Biology FInal

We so screwed :)

Characteristics of Living Things

1. Order
2. Reproduction
3. Growth and Development
4. Energy Processing
5. Regulation
6. Response to Environment
7. Evolutionary Adaption

Order

Structure; Highly organized, coordinated organisms that consist of one or more cells.

Reproduction

Able to reproduce; Organisms reproduce their kind and give rise to more offspring.

Growth and Development

Growth is controlled by DNA; Organisms grow and develop.

Energy and Processing

Having the means of converting energy to energy that can be used for food; Organisms utilize chemical energy that they have stored for their functions.

Regulation

The ability to regulate the internal environment; Organisms maintain homeostasis.

Response to Environment

Able to respond to stimuli; Organisms detect changes in their environment and respond to them.

Evolutionary Adaptation

Adaptations that evolved over generations to create greater reproductive success; Organisms evolve over many generations with traits that are best suited to their environment.

The Three Domains

Archaea: Consists of prokaryotes that usually live in extreme environments.

Bacteria: Consists of Prokaryotes, which are the most diverse and widespread prokaryotes.

Eukarya: All Eukaryotic Organisms (Protists, Animals, Plants, Fungi)

Prokaryotes

First to evolve.

Much simpler and usually much smaller than a Eukaryotic cell.

DNA is free floating and contains ribosomes.

Eukaryotes

More complex than a prokaryote.

Membranes subdivide eukaryotic cells into organelles that complete different functions.

Includes a nucleus that contains the cell’s DNA.

Controlled Experiments

Designed to compare an experimental group with a control group to test a hypothesis.

Dependent Variable

The thing that changes as a result of the independent variable; y-axis.

Independent Variable

The thing manipulated between the control and experimental groups; x-axis.

Deductive Reasoning

Making a claim based on data that is structured the same way as the data.

Inductive Reasoning

Making a claim based on pre existing evidence that is different than the data itself.

Hypothesis

A proposed explanation for a set of observations.

Leads to predictions that can be tested by making additional observations or by performing experiments.

Theory

Broader in scope than hypotheses and have larger bodies of evidence supporting them.

Explain how things happen.

Movement of Energy

Energy flows through an ecosystem and is gained and lost constantly.

Energy is not cycled.

Energy is released through organisms as heat and waste.

Think 10% rule.

Movement of Matter

Matter cycles through ecosystems.

Think phosphorous, water, carbon, nitrogen.

Natural Selection

The method proposed by Darwin that controls evolution. Based on the following observations:

Individual Variation in a population.

Overproduction of offspring.

When a population produces more offspring than the environment can handle.

Adaptation

Darwin’s Two Inferences

Individuals with traits best suited to the environment are more likely to reproduce and survive.

As a result of unequal reproductive success, over the course of many generations, a higher proportion of individuals in the population will have the advantageous traits.

Matter

Anything that occupies space and has mass.

Atom

Smallest unit of matter.

Proton

A subatomic particle with a single positive electric charge packed in the atom’s nucleus.

Neutron

A subatomic particle with no electric charge packed in the atom’s nucleus.

Electron

A subatomic particle with no electric charge packed in the atom’s nucleus.

Atomic Number

The number of protons in a particular element.

Atomic Mass

The total weight of an atom is usually equal to the amount of protons and neutrons combined (the mass number).

What makes an atom chemically reactive?

An atom is chemically reactive through its chemical bonds that are formed thanks to the sharings of electrons in its outermost shell (valence electrons).

Structure

Protons and Neutrons are tightly packed around the center

Electrons circle the nucleus forming a negatively-charged cloud

The number of electrons in the outermost shell determines the reactivity

Electron Shells go: 2-8-8 (called the octet rule)

\# of protons determines the element

Atomic number = # of protons

Atomic mass = # of protons + neutrons

\# of protons = # of electrons

Element

A substance that cannot be broken down into other substances.

Trace Element

Elements that are essential for humans, but only in minute quantities.

Compound

A substance consisting of two or more different elements.

Isotope

An atom with the same number of protons but a different number of neutrons than its normal atom.

Radioactive Isotope

 An isotope in which the nucleus decays spontaneously and gives off energy and particles.

