Microbiology Study Guide Chapter 7 & 8

Ionic Bonds

A type of bond where one atom gives up an electron to another, resulting in positive and negative charges.

Covalent Bonds

Bonds formed by the sharing of electrons between atoms.

Polar Covalent Bonds

Bonds with unequal sharing of electrons, resulting in partial charges.

Nonpolar Covalent Bonds

Bonds with equal sharing of electrons (same atoms & carbon/hydrogen atoms)

Hydrogen Bonds

Intermolecular forces involving a partially positive hydrogen atom bonded to a Partially negative atom.

Vanderwaals interaction-temporary and weak

Electronegativity

Greed for electrons ( Ability of an element to hold electron next to it.)

An unchangeable property of each element.

• Extreme difference - Ionic bond 

• Moderate difference - Polar Covalent (partial charges, use delta symbol for charge)

• Small Difference - NonPolar Covalent

Organic vs Inorganic

Organic- contains carbon and hydrogen

Inorganic- does NOT contain carbon and hydrogen

Macronutrients

Most abundant elements in living things 

Hydrogen,Oxygen,Nitrogen,Carbon

Phosphorus,Sulfur

Low atomic mass

capable of forming strong bonds

Micronutrients

Can be found in our body

Calcium, Iron, Zinc, Copper, Potassium Sodium, Magnesium

Isomers

Compounds with the same chemical formula but different structural arrangements.

-Structural connect differently

-Cis-Trans cis is same side trans is opposite sides

-Enantiomers- non-superimposible mirror images

Dehydration Synthesis

A chemical reaction that builds polymers by removing water and creating a covalent bond.

Hydrolysis

A reaction that breaks down polymers by adding water to break a bond.

Peptide,Polypeptide,Protein

Protein polymers composed of many amino acid subunits.

Have a job. Can find sulfur

Polysaccharides

Carbohydrate polymers composed of many monosaccharide subunits.

Store sugars.

DNA & RNA

Nucleic Acid polymers composed of many nucleotide subunits.(ribose, nitrogenous base, phosphate group)

Lipids

Sub units not monomer or polymers.

Hydrophobic molecules including fats, oils, and phospholipids.

FattyAcid and Glycerol → Triglyceride

Organic Molecules

Carbohydrates

Lipids

Proteins

Nucleic Acids

Monosaccharides (carbohydrate)

1 sugar 1 monomer of carbohydrates

Simple sugars

Can name general shape based on carbons (EX: Triose,Pentose,Hexose)

Disaccharides (carbohydrate)

Glycosidic Bond

• MALTOSE = Glucose Glucoe

• LACTOSE = Glucose Galactose

• SUCROSE = Frucose Glucose

Polysaccharides (carbohydrate)

Structural Polysaccharides

Modified glucose (NAG,NAM) (OH group replaced by —, no amino group, no double bonds.

Fatty Acids (lipid)

Saturated - we can’t add anymore hydrogen , no double bond

Unsaturated 1 or more double bonds

• Monounsaturated 1 double bond

• Polyunsaturated 2 double bonds

Triglycerides (lipid)

3 fatty acids on a glycerol backbone

This is how we store fatty acids

Phospholipid (lipid)

Has a hydrophilic head and hydrophobic “tails”

Has a phosphate group

Biological Membranes

Steroids (lipid)

Sterols(has hydroxyl group)

• Chelestrol

• Ergosterol

Cholesterol (steroid(lipid))

Vital molecule in cells

increases temp stabilize membranes, pre cursor for other steroids

Amino Acids (Proteins)

The building blocks of proteins connected by peptide bonds.

Peptide Bonds

Dehydration synthesis from an amino acid

Conjugated Proteins

Add Things

• Glycoproteins

• Lipoproteins

Protein Structure

Primary

• Primary sequence of amino acids

Secondary

• Hydrogen bonding is using backbone of amino acid (ncc)

• Alpha Felix and Beta Sheets

Tertiary

• R group interactions

• Electrostatic attraction, hydrophobic interactions metal ion coordination

  (-+- or +-+)

• Folding is essentially about charge

Quaternary

• Multiple peptides

Denaturation

Heat

Anabolic

building up a molecule require energy

Catabolic

Breaking down a molecule

Gibbs Free Energy

The energy in a molecule that COULD be released.

Enthalpy

Related to heat

About equal to the number of covalent bonds (more energy)

Entropy

About equal to number of molecules “the more you have the more chaos” (less energy)

Exergonic

EXITING ENERGY.

Spontaneous.

Gives energy 

(High energy to low energy)

Endergonic

ENTERING ENERGY

NonSpontaneous.

Requests energy 

(Low energy to high energy)

Carbon Sources (pptx. table)

Autotrophs

Fix CO2

Heterotrophs

Harvest preformedorganic molecules

Redox Reactions

Exchanging electrons from a reducing agent to an oxidizing agent

-Incremental energy harvesting prevents explosion

‘OIL RIG’ Oxidation is losing Reduction is gaining

NAD+,NADP+,FAD electron carriers

Modified nucleotides

Engage in moving electrons as “Intermediate holders”

ATP

Energy currency & Energy states

Couples endergonic and exergonic reactions

Bonds store a lot of energy

Enzymes (Biocatalysts)

Cofactor and Coenzymes (organic/Vitamins bond near active site)

Activation energy go down providing shortcut for reaction to happen

DO NOT change amount of energy available, DO NOT change deltaG, DO NOT provide energy

Inhibition (enzymes)

Competitive Inhibitors

Active site is taken

Allosteric Modification

A change in shape

• Inhibition altered active site

• Activation active site not altered

Feedback Inhibition

Changing the process because of the outcome

Glycolysis

Catabolic reaction that breaks down glucose into pyruvate.

