Biol 244 Lab Practical 1

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Scientific Method

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1. OBSERVATION about some phenomenon.

2. Questions, tentative answers (HYPOTHESIZE)

3. Design and conduct tests (EXPERIMENTS)

4. Collect data, summarize data, ANALYZE data

5. Draw CONCLUSIONS from the results

6. FUTURE RESEARCH

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Basic Attributes of a Valid Hypothesis

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-Predictable

-Testable

-Falsifiable

-Repeatable

-Verifiable

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Define: Hypotheses, Theory, Law

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Hypotheses: a tentative explanation of why certain observations about the physical universe are the way they are

Theory: a hypothesis that has been accepted after repeated tests; composed of 1 or more hypotheses that have never been rejected, which explain the same phenomenon

Law: descriptions of what we observe in nature; typically mathematical generalizations describing the precise relationships between 2 or more variables

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Adaption vs. Acclimation

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Adaptation: an entire species adapts over time (evolution)

Acclimation: Acclimation is a form of adaptation that an organism undergoes when transferred to a different habitat. It doesn’t take as long as evolutionary adaptation and it doesn’t affect the body composition of the entire species. Adjustment is made by modifying physical reactions to environmental changes, like shivering when exposed to cold weather.

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Oxygen Dissociation Curves

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Relate the saturation of the hemoglobin to the oxygen partial pressure in the blood. Above some partial pressure, the hemoglobin is totally saturated with oxygen (the hemoglobin is carrying the maximum amount of oxygen) and below a certain partial pressure, the hemoglobin is carrying little oxygen, or the hemoglobin releases the oxygen.

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Sample vs. Population

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Population: i.e., whitetail deer

Sample: a representative subset of a population from which one can make inferences about the entire population

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Parameter, Statistic

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Parameter: some measurable feature of a population, such as the population's mean size or the standard deviation of the size

Statistic: an estimate of the population parameter; obtained from analyzing a sample

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Variance, Standard Deviation

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Variance: the average squared deviation from the mean of all of the measurement observations; it is equal to the sum of the squares of the deviations of each sample from the average, divided by sample size minus 1 ('unbiased estimate of population variance')

Standard Deviation: square root of the variance

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Base units in metric system for temperature, mass, length, volume

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Temperature: degree

Mass: one gram

Length: one meter

Volume: one liter

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Quantitative vs. Qualitative Variables

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Quantitative variable: data differs in magnitude and can be ranked on some measurement scale

Qualitative variable: "big" vs. "small"; categorical data

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Discrete vs. Continuous Variables

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Continuous variables: a measurement could be of any conceivable value along a continuum (i.e., 1.25), includes decimals

Discrete variables: countable number of numerical values, categories, or codes. (i.e., number of leaves on a plant; 5) whole numbers only

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Nominal-scale, ordinal-scale, interval-scale, ratio-scale

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Nominal-scale: categorical data; qualitative, discrete variables (male, female; blue, green); no explicit ordering

Ordinal-scale: quantitative variables that are often discrete, but can be continuous; can be ordered (ranked slow to fast, low to high)

Interval-scale: ordered, quantitative data, may be either continuous or discrete; there is a directionality to interval data, and it can have +/- values (degrees Celsius, compass directions...)

Ratio-scale: ordered, quantitative data, can be continuous or discrete. constant interval size between any 2 units on the ratio scale (number of things, rates, physical or numerical measurements of objects, length of elapsed time...)

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Probability (p) value

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P-value is a measured likelihood of the deviation of some observed results from the value that was expected if the null hypothesis was true. A small p-value suggests that the alternative hypothesis is probably true.

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Parametric and nonparametric tests

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Parametric tests: t-test, regression (and correlation), and chi-square test; as long as the underlying population distribution is normal, parametric tests can be used

Nonparametric: type of statistics

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Normal distribution

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distribution often assumed for parametric tests, if plotted on a graph forms a normal curve

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Degrees of freedom

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N-1

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Slope, Intercept

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y = mx + b

Where:

y = value of dependent variable

m = slope of the line

b = the intercept of the line (point at which the line crosses the y-axis)

x = value of independent variable

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Correlation Coefficient (r)

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describes the kind of relationship that exists between 2 variables (positive correlation, negative correlation)

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Square of the correlation coefficient (r2)

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tells you the percentage of the variation of the dependent variable as explained by the variation in the independent variable

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Type I vs. Type II Error

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Type 1 error occurs when we reject a null hypothesis, when in fact the null hypothesis is true.

Type 2 error occurs when we accept the null hypothesis as true, when in fact the null hypothesis is false.

