BIOL 111 Midterm Terminology

genomes

all genetic material in an organism; all DNA found in a cell, consisting of nucleotide sequences (alleles) and genes

photoautotrophs

organisms that use photosynthesis to generate their own food (ex: green plants)

coevolution

mutually imposed selective pressures; reciprocal evolution between species as they interact with one another.

how did land plants reproduce in the harsh conditions for gametes

1. spores were encased in a tough coat

2. gametes were produced in complex multicellular structures

3. embryos were kept and nourished by the parent plant (embryo retention)

foraging theory

animals should eat foods that maximize their energy intake

factors to consider for organisms when foraging

1. abundance (don't want to waste time finding them)

2. catchability of prey (don't want to waste energy)

3. quality of prey (nutrients, fat content etc.)

4. competition (within species for the same prey)

5. predation risk (landscape of fear)

6. protection from toxins

landscape of fear

organisms in the middle of the food chain can get scared of predators and eat less, resulting in abundance of lower level organisms (ex: mother bears bring their cubs to the water to catch salmon, but there is a possibility that males might eat them)

why do some animals show population cycles

predation + competition (more individuals in a population, less resources and increased competition, more die off)

phylogeny

a tree that depicts the evolutionary relationships (ancestors and descendants) among a group of organisms with a COMMON ANCESTOR

what are the mechanisms of evolution

1. mutations

2. genetic drift

3. natural selection

4. sexual selection

5. gene flow

mutation

the driving factor of biodiversity: caused by changes in the gene sequences, creating new alleles which can change AA sequences and alter gene expression

genetic variation

diversity among genomes (makeup of gene frequencies) in one species

misdirected panspermia

microbes were brought to earth via global pollution (they attached themselves to spacecraft)

red algae

can be multicellular or unicellular, can reproduce asexually and sexually, appear red because of carotenoid pigment used in photosynthesis. absorbs blue light and reflects red light.

sporophyte phase

asexual phase of spore reproduction which produces zygotes (diploid) with two sets of chromosomes. they undergo meiosis to produce 4 cells (spores).

predation

one species hunts another for food; predator kills and consumes the prey (ex: weasels eat squirrels)

competition

two or more individuals or species use the same resource that is insufficient to supply both of them (ex: lynx and wolves both eat squirrels)

mutualism

two species both benefit from an interaction (ex: bears eat huckleberries, and disperse their seeds from their feces)

parasitism

one species benefits (takes resources from the host) and the other is harmed (but not immediately killed) (ex: parasitic wasp deposits its eggs inside the beetle)

primary producers

organisms produce their own food and energy from sunlight or soil instead of getting it from other organisms (ex: plants)

consumers

get energy and food from consuming other organisms

generalists

species that eat a variety of things and live in a wide variety of environments (ex: raccoons)

specialists

have a limited diet under certain conditions, and only live in specific environments (ex: pandas or koalas)

example of foraging theory

bears SHOULD eat high energy foods like salmon, instead of grass, since they hibernate in the winter (won't be eating then), but they only eat energy rich fish where it is abundant and accessible

bottom up control

when abiotic factors (ex: sunlight, temperature, water) control the abundance of primary producers, and thus the rest of the food chain

example of bottom up control

drop in temperatures results in less growth/more death of plants, resulting in less food for mid and higher level organisms, creating more competition

top down control

when predators control the abundance of lower trophic levels

example of top down control

more elk were introduced to the population (but nothing else changed): there are more predators so they consumed all the mid level consumers, which in turn creates an abundance of low level organisms (like grass), because there are no organisms anymore to eat the grass

keystone species

a species that has a disproportionately large effect on its environment relative to its abundance (ex: beavers, because they build dams that provide ecosystems for many other organisms, process nutrients, and filters water)

evolution

changes in allele frequency (gene variants) across generations

alleles

a sequence of nucleotides; we get one from each parent during reproduction, creating different variants of one gene (humans have 2, which is why we are called diploid organisms)

three genotypes

homozygous DOM- 2 identical dominant alleles (AA)

homozygous REC- 2 identical recessive alleles (aa)

heterozygous- 2 different alleles (Aa)

genes

a segment of DNA that codes for a specific function/trait

gene pool

all genes and alleles for each gene in one population

allele frequency

the amount of times an allele appears in a gene pool

(# of 1 type of allele)/(total number of alleles in pool)

quantitative/polygenic variation

the variety in a genetic population influenced changes in allele frequency in MULTIPLE genes, expressed by a RANGE of phenotypes that differ by degree (variation measured on a continuum). can be influenced by the environment

example of quantitative variation

height in humans, or beak sizes of finches

base insertion/deletion mutation

1 nucleotide base pair is inserted/deleted, shifting the entire sequence. this means completely new AAs are coded, producing different proteins, changing the function of the entire gene completely.

