BIO116 Exam #4

histone acetylation

acetylation of the histone tails promotes loose chromatin, which permits easier transcription; a type of epigenetic modification

DNA methylation

adding methyl groups to DNA inhibits transcription and usually has a longer-term effect; sometimes used in imprinting; a type of epigenetic modification

epigenetic modifications

modifications on DNA and nucleosomes that affect gene expression without changes in the nucleotide sequence; influence the phenotype, not the genotype; can persist and survive cell divisions, but most are removed during meiosis

imprinting

certain copies of the genes coming from the mother or father are silenced or repressed; only one copy of a gene in an individual, either from the mother or the father, is expressed, and the other copy is suppressed

Angelman syndrome

spontaneous deletion in the maternal chromosome, and paternal region 2 is silenced; only region 1 of paternal chromosome is the only thing expressed

Prader-Willi syndrome

deletion in paternal chromosome, and maternal region 1 is silenced; maternal region 2 is the only thing expressed; short stature and obesity

activators and repressors

two categories of regulatory transcription factors; often work in combination; expression of a gene can depend on a particular combination of activators and repressors

enhancer regulatory elements

What do activators bind to for transcription factors?

Silencer regulatory elements

What do repressors bind to in transcription factors?

alternative splicing

a single gene can produce multiple versions of mRNA based on inclusion/exclusion of exons; can determine sex and other characteristics

70%; very important

What percentage of genes in humans are alternatively spliced? Is alternative splicing important in humans?

constitutive exons

exons that are present in every version of the polypeptide the gene makes

alternative exons

exons that may or may not be included in the mature mRNA

1\.) produce tissue-specific versions of proteins

2\.) produce developmental stage-specific/sex-specific versions of proteins

3\.) alternate way to suppress/allow production of a protein

4\.) include/exclude exon with a premature stop codon

reasons for alternative splicing

length of the poly-A tail at the 3’ end, how many times is the protein translated, how much protein is being produced

factors that are responsible for controlling gene regulation in eukaryotes

glycocalyx/capsule

pink coating; a carbohydrate-based coating external to the cell wall; protective, adhesive, sticky; helps bacteria aggregate

bacterial chromosomes

composed of condensed DNA molecules; circular with no nuclear membrane

plasmid

double-stranded DNA that contains extra genes; supplements the circular chromosomes; not all bacteria have these

pilus

an elongate, hollow appendage used in transfers of DNA to other cells

flagellum

specialized appendage attached to the cell by a basal body that holds a long, rotating filament; movement pushes the cell forward and provides mobility; made of microtubules

cell wall

a semirigid casing that provides structural support and shape for the cell; made of peptidoglycan (proteins and carbohydrates)

outer membrane

some bacteria have this; similar to the cell membrane but also containing lipopoly saccharide; controls flow of materials and portions of it are toxic to mammals when refused

endospore

dormant body formed within some bacteria that allows for their survival in adverse conditions

situational

Do plasmids contain genes that are essential for life or situational?

conjugation

the way bacteria exchange genetic information; able to be done by plasmids and pilus

cell wall structure

What does gram staining provide information about?

gram positive

have a very thick cell wall; are PURPLE; peptidoglycan traps the crystal violet which masks the safranin dye

gram negative

have a much thinner peptidoglycan membrane with an outer lipid bilayer membrane; crystal violet is easily rinsed away, revealing the red safranin dye; is the color pink

gram-negative bacteria; the double cell membrane is a greater barrier to the antibiotics

Which type of bacteria are more likely to be antibiotic-resistant? Why?

smaller versions or polar side chains

How can antibiotics be specialized for gram-negative bacteria?

1\.) Lag

2\.) Logarithmic/exponential

3\.) Stationary

4\.) Death (not all species)

the phases of growth in bacteria

lag phase

bacteria cells adjusting to the new environment

logarithmic/exponential phase

bacteria cells divide like crazy

stationary phase

competition increases between the bacteria, growth slows; characterized by changes in gene expression

death phase

toxins are building up as they are produced by the bacteria; not all species will have this

1\.) Production of endospores/spores

2\.) Biofilm production

3\.) Toxin production

important events during stationary phase

quorum sensing

group behavior, density-dependent production of proteins; for example, if a lot of bacteria are producing auto-inducers, a lot of receptors are triggered all at once, producing biofilms and toxins; achieves the events during stationary phase

autoinducers

does the gene regulation of quorum sensing; how the bacteria notice they are in a stationary phase and noticing how dense the population is

autoinducer-1

tends to be species-specific; allows interspecies communication

autoinducer- 2

conserved among many bacterial species

virulence

one cell acting versus 1000s; severity of harmfulness; one bacteria may not cause a lot of harm, but altogether, that impact builds up

bacterial colonies

large aggregations of bacteria

1\.) biofilm

2\.) enzymes

3\.) toxins

Changes in gene expression by detection of chemicals during quorum sensing

Bacteria can coordinate the production of what three things? What is this based on?

endospores

if the population is large enough, or things have been degraded; it is produced; unequal cell division; produced in response to an environment in decline

clostridium, bacillus

endospores produced through asymmetric division within the cell wall; extremely resistant to heat, UV, and radiation

myxococcus/myxospores

starving cells send out signals to form fruiting bodies; decline in food resources causes the cells to lack nutrition; cells at the top become spores, and cells at the bottom die; type of endospore

True

T or F: Different genes are expressed when they are alone or when they are in biofilms.

biofilms

sticky substances that allow bacteria to adhere to each other and other surfaces; other species will join; changes allow cells to secrete these; ex. film on our teeth in the morning; typically have negative implications

