Micro lecture test 2 - Biochemistry

hydrophobic vs. hydrophilic

• a substance that does not mix well with water (non-polar) - lipid,

• a substance that mixes well with water (polar) - protein, nucleic acids, carbohydrates

lipids

organic molecules that serve as structural components of membranes and other parts of cells

• fatty acids

• triglycerides

• phospholipids (make up cell membranes)

carbohydrates

monosaccharides (sugars), disaccharides (storage, table sugar), polysaccharides (cell walls, starch

• glucose - body designed to process, and body will store

nucleic acids

long chains composed of nucleotides, and each nucleotide has three components

• five carbon sugar (pentose)

• nucleobase (nitrogenous base)

• phosphoryl group (phosphate)

proteins process

DNA → RNA → Proteins

DNA double helix

double stranded (mutation prevention), antiparallel, N bases: ATCG, sugar: Deoxyribose, use: genetic material

RNA

single stranded, short lived (avoids errors/mutations), N bases: AUCG, sugar: ribose, use: genetic material (viruses), messenger RNA, Ribosomal RNA, Transfer RNA

proteins

complex (20 different amino acids), uses: identification, reaction (enzymes), structural components of cell, antibodies, toxins, receptors (receive chemical messages)

levels of protein folding

primary and secondary

• teritiary and quarternary structure: its unique three dimensional shape

enzymes

biological catalyst (lowers activation energy)

• most are proteins (subject to environmental factors)

• rate of reactions catalyzed by enzymes is affected by many factors (temperature, pH)

denatured

when proteins lose their structure

oxidation and reduction reactions

redox reactions involve the transfer of electrons from one molecule to another

• reduction: gain of electrons

• oxidation: loss of electrons

oxidation and reduction reactions always occur together (OIL RIG)

phototrophy

light energy is absorbed to make high-energy molecule that donates electrons to acceptor (photosynthesis)

chemotrophy

high energy food molecule donates electrons to acceptor

• organotrophy aerobic - aerobic respiration

• organotrophy anaerobic - fermentation and anaerobic respiration

• lithotrophy aerobic - ammonia oxidation

• lithotrophy anaerobic - methanogenesis

enzyme functions (control reactions)

Energy in systems is recycled and repurposed.

 Energy-releasing reactions (catabolism) are coupled with energy-capturing reactions (anabolism).

• Example: Sugar catabolism releases energy cells use to synthesize proteins.

 In biology, enzymes manage energy transfer from one reaction to another.

 Enzymes lower the activation energy of chemical reactions, so they will

proceed

catabolism (the microbial buffet)

• Carbohydrates, lipids, and proteins are chemically broken down.

• Reactions are oxidative.

• Energy is released and transferred to ATP and NADH.

• Smaller biomolecules (amino acids, fatty acids, simple sugars) are produced.

energy transfers in biology

 Oxidation-reduction (redox) reactions occur together and transform matter and energy in biology.

• Oxidation: loss of an electron.

• Reduction: gain of an electron.

 Biomolecules donate electrons (oxidation); electron carriers (NAD, FAD, ATP) accept electrons (reduction).

 One molecule of NADH carries about three times as much energy as one

molecule of ATP.

Glycolysis: from glucose to pyruvate

 Carbohydrate (sugar) catabolism

 Glycolysis “splits” sugar molecules

 Energy is transferred to ATP.

 Glycolytic pathways include:

• Embden-Meyerhof-Parnas (EMP) pathway – most organisms (including us!)

• Entner Doudoroff pathway – many archaea and bacteria (esp. Gram neg.), photosynthetic organisms

• Pentose Phosphate shunt – most organisms (depends on cell and cell type)

 Glycolysis occurs in two stages:

• Stage 1 consumes energy (2 ATP).

• Stage 2 yields energy, which is transferred to 2 ATP and 2 NADH

Fermentation completes catabolism

 What happens to pyruvate determines fermentation and respiration

Fermentation

• Pyruvate is reduced; NADH is oxidized to NAD+

• NAD+ is required (!!!!) for glycolysis to occur

• Little to no ATP produced

• Fermentation products: organic acids, gas, alcohols

Respiration

• Pyruvate is oxidized; NAD+ and FAD+ are reduced (during Kreb’s)

• NADH and FADH2 carry electrons to ETC

• Lots of ATP (24-28ATP/ glucose) are made

Tricarboxylic acid cycle

 The complete breakdown of glucose requires the breakdown of two molecules of pyruvate to six molecules of CO2.

