Biol 251 Final

Processes microbes use to obtain energy

aerobic respiration, anaerobic respiration, fermentation

How to find out how microbes obtain their energy?

follow the energy, follow the electrons, follow the carbon

Fermentation

maintains a limited pool of NAD+, without which glycolysis could NOT continue; aerobic or anaerobe the final electron acceptor acetaldehyde/pyruvate ATP: 2

Alcohol fermentation

acetaldehyde is the final electron acceptor; 2 ATP: 1 glucose makes 2 ethanol; 2 stops using 2 enzymes

Lactic acid fermentation

pyruvate is the final electron acceptor; convert lactic acid back to pyruvate for aerobic respiration in muscles

Aerobic respiration

final electron acceptor is oxygen; 38 ATP produced in prokaryotes; 36 ATP in eukaryotes

Anaerobic respiration

final electron acceptor inorganic nitrate, sulfate, carbonate; variable ATP

Membrane of cell is a boundary

the ability of the cell to discriminate in its chemical exchanges with the environment is fundamental to life, and it is the plasma membrane that makes this selectivity possible

Functions of membranes

\-form specialized compartments by selective permeability

\-generate asymmetric protein distribution

\-mediate cell-cell recognition

\-serve as site for receptor molecule binding for cell signaling

\-controls and regulates sequences of multiple biochemical reactions

Membrane size

4nm thick

Selectivity of the membrane due to structure

\-hydrophobic/small molecules can pass through

\-large uncharged polar molecules and ions cannot diffuse through

Diffusion

net movement of particles from a volume of higher concentration to a volume of lower concentration

Gradient

change in the value of a quantity (such as temperature, pressure, or concentration) with change in a given variable and especially per unit distance in a specified direction

Osmosis

Diffusion of water through a selectively permeable membrane

Fresh water

< 1,000 mg of solute in 1 kg of solution (< 0.1% by mass)

Slightly saline

1,000 to 3,000 mg (1 to 3 g) of solute in 1 kg of solution (0.1 to 0.3%)

Moderately saline

3,000 to 10,000 mg (3 to 10 g) of solute in 1 kg of solution (0.3 to 1%)

Highly saline

10,000 to 35,000 mg (10 to 35 g) of solute in 1 kg of solution (1 to 3.5%)

Tonicity

the quality of the concentration of solute in one solution as compared with that in another solution

An erythrocyte in fluid that is hypertonic to its cytoplasm

undergoes plasmolysis

An erythrocyte in fluid that is isotonic to its cytoplasm

appears structurally normal

An erythrocyte in fluid that is hypotonic to its cytoplasm

undergo lysis

Chemical driving force

directional pressure on particles, that is the result of a concentration gradient

Electrical driving force

directional pressure on particles, that is the result of an electrical gradient

Passive transport

the cell expends no energy for transmembranal movement to occur

Active transport

the cell expends energy (usually provided by ATP) for transmembranal movement to occur; moves ions and molecules against a concentration and/or electrical gradient; requires energy

Primary active transport

transporter molecule obtains ATP (or other energy carrier) the energy that is needed to move cargo against a gradient

Secondary active transport

uses environment to provide energy

Diffusion through a channel

ion channels can be non-gated (always open) or gated (opens and closes in response to local conditions)

Leak channel

always open

Voltage gated channels

open and close in response to changes in membrane potential

Ligand gated channel

opens and closes in response to a specific extracellular neurotransmitter

Signal gated channel

opens (closes) in response to a specific intracellular molecule

Among ALL cells there are channels for only 5 kinds of monoatomic ion

H+, Na+, Cl-, K+, Ca2+

MOST ion channels are gated

they open/close in response to changes in the local environment

Facilitated diffusion

carrier proteins transport molecules down their concentration gradients

Bacteria need

\-macronutrients/elements in large amounts

\-micronutrients in small amounts

Ions/molecules cross the outer membrane of gram- bacteria through

OMP (outer-membrane porin) complexes; acts of diffusion through a channel; 3 wide linked tubes for big molecules

Glucose transported into bacterial cells

IIC protein transports glucose into the cytoplasm; acts of facilitated diffusion by a carrier-protein complex

Oligopeptides

how peptides and amino acids are transported into cytoplasm of bacterial cells

OPP (oligopeptide permease)

cells must use ATP; primary active transport

Di/Tri transporter

cell builds these as symporters coupled with H+

AA transporter

specific to an AA or a specific AA group; facilitated diffusion by carrier-protein complex

How fatty acids are transported into the cytoplasm of bacterial cells?

fatty acid transporters

Fatty acid transporter examples

\-E. Coli FadD; primary active transport

\-Bacillus subtilis A to E; primary active transport

Nucleic acids transported into cytoplasm of bacterial cells (primary active transport)

1. foreign DNA binds to protein receptor
2. proteins move DNA across cell wall
3. ComEC transports one DNA strand into the cytoplasm
4. the other DNA strand is digested by enzymes; membranal transporter proteins transport nucleotides into the cytoplasm

Siderophore

an organic molecule that is used by bacteria to capture iron ions (Fe3+) from the environment and transport them into the cytoplasm

Enterobactin (Ent)

E. coli siderophore; used by most gram- bacteria

Bacillibactin (BB)

Bacillis subtilis gram+ siderophore

How siderophores brought into bacterial cells?

Membranal siderophore permease protein complexes actively transport them into the cytoplasm

How prokaryotic digestive enzymes are exported into the environment?