stop codon mutation

when a sequence produces a BP that codes for a stop codon, instead of an AA. this terminates the sequence early, potentially producing a protein that is nonfunctional

deleterious mutations

most mutations: decrease the fitness of the organism (decreases reproductive success or survival rates)

genetic drift

random changes in allele frequency that can cause some alleles to disappear, reducing genetic variation. it can cause some traits to become very frequent, or even some can disappear completely.

natural selection

organisms that are well adapted to their environment are more likely to survive and reproduce. their favourable traits are passed on.

example of natural selection

a drought reduced the abundance of small seeds available, causing many small-beaked finches to die, as they didn't have any food. this caused the average beak size to increase after the drought, as they had to adapt to eating larger seeds.

sexual selection

when organisms decide who to reproduce with based on favourable traits.

intra-sexual selection

competition between males (same sex)

inter-sexual selection

males develop traits to attract females, who choose based on these traits. (ex: mating calls of frogs)

secondary sexual traits

traits that evolve as a compromise between natural and sexual selection that influence sexual success. (ex: breasts)

gene flow

movement of genes among populations via sexual selection. can increase genetic variation WITHIN a population because alleles are being exchanged, producing new geno + phenotypes. can decrease genetic variation BETWEEN populations, because they exchange allele frequencies, causing the populations to become more alike (in allele makeup).

evolutionary and ecological effects of global change

species become maladapted and decline to extinction if they don't change their phenotypes to suit their environment

extirpation

local extinction of a population/species

how can populations shift their phenotypes to match their environment better

1. they can move locations that they are better suited for

2. they can stay in the same place but change their phenotypes to suit the new optimum via plasticity or evolution

plasticity

the ability of individual genotypes to produce different phenotypes when exposed to different environments

ecological traps

when organisms mistakenly prefer habitats where they are less likely to survive than in other habitats that are changing rapidly (ex: flies lay their eggs on polarized glass surfaces because they think it's water).

what are microbes?

an organism (the first cellular form of life) that can cause disease, or prevent us from being sick. they are essential for all global nutrient cycles.

pasteurization

involves heating bacteria in a culture media to sterilize the culture (remove the microbes/bacteria).

koch's first postulate

the microorganism must be present in an organism suffering from disease, but not present in healthy organisms

koch's second postulate

the microorganism must be isolated from the diseased organism and isolated to be grown in a culture

koch's third postulate

the cultured microorganism should cause disease when introduced to a healthy organism

koch's fourth postulate

the microorganism should be re-isolated from the newly diseased organism and be identified as identical to the initial microorganism to show that it is the cause of disease

example of symbiosis in bacteria and animals

vibrio fischeri bacteria colonizes the bobtailed squid; v fischeri is a bioluminescent, which illuminates the squid's organs, camouflaging it

symbiotic relationship between humans and bacteria

we are 2% bacteria, which lives mostly in the gut. there is a 1:1 ratio of bacterial and human cells in our body, which can be flipped with each defecation event.

bacterial evolution

they go through many generations in a short time (ex: 600-700 generations in a few weeks) and have no fitness plateau

advantages of microbes being small

small cells grow faster than big cells, as there is a greater SA to V ratio (they can absorb more nutrients per volume unit, since volume grows faster than surface area

cell mechanisms

metabolism and replication (transcription and translation)

what is the role of metabolism in cells

cells generate energy to create new enzymes responsible for metabolism. more efficient metabolism leads to faster growth and faster reproduction.

what is the role of replication in cells

the division of biomass from one parent cell into two daughter cells and the replication of genetic information

cell processes

cells require a continuous input of energy to stay out of thermodynamic equilibrium (to keep the cell from turning back into data sequences)

population mechanisms

evolution and genetic variation through replication of individuals

population processes

natural selection occurs in a population through changes in allele frequency, fitness increases and reproduction creates competition

community mechanisms

consumption and nutrient cycling through food webs; populations are linked through consumption (food webs) to create communities

nutrient cycling

where energy and matter are transferred between living and non-living organisms (ex: animals/plants consume nutrients in the soil, which are released back into the environment through death and decomposition)

plasma membrane

the boundary of the cell forms a phospholipid bilayer to control movement in and out of the cell.

