Molecular bio exam 2

what is needed to form a cell?

amino acids to build things, store and transmit genetic information (nucleic acids), and membranes to protect from the environment

ribozyme

the first enzymes, formed by RNA folding, and helped catalyze replication of early RNA polymers

liposome

a hollow membrane-bound vesicle that forms spontaneously in aqueous environments

bacteria

single cell, doesn’t have a nucleus (DNA and RNA are free floating in cytoplasm), don’t have the organelles, divide through binary fission, DNA is circular, and minimal RNA processing

Archaea

single cell, don’t have a nucleus (DNA and RNA free floating in cytoplasm), divide through binary fission, DNA is circular, contains histone-like proteins, moderate RNA processing, and eukaryotic transcription and translation

Eukarya

single or multicellular, membrane-bound nucleus to house genetic material, internal organelles, divide through mitosis or meiosis, linear RNA, like histone proteins, extensive RNA processing, and eukaryotic transcription and translation

Eukaryotic animal cell components

plasma membrane, cytoskeleton, extraceullar matrix, nucleus, endoplasmic reticulum, Golgi apparatus, ribosomes, lysosome, mitochondria, lysosome, and peroxisome

eukaryotic plant cell components

plasma membrane, cytoskeleton, cell wall, vacuole, nucleus, endoplasmic reticulum, Golgi apparatus, ribosomes, chloroplasts, mitochondria, and peroxisome

plasma membrane

surrounds cells and organelles, a barrier between outside an inside of a cell or organelle

nucleus

contains cell’s genetic information, main location for transcription

nuclear envelope

surrounds the nucleus, contains an inner and outer membrane, each a lipid bilayer

nuclear pores

channels through the nuclear envelope

nucleolus

synthesize RNA needed in ribosomes (rRNA)

ribosome

synthesizes polypeptides during translation, consists of an RNA and protein complex, partially made in the nucleus, then sent to cytosol

endomembrane system

structures that synthesize proteins and transport them around or out of the cell. contains: endoplasmic reticulum, Golgi apparatus, secretory vesicles, and lysosome

Endoplasm reticulum (ER)

smooth ER: no ribosomes, involved in lipid and steroid synthesis

rough ER: ribosomes are embedded in the membrane, synthesizes membrane and secretory proteins and sends them to the Golgi

Golgi apparatus

stack of single-membrane vesicles, processes and packages secretory proteins and synthesizes polysaccharides, accepts transition vesicles from the ER, processes proteins, and sends them off in secretory vesicles

secretory vesicles

small single membrane vesicles, transport secretory proteins to the cell membrane, releases contents by fusing with cell membrane (exocytosis)

lysosome

formed from the golgi, similar in structure to secretory vesicles, contain hydrolase: enzymes that break down proteins, carbohydrates and fat

peroxisome

contain catalases that break down hydrogen peroxide, which can be toxic to cells (peroxisome can also generate hydrogen peroxide), single membrane structure, formed form the ER, but not apart of the endomembrane system

vacuole

single-membrane organelle, temporary storage and cell structure (turgor pressure), only found in plant cells

mitochondrion

energy production via breakdown of sugar, has both an outer (inter membrane space) and an inner membrane (matrix), has their own circular DNA which gets replicated (mtDNA)

cristae

folds in the inner membrane

chloroplasts

synthesize sugar from light energy, found in leaves and photosynthetic tissues, has outer and inner membrane, and has own DNA (cpDNA)

thylakoid

stacks of membrane, reaction here depend on solar energy, contain chlorophyl, which is green

stroma

fills the interior of the chloroplast, reaction here do not require solar energy

endosymbiont theory

a theory that mitochondria and chloroplasts evolved from ancient bacteria that formed a symbiotic relationship with primitive nucleated cells

cytoskeleton

fibrous protein filaments that define cell shape, also involve in movement, division, transporting organelles/macromolcules through cytosol

extracellular matrix

structural support, outside the plasma membrane

cell wall

made of cellulose

membrane functions: organization

need to separate the cell and organelle interior from exterior, keeps wanted substances in and unwanted substances out

membrane function: transport

membrane proteins regulate movement of molecules into and out of cells or organelles

membrane function: signal detection

receptor proteins bind to chemical signals outside the cell and transfer the message to the cell interior

membrane function: cell-to-cell interactions

membrane proteins allow cell-cell adhesion dn communication

fluid

lateral movement and elasticity of the phospholipid bilayer

mosaic

composed of both lipids and proteins

phospholipids

the most common membrane lipid, primarily composed membranes

membrane fluidity

phospholipids are not static, and move around

speed of movement depends on:

temperature, length of fatty acids, and saturation of fatty acids

Tm

the transition temperature, the temperature at which a membrane passes form a gel-state to fluid state

sterol (type of steroid)

a four-ringed hydrocarbon

cholesterol

acts as a membrane fluidity buffer (keeps within a desired range), composed 50% of eukaroytic membranes

high temperature

rigid structure prevents phospholipids from becoming too fluid

low temperature

bulky structure prevents phospholipid tails from binding too tightly and becoming rigid

glycolipids

lipid and a carbohydrate heard, either glycerol or spingosine based

membrane asymmetry

different phospholipid are kept on distinct sides of the membrane- polar head cannott easily pass through the hydrophobic middle

