BSC 2010

Attributes of living organisms…

• A common set of chemical parts (nucleic acids such as DNA and amino acids that make up proteins)

• All composed of similar structures (such as cells enclosed in membranes)

• Depend on interactions between structurally complex parts to maintain the living state

• Contain genetic information that codes for proteins

• Convert molecules obtained from their environment into new biological molecules

• Extract energy from the environment and use it to carry out life functions

• Replicate their genetic information in the same way

• Have a fundamental set of genes

• Evolve through gradual changes in their genetic information (mutations due to external or internal forces)

Viruses

• Contain genetic information, mutate, and evolve

• Considered living things by most biologists, but they are not composed of cells and cannot carry out functions on their own

Nucleic acids

molecules that can reproduce themselves and contain the information for synthesis of proteins

Prokaryotes

first organisms, made up of single cells containing genetic material and other structures enclosed in a membrane

Photosynthesis

a set of chemical reactions that transforms sunlight energy into chemical bond energy

Aerobic metabolism

•  a set of chemical reactions that releases energy from molecules using O₂

Anaerobic metabolism

• set of reactions that extracts energy without using O₂

Eukaryotes

cells with a nucleus

Endosymbiosis

(living inside another): a process by which certain organelles were created. Smaller cells were ingested by larger cells

Ex. Mitochondria, Chloroplasts

Cellular specialization:

cells in groups are able to specialize (perform different functions)

• Some cells might specialize in reproduction, nutrient absorption, etc.

Two kinds of research

• Discovery-based research

• Hypothesis-driven research

Discovery-based research

1. analysis of lots of collected data to find new patterns and generate questions or ideas

• No endpoint/question to the research

Hypothesis-driven research

testing answers to a specific question using the scientific method

• Scientific Method

  1. Make observations

  2. Ask a question, usually using why or how?

  3. Formulate possible answers to the question (alternative hypotheses)

  4. Make predictions: what will be true if my prediction is correct?

  5. Design and conduct an experiment

     1. Use statistical tests to calculate probability of observed data if hypothesis is correct

        a. If results support hypothesis, then repeat the experiment and ask new questions

        b. If results do not support the hypothesis, reexamine the experiment for uncontrolled variables and conduct the experiment again. If results are still not supporting hypothesis, then revise the hypothesis

All living and nonliving matter is composed of…

atoms!

Element (what is an element, how many, which are most abundant)

substance that consists of one type of atom

• 92 naturally occurring elements

• CHON (carbon, hydrogen, oxygen, and nitrogen) are the most abundant elements in living systems

Structure of an atom

• Protons (+)

• Neutrons (neutral = no charge)

• Electrons (-)

Atomic mass is measured in

measured in daltons/amu (1 dalton = mass of 1 proton or neutron)

• Mass of electrons is so low that it is ignored when calculating the atomic mass

Atomic number

elements are identified by the number of protons (atomic number)

Isotope

versions of elements with different numbers of neutrons

Mass number

 total number of protons and neutrons

Columns on periodic table

• have the same number of electrons in their valence shell (similar reactive properties)

Orbitals

• Every shell has an s orbital (one pair of electrons)

• Shells after the first shell also have a p orbital (3 pairs of electrons)

• Lower level shells have less energy than higher level shells

• s orbitals are lower energy than p orbitals

• Atoms with unfilled outer shells undergo chemical reactions 

  • Reaction = gaining or losing electrons

  • Atoms are stable when their valence shell is full

Octet rule

atoms with at least two electron shells form stable bonds when they have 8 electrons in their valence shell

Electronegativity

an atom’s tendency to attract electrons from another atom

• More electrons in the outermost shell = higher EN

• Electrons closer to the nucleus have higher EN

• EN increases from the bottom left of the periodic table (lowest EN) to top right (highest EN)

Ionic bonds

• High EN atom steals electron(s) from low EN atom to form charged particles

• The force of attraction between these charged particles is called an ionic bond

• Cation (positively charged atom)

• Anion (negatively charged atom)

• Salts: molecules held together by ionic bonds

Covalent bonds

• Each atom counts those electrons as part of itself

• Covalent bonds are very strong 

• Occur between similar EN atoms

• Nonpolar covalent: equally shared e

• Polar covalent: unequally shared e

Dipole-dipole interactions

electrostatic attractions that occur between polar molecules, where the positive end of one molecule is attracted to the negative end of another

Hydrogen bonds

Van der Waals interactions

• Random attractions due to movement of electrons creating temporary dipoles

• Occurs within all molecules (polar and nonpolar)

Stability of a molecule is closely associated with

 its level of energy

• Less stable molecules have higher energy and are converted during chemical reactions into lower energy, more stable molecules

Energy

capacity to produce a change

Kinetic energy

energy of movement (includes thermal, sound, and electromagnetic energy

Potential energy

stored energy (includes gravitational, elastic, chemical bond, and nuclear energy)

All changes in the universe involve….

