Specific terms and examples of things---Biology

enzyme that works in low pH

pepsin: works at pH of 2

non-conjugated protein

collagen triple helix

only polypeptides

conjugated protein

hemoglobin (and its haem groups)

polypeptides + non-protein groups

Fibrous protein

collagen, keratin

elongated, structural, insoluble

Globular protien

enzymes, insulin, hemoglobin

compact, functional, soluble

Microscopy stains

iodine (plants)

methylene blue (animals)

Atypical eukaryotic cells

Red blood cells: no nucleii

phloem sieve tube elements: no nuclei

skeletal muscle fibers: many nuclei

Aseptate hyphae: many nuclei

hybrid species

horse x donkey = mule (sterile)

Places with aquaporins

kidney, root hairs

totipotent stem cells

zygote

pluripotent stem cells

embryonic stem cells

multipotent stem cells

bone stem cells

examples of cell size as specialization

sperm: long and thin for mobility

egg: large, nutrient reserves

RBCs: concave, small volume, lots of surface area

Neurons: long axons for transmission

Muscle fibers: long and multinucleated: strong contraction

Adaptations to increase surface area to volume ratio

RBCs

kidney proximal tubule cells have microvilli and infoldings

positive feedback loops for climate change

ocean outgassing: warmer water holds less CO2, so it warms the atmosphere.

Ice & albedo: melting ice lowers reflectivity, meaning more absorption and more warming.

Permafrost/peat: warming = CO2 and CH4 (methane) release

Drough/fire: carbon and soot emissions = warming

Ocean upwelling

warmer ocean surface = more stratification (layer seperation).

less mixing = less nutrients go to euphotic zone.

Primary production decreases, impacting species

coral reefs

acidification = less carbonate ions, and weaker calcification

warming = bleaching (zooxanthellae loss)

phenology

biological timing, + climate cues

flowering, migration, nesting.

depends on photoperiod, and temp

mesocosm

controlled mini-ecosystem to test variable effects on stability

stability within ecosystem depends on

energy supply being reliable

nutrient recycling with minimal leakages

genetic diversity within species

climate within tolerance (temp and rainfall reasonable)

eutrophication

excess nitrogen and phosphate runoff = algae blooms

biomagnification

stuff that accumulates in organisms

top predators have highest concentrations

DDT, methylmercury

arrested succession

when the cycle of succession in an envionment is lowk stopped

grazing, drainage that dries wetlands, etc.

Example of modelling natural and sexual selection

Endler’s guppies:

manipulated predators to track trait changes

no predators = sexual selection dominates

weak predators = natural and sexual selection

strong predators = natural selection dominates

Hardy-Weinberg equation

p² + 2pq + q² = 1

p + q = 1

USED WHEN

no mutation

large population

random mating

no migration

no natural selection

endosymbiotic

the thing where chloroplast and mitochondria were taken into cell

Criteria for life

MR H GREN

metabolism, response, homeostasis, growth, reproduction, excretion, nutrition

how to tell trans fat

Hydrogen atoms are on opposite sides of the double bond

trans fat also has one or more double bonds

wtf is sucrose made of

glucose and fructose joined by glycosidic bond

what are covalent bonds

sharing of one or more pairs of electrons

what does increasing substrate do to rate of reaction

increases it

does not increase rate of reaction when there is non-competitive inhibitor

where are photosystem arrays

in thylakoid membrane in chloroplasts

what molecule is reduced by photosystem 1 during photosynthesis

NADP+

chemiosmosis

diffusion of protons (hydrogen ions) across concentration gradient, back into matrix through ATP synthase to generate ATP

H+ pumped into intermembrane space, or thylakoid space

pennicilin mechanism of action

it acts as a mechanism-based inhibitor on transpeptidase enzymes

action spectra vs absorption spectra

action spectra shows wavelenths that activate photosynthesis

absorption spectra shows the wavelengths absorbed by a pigment

what does NAD do in respiration

it accepts hydrogen from a substrate, becoming NADH.

