Proteins, DNA & RNA

• To be considered alive, something must consist of cells, be able to replicate, process information, acquire and use energy, and evolve.
• Experimental scientists ask questions that can be answered by measuring things and collecting data.
• Science involves formulating hypotheses and finding evidence that supports or conflicts with those hypotheses.

Terminology

Theory

• A broad explanation for patterns.

Hypothesis

• A testable statement that explains something observed.

Experiment

• Allows researchers to test a hypothesis.

Prediction

• A measurable or observable result that must be correct if a hypothesis is valid.

Hypothesis Testing

• There are two steps in hypothesis testing:
  • Precisely state the hypothesis and list its predictions
  • Design an observation or experiment to test those predictions

Characteristics of Good Experiment Design

• Including a control group, maintaining constant experimental conditions, repeating the test, and using a large sample size are all critical.

Cells

• Cell theory states all organisms consist of cells, cells spontaneously appear, and cells come from preexisting cells.
• All cells and organisms are thought to be related by a common ancestry.

Evolution

• Evolution is caused by natural selection
• all species are related by common ancestry
• species' characteristics can be modified from generation to generation, resulting in descent with modification

Evolution

• A change in population characteristics over time.

Natural Selection

• Explains the process of evolution.

Population

• A group of individuals of the same species living in the same area at the same time (millions of years).

Natural Selection Requirements

• Individuals must vary in heritable characteristics

• Certain heritable traits must help individuals survive better and reproduce more than others in a particular environment.

• Evolutionary change occurs because beneficial heritable traits lead to increased offspring production

• these traits become more common in the population over time causing a shift the overall characteristic

Natural Selection

• Acts on individuals.

Evolutionary Change

• Occurs in populations.
• Cells are related hence all organisms are also related
• Phylogenetic tress are used to show this

Tree of Life

• Eukaryotes have a nucleus.
• Prokaryotes do not have a nucleus.
• Bacteria and archaea are examples of prokaryotes.

Parts of an Atom

• Molecules consist of two or more atoms held together by covalent bonds.
• Atoms possess protons (+ charge), electrons (- charge), and neutrons (no charge).
• Mass number = # of protons + # of neutrons
• Atomic number = # of protons; defines the atom.

Isotopes

• Average mass of all isotopes for any element.

Covalent Bonds

• Covalent Bonds have two atoms sharing one or more pairs of electrons.
• Atoms want to have 8 electrons in their outer valence (outermost) shell.

Nonpolar Covalent Bonds

• Electrons are shared equally between two atoms

Polar Covalent Bonds

• Electrons are shared unequally between atoms.
• Electronegativity is how strongly an atom pulls shared electrons toward the nuclei in a bond
  • Controlled by the number of protons in the nucleus and the distance between the nucleus and the valence shell

Ionic Bonds

• Electrons are completely transferred from one atom to another.
• Atoms can gain or lose electrons to fill their outer shell creating Ions
  • Cations are positively charged ions that lose electrons
  • Anions are negatively charged ions that gain electrons

Hydrogen Bonds

• Weak interactions between two molecules or different parts of the same molecule.
• Result from the attraction between a hydrogen atom with a partial positive charge and another atom negatively charged.
• Single bonds involve one pair of electrons.
• Double bonds involve two pairs of electrons.
• Atoms prefer to have a filled outer shell (8 electrons) and will react accordingly
• Electrons are not always shared equally, shifting characteristics.

Water

• The rule of 2 states there will be 2 e- in an s orbital in the first circle
• The rule of 8 states there will be 8 e- in a p orbital
• Life is based on water as its an excellent solvent
• A solute dissolved into a solvent forms solution
• Water is polar, small in size, has a bent shape, highly polar covalent bonds, and overall polarity.
• Oxygen has a partial negative charge, and hydrogen has a partial positive charge.
• Hydrogen bonds can form between water molecules and polar solutes.

Hydrophilic

• Likes water.
• Ions and polar molecules stay in solution due to the reaction with water's partial charges.

Hydrogen Bonding

• Enables almost any charged or polar molecules to dissolve in water.
• Water can therefore dissolve polar and charged molecules.
• In diagrams of atoms, mass number = protons + neutrons and atomic number = protons
• A filled outer shell has 4 pairs of electrons/8 total electrons and is stable

Ion Formation and Ionic Bonding

• Atoms that lose electrons are positively charged.
• Atoms that gain electrons are negatively charged.
• Carbon and hydrogen share electrons equally.
• Oxygen and hydrogen result in hydrogen liking the electron more (electronegativity).
• "Charged" refers to lost or gained electrons.
• Electrons are pulled towards oxygen making it a polar molcule.
• Water molecules have hydrogen bonds and hold onto each other to stay together.

Non-polar

• Hydrophobic.

