BIO MT 2 (today)

Order

highly ordered structures

Response to environment

can respond to environmental stimuli (if environment changes, they can change)

Reproduction

ability to reproduce their own kind (without help)

Evolutionary adaptation

individuals with traits best suited to their environments have greater reproductive success and pass their traits to offspring (change over time)

Growth and development

consistent growth and development controlled by inherited DNA (over time, structure gets bigger and changes)

Regulation and homeostasis

can control internal environment within limits that sustain life (keeping the right environment for life to persist)

Energy processing

use of chemical energy to power activities (acquiring energy in one form and changing it to another for use)

Atom

Basic unit of matter

Molecule

A cluster of atoms held together by covalent bonds

Organelle

Structure made of large molecules that performs a specific function in a cell

Cells

The fundamental unit of life (most simple level of org that can do the 7 traits)

Tissues

Group of similar cells that performs a specific function

Organ

Structure composed of tissue providing a specific function for the organism

Organ systems

Several organs that cooperate in a specific function

Organism

An individual living thing

Population

All the individuals of a species living in a specific area (size of area not defined)

Community

The organisms in one ecosystem (made up of more than one population)

Ecosystem

All the organisms living in a particularly (usually large) area and the physical components with which the organisms interact (desert ecosystems in Sahara)

Biosphere

All of the environment on earth that supports life

TWO TYPES OF CELLS

1) Prokaryotic cells

1. Prokaryotic cells

▪ Simple (lack internal organization) and usually very small

▪ No nucleus or membrane-bound organelles

▪ Evolved first

2) Eukaryotic cells

▪ More complex – have internal organization

▪ Contain membrane-enclosed organelles, including a nucleus

▪ Larger cells than prokaryotes

BOTH PROK AND EUK HAVE DNA!!!!

Taxonomy

-Taxonomy names species and classifies them into a system of broader groups.

▪ Because organisms are grouped according to their similarities, taxonomy often reflects evolutionary history.

-Approximately 1.8 million species have been identified and named to date.

▪ Thousands more species are identified each year.

▪ Estimates of the total number of species range from 10 million to over 100 million.

Diversity of life is arranged in 3 domains

1) Bacteria

Most diverse and widespread PROK

2) Archaea

PROK that often live in extreme environments (Very hot, salty, etc.)

3) Eukarya

have eukaryotic cells and include

▪ Single-celled protists (big group of one-celled eukaryotes-diverse/invisible)

▪ Multicellular fungi, animals, and plants

Inductive reasoning

general conclusions drawn from a large number of specific observations

▪ E.g.: after two centuries of scientists discovering cells in every biological specimen they observed, they could conclude that “all organisms are made of cells”

Deductive reasoning

invent a hypothesis (proposed explanation) for something you observe. Design an experiment that tests the hypothesis and will provide simple results. This is the “scientific method”

Scientific Method

Observation

Stuff that gets noticed

Hypothesis

An idea that explains a phenomenon or a set of observations

Prediction

Describes a measurable or observable result that must be correct if a hypothesis is valid

Experiment

A test of the effect of a single, well-defined factor on a particular phenomenon (replicated and has a control)

Conclusion

Is the hypothesis supported or not by the results of the experiment (might return to step 2)

A useful scientific experiment

▪ It has one thing (one variable) that differs between the two treatments → one treatment is the experimental treatment and the other is the control treatment (the group where the variable is unchanged from ‘normal’)

▪ All conditions should be repeatable: you should be able to perform the experiment again in exactly the same way

▪ The outcome is easy to observe and something that can be measured

▪ The experimental design must allow for a large sample → lots of individuals in the test, or many tests performed

Qualitative data

Data in the form of descriptions (not numbers)

Quantitative data (what biologists use)

Numerical measurements

Then use STATISTICS

Result from statistical analysis of experiment to FALSIFY or SUPPORT hypothesis

If hypothesis is FALSE, it can be REJECTED

Hypotheses can NEVER be proven with absolute certainty

Science does NOT PROVE, only falsifies

Theory

A very strongly supported hypothesis

Limits of science

• Science can draw wrong conclusions, because people can make mistakes (or lie )

• Controls cannot always be used especially where experiments are done in nature

• Since scientific inquiry requires hypotheses to be testable and falsifiable, there are limits to the questions it can answer

Science deals only with observable, quantifiable, testable phenomena in the natural world

The central dogma

-The central dogma describes the basic flow of information in a cell.

