BISC 120- exam 3

prokaryotes

form colonies are single-celled organisms that make up domains bacteria and archae

what do prkaryotes form?

some species form colonies

prokaryotes come in variety of shapes, name them.

spheres(cocci)

rods(bacilli)

sprirals

describe the prokaryote cell-surface structures

unlike our cells, have a cell wall that maintains shape, protects the cell, and prevents bursting in hypotonic environement

what do most bacterial cell walls contain?

contain peptidoglycan, which is a network of sugar polymers cross-linked by polypepetides

what do archael walls contain?

this contains a variety of polysaccharides and proteins but lack peptidoglycan

what is the Gram stain used for?

used to classify bacteria by cell wall composition

what are the two types of gram ve bacteria?

gram +ve and gram -ve

gram positive bacteria are..

bacteria have simpler walls with a large amount of peptidoglycan

gram-negative bacteria are...

bacteria have less peptidoclycan and are more complex with an outer membrance that contains lipopolysaccharides

what is the capsule that reside on many prokaryotes?

many of them have a sticky layer of polysaccharide or protein surrounding the cell wall

what are the two types of capsules?

1. it can be dense and well-defined

2. can be a slime layer if it is not well organized

what do capsules help with?

both types enable adherence to the subtance or other individuals, prevent dehydration, and protect the cell from the host's immune system

what is the use of fumbriae?

these are hair like appendages that allow the prokaryotes to stick to their substrate or other individuals in a colony

what are pili (sex pili) and their function?

this is longer than fimbriae and function to pull cells togeter enabaling exchange of DNA

what are endospores

this is when water or nutrients are lacking

the cell copies its chromosome and surrounds it with a multilayered structure

describe motility in prkaryotes

about half of all prokayotes exhibit taxis, which is the ability to move toward or away from stimulus

what strucure is used for this movement to occur?

the flagella are the most common strucutures used

what is the DNA function in bacteria?

genes in signaling binary fisions, characterisitcs, signals and things to do as the bacteria

where is the chromosome located in bacteria?

it is in the nucleoid, which is a region with no membrane

what can some prokaryotes have in the nucleoid?

Plasmids are located in some prokaryotes, they are smaller rings of indeedendlty replicating DNA

- they are like additional genes used to genetically improve itself

What are microbes?

microscopic organisms

prokaryotic genes- tree of life, do they dominate it?

bacteria dominate the tree of life, estimates of 2.2 - 4.3 million species

what is binary fission?

this is how prokaryotes reproduce quickly and can divide every 1-3 hour under optimal conditions

what are the three key features of prokaryotic biology?

1. they are small

2. they reproduce by binary fission

3. they have short generation times

what can occur as a result of binary fission?

binary fission results are usually identical but differences can occur through mutations

what is the setting where mutations occur the most?

mutations are usually low but it can accumulate rapidly with short generation times and large populations

what is genetic recombination?

it combines the DNA from 2 sources and contributes to prokayote diversity

what is genetic recombination occur?

DNA from dif individuals can be combined by tranformation, tranduction, or conjugation

what is horizontal gene transfer?

this is the movement of genes between indidividual prokaryotes of dif species

describe the conjugation process?

this is the process through which DNA is transffered between two prokaryotic cells

1. pilus od the donor cell attaches to the recipeint

2. the pilus retracts, pulling the two cells together

3. DNA is transferred through temporary structure called the "mating bridge"

what is required for the production of pili?

a piece of DNA called the F factor (f for fertility) is reposnible to make pili

how can the F factor exist?

exists either as a plasmid or a segment of DNA within the bacterial chormosome

what is the function of the F plasmid?

its function is a DNA donor

what happens when a F+ cell can convert F- cell to what?

it converts to F+ cells if it transfers an entire F plasmid to the F- cell

what is it called when the F factor is in the chromosome of DNA?

it is the Hfr cells , named for high frequency of recombination which functions as donors during conjugation

what occurs in homologous segments of the chromosomal DNA from the Hfr cell?

the HFR cell recombines with that of the F- cell

what happens after the recombination of F- cell to HFR cell?