it then carries the hydrogen to the ETC

Decarboxylation of pyruvate in the link reaction

where does light-dependent reactions take place

on molecules embedded in bilayer of thylakoids

plasmodesmata

small channels between cells, like phloem seive tubes and their companion cells

systole vs diastole

systole = contract

diastole = relaxation

blood pressure is systolic/dystolic

external and internal intercostal muscles

external: contract, expanding ribs, inhalation

internaL: contract, ribs move inward, exhalation

coral

depend on sunlight for zooxanthellae photosynthesis

salinity 32-43 ppt

pH greater than 7.8 for calcium carbonate depositon

shallow waters

23-29 degrees C

obligate aerobes / anaerobes

cannot function without O2, and cannot function with O2

faculative anaerobes

switch between aerobic and anaerobic

does archaea do photosynthesis

NEVER

holozoic nutrition

animals ingest solid food and digest internally

saprotrophic nutrition

secrete enzymes onto dead matter and absorb products

decomposers

chemotrophic

oxidize inorganic compounds such as iron ions

fundamental vs realized niche

fundamental: full range a species could occupy without competition

realized: actual occupied range with competition

metabolism

network of enzymaatic reactions

the sum of all chemical reactions that occur within every cell of a living organism to sustain life

induced fit binding

the active site of enzyme chances slightly to better fit the substrate

what does denaturation do

disrupts weak bonds within enzyme, destroying shape of active site

examples of extracellular enzymes

amylase, trypsin, fungal cellulases

cyclical vs. linear metabolic pathway

cyclical: regenerates a starting molecule (Kreb’s cycle regenerates oxaloacetate)

linear: substrate flows to a diff end product (glycolysis to pyruvate)

feedback inhibition, and example

end product of a process binds allosterically to the first enzyme, slowing the pathway.

negative feedback loop

example: isoleucine inhibits threonine deaminase

mechanism based inhibition, and examples

inhibitor is processed by the enzyme into a reactive form, that irreversibly inactivates the active site

EX: penicillin and bacterial transpeptidase, aspirin acetylates COX enzymes

oxidation vs reduction

OIL RIG: Oxidation is loss, reduction is gain (of electrons)

link reaction

follow glycolysis

transports pyruvate into mitochondrial matrix

pyruvate loses a carbon, forming CO2 (3C turns into 2C)

forms an acetyl group when it loses a hydrogen atom

acetyl compound binds w coenzyme A to make acetyl CoA

why does fermentation occur

no O2 = ETC stops

fermentation regenerates NAD from NADH, to keep glycolysis going

makes lactic acid in muscles, ethanol in yeast and plants

Cell repiration product release stats

glycolysis (cytoplasm)—-uses glucose, ATP, NAD —→ 2 pyruvate, 2 NADH, 2 net ATP

link (mitochondrial matrix)—-uses 2 pyruvate, 2 NAD —→ 2 acetyle CoA, 2 CO2, 2 NADH, 0 ATP

Kreb’s (matrix)—-uses 2 acetyl CoA, 6 NAD, 2 FAD —→ 4 CO2, 6 NADH, 2 FADH, 2 ATP

ETC (inner membrane)—-uses FADH and NADH, and O2 —→ makes H2O, NAD, FAD, and 28-32 ATP

glycolysis steps and stuff

energy investment: 2 ATP made into 2 ADP. Glucose becomes frictose 1, 6 biphosphate. ADP made back into ATP, and fructose 1 6 biphosphate becomes 2 pyruvate. NAD made into NADH too.

pyruvate to lactate

lactate dehydrogenase is the enzyme that does pyruvate + NADH —→ lactate + NAD

yeast fermentation

pyruvate —→ ethanal + CO2 (decarboxylation)

then ethanal —→ ethanol

Kreb’s cycle

Acetyl CoA + oxaloacetate = citrate

the cycle replenishes oxaloacetate

for each acetyl CoA, 3 NADh, 1 FADH2, 1 ATP, 2 CO2.

