biol 203 exam 2

major domains of life

eukaryotes, prokaryotes (bacteria + archea)

cytoplasm

collective term that includes all contents of a cell that are within the cell membrane (except for nucleus in eukaryotes)

chromosome (Prokaryotic)

singular, circular, not membrane bound, and is organized in the nucleiod area of the cell

nucleiod

area in prokaryote containing the one chromosome circle

plasmids

mini circular piece of DNA/chromosome but is an unessential extra or copy

prokaryotes may have 1-100 of them

ribosomes

sites of protein synthesis

can either float freely in cytosol or (only in eukaryotes) be associated with the surface of the rough er organelle

cytoskeleton (prokaryotic)

long thin protein filaments that move materials within the cell and help to maintain cell shape

cell wall

protective exoskeleton that resists osmotic pressure generated by high solute concentration outside the cell

flagella

some prokaryotes have them to support movement

fimbriae

some prokaryotes have them to promote attachment to other cells/surfaces (little spikeys)

photosynthetic membrane

internal membrane complexes that contain enzymes & pigment molecules required for photosynthetic reactions to occur

(unique to photosynthetic bacteria)

prokaryotic cell contents

cytoplasm, chromosome ring, plasmids, ribosomes, cytoskeleton, cell wall…

some have flagella, fimbriae, photosynthetic membrane

eukaryotic cell contents

cytoplasm, ribosomes, cytoskeleton, nucleus, nucleolus, rough er, smooth er, golgi apparatus, peroxisomes, mitochondria…

some have chloroplasts, cell wall, vacuoles, lysosomes

biggest difference between prokaryotic and eukaryotic cells (and why organelles?)

eukaryotic are much larger, so they have organelles to compartmentalize cell volume into many small bins, allowing for the separation of incompatible chemical reactions and increased efficiency of chemical reactions via forced close proximity

nucleus

membrane bound organelle that houses the cell’s DNA (transcription of RNA from DNA occurs within)

**only in eukaryotes

nucleolus

site within the nucleus that manufactures & processes RNA molecules that assemble into ribosomal subunits

**only in eukaryotes

rough endoplasmic reticulum

site of protein manufacture & processing (it is also embedded with ribosomes)

**only in eukaryotes

smooth endoplasmic reticulum

primarily the lipid processing center (NO ribosomes)

**only in eukaryotes

golgi apparatus

does additional sorting, processing, & shipping of proteins when they leave the rough er and pass through it

**only in eukaryotes

lysosomes

hydrolysis of different types of macromolecules

**only in ANIMAL cell eukaryotes

hydrolysis

rxn that breaks an H2O, opposite of condensation/dehydration synthesis rxns

vacuoles

variety of functions: some act like lysosomes, some like storage depots for ions/pigments/toxin, can play structural roles when H2O builds up with what is being stored

**only in PLANTS, FUNGI, & SOME microeukaryotes

peroxisomes

centers for redox aka reduction-oxidation reactions (keeps highly reactive compounds separate & safe to react as intended)

**only in eukaryotes

mitochondria

converts chemical energy from (primarily) carbohydrates & fats into chemical energy stored as ATP

**only in eukaryotes

chloroplasts

contain enzymes & pigments that convert sunlight into chemical energy

**only in most PLANT & ALGAE eukaryotes

cytoskeleton (eukaryotic)

network of protein fibers that give cell shape & structural stability, and moves material within a cell (more complex than…)

cell wall (eukaryotic)

outside the plasma membrane, lends structural support to the cell

**only in FUNGI, PLANT, & ALGAE eukaryotes

extracellular matrix

supports animal cells (like their own version of cell wall)

Nuclear envelope

the double (inner and outer) membrane surrounding the nucleus, perforated with openings formed by nuclear pore complexes that cross both layers

Nuclear lamina

internal fibrous support for the nucleus, last layer between the inside of the nucleus and the innermost part of the nuclear envelope

What needs to go in and out of nucleus?

Messenger RNA (mRNA), newly assembled ribosomal subunits, nucleoside triphosphates & deoxynucleoside triphosphates (NTPs & dNTPs), and proteins responsible for copying DNA/ transcribing mRNA/ assembling ribosomes

What can go in/out the nucleus?

