Cell bio exam 2

what are examples of important activated carriers? what is the function of Nicotinaminde adenine dinucleotide

(ATP, NADH, FADH2)

What codon does the translation of an mRNA begin with?

AUG

Do ribosomes possess catalytic activity? What is the name of an enzyme that catalyzes the formation of a peptide bond?

Yes. Peptidyl transferase (contained within the large subunit)

what is sphinogomyelin and where is it found?

a type of sphinogolipid found in animal membranes

what is caroenoid

accessory pigments that serve to protect chlorophyll

understand active transport. what are the different types of active transporters

active transport moves solute agianst their electrochemica/concentration gradient-moving solutes away from thermodynamic equilibrum, thus energy input is needed. 1. coupled transporters: couple uphil transport with downhil transport 2 . ATP-driven pumps: couple uphill transport with the hydrolyssi of ATP

where do the sugars synthesized by the chloroplasts go?

exported to the cytosol for production of cellular ATP, starch, and other metabolities

which surface of plasma membrane are the carbohydrates found on?

extracellular surface

what side of membranes are the sugars of glycoproteins and proteoglycans on?

extracellular surface of plasma membrane

what occurs when electrons enter the electron transport chain, how are electrons transferred from one molecule to another?

first, electron transport begins when a hydride ion is removed from nadh and is converted into a proton and two high energy electrons. this reaction is catalyzed by nadh electrons are transfered spontaneously from low elecgron affinity to molecules with high electron affinithy

what are phospholipid translocators?

flip phospholipids

what is analogus between chloroplasts and mitochondria

inernal membrane is thylakoid in chloroplast, cristae in mitochondria matrix (mitochondria) is stroma (chloroplast)

what side of the plasma membrane are membrane-associated proteins on?

inner (cytosolic) surface

where in the mitochondria different steps of oxidative phosphorylation are occuring

inner membrae

permeability of the outer and inner mitochondrial membranes

inner membrane is impermeable becuase elecrochemical gradien of H+

requirements for chemiosmotic coupling in mitochondria?

inner mitochondrial membrane, high energy electrions (NADH and FADH2) two sets of prtoein complexes embedded in membrane (transferes electrons, pumps protons and syntehsizes ATP), protns to generage a H+ gradient

describe the different types of integral membrane proteins

integral membrane proteins are proteins directly associated with the membrane

pHs associated with different areas of chloroplast

intermembrane space= low pH matrix= high pH

define photosystem and describe basic structure

large, multi-protein complex. the antenna and photochemical reaction center

what different types of diffusion/movement occur?

lateral diffusion, rotation, flexion, transverese diffusion

how do the lipids affect movement of components in a membrane?

lipid components are usially in constant motion, thus making the membrane not a rigid structure

why is sugar oxidized in a stepwise manner instead of being used in one step?

becuase stepwise oxidation preserves useful energy compared to the simple burning of the same molecule. stepwise oxication has small activation energies that are overcoem by enzymes that work at body temp, and the free energy is stored in activated carrier molecules. in direct burning, there is a very large activation energy to overcome and all of the energy is released as heat, none is stored

what is the begining substrate? what is role of O2? why doe the cycle depend on molecular oxygen?

beginging substrate is acetyl coA, which is then converted ito co2

How does protein folding occur?

begins immediately as protein spins out of ribosome. N-terminal end is folded first while C-terminal end is still being synthesized. Folding is completed after release from the ribosome.

Small subunit of ribosome

binds mRNA and matches the tRNAs to the codons of the mRNA

is the membrane a rigid structure?

cannot be rigid, the are in constant motion

what is the basic structure of a sterol

carbon skeleton made of four linked rings, hydrophobic tail, and small hydrophilic head group. they are hydrogens bound to phospholipids

what occurs during dark reactions?

carbon-fixation reactions. ATP adn NADPH from light reactions are used as energy source (activted carriers) to convert CO2 into carbohydrate (carbon fixation). this occurs in stroma with formation of glyceradlehyde 3- phosphate, which is then transported to the cytosol

what are the primary functions of sterols?

cell membrane structure, affects fluidity and helps in signaling

voltage gated ion channels?

changes in electrical potential across a membrane

what are the five types of transmembrane channel proteins and what type of transport do they mediate?

channel proteins: passive transport mediated by the concentration or electricochemical gradient. the hydrophylic transmembrane channels alloow water soluble solutes to pass. 5 types are porins, aquaporins, gap junctions, plasmadesmata, and ion channels

how do selectivly permeable membranes regulate molecular traffic?

characteristics of materials being transported, membrane solubility charachteristics, presence of specific transmembrane transport prtoeins

what is simple diffusion? how does the hydrophobic interior of the membrane affect simple diffusion?

direct, unaided net movement of molecules into and through the lipid bilayer in the direction dictated by the concentrations of the solute on the two sides of the membrane

who is hans aldof krebs

discovered citric acid cycl, noble prize in physiology and medicine in 1953

what is cardiolipin?

