Bio Unit 1 P1: Chemistry and Cells

Biology

The scientific study of life.

Five Unifying Themed of Biology

-Organization

-Information

-Energy and Matter

-Interactions

-Evolution

Reductionism

A scientific approach that reduces complex systems to simpler components that are more manageable to study.

Emergent Properties

Novel properties in levels of biological organization that are absent from the preceding level.

Systems Biology

The exploration of the network of interactions that u derline the emergent Properties of a system.

10 Levels of Biological Organization

-Biosphere (all life on earth and all places where life exists)

-Evosystem (all living things in a particular area and all nonliving components with which they interact)

-Community (all organisms inhabiting an ecosystem)

-Population (all individuals of a specific species within a specific area)

-Organism (an individual living thing)

-Organ (a body part made up of tissues to perform a specific function in the body)

-Tissue (a group of cells that work together to perform a specialized function)

-Cell (life's fundamental and smallest living unit)

-Organelle (the functional components present int cells)

-Molecule (a chemical structure consisting of two or more atoms)

DNA

Deoxyribonucleic acid. The genetic material carried by chromosomes.

Genes

Each section of the DNA carried by a chromosome. Genes are units of inheritance.

Gene Expression

The entire process by which the information in a gene directs the production of a cellular product.

Genome

The entire array of genetic instructions that an organism inherits.

Genomics

Field of study where researchets study while sets of genes in one or more organisms.

Proteonomics

The study of sets of proteins and their properties.

Climate Change

A directional change to the global climate that lasts for three decades or more.

Evolution

A process of biological change in which species accumulate differences from their ancestors as they adapt to different environments over time.

Estimated number of species

10 million to 100 million

Three Domains of Life

-Domain Bacteria (consists of prokaryotic organisms, bacteria being the most widespread kind)

-Domain Archaea (prokaryotes made to live in Earth's extreme environments)

-Domain Eukarya (all eukaryotic organisms, separated into 3 kingdoms: kingdoms plantae, fungi, and animalia)

Decent with Modification

The accumulation of different traits from ancestors as a species adapts to a different environment over time. Natural Selection is a primary cause for this.

Theory of Natural Selection

Individuals inherit traits that are better suited to the local environment and are more likely to survive and reproduce because of these traits. Over generations, a higher and higher proportion of individuals in a population will have the advantageous trait.

Three related observations: individuals vary in traits that appear to be inherited, populations produce more offspring than can survive, and species are suited to their environments.

Process of Inquiry

The search for information and explanations to natural phenomena. Includes making observations, forming logical explanations ( hypotheses) an testing them.

Data

Recorded observations

Inductive vs Deductive Reasoning

Inductive: from specific observations, we derive generalizations.

Deductive: From generalizations, we extrapolate specific results we expect.

Controlled Experiment

An experiment that is designed to compare an experimental group with a control group.

Variables

A feature or quantity that varies in an experiment.

They can either be dependant, or independent.

Theory

A broader hypothesis that results in many new testable hypotheses, and is supported by a large body of evidence. They will either be thrown out or altered if new data comes out that doesn't fit the theory.

Matter

Anything that takes up space and has mass.

Element

A substance that cannot be broken down into other substances by chemical reactions.

Compound

A substance consisting of two or more different elements combined in a fixed ratio.

Essential Elements

Elements that an organism needs to live a healthy life and reproduce.

Humans need around 25 elements.

Which elements make up 96% of all living matter?

Oxygen, Carbon, Hydrogen, and Nitrogen

Trace Elements

Elements required by an organism, but only in minute quantities.

Atom

The smallest unit of matter that still retains the properties of an element.

Three most important subatomic particles

Protons, with one unit of positive charge

Electrons, with one unit of negative charge

Neutrons, with neutral charge.

Atomic Nucleus

The center of an atom where protons and neutrons are packed together. Protons give it a positive charge.

Dalton

A unit of measurement for atoms and subatomic particles.

How to read an element

Mass number: the number of protons+neutrons

Atomic number: the number of protons

Number of electrons: mass number- atomic number

Isotope

A different form of an element while staying the same element. Occurs from differing numbers of neutrons.

A radioactive isotope is one where the nucleus spontaneously decays, giving off particles and energy. This can lead to a change in protons, changing the element.

Energy and Potential Energy

Energy: The capacity to cause change.

Potential Energy: Energy that matter possesses because of its location or structure.

Electron Shells

The different energy levels of electrons. When an electron absorbs energy, it moved a shell further from the nucleus.

Valence Electrons and the Valence Shell

Valence electron: electrons on the outermost shell, called the valence shell.

Chemical Bond

Atoms with incomplete valence shells interact with certain other atoms to share or transfer electrons, completing the valence shell. The atoms remain close, held together in a chemical Bond.

Covalent Bond

The sharing of a pair of valence Electrons by two atoms.

Two or more atoms held together by a covalent Bond is a molecule.

Valence

The bonding capacity of an atom, determined by the number of electrons required to complete the atoms valence shell.