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3 assumptions implied when using a regression

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see unit 3

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Analysis of experimental results using a t-test; study Table 3.1-3.3

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see unit 3

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Assumptions for parametric analyses:

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1) the data were randomly and independently sampled from the population

2) data were sampled from a specified distribution

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logarithms, exponential functions, natural logarithms, common logarithms, antilogs

(4-2)

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Logarithm--> basic idea is that the logarithm of a product of 2 numbers is the sum of their logarithms, and adding 2 or more numbers is easier than multiplying 2 or more numbers.

natural log [ln]: the ln of a given number is the exponent 'y' that indicates the power to which base 'e' must be raised to obtain a given number 'x' -->

y = loge(x) = ln(x)

common log [log]: inverses of the exponential functions;

logax = y

exponential functions: for any given positive real number 'a', (a > 0), the exponential function with base 'a' is the function: x = a^y

antilogs: the inverse function

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pH

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pH = -log10 [H+]

[H+] = 10^-pH

the concentration of the hydrogen ion H+ in an acidic or basic solution is indicated by the pH

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serial dilutions

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adjust concentrations of chemical solutions by taking a factor of 1/10th

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acids, bases

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acid: any compound that releases hydrogen ions when dissolved in water

base: compound that accepts hydrogen ions while in water

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salts

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dissociate in water and do not release or absorb hydrogen ions

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ions

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molecules dissociate into ions; atoms in which total # of electrons does not equal the total # of protons

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membranes

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Cell membrane of living things consists of a lipid bilayer, with a variety of proteins embedded in and lying on the membrane

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plasma membrane

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outer membrane of the cell

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tonoplast

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membrane around the central vacuole

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fluid mosaic model

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see unit 4

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lipid bilayer

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composed of phospholipids and cholesterol

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polar vs. nonpolar

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polar molecules: large and cannot easily cross most cellular membranes

nonpolar molecules: i.e., lipids and gases, can cross bilayer easily

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diffusion, facilitated diffusion

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Simple diffusion: movement of matter (in the form of atoms or molecules) from areas of high concentration to low concentration

Facilitated diffusion: diffusion of molecules facilitated by a protein carrier across the membrane

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semipermeable

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selectively permeable; membrane decides what is allowed to pass through it by diffusion

Permeable: passing through is relatively easy

Impermeable: molecules cannot pass through the semipermeable membrane

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active transport

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the movement of materials against their concentration gradients, opposite the way they would move by diffusion

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osmosis

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the diffusion of water across a semipermeable membrane; refers only to the movement of water

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hypertonic, hypotonic, isotonic

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hypertonic: cells lose water when placed in these solutions

hypotonic: cells gain water when placed in these solutions

isotonic: normal; concentration on the outside of the cell is the same as the concentration on the inside

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osmotic pressure, turgor pressure, hydrostatic pressure

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osmotic pressure: a solution exerts a 'force' against the membrane because of the movement of water across the membrane into the solution

turgor pressure: osmotic pressure is counteracted by this pressure exerted on the elastic cell wall by the hydrostatic pressure inside the turgid cell (firm cell)

hydrostatic pressure:

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resolution

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resolving power of the instrument being used; a limitation of measurements is the degree of resolution

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Importance of cell membranes and fluid mosaic membrane model

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See unit 4

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Estimate osmotic strength of unknown samples using serial dilutions and regression

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See unit 4

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Impact of degree of resolution on precision

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High precision is obtained by using a given method or procedure correctly and consistently, using equipment that has a higher or finer degree of resolution.

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glycolysis

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The first step in both fermentation and aerobic respiration

Glycolysis is a pathway that occurs in the cytoplasm of the cell. Glucose is partially oxidized (broken down) to two, 3C molecules called 'pyruvate'. No CO2 is produced by glycolysis. Glycolysis occurs regardless of the presence or absence of oxygen (oxygen is not needed)

Glycolysis also produces two NADH molecules (see NADH)

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oxidized, reduced

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oxidized: loss of electrons

reduced: gain of electrons

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Krebs cycle (also called TCA cycle, citric acid cycle)

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Oxidizes acetyl coA to 2 CO2 molecules over a series of steps

take the pyruvate (formed from aerobic respiration) and break it down further to carbon dioxide and water. The energy in pyruvate has been transferred to various carriers (NADH, FADH2, ATP). These energy carriers are reoxidized by the electron transport chain (ETC).

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Electron transport chain

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Reoxidizes the energy carriers NADH, FADH2

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chemiosmosis

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produces ATP; makes up the last step (in addition to ETC) of aerobic respiration

The energy-coupling mechanism that uses the energy stored in the hydrogen ion gradient with ATP production

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ATP, NADH, FADH2

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NADH: nicotinamide adenine dinucleotide; can be viewed as a second type of 'energy carrier' that is produced by glycolysis

ATP:

FADH2:

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Pyruvate

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broken down glucose

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alcoholic fermentation (basic process)

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Ethanol is the end product of alcoholic fermentation. In addition, CO2 is an important byproduct of the reaction

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lactic acid fermentation (basic process)

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muscle cells, in the absence of oxygen, can continue glycolysis by a 'fermentation process that differs slightly from alcoholic fermentation. Even with little oxygen around, your muscle cells can continue producing a small amount of ATP for a brief period of time; end product is lactate

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anaerobic respiration (fermentation)

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basic chemical equation:

NADH, in plant and animal cells, is further harvested by the ETC and associated proteins to produce more ATP

Fermentation - yeast performing glyolysis to produce ATP (but they do not take the next 2 steps of aerobic respiration: Krebs cycle and ETC)

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aerobic respiration (basic steps and state specific cellular location where each step occurs: glycolysis, krebs, and electron transport chain)

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basic chemical eqn. of aerobic respiration:

C6H12O6 + 6O2 -->

6CO2 + 6H2O + approx. 30-32 ATP + HEAT

In aerobic respiration, glucose is oxidized completely to water and carbon dioxide if there is oxygen available.