▪ DNA is transcribed into RNA (similar to DNA)

▪ RNA is then translated into protein.

▪ Proteins are responsible for every activity/function in a cell: PROTEINS DO EVERYTHING!!

-A gene is the DNA sequence that corresponds to a specific protein product. ONE GENE = ONE PROTEIN

Producers (solar —> chemical energy)

▪ Producers absorb water (H2O), minerals, and carbon dioxide (CO2).

▪ Using photosynthesis, producers take energy from sunlight

▪ This evergy is used to rearrange the atoms in CO2 and H2O into

sugar molecules (rich in chemical energy)

▪ Producers then use or store these molecules

Consumers (eat molecules made by producers)

▪ Consumers take in the molecules made by producers and use cellular respiration to release the chemical energy

▪ Requires O2 from the air and releases CO2

▪ Producers also use cellular respiration

▪ Consumers then use both the energy and the atoms (matter) obtained from food to build new molecules.

Decomposers (break down what is left over)

▪ Decomposers act as recyclers

▪ Change complex matter into simpler chemicals that return to the

environment → once again available to producers.

▪ Break down wastes and the remains of dead organisms

▪ Key composers include bacteria, fungi, protists and small animals

Evolution by natural selection

• Evolution explains the unity and diversity of life

• All organisms living on Earth are modified descendants of common ancestors.

• Evolution explains the similarities and differences between all living organisms

Wallace and Darwin: Theory of NS

• Charles Darwin published the book On the Origin of Species by Means of Natural Selection in 1859.

Darwin made two main points:

1. He showed lots of evidence of evolution: that species descend

from their ancestors but change a bit along the way

2. He proposed that natural selection is the mechanism behind

evolution.

• Darwin’s theory explained how unity and diversity can be true

at the same time:

▪ Similar traits among organisms are explained by descent from common ancestors

▪ Differences among organisms are explained by heritable changes

building up

NS

-Natural selection connected two observations

1. Individuals in a population vary in their traits, many of which are passed on from parents to offspring

2. A population can produce far more offspring than the environment can support —>

• Those individuals best suited to the environment are more likely to survive and reproduce than the rest

• Over many generations, more and more individuals will have the advantageous traits

• Result: evolutionary adaptation, the accumulation of favorable traits in a population over time.

-The natural environment “selects” for beneficial traits

NS INVOLVES EDITING RATHER THAN CREATING

Mutation

• Mutation = DIFFERENCE in DNA = changed protein → changed body

• Individuals NEVER THEMSELVES evolve: the differences occur between one generation and the next

• Individuals cannot evolve (or their children evolve) because it is something they want or something that might be good in the future.

• Evolution happens because some individuals survive better right now and then go on to have more offspring

Ionic Bonds

Ionic bonds are electrical attractions between ions of opposite charge (between anions and cations)

▪ Ionic compounds are solids and dissolve easily in water

Covalent bonds

The sharing of a pair of valence electrons by two atoms (strong)

Electronegativity

• Electronegativity is a measurement of how attractive an atom is for the shared electrons.

