Exam 3 BIOL 2051 Brininstool

What are the core macronutrients

carbon, oxygen, nitrogen, hydrogen, phosphorus, and sulfur

What percentage of the dry weight of the cell is made of macronutrients?

96%

What percentage of the dry weight of the cell is made of other macronutrients found in some microorganisms?

3.7%

What are the macronutrients found in some but not all microorgansims?

potassium, sodium, calcium, magnesium, chlorine, and iron.

How many different elements can microbes metabolize?

62

What macromolecules are cells composed of?

proteins, lipids, polysaccharides, lipopolysaccharides, and nucleic acids.

Why is carbon needed?

is it needed to make organic compounds such as amino acids, fatty acids, sugars, nitrogenous bases

How do heterotrophs obtain carbon?

Through organic compounds

How do autotrophs obtain carbon?

Through CO2

How do autotrophs break down CO2 to obtain carbon?

Through CO2 fixation which involves

-calvin-benson cycle

-reverse citric acid pathway

-hydroxypropionate pathway

-acetyl-CoA pathway

•Most phototrophs and chemolithotrophs, many chemoorganotrophs

How do heterotrophs obtain carbon from organic compounds?

Use some of the same pathways as autotrophs but different entry ways.

•Many chemoorganotrophs, some phototrophs and chemolithotrophs (mixotrophic)

Where does the calvin benson cycle occur in heterotrophs?

chloroplast stoma

Where does the calvin benson cycle occur in autotrophs

carboxysomes

Calvin-Benson cycle

Cyclic carbon-fixing pathway that builds sugars from CO2; the light-independent reactions of photosynthesis.

What goes into the calvin-benson cycle

CO2, ATP, and NAD(P)H

Where does CO2 come from in the calvin-benson cycle for autotrophs

the environment

Where does the ATP and NADH come from in the calvin-benson cycle?

inside the cell, through respiration and or photosynthesis (etc)

What comes out of the calvin-benson cycle

sugar

what are the intermediates in the calvin-benson cycle?

3-phosphoglycerate

1,3-biphosphoglycerate

glyceraldehyde 3-phosphate

ribulose 5-phosphate

ribulose 1,5-phosphate

Reverse citric acid cycle

used for photosynthesis green sulfur in bacteria like chlorodium and used by chemolithostrophic bacteria and archaea.

What goes into the reverse citric acid cycle?

NADH, FADH, CO2, and ATP

What comes out of the reverse citric acid cycle?

sugar

Hydroxypropionate pathway

used by photosynthetic green nonsulfur bacteria Chloroplexus and species of thaumarchaeota

what goes into to the Hydroxypropionate pathway?

CO2, ATP, NADPH

What come out of the Hydroxypropionate pathway?

2 carbon glyoxylate used to build cell material.

Acetogenisis

Takes in CO2 and makes a 2 carbon acetate

What comes in in acetogenisis?

CO2, ATP, NADH, H2

What does oxic mean?

environment contains oxygen

What does anoxic mean?

environment lacks oxygen

aerobes

can grow and respire at full oxygen tention

anaerobes

cannot respire in the presence of oxygen

obligate anerobes

require oxygen to grow and respire. They use anerobic respiration as their metabolism.

Facultative aerobes

oxygen is not required but they grow better with it. They use aerobic and anaerobic respiration for their metabolism.

Microaerobic aerobes

Oxygen is required but at a much lower level. They use aerobic respiration for their metabolism.

aerotolerant anaerobes

can tolerate O2 and grow but can not respire. They use fermentation as their metabolism

Obligate anaerobes

O2 is harmful or lethal to the cell. They use fermentation or anaerobic respiration for their metabolism.

What does a reducing agent due?

reacts with oxygen to from water

What is a reducing agent used for?

To remove oxygen from a broth

Explain Thioglycolate broth

it is a reducing agent and is used to test an organisms requirement for oxygen, oxygen only present at air interface.

In lab, what conditions to aerobes need?

-a culture medium oxygenated

-allowed exposure to air

-vigorous shaking

-bubbling sterile air into the medium

In lab, what conditions to anaerobes need?

-oxygen excluded from culture medium

-bottles/tubes complelty filled and sealed with medium

-use a reducing agent

-anoxic jars

-anoxic glove boxes

What are the toxic forms of Oxygen

O2-, H2O2, OH

Is oxygen by itself toxic to anaerobic cells?

No, it is the by products produced during cell respiration.

How does catalase help break down toxic oxygen?

this enzyme helps break down hydrogen peroxide (H2O2) into 2 H2O and O2

How does peroxidase help break down toxic oxygen?

This enzyme helps break down hydrogen peroxide (H2O2) into 2 H2O and NAD+

How does superoxide dismutase help break down toxic oxygen?

It helps break down superoxide (O2-) into H2O2 and O2

How does superoxide reductase help break down toxic oxygen?

it helps break down superoxide into 2 H2O and 3 O2

Why is nitrogen needed?

to make amino acids and nitrogenous bases.

What is nitrogen fixation?

the use of nitrogenase to convert atmospheric nitrogen (N2) into ammonia (NH3)

What is a nitrifyer?

a cell that uses inorganic compounds ammonia and nitrite (NO2) for nitrification.