Energy transformation

Laws of thermodynamics

1. Energy cannot be created or destroyed (Total amount of energy in a closed system remains constant)

2. With each energy transformation, entropy increases

• Entropy: measure of disorder, how spread out energy is, how much of the energy is unusable

  • Increase in entropy implies that energy is becoming less concentrated and less useable, which is the natural tendency for energy 

  • After each energy transformation, some energy in the system becomes unavailable to do work

  • Only an input of energy can impose order on a system (ex. hot tea kettle cools down on its own but requires input of energy to be heated)

• Second law explains why some reactions occur spontaneously and others do not

  • If change in entropy is negative, rxn occurs spontaneously

  • If change in entropy is positive, rxn requires energy

Chemical reaction

occurs when atoms combine or change their bonding partners

• Ex: hydrolysis: molecule interacts with water, leading to breakdown into simpler molecules

Hydrolysis

molecule interacts with water, leading to breakdown into simpler molecules

Hydrolysis is exergonic and produces molecules with lower potential energy (stronger bonds)

Free energy

 amount of energy available to do work

(ΔG) = total energy change of a reaction

Exergonic reaction

negative ΔG, the reaction releases energy (chemical energy stored in bonds of the products is less than the chemical energy stored in the bonds of reactants)

Endergonic reaction

positive ΔG, the reaction requires energy to occur (bonds of product molecules contain more energy than bonds of reactant molecules)

Condensation reaction

two molecules combine to form a larger molecule, producing water as a byproduct

• Opposite of hydrolysis

• Condensation reactions are endergonic and produce larger molecules with more potential energy (weaker bonds)

Activation energy

• the energy that must be supplied for a reaction to begin

  • Energy to break the covalent bonds of reactants (before products can be formed, releasing energy)

  • both exergonic (spontaneous) and endergonic (non-spontaneous) require additional energy to initial the reaction

Reaction rate

• measures how fast products are made per unit of time

Factors that affect reaction rate

1. Activation energy

• If collision has sufficient energy to reach activation energy, then reaction can occur

• Lower activation energy → reaction is more likely to occur

2. Temperature

• Higher temperature increases number of collisions and energy of collisions, making it more likely that collision reaches the activation energy

3. Concentration

• Higher concentration = more likely to collide

Equilibrium

the state in which the rate of forward and reverse reactions is relatively equal and so the relative concentrations of reactants and products will not change

4 basic categories of molecules

• Carbohydrates

• Lipids

• Proteins

• Nucleic acids

All of these 4 biomolecules have carbon backbones

Functional groups

small clusters of atoms that influence the properties and reactivities of molecules

Methyl

Hydroxyl

Sulfhydryl

Aldehyde

Keto

Carboxyl

Amino

Phosphate

Macromolecules (definition and types)

large molecules formed by covalent bonds between smaller molecules

• Carbohydrates, lipids, nucleic acids, proteins

Polymers (definition and types)

Large molecules formed by covalent bonds between smaller molecules called monomers

• Carbohydrates, nucleic acids, and proteins are polymers, but lipids are not

Monomers

• building blocks of large macromolecules, also called residues

How are polymers created and broken down

• Created by condensation reaction, broken down by hydrolysis (reactions involving water)

Lipids (definition, composition, function)

structurally and functionally diverse group of compounds defined by their insolubility in water

• Made of hydrocarbons

• Hydrophobic because they have nonpolar covalent bonds (C-H and C-C)

• Store energy in C-C and C-H bonds

• Plays a structural role in cell membranes

Important property of lipids

• melting temperature

  • Melting point is determined by their size and how closely the molecules pack together

    • Larger lipid molecules and molecules that can pack tightly together have higher melting temperatures because there are more Van der Waals interactions

    • Held together by van der Waals interactions and the hydrophobic effect (when in water)

White fat

serves to store energy and provide thermal insulation that helps regulate body temperature

Brown fat

gets its color from iron-rich mitochondria and plays an important role in thermoregulation, particularly in infants

Triglycerides

(simple lipids): contains 3 fatty acid molecules and one glycerol molecule, are hydrophobic and nonpolar

Fatty acid

consists of a long nonpolar hydrocarbon chain with a terminal polar carboxyl group (COOH)

Glycerol

3-carbon molecule with 3 hydroxyl groups (OH)