• If sharing is unequal, electrons spend more time close to the more electromagnetic atom in the bond

• C and H have similar electronegativity

• O and N have similar electronegativity

• O and N MORE electronegative than C and H

NP Covalent bonds

Electrons shared equally between atoms

Polar covalent bonds

Unequal sharing of electrons between atoms

Hydrogen bonds

▪ Occurs when a region of partial charge on one molecule is electrically attracted to a region of partial charge on another molecule

▪ Often BETWEEN 2 different molecules

Weak

Constantly formed and destroyed

Important in descriptions behaviour of water molecules

Hydrogen bonds

▪ Occurs when a region of partial charge on one molecule is electrically attracted to a region of partial charge on another molecule

▪ Often BETWEEN 2 different molecules

Weak

Constantly formed and destroyed

Important in descriptions behaviour of water molecules

Molecule

Two or more atoms held together by covalent bonds

-can be same or diff elements

Bonds

-sharing pair of e- —> covalent bond

-attraction between 2 ions with opposite charges = ionic bond

-attraction between areas of opposite partial charge = hydrogen bond

3 Properties of Water (all linked to hydrogen bonds)

1) Moderation of Temp

Earth’s giant supply of water moderates temperatures, keeping them within limits that permit life.

▪ Water absorbs heat from warmer air and releases stored heat to cooler air.

▪ Water can absorb or release a large amount of heat with only a slight change in its own temperature.

-When water is heated, energy first disrupts H-bonds and makes molecules move faster.

▪ Heat must be absorbed to break hydrogen bonds. (Energy is required)

▪ Much of the heat is used to disrupt hydrogen bonds before the water molecules can begin moving faster → the temperature

only goes up a little

-Conversely, when water is cooled, more hydrogen bonds form.

▪ Heat is released when hydrogen bonds form. (Energy is released)

▪ This slows down the cooling process

2) Versatile solvent

-A solution: a liquid that is a homogeneous mixture of substances.

▪ A solvent is the dissolving agent of a solution.

▪ The solute is the substance that is dissolved.

-Water dissolves a huge variety of solutes necessary for life → anything that can make H-bonds with water can be dissolved in water

-Therefore water’s versatility as a solvent results from the fact that water molecules can form hydrogen bonds

3) Cohesion

Cohesion = tendency of molecules to stick together

▪ Hydrogen bonds hold water molecules together, making water much more cohesive than other substances

▪ Cohesion helps the transport of water against gravity in plants.

▪ Cohesion leads to surface tension → a measure of how hard it is to break the surface of a liquid.

The PH Scale

-used to describe acidity of a solution

-ranges from 0 (most acidic) to 14 (most basic)▪ Acidic solutions have pH values less than 7.

▪ Basic solutions have pH values greater than 7.

-Most biological fluids have pH values in the range of 6 to 8

-logarithmic and negative (every step is a 10x difference in the number of H+)

-more H+, more acidity, lower PH number ▪ Buffers are substances that minimize changes in concentrations of H+ in a solution.

▪ Buffers accept H+ if there are too much or donate H+ when there aren’t enough

Isomers

-Isomers are compounds with the same molecular formula but different structures and properties

-Isomers are important in biology

-organisms are sensitive to even subtle variations in molecules

-two isomers of a drug may have different effects

Hydrocarbons

Hydrocarbons are organic molecules consisting of only carbon and hydrogen.

▪ Many organic molecules, such as fats, have hydrocarbon components, but pure hydrocarbons are rare in cells

▪ Hydrocarbons can undergo reactions that release a large

amount of energy.

▪ Hydrocarbons are the major components of petroleum and (currently) provide much of the world’s energy.

-hydrophobic!!

4 main organic molecules

Carbohydrates (polysaccharides)

Proteins

Nucleic acids (DNA and RNA)

Lipids

Building polymers and breaking them down

-Cells link monomers together to form polymers by dehydration synthesis or dehydration reaction

▪ Generates a water molecule too!

-Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction.

▪ ‘Hydrolysis’ = “water – break”

▪ Requires a water molecule

1) Carbohydrates (sugars)

▪ The simplest carbohydrates are monosaccharides, or simple sugars (monomers); glucose is most common — C6H12O6

▪ Carbohydrate macromolecules are polysaccharides, or complex carbohydrates (polymers) composed of many monosaccharides.

