bio 205 microbiology exam 1

microbiology is important

diseases, food, research, microbiota

helps with study of all living things and is essential to understand all life on earth

hippocrates

Hippocratic oath, diseases have natural cuases

Hippocratic oath

widely known greek medical text, requires a new physician to swear, by a number of healing gods, to uphold specific ethical standards

Louis Pasteur

pasteurization, individual microbial strains have unique properties, fermentation caused by microbes, vaccines

Robert Koch

single microbe causes a particular disease, Koch’s postulates

carolus linnaeus

father of taxonomy: plants and animals, subcategories of taxa

Antonie van leeuwenhoek

first microscope lens, now of the first to observe microbes

how genetic methods can be used to determine phylogeny

distance methods involve calculating a genetic distance between every pair of species, and using the resulting distance matrix interactively to construct a tree

taxonomic ranks

domain, kingdom, phylum, class, order, family, genus, species

taxonomic domains

Archaea, Bacteria, Eukarya

what size is a eukaryote cell

10 to  100 μm

what size is a prokaryote

0.1 to 5.0

which domains have nuclei and which do not

no: bacteria and archaea

yes: eukarya

what makes up a bacteria cell wall

peptidoglycan

what makes up a archaea cell wall

polysaccharide and glycoconjugates

what makes up a plant cellulose cell wall

cellulose microfibrils and cross linking, glycan embedded in highly cross linked matrix

what is a fungi cell wall made of

gluten, chitin and glycoprotein

what are animal cell walls made up

tough carbohydrates

what are algae cell walls made up of

cellulose, hemicellulose, pectins

unicellular microbes

bacteria, archaea, fungi, protist

multicellular microbes

molds

acellular microbes

viruses

how are bacteria and archaea differ

archaea’s cell wall does not contain peptidoglycan and cell membrane uses ether linked lipids as opposed to ester linked lipids in bacteria

how various microbes affect humans and how do humans make use of them

many microbes can be unhealthy, they can cause diseases.

can help with digestion, absorb nutrients and take out bad bacteria

difference between a eukaryote and prokaryote

prokaryotes are always unicellular, smaller and circular genomes

eukaryotes are often multicellular, larger and linear genomes

coccus shape

round, circle

bacillus shape

rod, long oval

streptococcus

chain of cocci

staphylococcus

cluster of cocci

ribosomes are primarily constructed of

RNA 60 with some protein 40

endospore

protects the bacterial genome in a dormant state when the environment is unfavorable

vegetative cells

cells that actively grow, die easily

plasma membrane

outside of cell, made up of phospholipid layer and embedded membrane proteins

simple diffusion

molecules moving from a higher concentration to a lower concentration, no energy required

facilitated diffusion

ferry molecules across the membrane, high to low, require no energy

active transport

molecules from low to high concentration, need energy, comes on from of ATP

peptidoglycan

major component of bacterial cell wall , made of alternating sugars cross-linked by small peptides

peptide= amino acid

glycan = sugars

gram positive

stain purple

thicker cell wall

1 membrane

gram negative

stains pink

thinner cell wall

2 membranes

glycocalyces

a coating primarily made of sugars

allows cells to adhere to surfaces adding the infro to biofilms

Fimbriae

important for colonization of host and biofilms formation

for prokaryotes

short bristle like proteins

pili

envolved horizontal gene transfer ( F pilus)

singular

long

flagella

used to move in aqueous environment

stiff spiral filaments

spin

DNA is transcribed into RNA, which is translated into proteins

what does it mean that DNA replication is semi-conservative, and 5’ to 3’ direction

DNA molecules have both a new and an old strand

new strand is 5’ to 3’ and old strand is 3’ to 5’

DNA replication Initiation

the origin of replication where it beings

spread the strand apart

DNA replication elongation

New DNA strand grows inly in 5’ to 3’ direction

DNA polymerase

the main protein, an enzyme to catalyze

new nucleotide is needed to bring It in

topoisomerase

removes supercoils

a protein

DNA helicase

uses ATP to unwind

a protein

Sing Strand binding protein

keeps the strands from coming together

primase

DNA polymers require a primer, short starter strand usually RNA because DNA nucleotides cannot be directly added