Poor circulation leads to lack of nutrients, which leads to nerve damage and infection. These infections become chronic and form biofilms, which are resistant to antibiotics and far away from immune cells

Why do people with diabetes have trouble with their feet?

endotoxins

not actively secreted; give general symptoms such as fever, lethargy, etc.; lipopolysaccharides of the gram negative variety are the most common; part of the cell; much less toxic; only secreted when the cell dies

exotoxins

secreted to very specific targets and more specific symptoms; types are A-B, cytolytic, superantigen

A-B toxin

a two-component type of exotoxin; examples are Botulinum Toxin and tetanus

A component

the active toxin in the A-B toxin

B component

helps toxin bind to or enter a target cell in the A-B toxin

Botulinum Toxin

A-B toxin; rare disease coming from improperly preserved foods; it is an obligate anaerobe where there cannot be oxygen in the environment; antibiotics often don’t help; direct cause of death is often suffocation because the diaphragm does not get the signal to contract

When acetylcholine is released, the muscle contracts, but botulinum toxin blocks AC and the muscle relaxes and is unable to contract again.

What is the neurotransmitter-related reason for botulism’s effect on people?

tetanus

exotoxin example; obligate anaerobe, meaning there cannot be oxygen in the environment; caused by puncture wounds/rusty nails; toxin is released from the site of the growth

The tetanus toxin blocks the release of glycine, so the muscles can’t relax after being signaled to contract

neurotransmitter-related reason for tetanus’s effect on the body

energy production and formation of complex organic molecules (C-C bonds)

two main goals of metabolism

1\.) energy from the sun - phototrophic

2\.) energy from chemical bonds - chemotrophic

Two ways to produce ATP

1\.) build complex molecules from single carbon compounds - autotrophic

2\.) ingest pre-existing C-C bonds - heterotrophic

Two ways to get complex organic molecules (C-C bonds)

1\.) chemoheterotroph

2\.) chemoautotroph

3\.) photoautotroph

4\.) photoheterotroph

Four possible combinations for metabolism

oxygenic photosynthesis; cellular respiration (aerobic respiration); lactic acid fermentation; alcohol fermentation

metabolic processes found in both eukaryotes and prokaryotes

photoautotrophs and chemoheterotrophs

What are the only two combinations of metabolic processes that eukaryotes can do?

1\.) Anaerobic respiration

2\.) Photoheterotrophy

3\.) Lithotrophy

4\.) Nitrogen fixation

5\.) Fermentation of other organic acids

6\.) Methanogenesis (produces methane as a byproduct)

types of metabolic processes found ONLY in prokaryotes

False- prokaryotes have much greater metabolic diversity

T or F: There is much greater metabolic diversity in eukaryotes than in prokaryotes

anaerobic; toxic

Earliest lifeforms were _______ because oxygen was ___________.__

metabolic activity of some bacteria altered atmosphere to use oxygen to increase ATP and make it helpful

What did some bacteria do because oxygen was toxic?

pairs electron acceptors and electron donors

When it comes to electrons and metabolism, how do all eukaryotes pair?

sugars; oxygen

Bacteria pair electron donors and electron acceptors as well, but they have more options and can use electrons from other ________ and put them in molecules that aren’t ________.

oxygen

What is always the best electron acceptor?

lithotrophy

ability to use inorganic molecules to generate energy and build cells; many are chemoautotrophs and “rock eaters”; conversion of inorganic molecules to organic molecules

ammonia oxidizers

a type of bacteria that uses lithotrophy; ammonia is a source of electrons for production of ATP; found in soil, wastewater, etc.; critical to the nitrogen cycle

Nitrogen exists in many forms, including N2 gas, ammonium, ammonia, nitrite, nitrate, etc., so the cycle fixes N2 into usable forms for other organisms

Why is the nitrogen cycle necessary?

True- this is why the nitrite cycle is necessary

T or F: N2 gas is biologically unavailable to all eukaryotes.

bacteria and archaea in the root nodules; (lightning is one natural, unreliable example)

What fixes the nitrogen?

legumes

example of the co-evolution of plants and mutualistic bacteria that fix nitrogen

False- N fixation only happens in anaerobic environments

T or F: The enzymes that work in nitrogen fixation work well in aerobic environments.

1\.) recognize each other

2\.) adhere to each other

3\.) differentiated from each other

When it comes to multicellularity, cells need to :

unicellular

one cell exists, working alone

colonial

gray area between multicellular and unicellular; many species have slight division of labor

multicellular

many cells; animals and plants

individual (human) → organs → tissues → cells

Hierarchical organization

angiosperms

80% of extant plant species; flowering plants

Shoot System

→ Stems

→ Leaves

Root System

→ Roots

two systems and three organs of all plants

True

T or F: EVERYTHING is either a root, stem, or leaf, or a modified room, stem, or leaf.

1\.) anchor the plant

2\.) absorb nutrients and water from the soil

3\.) store carbohydrates

functions of roots

taproots

one larger vertical root with many lateral or branch roots

fibrous roots

mat of slender roots spreading out; no large central core

root hairs

extensions of single plant cells; increase absorptive surface area; not a multicellular branch

prop roots

a modification to roots; allows for extra support for plants that grow in swamps and warm/wet areas

storage roots

carrots, sweet potatoes, and radishes are examples of this storage root

buttress roots

similar to prop roots; have shallow roots and shallow soil

nodes

points where leaves are attached on the stem

internodes

stem segments between nodes

buds

point of growth of shoot on the stem

apical bud

a tip of plant/shoot

axillary bud

in the nodes of the stem

rhizomes

modified stem that grows underground to spread the plant

stolons

modified stem that grows along the surface of the ground to spread the plant