Polar and Charged

• Hydrophilic.
• NaCl and sugar dissolves in water
• Carbon and hydrogen are hydrophobic.
• Hydrophobic molecules do not dissolve in water

Cohesion, Adhesion, and Surface Tension

• Water interacts with its surroundings.
  • Adhesion is attraction between unlike molecules.
  • Cohesion is attraction between like molecules.
  • Surface tension is caused by cohesion at the surface.
• Water is more dense as a liquid than as a solid becoming is less dense so it will rise

Properties of Water

• Density: water is more dense as a liquid than a solid, and ice is less dense so it rises.
• High Specific Heat: energy is needed to raise the temperature of solutions.
• Hugh heat of Vaporization - energy needed to convert liquid to a gas

Water in Acid-Base Reactions

• Water molecules dissociate into a hydrogen ion (H+) and a hydroxide ion.
  • Acids add acid, increasing proton concentration.
  • Bases add base, decreasing proton concentration.
• Carbon is versatile with four valence electrons
• Carbons will therefore always form 4 covalent bonds

Carbon and Macromolecules

• Small molecular structures can come together to make bigger molecules
• Proteins, Carbohydrates, Nucleic acids, and Lipids
• Amino acids are building blocks of proteins
• A non ionized form of amino acids contains R groups which are also charged, nonpolar and polar

What Do Proteins Look Like?

• Polymers, or chains of amino acids
• Every part of the amino acid chain will change to form different proteins
• How to determine of an amino acid and R group is non polar/polar or charged
  • Polar: Contains oxygen
  • Nonpolar: contains carbon and hydrogen -Charged: Contains a charge
• Structure determines its functions
• Proteins have 3-dimensional structure with different protein stucture for different functions
• Polymerzation: Individual units into a combined structure

What Do Proteins Do?

• Proteins are crucial to cells
  • Catalysis: Enzymes speed up chemical reactions
  • Defense: Antibodies and complement proteins attack pathogens
  • Movement: Motor and contractile proteins move the cell or molecules
  • Signaling: Proteins convey signals between cells
  • Structure: Structural transport proteins carry materials; membrane proteins control molecular movement into and out of the cells

DNA & RNA

Purpose

• Transmission of information.

Phosphate

• Negative charge
• High energy structure
• Example is ATP
• Hydrophilic

Sugar

• Polarity (See OH groups).
• Numbering systems
• Compare ribose to deoxyribose
• Hydrophilic.

Base

• Purines have 2 rings
• Pyrimidines have 1 ring
• Site of sugar link
• Possible H bonding sites
• Hydrophobic
• Bases can form hydrogen bonds with other bonds
• Nucleotides polymerize to form DNA/RNA through covalent charges.
• A polymer has 5'-3' Orientation
• Base structure controlled by (Size/Polarity)
• Each strand is held together by covalent bonds

Nature of DNA Secondary Structure

• DNA follows two rules:
  • The total number of purines and pyrimidenes is constant
  • The number of A and T are equivalent and so too of C and G

DNA Structure

• Double helix
• Hydrogen bonds (G-C three bonds, A-T two bonds).
• Hydrophobic relationships
• Sugar and phosphorus are on the outside
• 5' to 3' on one side and 5' to 3'
• The bases are hidden in the middle because they are hydrophobic
• Hydrophilic and hydrophobic CH bonds
• Covalent attachments between nucleotides and phosphates

DNA

• Associated between strands
• Hydrogen bonds

Carbohydrates

Basic Definitions

• O-H bonds are polar and oxygen is negative.
• H is positive.

Polysaccharides

• Sugar polymers

Types of Polysaccharides

• Plants store sugar as starch, while animals store sugar as glycogen
• Cellulose is in plant-based cells
• Chitin is present in fungi cells
• Peptidoglycan is for bacterial cell walls

Carbohydrates Role in Cell Identity

Display information on the outer surface of cells, like Gycorportoes (proteins with carbohydrates). Carbohydrates store and provide chemical energy.

Lipids

• Carbon-containing compounds found in organisms
• Nonpolar and hydrophobic, possessing C and H bonds, with squiggly or straight lines
• Amphipathic; have both hydrophilic and hydrophobic parts.
• The three types of lipids found in cells include fats, steroids, and phospholipids
• Lipids have an -polar/charged head group and -non polar straight tail
• Phospholipids cant dissolve in water forming Micelles where water is used inside and outside of the cells

Phospholipid Bilayers

• Inside are hydrophobic
• The head/outside is hydrophilic
• Phospholipid bilayers have selectively permeable characteristics of lipid bilayers
• Small, nonpolar molecules cross the bilayer more easily.
• Polar molecules move slower.
• Charged molecules require the help of protein to facilitate movement
• More double bonds offer for more fluid

Affects on Membrane Permeability

• Number of double bonds in the tail.
• Tail length.
• Number of cholesterol molecules.
• Temperature.
• Unsaturated fatty acids
• • Double bonds form kinks, stopping the ability to compact and don't allow free rotation
• The more double bonds, the more fluid

Lipid Bilayers

• Lipids in constant lateral motion rarely flip to the other side of the bilayer with lipids stuck on the far side
• Movement is by simple diffusion where every molecule simply moves randomly

Moving Solutes Across Lipid Bilayers

• Materials move across the cell's membrane using:
  • Passive transport - which does not require energy
  • Active transport - which requires energy to move substances

Solute movement:

• There are solutes that include thermal energy and are inconstant with random motion
• Molecules move from high to low solute concentration.
• Equilibrium happens very fast: there are only small uncharged molecules - Equilibrium - molecules or ions distribution throughout a solution

Osmosis

• Where water moves quickly across the lipid bilayers a special case of diffusion is called osmosis
• Water flows from low to high concentration - so higher solutes reduce the overall amount of water

Test your knowledge of protein structure, function, and the roles of DNA and RNA. Questions cover amino acid sequences, R groups, nucleotide bonds, and Chargaff's rules. Explore the fundamental concepts of molecular biology.