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chlorophyll

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the molecules that capture the light energy and form an assemblage of molecules called a 'photosystem'

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light reactions (light dependent reactions)

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Occur in the chloroplast

1st step in photosynthesis

Captures light energy for the synthesis of ATP from ADP and the production of NADPH from NADP. These energy carriers then act as intermediates that transport energy to the next step of photosynthesis, the Calvin cycle.

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Calvin cycle (light independent reactions)

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Occur in the stroma of the chloroplast

Following the light dependent reactions, this occurs; both day and night. Carbon dioxide is reduced to glucose and other sugars, using the energy supplied by NADPH and ATP

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NADPH

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an energy carrier

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mitochondria (and basic structure of mitochondrion, relating its structure to aerobic respiration)

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Both the Krebs cycle and ETC occur inside the mitochondrion; the Krebs cycle occurs inside the inner membrane of the mitochondrion, in the matrix, whereas the ETC complex is embedded in the inner membrane of the mitochondrion.

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chloroplasts

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conduct photosynthesis

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stroma

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the dense, fluid-filled space inside the inner membrane; the Calvin cycle occurs here

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matrix

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the Krebs cycle occurs here

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intermembrane space

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fluid-filled space between the two membranes in the organelle

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photons

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particles of light

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fermentation vs. aerobic respiration (in terms of products and net ATP yield)

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see unit 4

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Cellular respiration and photosynthesis

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All living things use energy to do work and maintain order: grow, repair, move, and reproduce. Cellular respiration and photosynthesis are the 2 major metabolic pathways found in living things. By using photosynthesis, plants capture and store energy from the sun in the form of chemical bonds that hold sugars together. When they require energy for cellular work, plants can tap this stored energy by process of cellular respiration, a process by which living organisms convert the chemical energy stored in organic molecules into a form immediately usable by organisms, in the form of ATP

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Parafocal vs. Parcentered

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see unit 6

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importance of surface area to volume ratios

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metabolic requirements are a limit to the upper size of a eukaryotic cell

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Bacterial (prokaryotic) cells vs. Eukaryotic cells (plants and animals)

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location of chromosomes;

In eukaryotic - chromosomes are in nuclus

in prokaryotic - DNA is concentrated in the nucleoid region

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Interpolation vs. Extrapolation

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see unit 6

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mitochondria, extracellular matrix, cellulose, collagen, cristae, cisternae, flagella, centrioles, centrosome, basal bodies, microtubules

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mitochondria - organelles involved in cellular respiration; found in eukaryotic cells

cisternae - sacs that make up the ER

cristae - infoldings of the inner membrane

centrosome - structure that contains 2 centriols oriented at right angles

flagella - locomotory structures found in some animal cells and some plant cells

basal bodies - at the base of all eukaryotic cilia and flagella

microtubules - make up ER

extracellular matrix - (ECM) found outside of the plasma membrane

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cell cycle, interphase,

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Interphase: when cells are not dividing, they are in this part of the cell cycle. Interphase is NOT considered a phase of the 2 major types of nuclear division (mitosis, meiosis). During interphase, the cell is respiring, producig, and secreting materials, interacting with other cells, etc.

Interphase is divided into 3 parts: G1 (first gap), S (for replication of DNA) and G2 (second gap)

Throughout interphase, all of the cell's DNA is not tightly coiled into dense structures called chromosomes

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mitosis and meiosis

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Mitosis: ability to grow and replace cells through this process; in many animals, mitosis is also used for asexual reproduction; replaces somatic cells

Meiosis: special form of nuclear division that occurs only in gamete-producing tissues. Involved in the production of gametes

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Prophase

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Phase 1 of mitosis. The DNA is condensed into microscopically visible chromosomes

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Metaphase

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Phase 2 of mitosis: the chromosomes (made of 2 chromatids) move and line up at the center of the cell

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Anaphase

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Phase 3 in mitosis: at the start of anaphase, the sister chromatids separate from each other at the centromere. The chromatids now are called daughter chromosomes, to indicate they are considered to be separate chromosomes. The 2 identical daughter chromosomes separate and travel to opposite poles

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Telophase

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Phase 4 in mitosis: the last phase of mitosis; begins when the 2 groups of chromosomes reach the opposite poles. A nuclear membrane forms around each collection of chromosomes. The chromosomes begin to unwind and become chromatin, and the spindle disappears. The nucleolus reappears, signaling that the cell is beginning to produce RNA for protein synthesis.