BIO220 Lecture Exam 3 (Ch 7,8,9)

Most common elements (6) of living things

CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur)

-used to make organic macromolecules: carbohydrates, proteins, lipids and nucleic acids

Essential nutrients

Nutrients necessary for normal body functioning that must be obtained from food.

Two categories: macronutrients & micronutrients

Macronutrients

-required in large quantities; play principal roles in cell structure and metabolism

•Proteins, carbohydrates, lipids

Micronutrients (trace elements)

-required in small amounts; involved in enzyme function and maintenance of protein structure

•Manganese, zinc, nickel (vitamins and minerals)

Organic nutrients

contain carbon & hydrogen atoms and are usually the products of living things

-Methane (CH4), carbohydrates, lipids, proteins, and nucleic acids

Inorganic nutrients

-atom or molecule that contains a combination of atoms other than carbon and hydrogen

-Metals and their salts (magnesium sulfate, ferric nitrate, sodium phosphate), gases (oxygen, carbon dioxide) and water

Carbohydrates

macromolecules that contain carbon, hydrogen, and oxygen in a 1:2:1 ratio (ex: glucose C6H12O6)

-CHO

Proteins

macromolecules that contain carbon, hydrogen, oxygen, nitrogen & sometimes sulfur

-CHONS

Nucleic Acids

macromolecules that contain carbon, hydrogen, oxygen, nitrogen & phosphorus

-CHNOP

Lipids (fats)

macromolecules that contain mostly carbon & hydrogen with very little oxygen and sometimes phosphorous and nitrogen

-CHO NP

Heterotroph

organism that must obtain carbon in an organic form made by other living organisms (organic molecules like proteins, carbohydrates, lipids & nucleic acids)

Autotroph

organism that obtains carbon from CO2 (inorganic gas)

Main/largest reservoir of nitrogen

nitrogen gas (N2) in the atmosophere

fixation

To "fix" an element means that an organism converts it from a form that is not usable to organisms to a form that is usable to that organism and others.

Main/largest inorganic reservoir of hydrogen

water & H2 gas

Growth factors

organic chemicals that cannot be synthesized by certain organisms (Vitamins, Essential Amino Acids)

nutritional types

determined by where organisms get their carbon and energy

chemotroph

gain energy from chemical compounds/molecules

Phototroph

an organism that gets its energy from sunlight through photosynthesis

Chemoheterotroph

organism that must take in organic molecules for both energy and carbon

two categories: saprobes & parasites

Saprobe

free-living microorganisms that feed on organic detritus from dead organisms

parasites

organisms that live on or in a host and cause it harm

diffusion

Movement of molecules from an area of higher concentration to an area of lower concentration.

passive transport

Requires NO energy, Movement of molecules from high to low concentration, Moves with the concentration gradient

-diffusion, osmosis & facilitated diffusion

osmosis

Passive transport - Diffusion of water through a selectively permeable membrane (high to low concentration)

(remember Particle Party - water will move towards the area with the most solute particles (party) to reach equilibrium)

facilitated diffusion

Passive transport - requires a carrier/transport protein (but NO energy required) (from high to low concentration)

active transport

Energy-requiring process that moves material across a cell membrane against a concentration gradient (from low to high concentration)

- active transport, group translocation, bulk transport

hypertonic solution

Solute concentration is greater than that inside the cell; cell loses water/shrinks

hypotonic solution

Solute concentration is less than that inside the cell; cell gains water/swells & may burst

isotonic solution

a solution whose solute concentration is equal to the solute concentration inside a cell

Environmental factors that influence microbes

Temperature

Oxygen requirements

pH

Osmotic pressure

Barometric pressure

Psychrophiles

- below 15 degrees C

Mesophiles

• temperature 20-40 degrees C; (human body temperature is optimal)

Thermophiles

- optimum temperature greater than 45 degrees C

- ex. Archaea "extremophiles"

aerobe

aer="air", utilizes oxygen and can detoxify it

obligate aerobe

organism that requires a constant supply of oxygen in order to grow/live

facultative anaerobe

An organism that makes ATP by aerobic respiration if oxygen is present but that switches to anaerobic respiration or fermentation if oxygen is not present.

microaerophilic

requires only a small amount of oxygen

anaerobe

does not utilize oxygen (any organism that is able to live without oxygen)

obligate anaerobe

lacks the enzymes to detoxify oxygen so cannot survive in an oxygen environment

aerotolerant anaerobes

do not utilize oxygen but can survive and grow in its presence

capnophile

grows best at higher CO2 tensions than normally present in the atmosphere

acidophile

an organism that grows best at low pH; typically below pH 6

obligate acidophiles

grow at extreme acid pH (very low pH)

alkalinophiles

grow at extreme alkaline pH (very high pH)

halophiles

require a high concentration of salt

osmotolerant

do not require high concentration of salt/solute but can tolerate it when it occurs

barophiles

can survive under extreme pressure and will rupture if exposed to normal atmospheric pressure

Mutualism

symbiotic relationship in which both species benefit from the relationship

Commensalism

symbiotic relationship in which one organism benefits and the other is unaffected

Parasitism

symbiotic relationship in which one organism benefits and the other is harmed

Synergistic Relationship/Synergism

non-symbiotic relationship, but members cooperate to produce a result that benefits all

Antagonistic Relationship/Antagonism

non-symbiotic relationship, actions of one organism affect or harm the success or survival of others in the same community

biofilms

microbes living and working together on a surface

quorum sensing

The ability of bacteria to sense the presence of other bacteria via secreted chemical signals.

