Microbiology Exam 3 Flashcards by Katie De Leon

Totality of physical and chemical processes that occur in a cell.

Metabolism

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Synthesis of cell products

Requires energy

Anabolism

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Breakdown of large molecules into smaller ones

Releases energy

Catabolism

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Pathways of metabolic schemes are generally

complex and detailed

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All biochemical reactions need the presence of a specific and special class of proteins called

enzymes

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Properties of enzymes

Become physically attached to substrate
Participate in bonding
Do not become part of its products
Not used up by the chemical reaction
Can function over and over again

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Minimum energy input necessary for reactants to form products in a chemical reaction
Less if enzyme is present
More if enzyme is absent or in low concentration

Energy of Activation

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Types of enzymes

Simple
Protein alone
Conjugated or holoenzyme(enzyme with cofactor)
Protein (apoenzyme=inactive) + non-protein (organic/inorganic cofactors)

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The protein part of an enzyme

Apoenzyme

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Short (100 amino acids) to very long chains (10^6 amino acids)

Apoenzyme

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Molecular complexity (1-2-3-4-type of organization)

Apoenzyme

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Unique active or catalytic sites for substrates to fit

Apoenzyme

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Complex organic molecules, several of which are derived from vitamins (nicotinamide, riboflavin)
NAD = nicotinamide adenine dinucleotide
FAD = flavin adenine dinucleotide

Coenzymes

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Role of coenzymes

Carrier of functional groups [CO2, (NH3+ = amino group NH2), and others]
Work with apoenzyme to perform necessary alterations in a substrate
Removal of functional groups
Serve as transient carriers of specific atoms or functional groups during metabolic reactions

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These enzyme accessories can be
organic such as coenzymes
inorganic, such as Fe2+, Mn2+, or Zn2+ ions
Metals participate in precise functions between the enzyme and the substrate

Cofactors

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Role of cofactors

Activate enzymes
Help bring the active site and substrate close together
Participate directly in chemical reactions with the enzyme-substrate complex

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Specific region where the substrate binds to the apoenzyme

Site for reaction catalysis

Active or catalytic site

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Steps involved in a chemical reaction

Enzyme fits substrate at the active site and forms a complex
Bonds are formed between enzyme and substrate
Reactions occur on the substrate
Cofactor aids in the reactions
Product is formed and released
Enzyme attaches to another substrate molecule
Cycle is repeated

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C6H12O6 + 6O2 ==> 6CO2 + 6H2O + energy(ATP+heat)

Organic compounds + oxygen ==> carbon dioxide + water + energy

Aerobic respiration

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Oxidation or breakdown of glucose into two molecules of pyruvic acid
Occurs in the cytoplasm of all cells
It is the most commonly used sequence of reactions for the conversion of glucose into pyruvate
Produces 2 ATP’s, 2 NADH’s and 2 H2O molecules
Does not require oxygen

Glycolysis (Embden-Meyerhof-Parnas pathway)

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Discovered by Egleston and Krebs
Occurs in the cytoplasm of prokaryotes and in mitochondria of eukaryotes
Process the final 2-C molecule (Acetyl-CoA) coming from pyruvic acid obtained from the degradation of glucose (6C) via glycolysis
Cycle has 8 steps, reduces 2 FAD and 8 NAD’s, releases 2 CO2 and produces 2 ATP’s by substrate level phosphorylation

Tricarboxylic acid cycle (TCA) or Krebs cycle

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Occurs in cell membrane of prokaryotes and in mitochondria of eukaryotes
Made of a chain of special redox carriers that received electrons from reduced carriers
Produces 34 ATP’s and 6 H2O molecules
In aerobic metabolism, oxygen is the final electron acceptor and combines with H ions (protons) to form water
In aerobic metabolism, other ions may act as final electron acceptors

Electron transport system (ETS)

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Explains the origin and maintenance of electro-potential gradients across a membrane that leads to ATP synthesis, by ATP synthase (oxidative level phosphorylation)
The energy obtained is used to regenerate up to 38 ATP (this number may vary among microbes) for each glucose molecule catabolized