What 2 enzymes make up nitrogenase?

dinitrogenase reductase and dinitrogenase

What is the purpose of nitrogenase?

The fixing of nitrogen

heterocysts

a specialized cell that engages in nitrogen fixation and protects nitroginase. This part of the cell has no oxygen.

What are the 10 macronutrients?

Carbon, Oxygen, Nitrogen, Hydrogen, Phosphorus, Sulfur, Potassium, Magnesium, Calcium, Sodium

What is Phosphorus used for and what source does it come from?

is used to make nucleic acids and phospholipids. It is found in phosphate minerals and free phosphate.

What is sulfur used for and what source does it come from?

amino acids cysteine and methionine and other vitamins, iron-sulfur proteins. It is found in sulfates (SO42-) or sulfides (S2-)

What is Potassium used for and what source does it come from?

It is used for enzymes like pyruvate kinase and to maintain solute concentration. It can be found in free K+ and K salts

What is Magnesium used for and what source does it come from?

It is used for stabilizing ribosomes, membranes, and nucleic acids and is required by many enzymes like DNA polymerase. It can be found in salts in various minerals.

What is Calcium used for?

stabilizing the cell walls

endospores - calcium-dipicolinic acid complex

What is sodium used for?

marine microorganisms

stabilizes cell walls, binds to acidic amino acids

used by Na+-powered ATP synthase

What are the 11 micronutrients?

boron, cobalt, copper, iron, manganese, molybdenum, nickel, selenium, tungsten, vanadium, and zinc.

Micronutrients are needed in what kind of amounts?

very small amounts

Why is iron an important micronutirent?

It is needed for electron transport chain proteins

What is a siderophores?

these molecules bind to iron in the environment and transport it into the cell.

What are Enterobactins?

A molecule certain bacteria have to obtain iron from its environment.

What are Aquachelin?

A type of siderophore that aquatic species have that help them gather iron.

How do growth factors differ from macro and micro nutrients?

Growth factors can be made by the cell and or absorbed from outside sources.

What are the growth factors?

P A B A (p-aminobenzoic acid)

Folic acid

Biotin

B12 (Cobalamin)

B1 (Thiamine)

B6 (Pyridoxine)

Nicotinic acid (Niacin)

Riboflavin

Pantothenic acid

Lipoic acid

Vitamin K

Coenzymes M and B

F420 and F430P A B A (p-aminobenzoic acid)

Folic acid

Biotin

B12 (Cobalamin)

B1 (Thiamine)

B6 (Pyridoxine)

Nicotinic acid (Niacin)

Riboflavin

Pantothenic acid

Lipoic acid

Vitamin K

Coenzymes M and B

F420 and F430

true or false: organic compounds are needs in very small amounts for growth factors

true

Metabolism

sum of all reactions making energy

catabolic

the breakdown of molecules to make energy

anabolic

biosynthetic (uses energy)

Oxidation

loss of electrons

reduction

gaining of electrons

How are redox reactions coupled?

electron donor transfers electrons to acceptor

donor is oxidized and acceptor is reduced

electron carriers

Accepts the electrons that are oxidized and or carry electrons where they need to go.

they are membrane bound

freely diffusible coenzymes

what can glycolysis make form 1 glucose molecule?

2 pyruvate, 2 NADH, and 2 ATP

What is another name for glycolysis

Embden-Meyerhof pathway

what is chemiosmosis

it generates ATP using proton gradient

how many molecules of ATP can come from 1 NADH

3

where does the Calvin cycle take place?

the stroma

chemoorganotroph

an organisms that ferments sugars and a pathogenic bacterium that lives in the human body

chemolithortroph

an organism that uses chemical energy to oxidize H2S

photoheterotroph

an organism that generates ATP using light and that cant fix CO2 to build organic molecules

photoautrotrophic

an organism that uses oxygenic photosythesis

gluconeogenisis

the process of synthesising fluxe from other compounds

what are pentose sugars needed for?

for nucleic acid sythesis

what does lipases do?

breaks down lipids

in a pentose phosphate pathway anabolic or catabolic?

anabolic

explain oxidative phosphorylation

a proses where ATP is generated using energy realsed from the electron transport chain.

is oxidative phosphorylation anabolic or catabolic?

catabolic

how does NAD+ help enzymes

functions as a cofactor

What are the short term energy storage coumpounds?

Adenosine triphosphate (ATP)

What are the long term energy storage compounds?

glycogen, Poly-beta-dyroxybutyrate, and elemental sulfur

phosphate level phosphorylation

a phosphate is donated to ADP to make ATP

oxidative phosphorylation

a free phosphate is given to ADP to make ATP through ATP synthase

what does dehydrogenase do?

transfer two hydrogen atoms from organic compounds to several molecules acting as electron acceptors, thereby oxidizing the organic compounds and generating energy

What are examples of dehydrogenases?

Glyceraldehyde-3-P dehydrogenase: glyceraldehyde-3-P to 1,3-bisphosphoglycerate in glycolysis

What does Kinase do?

it phosphorylates

What are some examples of Kinases?

Hexokinase, pyruvate kinase.