Ion

An atom that either has more or less electrons than its normal  atom, having a charge.

Chemical Bond

An attraction between two atoms that results from the sharing, giving, or losing of electrons on the outer shell (valence electrons).

Covalent Bond

The strongest chemical bond where two atoms share one or more pairs of valence electrons, between metals and nonmetals.

Ionic Bond

A chemical bond in which two oppositely charged ions are attracted to each other. (Due to electronegativity, which is highest in Fluorine and Oxygen on the periodic table).

Hydrogen Bond

The weakest chemical bond in which a slightly positive hydrogen atom of one molecule is attracted to a slightly negative atom of another molecule.

Cohesion

Water molecules sticking together due to hydrogen bonds.

Adhesion

Water molecules sticking to other substances or things, due to hydrogen bonding.

Surface Tension

Measure of how difficult it is to break the surface of a liquid, because of strong hydrogen bonds.

Temperature

The intensity of heat. If water is heated up (thermal energy: the energy transferred through movement), then the water molecules increase in movement and speed and hydrogen bonds break at its boiling point, releasing vapor. Water has a stronger resistance to temperature change because of its strong hydrogen bonds. 

Evaporative Cooling

When a substance evaporates, the surface of the liquid left behind cools down. This is because the molecules that are the hottest with the greatest energy leave and are evaporated, leaving the temperature of the liquid left behind to cool down.

Density

Water is less dense as a solid than a liquid. Because of freezing, hydrogen bonds become stable and the length in between the molecules also become spacious and equal. This makes less molecules in ice than in water (water is moving).

Acidic

0-6 pH (more H+)

Negative

7 pH

Basic / Alkaline

8-14 pH (less H+ or more OH-)

Buffer

Adds H+ or OH

Carbohydrates

**Structure: Ring-like. Glucose, for example, has six carbons, making its ring in the shape of a hexagon. Composed of atoms in a ratio of 1:2:1 (C:H:O).**

**Monomer: Monosaccharides**

**Function: Structural Compounds, Storage Molecules, Quick Energy**

Lipids

**Structure: Fats are Hydrocarbon Chains (CH2). Triglyceride. Steroids are a type of lipid that has four carbon rings that are fused together. Phospholipids have fatty acid chains whereas triglycerides have three (they also have a phosphate group, tails are hydrophobic (doesn't like water) while the head is hydrophilic (likes water).**

**Monomer: No true monomer. Glycerol and Fatty Acids make up the typical triglyceride.**

**Function: Lipids are the most diverse group, due to a lipid being any molecule that does not mix well with water. Fats are for long-term energy storage and they help absorb vitamins. Steroids are most commonly used to make cholesterol, which is a precursor for making other steroids, such as sex hormones. Cholesterol is also used for making animal cell membranes.**

Proteins

**Structure:**  Made of peptide bonds that consist of amino groups, carboxyl groups, and amino acids.

**Monomer:** Amino Acids

**Function:** Makes hormones and enzymes, which help with bodily functions. Proteins control cellular shape and function.

Nucleic Acids

**Structure:** Consists of a nitrogenous base (ATCG) and a sugar-phosphate backbone. Adenine(A) is not Present in RNA and is replaced by Uracil(U) 

**Monomer:** Nucleotide

**Function:** Makes up the genetic material used by all organisms. (DNA) and (RNA)

Functional Groups

**Amino Group:** NH2 or H/N\\H

**Phosphate Group:** PO4

**Hydroxyl Group:** HO or H-O

**Carboxyl Group:** CO2H or O=C-O-H

**Carbonyl Group:** CO or C=O

**Sulfuric Group:** SH or S-H

Dehydration Synthesis

Facilitated by enzymes.

Links monomers together into polymers by removing water molecules.

Hydrolisis

Facilitate by enzymes.

Unlinks monomers from polymers by adding a water molecule.

Light Microscope

Uses a beam of visible light.

The light passes through a specimen (microorganism or thin slice of animal or plant tissue) and then through glass lenses.

The lenses bend the light in such a way that the image of the specimen is magnified as it is projected into your eye or a camera.

