Microbiology: Exam 2

anabolism

reactions that require energy to synthesize complex molecules from simpler ones

catabolism

reactions that release energy by breaking complex molecules intro simpler ones that can be used as building blocks

metabolism\`

sum of all the chemical processes carried out by an organism

oxidation

loss of electrons/energy; catabolism

reduction

gain of electrons/energy; anabolism

oxidizing agent

electron acceptor

reducing agent

electron donor

negative reduction potential

potential to donate electronsp

positive reduction potential

potential to accept electrons

autotroph

use CO2 for carbon

photoautotrophs

use CO2 for carbon and light for energy

chemoautotroph

use CO2 for carbon and inorganic compounds for energy

heterotroph

use organic compounds for carbon

photoheterotroph

use organic compounds for carbon and light for energy

chemoheterotroph

use organic compounds for carbon and energy

c6h12o6 + 602 → 6co2 + 6h20 + energy

respiration

6co2 + 6h20 → c6h12o6 + 6o2

photosynthesis

metabolic pathway

a series of chemical reactions required to convert substrate into product

catabolic pathway

convert the energy in molecules into a chemical form that cells can usea

anabolic pathways

use energy to construct complex molecules

endoenzymes

intracellular

exoenzymes

extracellular

enzyme activity

rate at which enzyme converts substrate to product

coenzyme

non protein organic molecule that carries electrons

cofactor

inorganic ion that improves fit of an enzyme

naming enzymes

end in -ase

competitive inhibitor

similar to substrate and binds to active siten

noncompetitive inhibitor

attaches to allosteric site and changes active site shape; reversible

feedback inhibition

regulates the rate of many metabolic pathways when an end product of a pathway accumulates and binds to and inactivates an early enzyme in the metabolic pathway

factors that affect enzyme activity

temperature, pH, concentration (substrates, products, enzymes)

anaerobic metabolism

catabolic pathways that do not use oxygen; glycolysis, fermentation, anaerobic respiration

glycolysis

In: glucose, 2 ATP; Out: 2 NADPH, 4 ATP, 2 pyruvate; anaerobic; cytoplasm; all organisms

phosphorylation

addition of a phosphate group to a molecule, increasing the molecule’s energy

substrate level phosphorylation (glycolysis)

captures energy by transferring phosphate directly from substrates to ADP, trapping the energy as ATP

fermentation

catabolic pathway in which final electron acceptor is an organic molecule; anaerobic; begins with glycolysis; pyruvic acid is reduced by electrons from NADH to NAD+, which is needed to continue glycolysis

lactic acid fermentation

pyruvic acid is reduced to lactic acid as NADH is oxidized to NAD+; lactobacilli, streptococci, mammalian muscle

alcoholic fermentation

pyruvic acid is split into acetaldehyde and CO2; acetaldehyde is reduced to ethanol as NADH is oxidized to NAD+; yeasts

butanediol fermentation

detected by Voges Proskauer test for acetoin; klebsiella pneumoniae

butyric acid fermentation

clostridium species; rancid butter and cheese

stages of aerobic respiration

pyruvate oxidation, Krebs cycle, electron transport

pyruvate oxidation

In: 2 pyruvate; Out: 2 CO2, 2 NADH, 2 acetyl CoA; pyruvate is decarboxylated and the resulting acetyl group is oxidized and NAD+ is reduced to NADH; 2-carbon acetyl group is linked to CoA to form acetyl CoA

Krebs Cycle

In: 2 acetyl CoA, 6 H2O; Out: 4 CO2, 6 NADH, 2 FADH2, 2 ATP; acetyl groups are combined with 4 carbon oxaloacetic acid to form 6 carbon citric acid and a series of oxidation steps harvest energy from the intermediates; in prokaryotes, cytoplasm; in eukaryotes, mitochondrial matrix

Krebs Cycle Step 1

2 carbon acetyl group is combined with oxaloacetate to form citric acid

Krebs Cycle Step 2

Citric acid is isomerized to isocitric acid

Krebs Cycle Step 3

Isocitric acid turns to alpha ketoglutaric acid as NAD+ is reduced to NADH

Krebs Cycle Step 4

alpha ketoglutaric acid is converted to succinyl CoA as NAD+ is reduced to NADH

Krebs Cycle Step 5

succinyl CoA is converted to succinic acid using H2O and CoA is released; GDP + P turns to GDP and ADP turns to ATP as GTP turns back to GDP