Chemiosmotic theory

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Glycolysis
Tricarboxylic acid cycle (Krebs cycle)
Electron transport system (ETS)

Aerobic respiration

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Anaerobic respiration

Fermentation | Fermentor

The anaerobic enzymatic conversion of pyruvic acid to organic acid or alcohol or other organic compounds producing energy in the form of ATP Incomplete oxidation of glucose or other carbohydrates in the absence of O2 Organic molecules can serve as final electron acceptors Inorganic salts can also serve as electron acceptors: NO3-, SO4^-2, CO2, ATP, organic acids, H2S, CH4 2 ATP's maximum per glucose molecule 25% of the energy of glucose transferred to ATP

Fermentation

Occurs in facultative anaerobes, aerotolerant, strict anaerobes Allows independence from O2 and allows colonization of anaerobic environments Enables microorganisms with a versatile metabolism to adapt to variations in the availability of oxygen Bacteria that digest cellulose in the rumen of cattle are largely fermentative providing the animal glucose, a source of energy The phosphogluconate pathway is an alternative anaerobic pathway

Anaerobic respiration | Fermentation *

A large tank used in industrial microbiology to grow mass quantities of microbes that can synthesize desired products These devices are equipped with means to stir, monitor and harvest products such as a variety of organic acids and alcohols in very large quantities

Fermentor

Pertains to the metabolic pathways that serve multiple functions in the breakdown, synthesis, and conversion of metabolites

Amphibolism

Metabolic pathways that connect anabolic and catabolic reactions to improve efficiency Intermediate compounds such as pyruvic acid and acetyl CoA serve multiple functions With comparatively small chemical modifications they can be converted into other compounds and enter a different pathway Catabolism of glucose furnishes numerous intermediates for anaerobic pathways that synthesize amino acids, fats, nucleic acids, and carbohydrates which can serve as building blocks for the synthesis of other compounds

Intermediary metabolism and amphibolic compounds

Reactions that produce and convert amino acids

Amination Transamination Deamination

Pyruvic acid can be converted to amino acids by adding NH4+

Amination

An amino acid such as (aspartic acid) and a carbohydrate (alpha ketoglutaric acid) will make another amino acid (glutamic acid) and oxaloacetic acid

Transamination

Amino acids can be used as a source of glucose (gluconeogenesis) releasing NH4+

Deamination

The study of the inheritance, or heredity, of living things

Genetics

The transmission of biological properties (traits) from parent to offspring The expression and variation of those traits The structure and function of the genetic material; and how this material changes

Scope

The genetic material of a cell that is found in several different forms, with the majority existing as large complexes of DNA and proteins

Chromosome

The sum total of the genetic material residing on chromosomes Viral genomes are different (DNA or RNA)

Genome

independently replicating, small double-stranded DNA molecules found in some bacterial species

Plasmid

Contain genes that are not essential for cell growth Bear genes that code for adaptive traits Transmissible to other bacteria DNA also present in chloroplasts and mitochondria

Plasmid

A site on a chromosome that provides information for a certain cell function A specific segment of DNA that contains the necessary code to make a protein on RNA molecule

Gene

The genetic makeup of an organism | Ultimately responsible for an organism's phenotype, or expressed characteristics

Genotype

The observable characteristics of an organism produced by the interaction between its genetic potential (genotype) and the environment

Phenotype

How many genes does the smallest virus have?

4 or 5

Genomes vary in

Size

What is the length of Escherichia coli?

1 micrometer

What has a single chromosome containing 4,288 genes?