Electronegativity

The attraction of a particular atom for the electrons of a covalent Bond. The stronger the electronegativity, the stronger it pulls things inwards.

Nonpolar vs Polar covalent bonds

Nonpolar: a covalent Bond between two atoms of the same element, where electrons are shared equally because both have the same electronegativity.

Polar: an atom bonded to a more electronegative atom, where the bond is not whated equally.

Ionic Bonds

When electronegativity is so unequal, the most electronegative atom strips an electron completely away from the other. This results in two ions. A positivity charged ion is a cation, while a negatively charged ion is an anion. The two attract eachother, forming an ionic bond.

These bonds form ionic compounds or salts.

Hydrogen bond

The noncovalent attraction between hydrogen and an electronegative atom. In living cells, the partners are usually oxygen or nitrogen.

Van der Waals Interaction

Ever-changing regions of positive and negative charge that allow all atoms and molecules to stick to eachother. Many occurring simultaneously is what allows geckos to stick to walls.

Chemical reaction

The making and breaking of chemical bonds, leading to changes in the composition of matter.

Chemical reaction formuals

The reactants are the starting materials, while the products are the resulting materials.

Some reactions are reverse able, shown by the arrow going both ways.

Chemical Equilibrium

The point at which the reactions offset one another exactly. Reactions are still occuring in both directions, but with no effect on the concentrations of reactants and products.

Cohesion

Hydrogen bonds holding a substance together.

Adhesion

The clinging of one substance to another.

Surface Tension

A measure of how difficult it is to stretch or break the surface of a liquid.

Kinetic Energy

The energy of movement.

Thermal Energy vs Temperature vs Heat

Thermal Energy: the total kinetic energy associated with the random movement of molecules.

Temperature: The average kinetic energy of molecules in a body of matter, regardless of volume,.

Heat: thermal energy in transfer from one body of matter to another.

calories (c )

The amount of heat needed to raise 1g of water 1°C, or the amount of heat releases when 1g of water cools by 1°C.

A Calorie (or kilocalorie) is 1000 calories.

Specific Heat

The amount of heat that must be absorbed or lost for 1g of that substance to change its temperate by 1°C.

Heat of Vaporization

The quantity of heat a liquid must absorb for 1g of it to be converted from the liquid to the gaseous state.

Evaporative Cooling

The surface of a liquid remaining and cooling down as it evaporates. It occurs because the hottest molecules are the ones most likely to leave as gas.

Solution

A liquid that is a completely homogeneous mixture of two or more substances.

The dissolving agent is the solventz while the substance being dissolved is the solute.

And aqueous solution is one with water was the solvent.

Hydrophilic vs Hydrophobic

Hydrophilic: any substance that has an affinity for water.

Hydrophobic: substances that are nonionic and nonpolar, repelling water.

Mole (mol)

6.02•10²³ aka Avagadro’s number.

Acid vs Base

Acid: A substance that increases the hydrogen ion concentration of a solution.

Base: A substance that reduces the hydrogen ion concentration of a solution.

pH of a Solution

The negative logarithm (base 10) of the hydrogen ion concentration.

Buffer

A substance that minimizes changes in the concentration of H+ and OH- in a solution. It does so by accepting hydrogen ions from the solution when they are in excess, and donating them when they have been depleted.

Organic Compound

A carbon-based compound formed when carbon bonds with up to four other atoms.

Hydrocarbon

Organic molecules consisting only of carbon and hydrogen.

Isomer

Compounds that have the same number of atoms of the same elements but different structures and therefore different properties.

Structural isomers differ in the covalent arrangements of their atoms.

Cis-trans isomer

Where carbons have covalent bonds to the same atoms, but the atoms differ in their spacial arrangements due to the inflexibility of double bonds.

Enatiomer

Isomers that are mirror images of each other that differ in shape due to the presence of asymmetric carbon, one that is attached to four different atoms or groups of atoms.

Functional Groups

Ones to know: hydroxyl, carbonyl, carboxyl, animo, sulfydryl, phosphate, and methyl groups.

First six are functional groups. All except sulfahydryl are hydrophilic. The methyl group is not reactive, but instead serves as a tag on molecules.

Macromolecules

Large carbohydrates, proteins, and nucleic acids. Called such for theit huge size and are all polymers.

Polymer

A long molecule consisting of many similar identical building blocks linked by covalent bonds. The repeating units are smaller molecules called monomers.

Enzymes

Specialized macromolecules that speed up chemical reactions.

Dehydration and hydrolosis reactions

Dehydration reaction: when a water molecule is lost in the bonding of polymers

Hydrolosis: polymers disassembled to monomers by this, a process which is the reverse of a dehydration reaction.

Carbohydrates

Sugars and polymers of sugars. Are monosaccharides, disaccharides, and polysaccharides.

They all have a carbonyl and hydroxyl group. Disaccharides are two monosaccharides joined by a glycosidic linkage, a bond of two monosaccharides joined by a dehydration reaction

Polysaccharides

Macromolecules, polymers with a few hundred tons few thousand monosaccharides joined by glycosidic linkages. Some serve as storage, while others serve as building materials for structures to protect the cell.