Small (<5 nm) molecules diffuse freely through pores; larger molecules need special transport proteins (with NLS and/or NES) to enter/exit

Nuclear localization signal (NLS)

short sequence of amino acids that allows large molecules to enter the nucleus via the pore complex

Nuclear export signal (NES)

short sequence of amino acids that allows large molecules to exit the nucleus via the pore complex

Importation into nucleus process

outside the nucleus, an importin beta (the truck driver) pairs with an NLS (or with NLS and importin alpha, which aids process by recognizing the NLS) -> goes through pore into nucleus and separates back into the original parts

Exportation from the nucleus process

inside the nucleus, an exportin pairs with an NES -> goes through pore to exit nucleus and separates back into the original parts

Endomembrane system

processes and distributes proteins bound for secretion from the cell, insertion into the plasma membrane, or lysosomes; (generally proteins manufactured in cytosol like those conditions, but the proteins listed above are for more varied environments and need to be manufactured/finalized in those more unique chemical conditions)

Entering the endomembrane system

proteins are synthesized in ribosomes that are free in the cytosol (even the ones on the rough ER are only there temporarily) and they carry a “molecular zip code” to get to correct endpoint; an ER signal sequence made by the ribosome binds to an SRP, halting synthesis; SRP binds to ER receptor and is released while the protein enters the ER via translocon; ER signal sequence is removed, protein synthesizes until completion

ER signal sequence

produced by ribosome, usually present in the first 20 synthesized amino acids, guides the protein and ribosome to the rough ER and detached when protein synthesis is complete; what the SRP binds to

Signal recognition particle (SRP)

binds to the ER signal sequence of a free ribosome, halts synthesis and drags it to the receptor and translocon

Translocon

point of entry in the rough ER for ribosomes to deposit proteins

Glycosylation

process through which proteins inside the rough ER interact with enzymes that catalyze the addition of carbohydrate side chains (ultimately produces glycoproteins)

Glycoproteins and where they go after production

produced via glycosylation of proteins in the ER; the added sugars promote folding, solubility, & embed info about final destination; travel via vesicle to cis face of golgi apparatus

Golgi directional orientation and cisternae

cis face is near the ER, trans face is near the plasma membrane; the enzymes in the cisternae (subsections and folds) are different due to various stages of maturation, with the trans end being older than the cis

Proteins in the golgi apparatus

proteins are further processed, sorted, and modified as they move through, and at the end their distinct tags bind to receptors that pinch off to form vesicles and transport them where they need to go

Mannose-6-phosphate tag (M6P)

special tag in proteins bound for lysosomes, made with a phosphate group added to a specific sugar on the surface

Main cytoskeleton components

actin microfilaments, intermediate filaments, microtubules

Actin microfilaments

7nm diameter, 2 strands coiled together; functions: maintains cell shape by resisting tension, moves cells via cell crawling or muscle contraction, divide animal cells in two, move organelles/cytoplasm in plants/animals/fungi (**little road that can rapidly build/change)

Intermediate filaments

10nm diameter, fibers (keratin, lamins, etc) would into thicker cables; Function: maintains cell shape by resisting tension, anchor nucleus and some other organelles (**little road that can rapidly build/change)

Microtubules

25nm diameter, hollow tube made of alpha/beta-tubulin dimers; Functions: maintains cell shape by resisting compression, move cells via flagella/cillia, move chromosomes during cell division, assist formation of cell plate during plant cell division, provide tracks for intracellular transport (**superhighway)

directionality/orientation of cytoskeleton components

the exterior, quick building end is called (+), the other interior end is called (-), BUT ITS NOT ACTUALLY CHARGED

Kinesin

motor protein that uses energy (ATP) to move towards the plus end of microtubles (away from organizing center)

Dynein

motor protein that uses energy (ATP) to move towards the minus end of microtubles (towards the organizing center)

Myosin

motor protein that uses energy (ATP) to move along actin filaments (the last ‘mile’)

Passive Transport

no energy(ATP) needed, movement with the gradient from high concentration to low concentration, leads to equilibrium, includes simple diffusion, facilitated diffusion, channel proteins, and carrier proteins

Active transport

uses energy (ATP) to enable movement against the concentration/electrochemical gradient, able to build up an unbalanced concentration & allows cells to concentrate valuable nutrients/ions, includes pumps and cotransporters