-sugar, pasta, vegetables

-CARBS ARE HYDROPHILIC

-polysaccharides = polymers of hundreds-thousands of glucose monomers

Polysaccharides

1. Starch: Energy storage polysaccharide of plants

▪ Starch coils into a helical shape

2. Glycogen: Energy storage polysaccharide of animals

▪ Humans and other vertebrates store glycogen mainly in liver and muscle cells.

3. Cellulose: Structural polysaccharide in plants (makes plant cell walls)

Polysaccharides

1. Starch: Energy storage polysaccharide of plants

▪ Starch coils into a helical shape

2. Glycogen: Energy storage polysaccharide of animals

▪ Humans and other vertebrates store glycogen mainly in liver and muscle cells.

3. Cellulose: Structural polysaccharide in plants (makes plant cell walls)

2) Proteins

-most elaborate and varied organic molecule

-each protein has its own unique structure

MONOMERS = AMINO ACIDS (20)

-same structure: amino group, carboxyl group, r group (side chain) (different for each amino acid, hydrophobic or philic, large or small)

Cells joining

• Cells join amino acids together using dehydration synthesis → resulting bond has a special name in proteins = peptide bond

• The cell creates a chain of amino acids that are in a specific order

• How does the cell know which amino acids to use?

• —> The central dogma; DNA —> RNA; Recall: DNA encodes this information

Protein structure determines function (4 levels)

1. Primary structure: the unique sequence of the amino acids in the chain

2. Secondary structure: two types of shapes can form via hydrogen bonds between the amino acids: alpha helix or beta-pleated sheet

3. Tertiary structure: various interactions between R-groups of specific amino acids

4. Quaternary structure: occurs when multiple separate subunits come together

Denaturation

-loss of a protein’s fold/structure

-denatured protein is biologically inactive

-irreversible

3) Nucleic Acids

-Nucleic acids are macromolecules that encode information required to build proteins (nucleic acids are polymers)

-MONOMER = NUCLEOTIDES (all have a phosphate group, sugar, and nitrogenous bases—A, C, G, T/U)

▪ The sequence of nucleotides determines the sequence of amino acids along a polypeptide chain.

Two types of nucleic acids:

1. DNA (deoxyribonucleic acid)

2. RNA (ribonucleic acid)

-Nucleic acid polymer is made by dehydration synthesis of nucleotides

DNA + RNA

DNA—A, C, G, T

RNA—A, C, G, U

A pairs with T, C with G

DNA is in nucleus; unzips when it is time to make RNA copy

RNA can perform many functions:

▪ Carry the message of the nucleotide sequence from the nucleus to

other parts of the cell (messenger RNA – mRNA)

▪ Make a structure used in forming proteins (transfer RNA – tRNA;

ribosomal RNA – rRNA)

▪ Structures are made via base pairing (A to U; C to G) within RNA

molecules

▪ Results in 3-D shapes necessary for their various functions

4) LIPIDS

-Lipids consist mostly of carbon and hydrogen atoms linked together by non-polar bonds

▪ Unifying feature of lipids: they are hydrophobic (water-fearing) → they do not mix well with water

▪ Not macromolecules or polymers

▪ The most biologically important lipids are fats, phospholipids, and steroids.

Lipids: fats

• Fat molecule aka triglycerol = 3 fatty acids linked to a glycerol

• Main function is energy storage (2X better than starch; can hold twice as much energy per gram)

• Fatty acids can vary in whether they are saturated or unsaturated

Fatty acids

-Fatty acids are components found in fats and in phospholipids.

-Fatty acids vary in length (number of carbons) and in the number of double bonds.

▪ Saturated fatty acids have the maximum hydrogen atoms possible and no double bonds

→ Solid at room temperature, can pack closely together due to straight shape (found in animals)

▪ Unsaturated fatty acids have one or more

double bonds. → Liquid at room temperature, cannot pack closely together due to bent shape (found in plant seeds)

Lipids: Phospholipids

• Phospholipids are similar to fats, but a hydrophilic phosphate group (the head) replaces one fatty acid (there are two fatty acids = the tails)

• Phospholipids are amphipathic (have both hydrophilic and hydrophobic regions)

• Forms bilayers, the basis of cellular membranes.