flippase

protein that facilitates the movement of a phospholipid from one side to the other

membrane proteins

proteins associated with lipid bilayer membrane

asymmetry of membrane proteins

proteins have distinct structures on one side of the membrane vs the other and cannot change sides

lipid raft

a section of membrane that moves together, rich in cholesterol and sphingolipids, and allows specific proteins to travel together

membrane transport

maintenance of a specific internal chemical environment for proper function by controlling what can cross the membrane

selectively permeable

controlled passage of ions and small molecules across a membrane

concentration gradient

difference in concentration of substance across a membrane, solutes will move from higher to lower concentration

electrochemical potential

difference in concentration and charge of a charged substance across a membrane, a substance will move down electrochemical gradient

membrane potential

determined by the equilibrium potentials of all ions permeable to the membrane, maintained by transportaters to keep around -60 mV

simple diffusion

molecules pass freely across membrane, following the concentration gradient towards equilibrium

facilitated diffusion

polar and charged molecules move down electrochemical gradient toward equilibrium, facilitated by channel proteins or carrier proteins

channel proteins

transmembrane protein channel open to both sides of membrane at once, includes aquaporins (water) and ion channels

carrier protein

transmembrane proteins that bind to a specific substance, change conformation, and unbind substrate on the other side of protein. transporting molecules in the direction of concentration gradient so doesn’t require energy

antiporter

carrier proteins that can move two molecules at the same time, moves both in opposite directions

symporter

carrier protein that can move two molecules at the same time, in the same direction

active transport

requires energy input, moves molecules against electrochemical gradient (ex: sodium potassium pump)

trancription

the information in DNA is converted to RNA (RNA synthesis)

translation

the information in RNA is converted into a polypeptide (protein), genetic code translates a nucleotide sequence into amino acid sequence

Process of RNA synthesis

1. RNA polymerase bind to promoter sequence and unwinds the DNA and synthesizes RNA strand

2. RNA strand is elongated until reaching the terminator sequence, RNA is synthesized 5’ to 3’

mRNA

the RNA sequence transcribed from DNA

coding sequence

region that will be translated

5’ untranslated region (UTR)

regulates ribosome binding

poly(A) tail

untranslated region, increases stability of mRNA

control elements

regions of DNA that are regulatory

transcription factors

can modify transcription and gene expression

gene regulation

why we have different cell types if all cells have the same DNA

codon

a series of three nucleotides that encode an amino acid

three pockets in the ribosome

-A-site: new amino acid is brought in

-P-site: peptide bond is formed with the growing polypeptide chain

-E-site: exit site

tRNA (transfer RNA)

“adaptor” molecule that connects mRNA codon to the correct amino acid

amino acid attachment site

binds to a specific amino acid, there are 20 different tRNAs — one for each amino acid

anticodon loop

reads the genetic code of the mRNA

aminoacyl tRNA

tRNA once bound to an amino acid

Translation (RNA)

1. tRNA + amino acid: binds to appropriate codon at the ‘A’ site

2. peptide bond is formed with aa at the ‘P’ site: chain is transferred

3. empty tRNA leaves the ribosome from the ‘E’ site

translation initiation

initiation factors help small subunit of ribosome and initiation tRNA bind to the mRNA and large subunits binds, initiator tRNA located in the P site

elongation

tRNA enters the A site, anticodon binds codon

termination

ribosome reaches the stop codon (enters the A site)

release factor protein

bonds to the stop codon, final tRNA unbends, large and small ribosome subunits unbind from the mRNA

protein folding

can occur spontaneously after translation, others requires involvement of chaperone proteins. chaperon proteins require energy input, folding with chaperons can occur min- or post-translation

post-translational processing

chemical modifications made to polypeptides to make them function, often occurs in the Golgi

the endomembrand system

dynamic, interconnected system of cytoplasmic membranes, including the ER, Golgi, endosome, lysosomes, and nuclear envelope

trafficking

movement of proteins and lipids between organelles

the endoplasmic reticulum (ER_

accounts for 50-90% of membrane in an average cell, consists of large, flattened or tubular cistenae with or without ribosome

the rough ER

contains ribosomes, synthesizes: membrane proteins, secretory proteins, glycoproteins; glycosylation: begins glycosylation of future glycoproteins; protein folding: assists with folding, quality control

the smooth ER

no ribosomes; synthesizes: steroid, membrane lipids; detoxifies: drug detoxification (liver cells); calcium storage: can contain high concentration of Calcium 2+

barbiturates

depressants broken down in the smooth ER

calcium ATPase

moves calcium against its concentration gradient to fill smooth ER with calcium

regulated release from the ER

can trigger cellular process

the Golgi apparatus

stack of separate single-membrane cisternae, protein and lipid processing, and packages and send proteins and lipids to next destination

Cis-golgi network (CGN)

between ER and Golgi stack

Trans-golgi netwrok (TGN)

between the Golgi stack and membrane (furthest away from ER)

Anterograde movement

toward the plasma membrane

retrograde movement

towards the ER

stationary cisterns model

vesicles fuse in and out of the cisternae

cisternae maturation model

anterograde movement is accompanied by maturation of proteins to be secreted