Gated channels

channel protein that can open/close in response to signals like charge asymmetry (think pitt bridges/tunnel that open/close/change depending on traffic

Channel proteins (and/or ion channels)

type of facilitated diffusion/passive transport for large, polar molecules and ions that is open and allows for passage from one side to the other, follow the concentration and/or electrochemical gradients, can vary in their selectivity (like size of opening, types of residues, etc) for specific types to pass through, (think tunnel)

Carrier proteins

type of facilitated diffusion/passive transport that picks up solute on one side of membrane, undergoes conformational change, and releases solute on other side of the membrane; *still must go with gradient, but is more selective so unwanted molecules can’t sneak across* (think pacman that eats/poops it out)

Pumps

type of protein involved in primary active transport, uses energy in the form of ATP to transport molecules/ions in a directed manner, often against the electrochemical gradient, allowing for concentrations/charges to build up

Sodium potassium pump key details

3Na+ out, 2K+ in, 1 ATP used–> 1 ADP + P; keeps going nonstop so charge builds up

Cotransporters

type of protein involved in secondary active transport, uses electrochemical gradient generated by ATP pump (*energy not directly used*) to transport different molecules/ions in a directed manner, often against the electrochemical gradient ADD MORE??

Diffusion

spontaneous movement of molecules and ions (can only occur with gradient, if one exists)

Simple diffusion

only for molecules that are small enough, nonpolar enough to cross bilayer membrane by squeezing through, spontaneous movement of molecules that can only occur with the gradient

Osmosis

diffusion of water down its concentration gradient, can cause changes in both volume and concentration (if there is a semipermiable bilayer that solute can’t cross, water will cross to even out concentrations)

Tonicity

how the concentration of solutes outside the membrane-bound vesicle or cell changes the vesicle/cell volume

Hypertonic

outer concentration > inner concentration, net flow of water is leaving the vesicle/cell, results in shriveling

Hypotonic

outer concentration < inner concentration, net flow of water is entering the vesicle/cell, results in lysing/bursting

Isotonic

outer concentration = inner concentration, net flow of water is zero but there is still movement occurring at equal rates in both directions, at equilibrium

Amphipathic proteins

proteins involved with lipid membranes that contain both hydrophilic and hydrophobic regions

Discovery of lipid bilayer model

was “sandwich model” until bilayer frozen and pulled apart to reveal membrane proteins that appeared as pits/mounds, became “fluid-mosaic model”

1st law of thermodynamics

energy can’t be created or destroyed, only transferred/transformed

Potential energy (bio context)

energy of position, energy stored in chemical bonds, higher in long weak bonds (nonpolar, equal e- sharing, easier to break) than short strong bonds (polar, unequal e- sharing, harder to break)

Kinetic energy (bio context)

molecular motion, usually in the form of thermal energy (heat)

Lamins

type of intermediate filament that holds down chromosomes

Centrosomes

where microtubules originate from, the microtubule organizing center (MTOC) in eukaryotes

Enzymes in metabolic pathways

they work together in an assembly line-like process, regulated by feedback inhibition

Noncovalent interaction enzyme activity regulation

competitive inhibition, allosteric regulation/activation/inhibition

covalent modification enzyme activity regulation

phosphorylation

Feedback inhibition

regulates some metabolic pathways when the final product of the pathway inhibits an enzyme earlier in the pathway to prevent waste of resources

Phosphorylation

a phosphate group is added to an enzyme, which can increase OR decrease activity depending on the enzyme

Allosteric regulation

a molecule binds somewhere on an enzyme other than the active site,triggers a shape change so the substrate can/cant bind to active site; activation makes enzyme more active, binding of inhibitor is inhibition and enzyme becomes less active

Competitive inhibition

the regulatory molecule (inhibitor) fits into active site to block substrate, competes with substrate for the enzyme’s active site

Coenzymes

organic molecules that reversibly interact with enzymes, tends to associate with active site and interact with bound substrates in ways that stabilize the transition state; ex: NADH, FADh2

Cofactor

inorganic ions that reversibly interact with enzymes, tends to associate with active site and interact with bound substrates in ways that stabilize the transition state; often Mg+2, Zn+2, Fe+2