Scanning Electron Microscope

Used to study the detailed architecture of cell surfaces, using an electron beam to scan the surface of a cell or other sample; the beam excites electrons on the surface, and these electrons are then detected by a device that translates their pattern into an image projected onto a video screen.

Transmission Electron Microscope

Used to study the details of internal cell structure. It aims an electron beam through a very thin section of a specimen, then stains the section with atoms of heavy metals, then electrons are scattered by these parts, and the image is created using the pattern of the scattered electrons.

Surface Area and Volume and Cell Size

Large cells have more surface area than small cells, but compared to the same volume, small cells have more surface area.

Differences Between Plant and Animal Cells

Plant cells have chloroplasts that allow photosynthesis, animal cells do not.

Plant cells also have a cell wall additional to the cell membrane to provide better structure and better protection.

Plant cells do not have lysosomes which break down unneeded parts of the cell (ex. damaged mitochondria), instead the vacuoles take on lysosomal functions.

Cell Membrane

Phospholipid bilayer, hydrophilic heads on outside, hydrophobic tails inside. Proteins to allow transportation in and out of the cell. Function is to regulate substances going in and out of the cell, and to provide a boundary and division between the inside and outside of the cell.

Cell Wall

**Thin, flexible primary cell wall on outside with pectin to stick to other cells, plasma membrane in middle, secondary cell wall on inside. Inside cell wall includes fibers of cellulose with polysaccharides and proteins. Function is to provide better protection from fluid and substances outside the cell, provide better structure, and to prevent mechanical stress.**

Cytoplasm

The substance inside the cell that props up organelles in the cell, consists of many types of molecules and materials (including organelles) that float around the cell.

Nucleus

**Consists of a nuclear envelope with a double membrane and pores which regulate entry and exit of molecules, a nucleolus in the center of the nucleus (synthesizes rRNA), and chromatin (contains DNA) in between. Function is to control and direct the cell’s activities through protein synthesis based on the encoded DNA. (Also site of RNA transcription and DNA replication)**

Ribosome

**Ribosomal RNA, ribosome is bound to rough ER or free, structurally identical. Function is to synthesize proteins from mRNA.**

Endoplasmic Recticulum

**Smooth ER: lacks ribosomes, functions to synthesize lipids, and pump calcium ions into the interior of the ER to trigger the cell to contract when nerve signal stimulates muscle cells.**

**Rough ER: Has bound ribosomes. Ribosomes synthesize polypeptides, and inside the ER the polypeptide turns to a glycoprotein by molding it into a 3D shape and adding sugars and a transport vesicle takes the protein out of the ER to some other part of the cell.**

Mitochondria

**THE POWERHOUSE OF THE CELL. Outer membrane → Intermembrane space → Inner membrane → Mitochondrial matrix which has folds called cristae and mitochondrial DNA and ribosomes. Function is to carry out cellular respiration and convert sugars and other chemical energy into ATP. Cristae increases surface area allowing for more ATP production.** 

Chloroplasts

**Double membrane, thick fluid called stroma, interconnected sacs called thylakoids which stack into a granum, or grana. Function is to convert light energy into chemical energy of sugar molecules. Green chlorophyll in the thylakoids traps solar energy.**

Golgi Apparatus

Stacks of flattened sacs, number of stacks correlates to the activeness of the cell in protein secretion. Transport vesicles from ER fuse with the golgi apparatus and the protein from the sac is modified and sorted as it goes through the stacks until it reaches the other side to ship off the finished product in another transport vesicle.

Vacuoles

**Large vesicles. Contractile vacuoles expel water out of the cell. In plants, digestive functions much like lysosomes occur here. Vacuoles in flower petals contain pigments which attract insects. Some vacuoles may also contain poisons to protect the plant from herbivores. A plant cell has a large central vacuole which helps absorb water and enlarge. It also keeps vital chemicals and stores toxic waste products that may be harmful.**

Lysosomes

**Breaks down products including food and damaged organelles, where then the nutrients are expelled into the cytoplasm/cytosol. Lysosomes (with digestive enzymes) fuse with food vacuoles or vesicles.**

Endosymbiotic Theory

Eukaryotic cells originated from prokaryotes

**Theory: A long time ago in a galaxy far far away,** Prokaryotes had diversity, some had photosynthetic abilities, and then there were photosynthetic bacteria. Some prokaryotes were larger so they could engulf others to become larger too. Some of these large cells engulfed the photosynthetic bacteria and non-photosynthetic bacteria. Instead of getting digested, they remained intact and lived as symbiotes. Bacteria that used oxygen to produce food soon became mitochondria, and bacteria that used sunlight energy to produce food became chloroplasts. Mitochondria developed first because most eukaryotes all have mitochondria. 