Goes twice per glucose (2 acetyl CoA’s from link reaction)

what does light dependent reaction make

ATP and NADPH, in the thylakoid membrane

what does Calvin cycle do

uses ATP and NADPH to fix CO2 into triose phosphate in stroma

where does oxygen come from in light dependent reaction

from the H2O, not the CO2.

released from photolysis in PSII

chlorophyll a

the reaction center. all others are antenna pigments

Free-air carbon dioxide enrichment

lots of CO2 in controlled environment, increases photosynthesis

photolysis

light splits water

2 H2O —> 4 H + 4 e + O2

IN PHOTOSYSTEM 2 (mainly in grana)

the H+ ions are used for chemiosmosis

wtf does photosystem 1 do

reduces NADP to NADPH (for use in calvin cycle)

in stroma lamellae

wtf is Rubisco and carbon fixation

most common enzyme on planet

adds CO2 to a 5-carbon sugar, RuBP (ribulose 1 5 biphosphate)

this makes an unstable 6 carbon sugar, which breaks into 3-PGA (3-phosphoglycerate)

takes place in stroma, first step of Calvin cycle

Calvin Cycle

3 molecules CO2 plus Rubisco —→ carbon fixation

6 ATP to 6 ADP

6 NADPH to 6 NADP + H

regeneration of RuBP

3 ATP to 3 ADP

plasmolysis

happens to plant cells in hypertonic solutions. The cell becomes shriveled

crenation

happens to animal cells in hypertonic solution (cell shrinks)

water potential

potential energy of water per unit volume

more solute = lower water potential

more pressure = higher water potential

uses the lil trident symbol

water moves from high water pot. to low water pot.

sum of (pot. solute) and (pot. pressure).

quorum sensing

bacteria

cells secrete autoinducers at low constant rates

alter gene expression when threshold is reached

it is COMMUNITY signalling

signalling categories in animals

hormones: endocrine glands

neurotransmitters: released at synapses

cytokines: small proteins from many cell types

calcium ions: universal intracellular second messenger (for muscle and neurons)

hormone amines

melatonin, thyroxin, epinephrine

hormone peptides

insulin, glucagon, ADH

hormone steroids

oestadiol, progesterone, testosterone

neurotransmitter amines

dopamine, norepinephrine

neurotransmitter amino acids

glutamate, glycine

transmembrane vs intracellular receptors

transmembrane binds hydrophilic ligands outside

intracellular binds lipi-soluble ligands inside cytoplasm/nucleus

GPCRs

GPCR binds ligand, and the receptor changes shape.

the GDP leaves the alpha subunit, and GTP binds to it.

the alpha/GTP thing dissociates from beta-gamma complex, and they trigger other things

RESET: the GTPase on alpha subunit hydrolyses GTP, resetting it to GDP and starting everything over.

epinephrine and cAMP

epinephrine binds beta adrenergic GPCR —→ activates adenylyl cyclase, which produces cAMP (cyclic AMP)

cAMP activates PKA (Protein kinase A) which phosphorylates different enzymes

EX: activates glycogen phosphorylase, inhibiting glycogen synthase

Receptor tyrosine kinase

ligand binding (like insulin) leads to receptor dimerization, and autophosphorylation on tyrosines

recruits signalling proteins, increasing glucose uptake

receptor-ligand vs enzyme substrate binding

receptor-ligand doesn’t change the ligand.

oestradiol

acts in ovary, uterus, and brain to modulate GnRH release.

Stimulating GnRH increases LH and FSH

Action potential

resting is around -70 mV

threshold is about -55 mV

depolarization: Na channels open, and Na comes inside to about +30 mV

repolarization: Na channels close, K goes out.

hyperpolarization: overshoot resting, go to -80 mV

refractory period: prevents backflow

saltatory conduction

jumping thing between nodes of myelinated axon

what does action potential even do

action potential opens calcium channels

vesicles release neurotransmitter by exocytosis

diffusion across cleft

binding to postysynaptic receptors

how does a signal move along axon

local Na diffusion depolarizes the next section of the axon

refractory period prevents backward movement (neuron can’t immediately fire another signal)

summation

spatial summation: many inputs at once

temporal summation: one input firing rapidly

axon hillock: little triangle thingy connecting body of neuron to axon. This is the site of integration of signals.

nociceptor

pain receptor

Spinal cord

integration center for unconscious processes

white matter = signals

grey matter = synapses

coordinates reflexes and unconscious actions faster than brain

baroreceptors

blood pressure

chemoreceptors

CO2 and pH

efferent vs afferent

afferent = going to brain

efferent = away from brain