-sense how many others are around them

Biofilm establishment

Microbes:

1. attach to a surface

2. secrete glycocalyx

3. perform quorum sensing

4. become in sync genetically

5. secrete digestive enzymes & harvest food in unison

binary fission

type of asexual reproduction in which an organism replicates its DNA and divides in half, producing two identical daughter cells

generation time (doubling time)

the time it takes for a complete fission cycle (time it takes for microbial population to double in number)

-examples: E.coli = 20 minutes, Staph. aureus = 30 minutes

exponential growth

Growth pattern in which the individuals in a population reproduce at a constant rate

Each new fission cycle increases the population by a factor of 2

Lag phase (population growth curve)

"flat" period of adjustment, enlargement; little growth

Exponential growth phase (population growth curve)

a period of maximum growth will continue as long as cells have adequate nutrients and a favorable environment

Stationary phase (population growth curve)

rate of cell growth equals rate of cell death caused by depleted nutrients and O2, excretion of organic acids and pollutants

Death phase (population growth curve)

as limiting factors intensify, cells die exponentially

Three Methods of Analyzing Population Growth

-Turbidity

- Viable colony count

-Direct cell count

Turbidity

degree of cloudiness; reflects the relative population size

viable colony count

spreading samples on plates, then counting the colonies that grow; counts only live cells

direct cell count

count all cells present; automated or manual

enzyme

A type of protein that acts as a biological catalyst to speed up (catalyze) chemical reactions in a living thing; not permanently altered by the reaction

enzymes catalyze (speed up) reactions by

decreases/lowers the activation energy necessary to initiate the reaction

active site

the region on the enzyme where the substrate binds and chemical reaction takes place

denaturation

protein/enzyme destruction - losing its specific structure and hence function (structure & function is destroyed); can be caused by changes in pH or salt concentration or by high temperature.

competitive inhibition

inhibitor outcompetes the substrate for the active site so that the reaction can't take place.

noncompetitive inhibition

regulator molecule "closes the active site for business," by torqueing the enzyme by binding to a regulatory site (it does not bind directly to the active site like a competitive inhibitor).

enzymatic repression

represses at the genetic (DNA) level to stop enzyme production, and therefore, activity.

Aerobic cellular respiration

Producing ATP with oxygen by breaking down glucose (36-38 ATP);

3 steps: glycolysis, Krebs Cycle & Electron Transport Chain (ETC)

Glycolysis - ATP produced?

net of 2 ATP

produced by substrate level phosphorylation

Glycolysis

-Glucose (6 carbons) broken down into 2 molecules of pyruvic acid (3 C)

substrate level phosphorylation

simple process of using a substrate and an enzyme to make ATP

Krebs/TCA Cycle

•Processes pyruvic acid (pyruvate, 3 C each) and generates 3 CO2 molecules

•Produces: ATP, NADH and FADH2 (electron carriers)

Glycolysis - where does it take place?

-takes place in the cytoplasm of the cell (prokaryotes & eukaryotes)

Krebs/TCA Cycle - ATP produced?

•2 ATPs are generated per glucose that began with glycolysis (1 ATP per pyruvate)

-produced by substrate-level phosphorylation

Krebs/TCA Cycle - where it occurs

-takes place in the cytoplasm of prokaryotes

-takes place in the mitochondrial matrix in eukaryotes

Electron Transport Chain (ETC) - where it occurs

•Eukaryotes: Inner mitochondrial membrane

•Prokaryotes: Cell membrane

Krebs Cycle - what happens to the carbons originally from glucose?

all released as CO2 as a byproduct

Reduction & Oxidation mnemonic: OIL RIG

oxidation is loss (of electrons/hydrogen ions)

reduction is gain (of electrons/hydrogen ions)

ETC - first steps

NADH enters the ETC first and is oxidized to NAD+

FADH2 enters 2nd further down the ETC & is oxidized to FAD

Oxidative phosphorylation

produces a lot of ATP by the oxidation of molecules

ETC - ATP produced?

net 34 ATP

produced by oxidative phosphorylation

ETC final electron acceptor (aerobic respiration)

O2 (to produce water)

Where ETC occurs?

•Eukaryotes: Inner mitochondrial membrane

•Prokaryotes: Cell membrane

Anaerobic respiration

•Functions like aerobic respiration except it utilizes oxygen containing ions, rather than free oxygen, as the final electron acceptor of ETC

-some microorganisms can utilize other electron acceptors instead of oxygen (oxygen is not required)

fermentation

A catabolic process that makes a limited amount of ATP from glucose (2 ATP/glucose molecule) without an electron transport chain and that produces a characteristic end product, such as ethyl alcohol or lactic acid.

-occurs in cytoplasm of cell

purpose of fermentation

to regenerate NAD+ so glycolysis can continue

Alcoholic fermentation

-occurs in yeast

-produces ethyl alcohol & CO2 (waste products) in addition to 2 ATP

lactic acid fermentation

-occurs in human and animal muscles and lactic acid bacteria

-produces lactic acid (waste product) in addition to 2 ATP

Photosynthesis - Light Dependent Reactions

•Light energy is captured and converted to chemical energy: ATP and NADPH

Photosynthesis - Light-Independent (Calvin Cycle) Reactions

•The energy from ATP and NADPH (from the light-dependent reactions) is combined (fixed) with CO2 as a carbon source and stored as glucose which can be used by the organism for energy.

ETC - commonality between Cellular Respiration & Photosynthesis?

Both embedded in membranes:

-Respiration (mitochondria or plasma membrane)

-Photosynthesis (chloroplast)

DNA - complementary base pairing

A-T (Adenine-Thymine)

G-C (Guanine-Cytosine)

(no uracil in DNA)

RNA - complementary base pairing

A-U (Adenine-Uracil)

G-C (Guanine-Cytosine)

(no thymine in RNA)