Krebs Cycle Step 6

succinic acid is converted to fumaric acid as FAD is reduced to FADH2

Krebs Cycle Step 7

fumaric acid is converted to malic acid using H2O

Krebs Cycle Step 8

malic acid converts to oxaloacetic acid as NAD+ is reduced to NADH

electron transport

transfers electrons from NADH to FADH2 to oxygen through a series of membrane bound electron carrier molecules

oxidative phosphorylation

addition of phosphate to ADP to form ATP using energy transferred in electrons

electron transport and oxidative phosphorylation

in: 10 NADH, 2 FADH2, 6 O2; Out: 34 ATP, 12 H2O

chemiosmosis

formation of ATP by ATP synthase (ATPase)

Total Energy from Aerobic Respiration

2 from Glycolysis; 2 from Krebs Cycle; 34 from oxidative phosphorylation; 38 ATP total

Complex I

NADH dehydrogenase complex

Inorganic electron acceptors in anaerobic respiration

nitrate, sulfate, ferric iron

light reactions

light is absorbed by chlorophyll and energy is used to generate ATP and NADPH

dark reactions

calvin cycle; CO2 is reduced to carbohydrate using energy in ATP and hydrogen atoms from organic NADPH or inorganic H2S molecules

bacterial photosynthesis

hydrogen to build carbohydrates comes from H2S and elemental sulfur is produced as a byproduct

photosynthesis in plants

hydrogen to build carbohydrates comes from H2O and O2 is produced as a byproduct

cyclic photophosphorylation

excited electrons are passed through an electron transport chain and energy depleted electrons are returned to chlorophyll

noncyclic photoreduction

excited electrons are passed through an electron transport chain then transferred to NADP to form reduced NADPH; electrons in chlorophyll are replaced from water which is split into electrons, protons, and O2 in photolysis

photosystem II

In: water, light; Out: oxygen, ATP; first; P680

photosystem I

In: light, e- from photosystem II; Out: NADPH; second; P700

Calvin Cycle

carbon fixation: rubisco converts 6 carbon compound to 3PGA; reduction: ATP and NADPH are used to convert 3PHGA to G3P and ATP and NADPH turn to ADP and NADP+; regeneration: G3P make glucose or are recycled to regenerate RuBP

Watson and Crick Model

double helix, rule of complementarity, antiparallel

methylation

bacteria silence DNA with big CH3 molecules

cistron

1 complete gene with an area for promoter to attach; recipe for 1 complete protein

gene

DNA sequence that creates an amino acid chain

locus/loci

where gene is located on chromosome

semiconservative model of DNA replication

1 dna strand is template for new one so there is 1 old strand and 1 new strand

plasmids

extra genetic information that is helpful but not needed

gene

basic unit of heredity

central dogma

dna is replicated to provide daughter cells with dna; dna is transcribed to mrna; mrna is translated into protein on ribosomes (rRna)

retroviruses and reverse transcriptase

transcribe RNA to DNA

replication fork

site of replication for prokaryotes

dna helicase

separates two strands of DNA by breaking hydrogen bonds between them

DNA gyrase

relieves supercoiling of DNA

DNA polymerase III in prokaryotes

adds nucleotides to replicate DNA and proofreads

leading strand

strand of DNA that is made continuously

okazaki fragments

small pieces of dna replicated on lagging strand

lagging strand

strand of DNA that cannot be replicated continuously

replication

both strands act at templates to direct the synthesis of new complementary strands

transcription

one strand of DNA acts as a template to direct the synthesis of a new complementary strand

translation

an RNA molecule uses a ribosome to create a polypeptide chain

RNA primase

creates a short RNA primer complementary to each strand

DNA polymerase I

removes primer and replaces it with DNA

DNA ligase

joins the sugar phosphate backbones together

lymeraseRNA

separates two DNA strands and makes a complementary rna copy of one of the strands by linking rna nucleotides together, adding them one by one to a 3’ end

promotoers

sequences of nucleotides in dna that are recognized by rna polymerases as places to start transcription

exons

coding regionsi

ntrons

non coding regions

ribosomal rna

forms part of the structure of ribosomes where proteins are constructed

subunits of prokaryotic ribosome

30S and 50S

subunits of eukaryotic ribosome

40S and 60S

messenger RNA

directs the synthesis of one polypeptide chain; read by ribosome

codon, sense codon

a sequence of 3 nucleotides in an mrna sufficient to specify 1 amino acid

start codon

AUG, methionine; where to begin translation

stop codon, nonsense codon, terminator

UAA, UAG, or UGA; signals where on mrna the ribosome will stop translation