Escherichia coli

What has a chromosome that measures about 1 mm if stretched out it will be about 1,000 times its length

Escherichia coli

A human has about ______ genes distributed into __ chromosomes

30,000; 46

DNA structure

Nitrogenous bases (purines and pyrimidines) Five carbon (pentose) sugars Nucleotide Other terminology

DNA copies itself just before cellular division by the process of

``` semiconservative replication DNA replication (each 'old' strand is the template upon which each 'new' strand is synthesized) Leading strand Lagging strand ```

replicated at two forks as directed by DNA polymerase III At each fork, two new strands are synthesized - one continuously and one in short fragments Mistakes are proofread and removed

circular bacterial chromosome

Types of RNA molecules

``` Messenger RNA (mRNA) Transfer RNA (tRNA) Ribosomal RNA (rRNA) Primer ```

Carries the DNA master code to the ribosome

mRNA

A cloverleaf shape, carries aminoacids to ribosome during translation

tRNA

Structural form of RNA that together with a protein makes a ribosome and participates in protein synthesis

rRNA

An RNA that can begin DNA replication

primer

Cellular structure where protein synthesis occurs Assembly of the small and large subunits results in specific site (P and A) for holding the mRNA and two tRNAs with their aminoacids

ribosome

The flow of genetic information | DNA replication => Transcription => Translation

dogma of biology

mRNA synthesis | The process by which a strand of RNA is produced from a DNA template

Transcription

a newly transcribed RNA molecule

Transcript

Protein synthesis | The process of decoding the messenger RNA code into a polypeptide

Translation

Codons of mRNA that specify a given aminoacid The 4 different nitrogen bases of RNA in all possible combinations of 3 64 codons or triplets (4^3=64) The universal language of life!

Genetic code

Coding sequences (exons) are interrupted at intervals by segments called introns that are not part of the protein's code

The split gene of eukaryotes

transcribed but not translated | junk DNA

introns

removed by RNA splicing enzymes before translation

introns

Genes are active only when their products are required

gene regulation

Genetic function in prokaryotes regulated by a specific collection of genes

operon

consist of a coordinated set of genes, all of which are regulated as a single unit

operon

Types of operons

inducible (turn or switch on) | repressible (turn or switch off)

Best understood operon, accounts for the metabolism of lactose in E. coli

lac operon

illustrates how inducible genes are controlled by substrate

lactose (lac) operon

Control of a gene through excess nutrient | Proof that the environment has a great influence on gene expression

repressible operon

Changes in the genetic code can occur by two means:

1. Mutation (permanent changes in the nucleotide sequence of an organism's genome) 2. Genetic recombination

Types of mutation

Point mutation Nonsense mutation Frameshift mutation

A change that involves the loss, substitution, or addition of one or a few nucleotides Genotype changes but not the phenotype

Point mutation

A mutation that changes an amino acid-producing codon into a stop codon, leading to a premature termination of a protein

Nonsense mutation

An insertion or deletion mutation which changes the codon reading frame from the point of the mutation to the final codon Almost always leads to a nonfunctional protein

Frameshift mutation

Mutations can either be _______

spontaneous (low frequency) or chemically-induced

Genetic recombination in prokaryotes occurs through the processes of:

Transformation Conjugation Transduction

In eukaryotes, genetic recombination occurs through

sexual reproduction

Genes that can relocate from one part of the genome to another, causing rearrangement of genetic material May have either beneficial or harmful consequences for the organism involved

Transposons

Palindromes:

Inverted repeats of an order of nitrogen bases Occur in all cells Vary in size Involved in heavy regulatory function Binding sites for enzymes Provide starting sites for DNA replication Relieve tension in DNA structure

Palindromes are cut or cleaved by ______ at desired sites

restriction enzymes (RE)

They recognize foreign DNA and nick them at these sites

restriction enzymes (RE)

Name 3 restriction enzymes:

EcoRI, HindIII, HaeIII

Types of enzymes

Exoenzymes Endoenzymes Constitutive Regulated enzymes

Extra-cellular action Hydrolysis Penicillases, cellulase, amylase

Exoenzymes

Intra-cellular action | Most are of this type

Endoenzymes

Always present and in constant amount in cell regardless the amount of substrate

Constitutive enzymes

Not in constant amounts in cell Produced only when substrate is present (inducible) Turned off when substrate is absent (repressed)