DOES NOT USE OXYGEN

2 ATP > 4 ATP> 2 ATP & 2 NADH

Pyruvate oxidation (happens twice)

A transition reaction

NO ATP is produced

1 NADH produced PER pyruvate

Citric Acid Cycle / Kreb’s Cycle (happens twice)

Takes 2 things (Acetyl CoA & combines to one)

1 ATP produced

3 NADH produced

1 FADH2 produced

Cellular Respiration

A process taht breaks down food to produce energy for cells

EX: breaking down glucose to produce ATP

Can fail when no final electron acceptor is available. Genetic reasons: no genes for ETC proteins or cytric acid cycle enzymes.

Carbon Dioxide CO2

Is the most oxidized from of carbon

EMP Pathway-

Used by most microbes/animals

Entner-Doudoroff (ED) Pathway-

Along with EMP or alone depending on bacteria

Pentose Phosphate Pathway (PPP)-

Synthesis of nucleotides/amino acids

Electron Transport Chain (ETC)

NADH > Protein Complex > Energy given off during transportation and then used to pump hydrogen into inter membrane space.

Aerobic Respiration

Aerobic Respiration

Use oxygen to complete

Anaerobic Respiration

Does not use oxygen but still…

Chemiosmosis

The movement of ions across a selectively permeable membrane, generating ATP.

Uses hydrogen ions as a source of energy

Lost energy stored as a concentration gradient

Proton motive force drive ATP production ,nutrient transport, flagella rotation.

Oxidative Phosphorylation-

Energy in concentration gradients

Fermentation

An anaerobic process that converts pyruvate into other compounds, such as lactic acid or ethanol. (Deals with overload of NADH and Pyruvate)

Does not go through the process aerobic and anaerobic go through

Lactic Acid Fermentation

Acid decreases ph and increases acidity in environment causing denaturing of nearby proteins.

Pyruvate accepts an electron chamging to lactic acid

Homolactic

Produces lactic acid

Heterolactic

Produces more than just lactic acid

Alcohol Fermentation

2 Steps =release CO2 and Convert the rest to a hydroxyl group

Pyruvate changes to ethanol

Other Fermentaton Pathways

organisms are related to pathways and end products.

It is possible to differentiate microbes based on what and how they ferment.

Lipid Catabolism

Break ester bonds to get fatty acid off

Lipases,Phospholipases, beta oxidation

Lipases

Breaks down lipids

Phospholipases

Breaks down phospholipids

Beta oxidation

Breaks off 2 carbons at a time turn into acetyl-CoA

Produces FDH2,NADH,Acetyl-CoA

Protein Catabolism

How we break down proteins

Proteases, Deaminases

Proteases (extracellular & intracellular)

Extracellular > Break down proteins into smaller fragments

Intracellular > Breakdown proteins into amino acids

Deaminase

removes amino group and uses left overs

Light reactions

Provide energy (ATP) and electrons (NADPH)

Oxygenic

Oxygen producing

Anoxygenic

produces something other than oxygen (like sulfur or sulfate ions)

The Calvin Cycle (Dark Reaction)

You need ATP, High energy electrons, and Carbon for this reaction.

There are other alternative CO2 Fixation Pathways*

Carbon Fixation

Connecting of the CO2 and then breaking into 2 3carbon molecules

(CO2 is connecting to an organic form of carbon)

Reduction Oxidation

Passing electrons from NADPH

Regeneration of RuBP

Regenerates 3 5carbon molecules using energy(ATP)

Carbon Cycle

l

Carbon Fixation

make organic carbon molecules

Methanogenisis

Methanogens- CO2 to make methane (CH4)(Bad)

Methanotrophs- oxidize methane into CO2 (Good)

Respiration

Organic carbon molecules turned back into CO2

Why is Carbon(CO2) needed?

Used to create other carbonaceous molecules

Autotrophs fix carbon

Heterotrophs steal carbon

Nitrogen Cycle

Ammonification

Nitrogenous waste turned into ammonium

Nitrification

Takes ammonia turns it into Nitrite which is then turned into Nitrates

Denitrification

Turns nitrate and turns it into N2(g)

Nitrogen fixation

Bacteria incorporate N2(g)

Assimilation

makes nitrogenous compounds

Why is Nitrogen (N2(g)) needed?

Accessing Nitrogen is hard

Bacteria can alter nitrogen for themselves and indirectly help other organisms (break it down into organic molecules.

Plants/phytoplankton can’t incorporate atmospheric nitrogen gas

Ammonia/Ammonium aren’t easily used

Eutrophication

Man made fertilizers release nitrogen and phosphorus via runoff

Nutrient runoff > Algae Growth > Death of Aquatic Algae > Anaerobic/ inhospitable environment

Sulfur Cycle

Fungi & Bacteria: convert organic sulfur in detritus > Hydrogen Sulfide (H2S)

Anoxygenic photosynthetic bacteria and chemoautotrophs

• Hydrogen Sulfide(electron donor)>sulfate

• Leads to stratification of hydrogen sulfide in soil

• Deeper= more anaerobic=more hydrogen

Why is Sulfur Needed?

Cysteine & methionine

Vitamin Synthesis (CoA)

Many plants and bacteria can use sulfate as a sulfur source

Different organisms use different pathways to produce different products

Different organisms use different pathways to produce different products