Topic 1: Biology Review and an Introduction to Statistics

Science

• at the heart of science is inquiry

  • inquiry - search for information and explanations

two main steps:

1. making observations

2. forming a hypothesis

Making Observations

• describes natural structures and processes through observations and analysis of data

  • data - recorded observations

    • qualitative - observations with senses

    • quantitative - measured using instruments

• inductive reasoning - derive generalizations based on a large number of specific observations

• deductive reasoning - specific results that are derived from general premises

Forming Hypotheses

hypothesis - a testable prediction based on observations

• results can either support or refute the hypothesis

• NEVER say the hypothesis is correct or true

Null and Alternative Hypotheses

• always start with a null hypothesis (H0)

  1. null hypothesis - a hypothesis which the researcher tries to disprove, reject, or nullify

  2. i.e. there will be no difference in headache relief between individuals who take Tylenol and those who don’t

after the null, list all the alternative hypotheses (H1, H2, H3…)

1. alternative hypothesis - a hypothesis that may be supported by the data

Scientific Method

• most scientific inquiries do not follow a perfectly structured form

scientists can be working with the wrong hypothesis and have to redirect research

Hypothesis vs Theory vs Law

Experiments

start with an observation and a hypothesis

• use control groups and experimental groups

  • well designed experiments should include:

    1. independent variable

    2. dependent variable

    3. control group (+ or -)

    4. constants

    5. multiple trials (in the scientific community 3 is the accepted minimum number of trials)

Variables vs Constants

• A variable is something that is changed in the experiment

• A constant is something that does not change throughout the experiment

• independent variable - the one factor that is changed by the person running the experiment

  • represents a quantity that is being manipulated during the experiment

• dependent variable - the factor which is measured in the experiment

  • represents the quantity whose value depends on how the independent variable is manipulated

Experimental Controls

• Control group - expected results

• Experimental results - experimental results

• COMPARE the two

Control Groups

• controls are essential elements of an experiment:

  • they help eliminate experimental errors and biases of researchers

  • results of the control experiments validate statistical analysis of the experiment

  • reliability of the experiment increases

NOTE: controls are NOT constants

Types of Control Groups

• There are two types of control groups:

Statistics

• scientists typically collect data on a sample of a population

• the first step in analysis is to graph the data and examine the distribution

• typical data will show normal distribution

  • bell shaped curve

Measures of Central Tendencies

• central tendencies - the center of the distribution can be described by the mean, median, and mode

  • mean - the average of the data set

  • median - the middle number/value of the data set

  • mode - the value that occurs most often in a data set

    • not usually used to measure central tendency

Measures of Variability

• variability - the measure of how far a data set diverges from the central tendency

  • measured by range and standard deviation

• range - the difference between the largest and smallest value of a data set

  • large range = greater variability

  • smaller range = smaller variability

  • often used in conjunction with standard deviation

• standard deviation - a measure of how spread out the data is from the mean

  • low standard deviation - the data is closer to the mean

    • the independent variable is likely causing changes

  • high standard deviation = the data is farther from the mean

    • factors other than the independent variable are likely causing changes

  • 1 standard deviation from the mean in either direction on the horizontal axis represents 68% of the data

  • 2 standard deviation from the mean in either direction on the horizontal axis represents 95% of the data

  • 3 standard deviation from the mean in either direction on the horizontal axis represents 99% of the data

  • formula:

• there are four steps to solve for standard deviation

  1. find the mean

  2. determine the deviation from the mean for each data point and square it

  3. calculate degrees of freedom (n-1), n is the sample size

  4. put it all together and calculate s

Standard Error of the Mean

• used to determine the precision of and confidence in the mean value

• based on:

  • standard deviation

  • the number of data points

• low standard error = increase in confidence

  • commonly given as +/- 2 SEM (95% confidence)

• formula:

Error Bars

• standard error bars are often added to graphs

• if error bars overlap, the difference is not significant

• if error bars do not overlap, the difference may be significant

Topic 1: Structure of Water and Hydrogen Bonding

Chemistry Review

• essential elements - of the 92 naturally occurring elements, 20-25% are essential to survive and reproduce

  • CHOPN make up 96% of living matter

• trace elements - of the 92 naturally occurring elements, these are required by an organism in very small quantities

• atomic mass - number of protons plus number of neutrons averaged out over all naturally occurring isotopes of an element

• Periodic Table

  • elements in the same period have the same total number of electron shells

  • elements in the same group have the same number of valence electrons

• Types of Bonds

  • elements want to be stable

    • achieve this by forming chemical bonds with other elements

      • octet rule - elements will gain, lose, or share electrons to complete their valence shell and become stable

  • chemical bonds - a attraction between two atoms, resulting from the sharing or transferring of valence electrons

    • electronegativity - the measure of an atom’s ability to attract electrons to itself

  • covalent bonds - when two or more atoms share electrons (usually between nonmetals)

    • forms molecules and compounds

      • single bond - 1 pair of shared electrons

      • double bond - 2 pairs of shared electrons

      • triple bond - 3 pairs of shared electrons

    • there are two types of covalent bonds: non-polar covalent bonds and polar covalent bonds

