development toward cellular properties within membrane-bound compartments

  • Notes and clarifications

    • The transcript contains some spelling and typographical errors (e.g., “proteins” where “protons” is meant, “C=0” for carbonyl, etc.). Where explicit, corrections are noted in parentheses to aid understanding while preserving the transcript’s sequencing.

    • Key equations/formulas mentioned or implied in the transcript are included in LaTeX format where relevant, for example:

    • Carbohydrate general formula: (extCH<em>2extO)</em>n( ext{CH}<em>2 ext{O})</em>n

    • Water (dissolution) context: H2OH_2O

    • Glucose energy conversion to ATP: (described conceptually; ATP is the energy currency of the cell)

    • Dehydration synthesis for glycosidic bond formation:
      extMonosaccharide<em>1+extMonosaccharide</em>2<br>ightarrowextDisaccharide+H2Oext{Monosaccharide}<em>1 + ext{Monosaccharide}</em>2 <br>ightarrow ext{Disaccharide} + H_2O

    • General polysaccharide structure: ext{Polysaccharide}= ext{(monosaccharide)}_n ext{ (n > 2)}

  • Summary of key themes across the transcript

    • Matter, atoms, and the structure of atoms underpin all biological substances

    • Chemical bonds (covalent, ionic, hydrogen) and electronegativity drive molecule properties and interactions (polarity, solubility, bonding patterns)

    • Water’s unique properties support life via solvent capabilities, hydrogen bonding, and temperature regulation

    • Biomolecules (carbohydrates, lipids, proteins, nucleic acids) form the core macromolecular infrastructure of life, with specific functional groups dictating chemical behavior

    • Membranes (phospholipid bilayers) provide compartmentalization, regulate transport, and support signaling

    • The origin of life is explored through staged hypotheses involving monomers, polymers, membranes, and emergent cellular properties, with proteins, RNA, and DNA playing central roles in early biochemistry