Bio 440 Lecture 2 Exam

Energy from the sun is transformed into chemical energy by which group of organisms?

autotrophs

photoautotrophs

organisms that carry out oxygenic photosynthesis

Provide summary reaction for aerobic respiration

Sunlight → carbon dioxide + water → energized into electrons (glucose)

Reverse aerobic respiration

carbon dioxide + water + energy ← glucose + oxygen

Chemoheterotrophs

requires performed source of organic molecules as source of energy to make ATP and needs fermentation, anaerobic respiration, aerobic respiration EX: kingdom animalia, kingdom fungi, some protista

Metabolism

all chemical reactions occur in a cell

Catabolism

degradation ; breaks down molecuels

Anabolism

biosynthesis ; forms molecules

Requires energy?

anabolism ; phosphorylation

Releases energy?

Catabolism ; hydrolysis

Which molecule links catabolism and anabolism

Sub units

ATP

Adenosine triphosphate

Where are high energy bonds located in ATP

upon hydrolysis bonds between 3rd or 2nd phosphate group

Role of ATP in metabolism

energy ; pays for everything

Oxidation

loss of electrons and H atoms

Reduction

gain of electrons and H atoms

Redox Reaction

oxidation and reduction coupled together

How is energy transfer related to oxidation-reduction

involves the transfer of electrons from one molecule to another

Oxidation

loss of electrons and energy is released when molecule is oxidized

Reduction

refers to gain of electrons and energy is stored in reduced molecule

In the following reaction, identify which molecule is oxidized, reduced; AH2 + B → A + BH2

AH2 is oxidized to A, B is reduced to BH2

Formula for complete oxidation of one molecule of glucose in the presence of O2 to CO2 and H2O, which is oxidized which is reduced

C6H12O6 + 6CO2 + 6H2O + energy (ATP); C6H12O6 is oxidized to CO2, O2 is reduced to H2O

Catalysts

substance that increases rate of chemical reaction

Enzymes

Protein catalysts

What role do enzymes perform in cells

Speed up chemical reactions by lowering activation energy

What does the suffix -ase mean

Enzymes will often end in -ase

Why can’t heat be used to increase speed of chemical reactions in cells

heat will cause denaturation

Ribozymes

ribonucleic acid enzyme that catalyzes chemical reaction

Substrate

cock and key fit between enzyme and substrate

Are enzymes specific for their substrate and what determines the specificity

Yes, the binding into the active site determines specificity

Reaction showing interaction of enzyme, substrate, and resulting products

E + S → ES Complex → E+P

What is the induced fit model of enzyme, substrate interaction

Induced fit: when substrate fits into enzyme the enzyme adjusts to fit substrate

How does PH affect enzyme activity

enzyme sensitive to PH, changes lead to enzyme active site change shape and charge; extreme PH → denaturation

What is meant by substrate saturation of an enzyme

When all enzyme active sites are filled up by substrate molecules = maximum capacity

Cofactors

assist enzyme in catalyzing reactions

Coenzymes

helps transfer chemical groups between enzymes

Name 2 coenzyme that act as hydrogen atom/electron carriers

NAD+ and FAD

What do NAD+ and FAD role in glycosis and aerobic respiration

act as electron carrier during glycosis and aerobic respiration

Which role do vitamins play with regard to coenzyme structure

NAD+: niacin Vitamin B3, FAD: riboflavin Vitamin B2

The bacterial enzyme which forms the peptide crosslinks in peptidoglycan is called

bacterial transpeptidase

if these peptide bonds are not formed what will happen if the bacterium is growing in a hypoosmotic environment

peptidoglycan is weakened

Alexander fleming discovered penicillium produced an antibiotic called ____ which belongs to the ____ group of antibiotics

Penicillium, domain eukarya

penicillin acts as an ______ inhibitor of which bacterial enzyme

irreversible, competitive; bacterial transpeptidase

When penicillin binds to its target, which function is inhibited

Transpeptidase

what is the consequence of the activity of penicillin

turns off

penicillin cannons cross the hydrophobic ___ of many gram-negative bacteria. Semi synthetic beta-lactams such as ampicillin and amoxicillin are chemically modified penicillin which can cross the ____ of many grma negative bacteria thus amoxicillin and ampicillin have broader _____t han penicillin