      • non-polar covalent - electrons are shared equally between two atoms

      • polar covalent - electrons are not shared equally between two atoms

        • unequal sharing of electrons results in partial charges of the O and Hs of a water molecule

  • ionic bonds - the attraction between oppositely charged atoms (ions)

    • usually between a metal and a nonmetal

    • forms ionic compounds and salts

    • occurs when there is a transfer of electrons

  • hydrogen bonds - the partially positive hydrogen atom in one polar covalent molecule will be attracted to an electronegative atom in another polar covalent molecule

  • intermolecular bond - bond that forms between molecules

    

Properties of Water

1. polarity

   • unequal sharing of electrons makes water a polar molecule

2. cohesion

   • attraction of molecules to other molecules of the same kind

   • hydrogen bonds between H2O molecules hold them together and increase cohesive forces

   • allows for the transport of water and nutrients against gravity in plants

   • responsible for surface tension = allow liquids to resist external force

3. adhesion

   • the clinging of one molecule to a different molecule

     • due to polarity of H2O

   • in plants, this allows for water to stick to the cell walls to resist the downward pull of gravity

4. capillary action

   • the upward movement of water due to the forces of cohesion, adhesion, and surface tension

   • occurs when adhesion is greater than cohesion

   • important for transport of water and nutrients in plants

5. temperature control

   • high specific heat - water resists changes in temperature

   • how? hydrogen bonds!

     • heat must be absorbed to break H bonds, but heat is released when H bonds form

     • importance of high specific heat:

       • moderates air temperature

         • large bodies of water can absorb heat in the daytime and release heat at night

       • stabilizes ocean temperature

         • benefits marine life

       • organisms can resist changes in their own internal temperature

   • evaporative cooling - water has a high heat of vaporization

     • the molecules with the highest kinetic energy leave as gas

     • importance of evaporative cooling

       • moderates earth’s climate

       • stabilizes temperatures in lakes and ponds

       • prevents terrestrial organisms from overheating (think sweating in humans)

6. density

   • as water solidifies it expands and becomes less dense

     • due to hydrogen bonds

     • when cooled, water molecules move too slowly to break the bonds

       • allows marine life to survive under floating ice sheets

7. solvent

   • dissolving agent in a solution

   • water is a versatile solvent

     • its polar molecules are attracted to ions and other polar molecules it can form hydrogen bonds with

   • solution - homogenous mix of two or more substances

   • solvent - dissolving agent in a solution

   • solute - substance that is dissolved

     • “like dissolves like”

   • water can interact with sugars or proteins containing many oxygen and hydrogen atoms

   • water will form hydrogen bonds with the sugar or protein to dissolve it

   • ionic compounds

     • the partially negative oxygen in water will interact with a positive atom

     • the partially positive hydrogen in water will interact with a negative atom

Topic 2: Elements of Life

Carbon

• organic chemistry - the study of compounds with covalently bonded carbon

• organic compounds - compounds that contain carbon and hydrogen

  • carbon has 4 valence electrons

• carbon can form single, double, or triple covalent bonds

  • a single carbon can form up to four covalent bonds

    • can form long chains

  • most commonly formed with hydrogen, oxygen, and nitrogen

  • the type and number of covalent bonds carbon forms with other atoms affects the length of the carbon chain and shape of the molecule

Carbon Chains

• carbon can use its valence electrons to form covalent bonds to other carbons

  • this links carbons into a chain

• hydrocarbons - organic molecules consisting only of carbon and hydrogen

  • a simple framework for more complex molecules

  • carbon chains form the skeletons of most organic molecules

    • skeletons can vary in:

      • length

      • branching

      • double bond position

      • presence of rings

    • many regions of a cells organic molecules contain hydrocarbons

• functional groups

  • chemical groups attached to the carbon skeleton that participate in chemical reactions

    • MEMORIZE

      • hydroxyl group

      • carbonyl group

      • carboxyl group

      • amino group

      • sulfhydryl group

      • methyl group

      • phosphate group

Topic 3: Introduction to Biological Macromolecules

Molecular Diversity due to Carbon

• variations in carbon skeletons allows for molecular diversity

• carbon can form large chains known as macromolecules

• four classes of macromolecules (molecules made of smaller subunits):

  • polymers

    • carbohydrates

    • proteins

    • nucleic acids

  • lipids → does not include true polymers and are hydrophobic molecules

  • nitrogen is important in building proteins

Formation and Breakdown of Macromolecules

• polymers - chain-like macromolecules of similar or identical repeating units that are covalently bonded together

• monomers - the repeating units that make up polymers

• dehydration reaction - bonds two monomers form with the loss of water

  • the -OH of one monomer bonds to the -H of another monomer forming water which is then released

  • A + B → AB + H2O

• hydrolysis reaction - breaks the bonds in a polymer by adding water

  • one -H of the water bonds to one monomer and the remaining -OH of the water attaches to the other monomer

  • AB + H2O → A + B