Structural and Storage Polysaccharides

Storage:

Starch- a polymer of glucose monomers, stored as granules within cells in plants. Synthesizing starch allows plants to store excess glucose.

Glycogen- a polymer of glucose that is like amylopectin but more extensively branched. Vertebrates store glycogen in liver and muscle cells, release glucose when the demand for energy increases.

Structural:

Cellulose- a major component of the tough walls that enclose plant cells. It is the most abundant organic Compound in earth.

Chitin- the carbohydrate used by arthropods to build their exoskeletons.

Lipids

Grouped together since they mix poorly/ if at all with water. There are three types to know.

Fatty acid: a long carbon skeleton. The completed fat consists of three fatty acids linked to one glycerol. Saturated fats have no double bonds between carbons, while unsaturated fats have one or more double bonds. Trans fats are unsaturated fats turned into saturated fats.

Phospholipid: similar to a dark but only has two fatty acids. There is a phosphate group joined on instead.

Steroids: lipids characterized by a carbon skeleton consisting of four fused rings. Cholesterol is a crucial steroid in animals, and so are other hormones.

Catalyst

A chemical agent that selectively speeds up chemical reactions without being consumed in the reaction.

Peptide Bond

Bond between amino acids. A polymer of amino acids is called a polypeptide. It is a covalent Bond.

Protein

A biologically functional molecule made up of one or more polypeptides folded and cooked into a specific three dimensional structure.

Amino Acid

An organic molecule with both an amino group and a carboxyl group. At the center is a carbon atom, paired with the amino group and carboxyl group. Attached also is the r/side group, which can be a number of things.

Four Levels of Structure

Primary Structure: a protein's sequence of amino acids. Dictates the other levels of structure.

Secondary Structure: the coils and folds of polypeptide chains that contribute to the proteins shape. Can form alpha helix of beta pleated sheets.

Tertiary Structure: the overall shape of a polypeptide resulting from interactions between side chains.

Quarternary Structure: overall proteins structure that results from the aggregation of the polypeptide subunits.

Denaturarion

A protein being destroyed and unraveling and losing shape due to pH , salt concentration, temperature or other environment changes. Misshapen proteins are biologically inactive.

Nucleic acids

Polymers made of monomers called nucleotides, called polynucleotides. Nucleotides are made of a nitrogenous base, a five-carbon surga (pentose), and one to three phosphate groups.

Pyrimidine vs Purines

Two families of nitrogenous bases.

Pyrimidine: one six-membered ring of carbon and nitrogenous atoms. The members are cutosinez thymine, and uracil.

Purines: larger, with a siz-membered ring fused to a five -membered ring. The members are adenine and guanine.

Kinds of Microscopes

Light Microscope (LM): visible light passes through the specimen and through glass lenses refracting the light so that the image of the specimen is magnified.

Electron Microscope (EM): a beam of electrons is focused through the specimen or onto its surface. Resolution is related the wavelength of light used for imaging.

Scanning Electron Microscope (SEM): good for topographical studies. The electron beam scans the surface, exciting the electrons in the surface. This pattern of electrons is translated in a video screen.

Transmission Electron Microscope (TEM): used for studying internal structure. Electrons are aimed through a thin section of the specimen. The specimen has been tainted by heavy metals to enhance electron density.

Organelle

Membrane - enclosed structure within eukaryotic cells.

Cell Fractionation

A technique for studying cell structure and function. Broken up cells are placed in a tube and spun in a centrifuge, resulting ij tbr largest cell components to settle on the bottom, forming a pellet. This is repeated until there are a series of pellets.

Cytosol

The semifluid inside a cell in which all sub cellular components are suspended.

Nucleus vs Nucleoid

Nucleus: where most DNA of eukaryotic cells is. Enclosed within the nuclear envelope, separating it from the cytoplasm.

Nucleoid: wherelst DNA of prokaryotic cells is.

Cytoplasm

The interior of cells. For eukaryotic cells, this is the region between the Nucleus and plasma membrane

Cytoplasm

The interior of cells. For eukaryotic cells, this is the region between the Nucleus and plasma membrane

Chromosome

Structures that carry the genetic information. Each chromosome contains one long DNA molecule associated with many proteins, I cluding small basic ones called histones. The complex of DNA making up chromosomes is called chromatin.

Nucleolus

A prominent structure within the nondividing nucleus. Here ribosomal RNA is synthesized from genes in the DNA. Proteins from the cytoplasm are also assembled with rRNA until large and small subunits of ribosomes.

Ribosomes

Complexes made of ribosomal RNA and protein, and carry out protein synthesis.

Endomembrane System

The different membrane-bouns organelles of eukaryotic cells. Includes the nuclear envelope, endoplasmic reticulum, the golgi apparatus, lysomes,the plasma membrane z and various vesicles and vacuoles.

Vesicles

Small, membrane bound sacs that hold, transport, or digest materials between organelles.

Endoplasmic Reticulum (ER)

An extensive network of membranes that accounts for more than half the total membrane in eukaryotic cells. Split into two different regions .