\-SecY pore complexes are used by bacteria and archaea

\-energy for export is provided by the SecA ATPase

Genome

the totality of genetic information belonging to a cell or an organism

Ploidy

number of sets of chromosomes in a cell

Largest archaeal genome

Methanosarcina acetivorans (5,751,492 bp)

largest bacterial genome

Sorangium cellulosum (13,033,779 bp)

Largest known genome

Canopy plant (Paris japonica) 150x10^9 bp

Smallest known genome

Nasuia deltocephalinicola 112,031 bp; 137 protein coding genes; lives inside leaf hopper organ

Bacteriome

specialized insect organ that holds bacteriocytes

Bacteriocyte

specialized insect cell that hold symbiotic bacteria in its cytoplasm

Human genome size (chromosomal DNA; nucleus)

\-female 6.062x10^9 bp

\-male 5.963x10^9 bp

Human genome size of mitochondrial DNA (mtDNA)

\-16,569 bp

\-1-10 mtDNA per mitochondrion

\-c. 80-2000 mitochondria per cell

Information in human mitochondrial DNA

\-mitochondrial DNA(mtDNA)

\-circular DNA molecule

\-13 genes for proteins

\-24 genes for rRNA and tRNA

\-16,569 bp

Relationship between genes and chromosomes

genes are part of the chromosomal DNA molecule

Gene

a sequence of nucleotides that can be transcribed by proteins to build an RNA molecule

Plasmid

\-small circular molecule of DNA that usually includes at least one gene

\-a single prokaryotic cell can have different plasmids that hold different genes

Transcription

process by which all cells use proteins to make an RNA copy of a DNA sequence

Translation

process by which ribosomes use information in mRNA to build proteins

horizontal gene transfer (HGT)

passing of genetic information between cells other than that which occurs between parent and offspring; through transduction, conjugation, and transformation

Pilus

fiber that is made of many proteins and extends outside of a prokaryotic cell; used to attach to other cells or to surfaces; used for movement; pili can be used to transfer DNA

Structure of bacterial pilus

tube; helical arrangements of multiple proteins noncovalently attached; linear DNA can travel through lumen (single strand)

\-tube size 2.8nm or 28 angstrom

1 angstrom

10^-10 m

F plasmid

plasmid that holds information for building a conjugative pilus, and that can be transferred between cells via that conjugative pilus

IS

insertion sequence

oriT

origin of transfer; one DNA strand that will be transferred to another cell and is cut here by enzymes

Origin of replication

F plasmid can be replicated by the same proteins that replicate chromosomal DNA

Conjugation

how bacteria share genetic information

Conjugation process

1. pilus of F+ donor plasmid attaches to F- recipient cell; pilus contracts, drawing cells to make contact with one another
2. one strand of F plasmid DNA transfers from donor cell to recipient cell
3. Donor synthesizes complementary strand to restore plasmid ; recipient synthesizes complementary strand to become F+ cell with pilus

Does HGT occur among archaea?

archaea can construct pilus and use plasmids for conjugation

Can conjugation occur between 2 different species of prokaryote?

yes; it can happen within bacteria and within the archaea; it can happen between bacteria and archaea

Can an F plasmid recombine with a bacterial chromosomal DNA molecule?

\-Yes! Enzymes can catalyze the breaking of old covalent bonds and the making of new bonds

\-The F plasmid can become part of the prokaryotic chromosomal DNA molecule

Hfr cell (high frequency of recombination)

cell in which F-plasmid DNA has been integrated into the chromosomal DNA molecule; When the Hfr cell replicates its DNA and divides, the daughter cells receive the Hfr chromosomal DNA

Can chromosomal DNA be transferred from one prokaryote to another?

\-During conjugation, some or all of the chromosomal DNA from the donor cell will be transferred into the recipient cell (a single strand of DNA is transferred)

\-Enzymes then exchange recipient chromosomal DNA with donor DNA

Natural transformation

process by which prokaryotic cells take foreign DNA out of the environment and insert it into their own chromosomal DNA molecules

Natural transformation process

1. foreign dsDNA binds to protein receptor
2. ComEC binds to incoming dsDNA
3. one DNA strand is digested by nucleases
4. the other strand is transported across the plasma membrane into the cytoplasm
5. enzymes insert the foreign DNA into the bacterial chromosomal DNA molecule

Why is natural transformation significant?

Prokaryotes can deliberately take up DNA that potentially came from any organism, and insert it into their chromosomal DNA, to be replicated and passed onto their descendants

\-eukaryotic cells CANNOT do this

Microbial growth

an increase in the number of cells (not the size of cells)

sexual reproduction

reproduction in which two sets of parental genetic information are used to produce a new complete organism

asexual reproduction

reproduction in which only one set of parental genetic information is used to produce a new complete organism; results in clones that are genetically identical to the parent

\-prokaryotes: binary fission

\-unicellular eukaryotes: mitosis

Binary fission

among prokaryotes, reproduction by means of cell division


1. cell replicates its DNA
2. cytoplasmic membrane elongates, separating DNA molecules
3. cross wall forms; membrane invaginates
4. cross wall forms completely
5. daughter cells

Budding ex: yeast

reproductive cell division in which daughter cells are initially not identical in terms of size, shape, and function


1. nucleoid is replicated
2. new nucleoid moves into bud
3. young bud
4. daughter cell

Physical microbial growth requirements

temperature, pH, osmotic pressure

Chemical microbial growth requirements

macroelements, microelements, O2, organic growth factors

Temperature range of microbes

minimum, maximum, optimum

Hyperthermophile

\>80 C

Thermophile

50-80 C

Mesophile

20-45 C

Psychrotroph

best at room temp but can tolerate colder temp 4-25 C

Psychrophile

-20-20 C

Danger zone; rapid bacteria growth

15-50 C

Many bacteria survive; little growth

5-15 C