what is the role of the membrane in the dual system of the cell

the membrane prevents the products of metabolism from diffusing away from each other, and permanently links the information and metabolism systems.

composition of plasmamembrane

hydroPHILic head (polar)

hydroPHObic tail (nonpolar); the tails arrange themselves in the middle away from the water, the hydrophilic heads attract water and prevent it from going through the nonpolar middle area

transport proteins

embedded in the plasma membrane (span across); channels that allow the passage of certain molecules and ions. allows sugars and amino acids in.

signal molecules

surface receptors that bind to external molecules in the extracellular space to general intracellular signals to regulate cell behaviour

adhesion proteins

hold cells together or binds cells with extracellular matrix

what is the dual system of the cell

metabolism and information, enclosed by the membrane

information in the cell

the cell stores information necessary to synthesize the metabolic system

example of evolution by natural selection

when information and metabolic system is enclosed in the same membrane; the information system that synthesizes a more efficient metabolic system will be replicated more rapidly

how does a genome store information

a single molecule of double stranded DNA in a closed loop (circular bacterial chromosome) is stored in the nucleoid. also some smaller circles of DNA called plasmids.

genome makeup

2 million BP that encodes 2000 genes.

plasmid

small ring shaped DNA molecules. some can encode for conjugation that results in horizontal gene transfer. they can also encode for functions that benefit the host bacteria (can code for antibiotic resistance).

how are plasmids involved in horizontal gene transfer

some plasmids can code for conjugation that results in plasmid transfer via a pilus. a conjugative plasmid contains all necessary genes for it to transmit itself into another bacteria via conjugation

conjugation

a mechanism of horizontal gene transfer where DNA is transferred from a donor to receipient bacterium by direct contact (transfer of plasmid)

DNA replication process

1. DNA-A recognizes origin of replication (which is where 2 replication forks are formed)

2. Helicase unwinds DNA (one on each RF, moving in opposite directions).

3. RNA primer creates a binding site on each single strand of DNA

4. DNA polymerase adds the complementary nucleotide.

5. the two RFs meet at termination site and daughter chromosomes separate.

chromosome replication role in cell division

1. bacterial chromosome replications (2 daughter chromosomes inside mother cell

2. cell begins to divide, daughter chromosomes move apart

3. cell wall is formed between 2 cells, FtsZ ring initiations septum formation

4. cell division is complete and daughter cells separate

central dogma

DNA into mRNA via transcription, mRNA into protein via translation

ribosome (tRNA) function

translates mRNA into protein by binding to an amino acid and bringing it to the corresponding triplet codon on the strand of mRNA.

what bond holds amino acids together to form a chain

peptide bonds

silent mutation

when 1 nucleotide (BP) is replaced with another BP that codes for the same amino acid, since the genetic code is redundant.

frozen accident theory for why the genetic code is redundant

the genetic code was discovered a long time ago and it stuck; the code cannot accept new variations

why are there only 20 amino acids but 64 codons

because several different codons can encode for the same amino acid

general timeline of life on earath

1. phototrophic bacteria

2. cyanobacateria

3. macroscopic eukaryotes

4. algal kingdoms

5. invertebrates

6. vascular plants

7. mammals

8. humans

what are the main differences between living and non-living organisms

living organisms are able to self-replicate and have heritability because they are able to evolve, and have a metabolism, so they are complex.

what is panspermia

the idea that life did NOT evolve on earth; it started somewhere else and ended up on earth

undirected panspermia

the idea that microbes were dispersed from planet to planet, by meteors.

what does undirected panspermia imply

that bacteria is stable and can survive extreme conditions, like atmospheric heating and impact and can be recovered (as they were dispersed across planets)

objections to undirected panspermia

1. solar systems are very far away from each other, it is not reasonable that they could travel those distances in a reasonable amount of time.

2. there is a low probability of capture; probably a lot of debris from mars since it is relatively close, but mars and earth are the same age.

directed panspermia

the idea that life was brought to earth purposefully