Fatty acids and glycerols are combined by

• 3 condensation reactions → connected by ester bonds

  • Ester bond O-C=O

Triglycerides are excellent stores for

 chemical-bond energy

2 classifications of triglycerides

1. Fats: solid at room temperature

2. Oils: liquid at room temperature

Fatty acid chains can vary in…

length and structure

Composition of fatty acid chains

 amphipathic: have a hydrophilic end (COOH) and long hydrophobic tail (many hydrocarbons connected to eachother)

Saturated fatty acids

• all the bonds between the carbon atoms in hydrocarbon chain and single bonds because carbons are saturated with hydrogen atoms

• Relatively straight molecules and therefore are able to pack closely together, creating a higher melting point

• Usually solid at room temperature

Unsaturated fatty acids

• hydrocarbon chain has one or more double bonds between carbons atoms because carbons are not fully saturated w/ hydrogen

• The double bonds create kinks that prevent unsaturated molecules from packing together tightly → lower melting temperature and are usually liquid at room temperature

Phospholipids

similar to fatty acids but a charged phosphate molecule replaces one of the fatty acids

• Also amphipathic

• Creates a phospholipid bilayer in water, which is the substance of cell membranes

Lipoproteins

Phospholipids can form single-layer spherical structure that have hydrophobic interiors and hydrophilic exteriors which are used for transporting lipids in aqueous solutions

Carotenoids

 lipids that can absorb energy from particular wavelengths of light

Steroids

important lipids in plants and animals, Examples: Cholesterol, Estrogen

Biological roles of carbohydrates (4)

• Source of stored energy

• Transport stored energy within complex organisms

• Structural molecules that give many organisms their shape

• Recognition or signaling molecules that can trigger specific biological responses

Carbohydrates

 large group of molecules that have similar composition, but differ in several important properties

General formula of carbohydrates

 C_m(H₂O)_n

Simple sugars

carbohydrates with 12 or fewer carbons

Most carbons in carbohydrates are attached to…

hydroxyl groups

Monosaccharides

• Simple carbohydrates

• Usually in a ring form (sometimes linear)

• Consist of 5 or 6 carbons atoms (either called pentoses or hexoses)

• 3D structures of polymers depends on the isomers of the simple sugars

• Different monosaccharides often have the same chemical formula and are structural or stereoisomers

Disaccharides

composed of two monosaccharides joined in a condensation reaction

Glycosidic linkage

bond that connects monosaccharides

The main carbohydrates in cells and readily break down to release energy

Monosaccharides and disaccharides

Oligosaccharides

carbohydrates composed of 3-10 monosaccharides joined by glycosidic bonds

• Also can have functional groups which give them additional properties

• Often covalently bonded to proteins or lipids, where they serve as recognition signals affecting the molecule’s function and solubility

Polysaccharides

large polymers of hundreds to thousands of monosaccharides connected by glycosidic bonds

2 forms of polysaccharides

1. Linear chains of monomers (attached via 1,4 glycosidic bonds)

2. Branched chains of monomers (from 1,6 glycosidic bonds)

Linear polysaccharides

Linear chains can align closely and form hydrogen bonds w/ neighboring chains → form dense sheets or strong fibers that are resistant to breaking

• Ex. cellulose: component of plant cell walls (most abundant carbon compound on the planet)

• Ex. chitin: arthropod skeletons

Branched polysaccharides

• Ex. Starches: principal energy storage compound of plants

• Ex. Glycogen: principal energy storage in animals, fungi, and bacteria

  • Both water-insoluble

  • Note: starches and glycogen contain both types of bonds

  • Energy is stored as glycogen instead of glucose because high glucose levels cause water to enter cells

Nucleic acids

 polymers that store, transmit, and express genetic (hereditary) information

2 types of nucleic acids

• DNA (deoxyribonucleic acid)

• RNA (ribonucleic acids)

Nucleotide

building blocks (monomers) of nucleic acids

3 components of nucleotides

1. Monosaccharide (pentose ribose or deoxyribose)

2. Nitrogen-containing base

3. One to three phosphate groups

Nucleoside vs. nucleotide

Nucleosides have no phosphate

Nucleotide is a nucleoside plus 1-3 phosphate groups

Types of bases in nucleic acids

• Pyrimidine: single-ring structure

• Purine: fused double-ring structure

Purines

• Pure as gold (adenine and guanine)

Pyrimidines

• Cytosine, Thymine, Uracil

Major differences between DNA and RNA monomers and strands

1. The monosaccharide in DNA is deoxyribose, while in RNA it is ribose

2. DNA has nucleotides CTAG (cytosine, thymine, adenine, guanine), while RNA replaces thymine with uracil

3. RNA is usually single stranded, while DNA is double-stranded