double phospholipid that countains four fatty acids. help make membrane especially impermeable

what is substrate-level phosphorylation? what is oxidative phosphorylation?

substrate-level: oxidation of food molecules directly coupled to atp synthesis oxidative-level: atp generaged in reactions using enrgy from NADH, takes place in mitochondrial membranes

which organelle is primarily responsible for glycosylating glycolipids?

sugars are added to the membrane in the Golgi bodies

what are couple transporters? what are symports and uniports?

symport= 2 solutes move in same direction antoport= two solutes move in opposite direction

what sides of the membrane are peripheral membrane proteins on?

the peripheral (outside) edges

understand passive (facilitated) transport. what are uniports and what kinds of membrane transport are they used for?

uniports transport a single solute across the membrane passively down concentration or electrocmehical transport

are ion channels fast or slow?

very fast

different ways that ion channels can be gated? why stimuli regulates ion channels?

voltage-gated: changes in electrical potential across a membrane ligand-gated: controlled by the binding of specific ligand (hormone, econdary messenger, ATP) mechanically-gated: open and close in response to mechanical forces that act on membrane

where are the protons that are pumped fromteh inner mitochondrial membrane come from?

water is a reservior of h+

what are the forces by which the lipid molecules in a membrane are held together?

weak hydrophobic forces and van der waals forces

What is the P Site?

where the amino acids on the tRNA make a peptide bond with the amino acids on the rRNA at the A site forming a long amino acid chain

What is the A Site?

where the new incoming tRNA bind to mRNA

how are metals involved in the pumping of protons and the transport of electrons across the inner membrane?

withing the three electron transport enzyme complexes, the elecgrons move manly between metal atoms that are tightly bound to the proteins, Iron-sulfer centers are in the NADH dehydrogenase complex cytochromes (bound heme group) is cytochrome c reductase complex copper atoms in cytosome C oxidase complex

describe porins, aquaporins, and ion channels

porins: beta barrel proteins found in outer membranes. they are large pores with low specificity aquaporins: fast movement of water, this is found in kidnesy ion channels: smallest porse size, selectivity involes pore size and distribution of charged amino acids in pore. the rate of transport

Where are ribosomes synthesized?

Synthesized in cytosol, then transported to nucleus to create small and large subunit

describe process of citric acid cycle

1. acetyl coA starts common pathway for degradation of 2-carbon acetyl residues. Generates NAdh by oxidizing acetyl coA to Co2

What are the five major functions of membranes?

1. boundary and permeability barriers (creates compartments) 2. working platforms/surface area (endoplasmic reticulum) 3. regulates transport of molecules and ions 4. signaling (detect and transmit electrical and chemical signals) 5. cellular growth and motility

what are the three stages of cellular metabolism/

1. glycolysis: partial oxidation of glucose and production of ATP int eh absence of oxygen

describe 2 important experimental methods that provide evidence for the lateral diffusion of proteins in a membrane

1. hybridiztion of cells: mouse and human proteins are conugated to different fluorescent dyes. fusion of cells create mouse-human hybrid cell and then the proteins are distributed evenly througout time 2. fluorescence recover after photobleaching: unbleached cell surface is labeled with fluorescent dye. a laserbeam then bleaches a surface, but the fluorescent molecules diffuse into the bleached area overtime.

describe the three most important aspects of lipid composition that affect membrane fluidity and understand the underlying reasons for each.

1. length of fatty acid tails: shorter tails= more fluid membrane (van der waals force interactions). longer chain=more stable 2. degree of saturation of fatty acid tails: unsaturated faty acid tails hinder close packing, thus increasing fluidity. saturated fatty acids makes for close packing, making the membrane more stable and less fluid 3. sterol content: sterols decrease fluidity as temp increases becuase phospholipid movement is restrained. at low temp, sterolss increase fluidity because the phospholipids are prevented from packing close

different protein complexes tath are prt of electron transport chain, which one uses most of the oxygen that we breathe?

1. nadh dehydrogenase complex 2. cytochrome c reductase complex 3. cytochrome c oxidase complex

explain the two methods used by animal cells to make ATP and where do these events occur?

1. oxidation reactions of food molecules are directly coupled to the energetically unfavorble reaction of ATP synthesiss. this is produced during glycolysis 2. ATP is generaged in reactins which use enrgy from the activated carrier NADH. this takes place in the mitochondrial membranes

what are the four classes of ATPase pumps and what are they used for?

1. p-type: cationic transport found in plasma membrane (Na+ and K+) 2. V-type: pump protons into vesicles, vacuoles, and lysosomes 3. F-type: found in bacteria, mitochondria, and chloroplasts where they are integral part of mechanism that produces ATP 4. ABC-type: found in plasma membrane and organelle membranes involved in nutrient uptake, protein export, and removal of detoxified drugs.

what is generated GTP used for? what is end product of ciric acid cycle?

3 NADH, 1 FADH2, 1GTP, and releases 2 moecules of CO2. GTP exchanges phosphate group with ADP to form ATP because ATP is not directly formed int eh citric acid sycle

How many codons specify one amino acid?