**Facts that support**:

These two organelles have their own DNA (bacterial DNA) separate from the nucleus.

They are similar in size with bacteria

They divide similarly to bacteria

Plasma Membrane Structure and Function

Phospholipid Bilayer

*Hydrophilic head*

*Hydrophobic tail*

*Glycerol backbone*

*Tails face each other and heads face external*

*Allows/regulates substances in and out of the cell*

*Acts as boundary that separates reactions*

The proteins associated with the plasma membrane and their functions

**Transport proteins**

**Allows specific ions or molecules to pass in and out of cell**

**Facilitated Diffusion: passive transport (no energy, driven by concentration gradient)**

**Active Transport requires ATP, substance driven against concentration gradient)**  

**1Solute binds, 2ATP provides energy for shape change, 3Solute released, 4protein returns to original form**

Enzymes

Lines the cell membrane and allows the transfer of molecules.

Attachment Proteins

Attach to extracellular matrix and cytoskeleton, 

Helps support membrane

Coordinates external and internal changes.

Receptor Proteins

Receives signaling molecules from outside

Relays message to inside the cell by activating other molecules

Glycoproteins

Provide structural stability and protection

Glycans (glycoproteins contain glycans attached to their polypeptide side chains)

Glycans can shield the protein from proteolysis and prevent protein aggregation

Serve as id tags for other cells → glycans can be recognized by other proteins or molecules and mediate cell-cell interactions and binding

 events

Carbohydrates attached to proteins on surface of membrane

Support immunity response (immunological)

Specific antigen onto which antibody binds is based on the carbohydrate it contains

Junction Proteins

Separates tissue spaces and regulate selective movement of solutes across membranes

Barriers, creates tight junctions between cells

Passive Transport

Facilitated Diffusion (Substances driven with concentration gradient, no energy expended) and Osmosis(diffusion of water).

Active Transport

Energy is expended to move a solute against concentration gradient — toward the side where solute is more concentrated. Requires ATP.

Hypotonic

Lower solute concentration than the cell. Water will rush into the cell. 

Cell Lysed     

Isotonic

Equal solutes level (normal water)

Cell normal

Hypertonic

Higher solute concentration outside the cells than in the cell.

Water will rush out of the cell and the cell will shrivel.

Kinetic Energy

**Energy of motion, other moving objects transfer motion to other objects.**

Thermal Energy

Type of kinetic energy, random movement of atoms/molecules.

Heat

**Thermal energy transferred from one object to another.**

Potential Energy

**Energy possessed by matter from its location or structure**

**Molecules contain potential energy because of arrangement of electrons**

Chemical Energy

**Potential Energy waiting to be released in chemical reaction**

**Most important type for organisms—** ***energy that can be transformed to power the cell***

Exergonic Reaction

**Reactant(w/more potential energy) releases energy to turn into product.**

Endergonic Reaction

**Requires net input of energy — (little potential energy → energy rich product)**

Coupled Reactions

**Use of energy from exergonic reactions to fuel endergonic reactions**

**ATP is key for energy coupling**

The Structure and Function of an enzyme and its substrate

**Enzymes are proteins - biological catalysts**

**Speed up reaction by decreasing activation energy for reaction**

**Substrate: specific reactant for enzyme**

**substrate fits into active site (pocket/groove)**

Substrate

Specific reactant for enzyme.

Inhibitor

Chemical that interferes with activity.

Competitive Inhibitor

**Reduces productivity by physically blocking active site**

**Can be overcome by abundance of substrate>inhibitor**