Outer membranes; outer membranes; spectrum

it was discovered these penicillin-reisstant staphylococcus aureus were making an enzyme called beta lactamase which hydrolyzes the beta lactam ring of penicillin, ampicillin, and amoxicillin, destroying their ability to inhibit____

beta lactamase; bacterial transpeptide

methicillin could not fit into the ___ of bacterial beta-lactamases.

active site

aureus infections was to use clavulanic acid, a ____ inhibitor of beta-lactamase

Competitive inhibitor

MRSA produce a mutant bacterial ____ to which beta-lactam antibiotics cannot bind thus MRSA can grow in the presence of beta-lactam antibiotics

transpeptidase

Vancomycin prevents _____ of peptidoglycan by binding to the peptide tails of peptidoglycan preventing bacterial transpeptidase from forming peptide crosslinks

crosslinking

Metabolic pathway

connected reactions that convert starting molecule into end product; each step catalyzed by enzyme

What are intermediates of a metabolic pathway

intermediates molecules formed by step by step conversion of substrate to final product

glycosis

first step in breakdown of glucose to take energy for cellular metabolism, occurs in cytoplasm of bacterium, in eukaryote glycosis occurs in cytoplasm, does not require O2

Is ATP produced in glycosis synthesized by substrate level phosphorylation or oxidative phosphorylation using chemiosmosis

ATP produced in glycosis synthesized by substrate level phosphorylation

Why are 2 ATP used at the start of glycosis

2 ATP molecules used to make more reactive, easier to break down

During glycolysis, high energy electrons are stripped from glucose and transferred to NAD⁺. Could the high energy electrons of reduced NADH be used to perform cellular work? Explain.(hint: requires ETC. see respiration section)

Yes, requires electron transport chain (ETC)

Do glycolytic intermediates play any role in biosynthetic reactions/anabolism? Explain.

Yes diverted into anabolic pathways to synthesis biomolecules

Is glycolysis common to both fermentation and aerobic/anaerobic respiration?

Yes, glycosis is first step in fermentation and aerobic respiration

What will happen if NADH is NOT oxidized?

If NADH is not oxidized, cell will run out of NAD+ which is needed for glycosis

If a bacterium is living anaerobically and lacks an ETC, how can it oxidize NADH?

must rely on fermentation to oxidize NADH

Describe atmospheric conditions on primitive earth.

methane, ammonia, hydrogen, water vapor, carbon dioxide and anoxic= no amount of free o2

Why did the first cells have to perform fermentation?

bc no O2 in atmosphere for aerobic respiration

Fermentation

Chemical breakdown of a substance by bacteria yeast or other microorganisms

Who first described fermentation as "life in the absence of air"?(Pasteur)

Louis Pasteur

Describe the steps involved in lactic acid fermentation and describe which organisms carry out these processes.

1 glucose broken down into pyruvate through glycosis producing 2 ATP and 2 NADH

2 pyruvate is reduced to lactiv acid by lactate dehydrogenase while NADH is oxidazed back into NAD+

Describe the steps involved in alcoholic fermentation and describe which organisms carry out these processes.

1 glycosis breaks down glucose into pyruvate producing 2 ATP and 2 NADH

2 Pyruvate is decarboxylated to acetaldehyde and CO2

3 acetaldehyde is reduced to ethanol by alcohol dehydrogenase with NADH oxidized to NAD+

How much ATP is produced from the fermentation of one molecule of glucose?

fermentation produces 2 ATP per glucose molecule

Are the endproducts of fermentation pathways of any commercial/beneficial use?