 Remember 1 glucose = 2 pyruvates = 6 CO2

• Pyruvate is broken down to form acetyl-CoA and CO2.

• 1 NAD is reduced to NADH

• 3 NAD are reduced to NADH

• 1 FAD is reduced to FADH2

• 1 ATP is made

 Overall, the complete catabolism of one glucose molecule requires two rounds

through the TCA cycle.

lithotrophs

 An alternative route to get electrons for ETS and PMF generation

 An inorganic, reduced molecule serves as the electron donor instead of an organic compound.

• Ferrous iron (Fe2+)

• Ammonium ion (NH4+)

• Hydrogen gas (H2)

 Oxygen or an alternate gas serves as the final electron acceptor for ETS.

 Unique energy pathway used only by some types of bacteria

Respiration vs Lithotrophy

respiration: the overall process of catabolism from substrate breakdown to reduction of a terminal electron acceptor

lithotrophy: a related bacterial process that transfers electrons from an inorganic molecule such as iron or ammonia

• both respiration and lithotrophy may ultimately transfer electrons to O2

anerobic respiration

some bacteria can use alternative electron acceptors to complete respiration instead of oxygen

• anerobic respiration

photosynthesis and carbon fixation

▪ All the oxygen we breathe comes from photosynthesis—much of it by microbes.

▪ The photolysis of water releases oxygen atoms, which form oxygen gas:

2 H2O (light absorbed) → O2 + 4 H+ + 4e–

requirements for biosynthesis

 What is required for cell growth?

 Assemble carbon skeletons.

• Organic carbon to produce carbon skeletons

• CO2 fixation (autotrophs)

• Consume organic compounds (heterotrophs)

 Fix nitrogen, sulfur, and phosphorus.

• Microbes “fix” inorganic elements, making them available for biosynthesis.

 Spend energy.

• ATP and NADPH

 Reduce carbon skeletons (add electrons).

• Biosynthesis of more complex organic compounds through

oxidation/reduction

nitrogen fixation and ammonia incorporation

 Microbes “fix” inorganic nitrogen into biologically usable forms:

N2 + 8 H+ + 8e– → 2 NH3 + H2 + 16 ADP + 16 Pi

 Rhizobia are plant symbionts that convert atmospheric N2 to ammonium ions.

• Associated with soybeans and other legumes

 Ammonium ion is quickly incorporated into amino acids to avoid toxicity

diversity of life

there are 30 phyla of bacteria from which species can be cultured in the lab

• microbiologists estimate there may really be over 1000 more phyla we have yet to see

seven major phyla (super phyla) are known to impact human health and ecosystem

diversity of life continued

Gram-positive Bacillota (also called Firmicutes) and Actinomycetota (f. Actinobacteria)

• thick cell walls that resist drying

• includes Bacillota that produce endospores and Actinomycetota that produce antibiotic

Cell wall-less Mycoplasmatota (f. Within firmicutes)

• smallest and simplest self-replicating bacteria

• evolved from Bacillota but characteristically lacks cell walls

Gram-negative Pseudomonadota (also called Proteobacteria) and Bacteroidota (f. Bacteroidetes)

• Pseudomonoadota is a very diverse phylum that includes species capable of a wide range of metabolism

• members of the Bacteroidetes phylum are all Gram-negative rods; most are obligate anaerobes

Spirochaetota (f. Spirochetes)

• Spirochaetota share a distinctive form: tightly

Cyanobacteriota (f. Cyanobacteria)

• Cyanobacteriota include tiny marine bacteria as well as massive

incubators of pathogen evolution

pathogens today continue to evolve and occasionally a new version emerges that causes human or animal disease

gram positive associated phyla

bacteria with gram positive cell walls

Bacillota (f. Firmicutes)

• tough skin

• several layers of peptidoglycan supported with teichoic acids

• low G+C (guanine and cytosine content)

Actinomycetota

• Peptidoglycan with an additional thick waxy coat

• high G+C content

Phylum Bacillota: endospore formers

inert heat-resistant spores that can remain viable for thousands of years

• resist drying, freezing, and chemical disinfectants

spore forming genera: Bacillus, Clostridium

Phylum Bacillota: Lactic Acid Bacteria

Gram-positive, nonendospore sorming bacilli

• lactic acid bacterua