this becomes a new genetic variant on which evolution can act

metabolism

is the totality of an ogranisms chemical reactions

metabolic pathways

they begin with specfic molecule (substrate or reactant) and end with a product

catabolic metabolic pathways

release energy by breaking down complex molecules into sompler compounds

what is an example of catabolic pathways?

cellular respiration- breaks down glucose in the presence of oxygen

CATabolic acronym

think of CAT, they break things hence when you think CATabolic rxn, think of large molecules being broken down into smaller pieces

anabolic metabolic pathways

consume energy to build complex molecules from simpler ones

example of anabolic pathways

photosynthesis- builds alrger organic compounds out of smaller molecules

ANAbolic acronym

think of body builders, take ANAbolic steroids to get bigger hence when u think of anabolic rxn think smaller molecules being pieced together to build larger ones

What is chemosynthesis?

this is the use of inorganic energy sources to synthesize larger molecules

what are chemoautotrphs?

they feed on chemicals that are good electron donors (hydrogen sulfide, sulfur, or iron)

what are the most common chemoautotrophs?

most of the chemoautrophs are extremophiles that live in hostile envirnments (dee sea vents)

e.g. tubeworms in deep sea vents host chemosynthetic bacteria that convert CO2 to org compounds

what are photoautotrphs?

they trap light energy and convert it into chemical energy (photosynthesis)

photoautotropic bacteria perform what?

they may perform oxygenic photosynthesis or anooxygenic photosynthesis

Chemoheterotrophs

they obtain carbon from other living organisms

- they breakdown bonds in complex molecules and harvest energy (cellular respoiration)

where are choloroplasts hypothesized to evolve from?

chloroplasts are hypothesized to evolved from ancient photoautotrophs bacteria

where did mitochandria evolve?

mitochondria evolved from a chemoheterotropic prokaryote

what are the three types of catabolic pathways

aerobic respoiration, anaerobid respiration, and fermentation

how do prokaryotic metabolisms vary with respect to O2?

1. obligate aerobes require )2 for cellular respiration

2. obligate anaerobes are posisoned by O2 and live by fermentation or use subtances other than O2

3. faculative anaerobes can use O2 if it is present or carry out fermentation or anerobic respiration

what do obligate aerobes require?

they require O2 for cellualr respiration

what do obligate anaerobes require?

they do not need O2 because they get posined by O2

- they live by fermentation or use subtances other than O2 for anaerobic respiration

what does the facultative anaerobes require?

they can use O2 IF it is present or carry out fermentation or anaerobic respiration (all three "systems")

what is the function of photoheterotrophs?

they cannot use CO2 so they must breakdown larger organic molecules (other orgs.) to obtain energy

- they capture ligth energy to convert to chemical energy

what happened to the Monera kindgom?

it expanded into the protista kindgom, aka Whittaker's 5 Kingdom Classification

what is Carl Woese 3 domain system?

this is the diagram where bacteria and archae seperate

what is metagenomics

this is used to examine bacterial genomes from environmental samples

- vast majority undescribed

major phyla the textbook dicusses

1. phyla exhibit

2. prescence in the environment

what is a proteobacteria also known as ohylum pseudomonadota

this is a gram negative bacteria including, photoautotrphs, chemoautotorphs, and heterotrophs

what does gram + vs and gram - ve refer to in the cell?

it refers to the location of the peptidoglycanlayer

- we have this purple stain color in gram +ve because

- we have

what is the difference btwn the gram +ve and -ve bacteria?

the gram -ve is organized differently, first layer of plasma membrane, then the peptidoglycanlayer, then another layer of membrane

- sanwhich of membrane and the ham is the peptidoglycanlayer

the gram +ve bacteria are organized like:

1. plasma membrane layer

2. peptidoglycanlayer

what do heterotrophic proteobacteria consist of (A LOT)?

they consist of A LOT of pathogens

pathogens may cause

- gonorrhea

- cholera

stomach ulcers

What is a pathogen?

disease causing organism, bacteria to pathogen (?)

where do chalmydias typically live?