Regulated enzymes

Factors affecting enzyme activity

``` Temperature The higher the more unstable or labile pH and chemicals Osmotic pressure Heavy metals ```

Occurs when weak bonds of apoenzyme are broken Distorts the shape of the enzyme Prevents the substrate from attaching to the active site

Denaturation

Add or remove functional groups

Transfer reactions

When a molecule loses or gives or donates electrons | Liberation of energy

Oxidized

Gains or receives or accepts electrons | Gains energy

Reduced

These reactions are common in microbial cells and indispensable for life processes

Redox reactions

Group of enzymes that can remove electrons from one substrate and add them to another

Oxireductases

Types of enzymes according to the chemical group transfer they perform

``` Aminotransferases: NH3+ Phosphotransferases: PO4^3- Methyltransferases: CH3 Decarboxylases: CO2 Dehydrogenases: H+ Transferases: C, N, P, S Hydrolases: H20 Isomerases: Isomeric Lyases: Double bonds Ligases: Form bonds Lipases: Fats Deoxyribonucleases: DNAase Synthetases/polymerases: Synthesis Cellulase: Cellulose Lactase: Lactose Aldolases: Aldehydes Oxidases: Oxidation ```

Aminotransferases

NH3+

Phosphotransferases

PO4^3-

Methyltransferases

CH3

Decarboxylases

CO2

Dehydrogenases

H+

Transferases

C, N, P, S

Hydrolases

H20

Isomerases

Isomeric

Lyases

Double bonds

Ligases

Form bonds

Lipases

Fats

Deoxyribonucleases

DNAase

Synthetases/polymerases

Synthesis

Cellulase

Cellulose

Lactase

Lactose

Aldolases

Aldehydes

Oxidases

Oxidation

Key common words that describe the action of enzymes:

Add, remove, cleave, bond, hydrolize, dehydrolize, change, alter, break, catalyze, digest, transform, attach, synthesize, convert, etc.

These reactions proceed in a systematic, highly regulated manner that maximizes the use of available nutritents and energy

Metabolic reactions

Regulation of __________ is the regulation of enzymes by an elaborate method of checks and balances

metabolism

These reactions occur in a multi-step series or pathway, with each step catalyzed by an enzyme

Metabolic reactions

Patterns of metabolic pathways

Linear Cyclic Branched

Other molecules with a structure similar to the normal subtrate can occupy the enzyme's active site

Competitive inhibition | Direct control on the behavior of enzymes

End product being fed back into the system negates (cancels) an enzyme's activity A+B---------Enzyme---------> C C will build up and cancel the catalytic action of the enzyme

Feedback control | Direct control on the behavior of enzymes

These enzymes have an additional regulatory site for the attachment of molecules other than the substrate. Distort active site so no binding to substrate occurs without denaturation.

Allosteric enzymes

Control of enzyme synthesis

Enzyme repression | Enzyme induction

Excess product turns off genetic program in DNA

Enzyme repression

Enzymes appear only when suitable substrates are present Synthesis induced by its substrate Adaption to the environment Ex. E. coli will produce lactase in the presence of lactose to yield gluose and galactose E. coli will produce sucrase in the presence of sucrose to yield glucose and fructose

Enzyme induction

Capacity to do work or cause change

Energy | Bioenergetics

Energy that is not spent

Potential energy

Energy that is freed

Kinetic

Cells extract energy from _____ and apply it towards useful work

bonds

When energy is released then the reaction is

Exergonic

When energy is absorbed then the reaction is

Endergonic

``` High energy phosphate molecule Stores and releases energy Unique molecular structure A temporary energy repository Bond releases energy when broken Negatively charged (PO4^3-) ```

Adenosine triphosphate (ATP)

The high energy charge originates in the orientation of the phosphate groups Negative charges impose strain on bonds Removal of the terminal PO4^3- releases the bond energy Formed by substrate level phosphorylation and photophosphorylation

Other properties of ATP