Yes, yogurt, buttermilk, kefir, cheese made through lactid acid fermentation by lactid acid bacteria

human microbiome

collection of microorganisms that live on and in the human body

Intestinal microbiome

community of microbes that reside in human digestive tract

What are lactic acid bacteria? (LAB's).

group of gram positive bacteria that produce lactid acid as a end product of fermentation

How do lactic acid bacteria make ATP?

generates ATP through substrate level phosphorylation

How may LAB's and other members of the human microbiome be helpful to humans?

contributes to vitamin synthesis, immune activation, and modulation, bioactive inhibation of pathogens

What are examples of probiotics?

lactobacillus and bifidobacterius

How may probiotics promote good health in humans/animals?

live microorganisms that when consumed offer health benefits

what are "pre-biotics"?

non digestable fibers that promote growth of beneficial bacteria in gut

What are some of the negative consequences when humans take broad spectrum antibiotics?

can disrupt normal balance of mcirobiome, killing both harmful and beneficial bacteria leading to candida overgrowth

What are fecal transplants? How may they be useful?? Explain

transferring of stool from healthy donor into gut of patient to restore natural balance of bacteria, effective in treating C. dificle infections

Anaerobic

without oxygen

Aerobic

With oxygen

Why was the evolution of porphyrin molecules important?

important to photosynthesis and cellular respiration

How did the evolution of chlorophyll and oxygenic photosynthesis change the Earth’s atmosphere?

allowed organisms to perform oxygenic photosynthesis, uses water as electron donor and produces oxygen as byproduct → cyanobacteria were first organisms to perform oxygenic photosynthesis leading to great oxygenation event

 What was the significance of evolution of cytochromes and the electron transport chain?

allowed for development of electron transport chain important to aerobic respiration, ETC enables more efficient ATP production through oxidative phosphorylation providing more energy

Does fermentation use internal organic or external inorganic terminal electron acceptors?

uses internal organic terminal electron acceptors and occurs in absence of oxygen

Does aerobic respiration use internal or external terminal electron acceptors?

uses external inorganic terminal electron acceptors like oxygen

The pyruvate dehydrogenase (PDH) complex catalyzes the reactions we described as the “Krebs Prep”. Where is this complex located in prokaryotes? In eukaryotes?

located in cytoplasm of prokaryotes and in mitochondria of eukaryotes

Write an equation describing the reactions catalyzed by the PDH complex, the "Krebs Prep".

pyruvate + NAD+ + CoA → Acetyl-CoA + NADH + CO2

What is “oxidative decarboxylation”? (removal of electrons and release of carbon as carbon dioxide)

removal of electrons and release of carbon as carbon dioxide

How do carbons from glucose enter the Krebs/TCA cycle? As_______(as acetyl group donated from Acetyl-CoA. The acetyl group still carries 2 carbons and lots of high energy electrons which once were part of glucose).

acetyl

Write a reaction for the first step of  the Krebs Cycle.

pyruvate + NAD+ + CoA → Acetyl-CoA + NADG + CO2

Why is the Krebs Cycle also called the TCA Cycle (Tricarboxylic Acid Cycle) or Citric Acid Cycle?

carbons from glucose enter the krebs cycle as an acetyl group donated by acetyl-CoA

Prior to evolution of respiration, did some of the enzymes of the Krebs Cycle play a role in anabolism?

yes, for amino acid and nucleotide synthesis

Do some Krebs Cycle intermediates act as reactants for anabolic/biosynthetic pathways

yes: some Krebs Cycle intermediates are used in amino acid synthesis and nitrogenous base synthesis for nucleotides

Describe how many NADH, FADH₂, CO₂ ,ATP are produced per glucose molecule in the Krebs Cycle.

6 NADH 2 FADH2 4CO2 2 ATP

Where is the Krebs Cycle located in bacteria?(cytoplasm) eukaryotes(mitochondria)?

Bacteria: cytoplasm

Eukaryotes: mitochondria

What major function does the Krebs Cycle perform in respiration?

removes all the remaining high energy electrons which once were part of glucose, finishes oxidation, transfers the electrons to NAD+ and FAD for transport to the ETC; while removing the electrons, Krebs Cycle finishes tearing apart the carbon  skeleton of what was once glucose, releasing the carbons as carbon dioxide

Do anaerobes have some enzymes of the Krebs Cycle?

yes; these enzymes probably first evolved in biosynthetic pathways, can function without molecular oxygen photosynthetic pigments (bacteriochlorophyll and chlorophyll a) and anoxygenic and oxygenic photosynthesis.

Impacts on Earth’s atmosphere when chlorophyll a evolved?

increase in O2 levels

which organism first evolved chlorophyll a?

cyanobacteria