DNA ligase

will take chances of DNA and will connect them

gets rid of primers

NTPS have three phosphate groups and lose two when they are incorporated into DNA

difference between leading and lagging strand synthesis

leading: strand continues

lagging: non-continues in chunks

the difference between DNA replication and transcription

use NTPS instead of dNTPs

only copies one strand

many mRNAs instead of a large DNA genome

splicing in transcription

noncoding introns get transcribed from the pre mRNA

happens in RNA

frameshift mutation

the insertion or deletion of nucleotide bases in numbers that are not multiples of 3

the 3 types of RNA and their functions

mRNA: messenger, DNA→RNA→ proteins

rRNA: main catalyzer, causes amino acids to attack

tRNA: transfer, does the decoding, translation book of the cell

how are tRNAs structure allow them to be the translation book of the cell

one end has specific anticodons that can base poor with specific codons

what is the start codon

AUG

steps of translation elongation

1) new charged tRNA enters A site

2) chemistry: growing peptide chain is temporarily moved from tRNA in P site to A site

3) two tRNAs are translocated move one site to another A→P→E

4)the tRNA in the E site leaves

how do stop codons and release factors allow translation termination to occur

they lead the release of protein

silent mutation

codon that codes for the same amino acid

missense

codon substitution of a different amino acid

nonsense

protein is not finished making because a stop codon is placed

loss of stop

skipping the stop codon until the next stop codon is placed

frame shift

insert or delete a nucleotide that is not a multiple of three

three types of DNA repair mechanisms

proofreading: ribosome makes sure base paring is correct

mismatch repair: scan DNA for base pairs who are not adjacent from each other

excision repair: DNA is not damaged enzymes scan too see if DNA is too bulky

replica plating

looking for mutation called autotroph ( does not have enzymes to make specific mutation)

purpose of the Ames test

looking at a chemical compound and see if it causes mutations or not

transformation

transfer of plasmids, DNA outside the cell brought into the cell, induced by heating an organism or an electric current

conjunction

transfer of plasmid, most common in nature, sex pilus

transduction

virus moves DNA from one cell to another, least common

plasmid

a genetic structure in a cell that can replicate independently of the chromosome

operon

prokaryotic gene cluster with a single promoter

allows protein synthesis to be controlled in responds bc of the need of cells

lac operon

repressor acts normally and transcription doesn’t happen lactose proteins dont produce

promoter

define the direction of transcription and indicate which DNA strand will be transcribed

activator protein

increases transcription

repressor protein

decreases transcription

repressor system

binding to the promoter reign of the gene, which prevents the production of messenger RNA

regulon

multiple operons are controlled by a single system

sigma factors

RNA polymerase must have a sigma to bond to a promoter, helps with strength conditions

molecular cloning

used to manipulate DNA sequences in the laboratory

restriction enzymes

edits DNA

bacterial enzymes produced as a protection mechanism to cut and destroy foreign cytoplasmic DNA

Sticky ends

are cuts of DNA that have DNA fragments on either side of the cut by the restriction enzyme

blunt ends

cut DNA symmetrically

why do designed plasmids usually contain an antibiotic resistance gene

it allows scientists to easily detect plasmid containing bacteria when the cells are grown on selective media

Multiple Cloning Site

plasmid containing multiple restriction enzyme recognition sites, for flexability and versatility

two methods used to perform transformation artificially

heat shock and electroporation

why does DNA move through the gel

Neg DNA is attracted to positive electrodes

how does agrose affect different sizes of DNA in different ways

smaller fragments of DNA are separated on higher concentrations of agarose while larger molecules require a lower concentration of agarose

purpose of PCR technique

amplifies DNA

required materials to run PCR

template, building blocks, enzyme, 2 artificially synthesized primers , right conditions

three step PCR cycle

1) DNA strands are separate by heating

2) Allow primers to bind ( cooldown)

3) DNA polymerase extends new strands ( heat up again)

why does PCR use a special polymerase

designed to withstand high temperatures

Sanger sequencing

uses small amount of dideoxynucleotides, each DNA brand will grow a diff color

next generation sequencing

for large DNA, can sequence different DNA together