Lipids: Steroids

• Steroids are lipids with carbon skeletons bent to form 4 fused rings.

• Cholesterol is a steroid → all steroids are made from cholesterol as the starting molecule

• One example of steroids is sex hormones

CH. 3 Cell Structure and Function

Every cell has:

Plasma Membrane

▪ Barrier that separates the internal environment from the external

environment.

▪ Controls flow of materials in and out of the cell → Selectively permeable.

▪ Important component of waste disposal and secretory processes.

Chromosomes

Strands of DNA that carry genes

Ribosomes

▪ Tiny structures that make proteins according to instructions from the DNA.

Cytoplasm

▪ The interior of the cell.

▪ In eukaryotic cells, the cytoplasm refers to the area inside the cell excluding the nucleus.

• Cell STRUCTURE is highly connected to cell FUNCTION!

PROK cells

—> Prokaryotic cells are small, relatively simple cells

▪ Do not have a nucleus or membrane-bound organelles.

▪ 1/10th the size of a eukaryote.

▪ Much less DNA (fewer genes)

▪ i.e. Bacteria, archaea

EUK Cells

—> Eukaryotic cells are larger and more complex

▪ Have a nucleus, cytoskeleton, and membrane-bound organelles that have distinct functions

▪ Larger genome (more genes)

▪ i.e. Animals, plants, fungi, protists

PROK cell structure

A prokaryotic cell has a plasma membrane and is usually encased in a rigid cell wall.

▪ The cell wall may be covered by a sticky capsule.

-Inside the cell, the location of the DNA is called the nucleoid region.

▪ In contact with cytoplasm (no membrane)

-On the exterior surface there can be processes called fimbriae and flagella.

EUK Cell structure

-Eukaryotic cells are partitioned by membranes into functional compartments

-Compartments = “membrane-bound organelles”

What’s the benefit of compartments?

→ Increases efficiency

• Allows incompatible chemical reactions to be separated

• Keeps enzymes that cooperate close together

• Higher local concentrations of molecules

PROK AND EUKS: similarities and differences

Commonalities:

• Both have cell membranes.

• Cytoplasm.

• Chromosomes/genes/DNA.

• Ribosomes.

Differences:

• Nucleoid region vs. nucleus.

• No membrane-bound organelles vs. complex

membrane-bound organelles.

• 1-10 mm vs. 10-100 mm.

EUK: animal vs. plants

Animal cells only (missing in most plants):

▪ Lysosomes

▪ Centrioles

Plant cells only (missing in animals):

▪ Chloroplasts (green organelles that convert sun to chemical energy)

▪ Rigid cell wall (gives plant structure)

▪ Central vacuole (liquid that pushes and makes cell pressurized; what males plant stand)

NOTE: both cell types are EUKARYOTIC

Why are cells small

• natural law limits size of cells

At minimum, a cell must be large enough to house the parts it needs

to survive and reproduce.

• The maximum size of a cell is limited by the amount of surface area

needed to obtain nutrients from the environment and dispose of wastes.

-As a cell gets bigger, the cell’s volume increases much faster than its

surface area

• A very large spherical cell does not have enough surface area to support the large volume of cytoplasm inside

Why is surface area important

Surface area is important because cells get nutrients and dispose of

wastes using a process called diffusion

• Diffusion is slow and operates best over very short distances

• Diffusion works best to supply cells when there is a large surface area compared to the volume of the cell

• We also see this pattern in organ systems that rely on diffusion – they

have a lot of surface area too!

-Surface area often connects structure to function

4 functional groups of structures in EUK

1. The nucleus and ribosomes carry out the genetic control of the cell.

2. Organelles involved in the manufacture, distribution, and breakdown of molecules include the endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, and peroxisomes.

3. Mitochondria in all cells and chloroplasts in plant cells function in energy processing.

4. Structural support, movement, and communication between cells are the functions of the cytoskeleton, plasma membrane, and plant cell wall.