rely on animal species

describe what chlamydia is

all species of chamydia parasitize animal cells and have a gram negative walls lacking peptidoglycan

describe what a Spirochetes- spirochaetota is

these bacteria are helical, gram negative, heterotrophs that spiral through the environment by rotatin internal filaments

- this bacteria reside in ticks and when a tick bites you the bacteria enters your blood stream generating lime disease

cyanobacteria

this is a gram-negative bacteria

- free living photoatrophic bacteria

gram-positive bacteria

this is a diverse group

- vast majority of them are free living bacteria meaning they mostly live in soil, water, etc.

how is archaea decribed?

this is almost a bridge between bacteria and eukaryotes

extremophiles are a type of archae, describe them and their habitat

this is an archaea that live in extreme envirnoments, uninhabitable for most organisms

what do extreme halophiles require?

this requires/tolerates highly saline enviroments

what do extreme thermophiles consist of

they have adptions that make their DNA and proteins stable at high temps (above 100C)

mathogens

are obligates anaerobes that produce methane as a by-product of their metobolism

where are methanogens found?

found in diverse environements

- underice in Greenland

- swmaps and marshes

- guts of cattle, termites and other herbivores

what is TACK archae

this is a subgroup composed of the remaining, closely realted clades of archae

what is a lokiarchaeotes

this is a recntly discovered group closely realted to the TACK archae may represent the sis group (asgard archae) of the eukaryotes

what roles do prokaryotes have?

they play major roles in the recycling of chemical elements btwn the living and nonliving components of the enviro.

- help during decomposition and minerilazation that release simple&soluble organic and inorganic coimpounds for other organisms to use it

what does it mean when prokaryotes conduct chemical conversion

prokaryotes convert some molecules to forms that can be used by other organisms

what do nitrogen fixing bacteris do?

they are able to metabolically pull N2 out of the air and incorparate this N2 for the use of other organisms (they convert N2 to ammonia etc.)

what is an example of nitrogen-fixing bacteria?

example of rhizobia bacteria living in legume roots which provide a safe home for them. meanwhile rhizobia bacteria in roots are able to fix N2

what does symbioses mean

this is a long term biological interaction btwn two dif species that live in close physical and/or physiological contact with each other

who is involved in the symbioses structure?

two partners invovled:

symbiont- the smaller pair

host- the larger pair (can be viewed as habitats of the symbiont

what was the example of symbiosis from lecture?

the Hawaiian bobtail squid, the squid is the host and the Vibrio fischeri are the symbiont

- the symbiont help protect the squid from predators by the luminiscent light

Human microbiome

animals are hosts to millions of prokaryotes that compose our microbiota

normal flora

this is composed of microorganisms growing on body surfaces of healthy individuals

what do beneficial microorganisms help with?

tehy serve as a physcial barrier to prevent the invasion of pathogens (competitive exlcusion)

what is competitive exclusion?

these are microorganims that create a physical barrier to prevent invasion of pathogens

- it covers bindings sites to prevent pathogens from landing on epithelial surfaces

- compete for nutrients

- may exlcude antimicrobial peptides

food production benefits human health by?

huamns reap many benefits from bacteria including the production of many foods

- yogurt

cheese

wine

fermented cabbage

describe DNA technology

DNA polymerase from Pyrococcus furiosus is used in the polymerase chain reaction (PCR) DNA amplification technique

- whole system reliant upon polymerase

CRISPR-Cas9 system

is an adaptive immune response, in response to viruses

- this helps prokaryotes defend against viral attacks, has been developed as a gene-altering tool

what dos "Cas9" mean in the title?

this is the section where enzymes are released (??)

what is a virus?

a virus is an infecitious particle consisting of genes packaged in a protein coat

- sometimes it contains an outer envelope/membrane

what do viruses require?

they require a host to replicate (obligate, intracellular parasites) and they exist in a shady area between life-forms and chemicals, leading a kind of "borrwed life"

what is the first hypothesis of the origin of viruses expalined in lecture

the progressive or escape, hypothesis states that viruses arose from genetic elements that gained the ability to move btwn cells