64 codons for 20 amino acids

What end of the growing polypeptide chain are amino acids added to?

C-Terminal

Large subunit of ribosome

Catalyzes formation of peptide bonds that link amino acids together in polypeptide chain

explain how charged and uncharged molecules are affected by the gradients

For charged molecules and ions, the difference in electrical potential across a membrane is an additonal force that drives movement across a membrane. most cell membranse have a voltage across them (electrical potential, sytosolic side is usually negative)

Free ribosome

Free in cytosol

What are the primary functions of the 5' cap and poly A tail?

Increase the stability of the mRNA;Facilitate mRNA export from the nucleus to the cytoplasm;

Describe the basic structure of a phospholipid

Lipid head group (polar) with fatty acid tail (nonpolar)

What are heat shock proteins and what do they do?

Molecular chaperons that help guide protein folding.

name, locate, and describe function of protein complexes that are part of the oxidative phosphorylation process that occur in the inner mitochonrial membrane

NADH dehydrogenase complex, cytochrome c reductase complex, cytochrome c oxidase compex. electrons pass spontaneously from molecules that have low affinity for their avaliable electrons, adn lose them easlity to mlecules with a higher eletron affinity

what are functions of NADH and FADH2 in the process of oxidative phosphorylation

NADH is a carier of high energy electrons. NADH donates its high-energy electrsons to the electron transport chain. these electrons then enter the electrontransport chain and are passed along the chain to moecular oxygen to form water. molecular oxygen is the final acceptor of electrons

what are the activated carriers created by chloroplasts?

NADPH-high energy hydrogen and electron donor and ATP

What is a proteasome?

Protein destruction machines

What site on the small ribosomal subunit does the initiator tRNA bind?

P-site

How is the end of the protein-coding message signaled? What are the release factors?

Proteins called release factors bind to stop codon positioned on the A-site. (UAG, UAA, and UGA are stop codons)

What is the initiator tRNA and what amino acid does it carry?

Starts translation, carries the amino acid Met.

Why is the formation of a peptide bond energetically favorable?

The formation of each peptide bond is energetically favorable because the growing C-terminus has been activated by its covalent attachment to a tRNA molecule. The peptidyltRNA linkage that activates the growing end is regenerated during each addition.

Where are ribosomes located within the cell?

They are made in the cytoplasm, then transported to the nucleolus to assemble the large and small ribosomal subunits, then the 2 subunits move back to cytosol via nuclear pores

what is an anticodon?

a set of three consecutive nucleotides that pair with the complementary codon in an mRNA molecule

how are membrane-associated proteins embedded in the monolayer?

amphiphthetic alpha helix

what is ATP syntahse and its function?

an enzyme that creates a hydrophilic pathway across the inner mitochondrial membrane that allows protons to flow down their electrochemical gradient

what are membrane-associated proteins?

associatd with the cytosolic surface of the membrane via the amphipathetic alphahelix embedded in monolayer

Bound ribosome

attached to membranes of endoplasmic reticulum

how are peripheral membrane proteins bound to the bilayer?

bound indirectly by weak, noncovalent interactions with other membrane proteins

what are names of fat cells that can oxidize food molecules? what is name of process and underlying mechnism

brown fat cells. innermembrane of brown fat cells contain special transport protein that moves protons down electrochemcial graident.

what is the primary sterol found in animal cells and what membrane is it found in?

cholesterol, it is found in plasma membrane

define antenna complex

cluster of chlorophyl and accessory pigments (carotenoids) molecules that absorb light energy and pass virtual photons to photochemical reaction center via FRET

what are the different gradients that are involved with transport across a membrane?

concentration and elctrochemical gradient

what two gradients drive simple diffusion and passive/facilitated transport?

concentration and electrochemical gradient

ligand gated ion channels

controlled by the binding of specific ligand (hormone, econdary messenger, ATP)

How is the electrochemical gradient involved in coupled transport?

coupled transporters transport two different solutes simultaneously or sequencentially by coupling the uphill transport of one solute across the membrane (passive transport) to the downhill transport of another (active transport=needs energy)

what is chemosmotic theory

created by peter d. mitchell. biological energy transfer

understand how membrane orientation is maintained during vesicular trafficking

cytosolic surface is always cytosolic surface and luminal surface is always extracellular surface. two leaflets make up one unit membrane. different surfaces of the membrane have different types of phospholipids, glycolipids, and proteins

what are sphingolipids

derived from spingosine, not glycerol

how do aminoacyl-tRNA synthetases couple tRNAs to the correct amino acid?

different synthetase enzyme for each amino acid. Enzyme attaches amino acid to 3' end on tRNA. Step 1: Amino acid is activated through linkage of carboxyl group to AMP Step 2: AMP-linked carboxyl group on amino acid is transferred to hydroxyl group on sugar at 3' end of tRNA molecule

are peripheral membrane proteins easy or difficult to isolate for biochemical studies?

easy to isolate

what is electrochemical graident? how does electrochemical gradient affect passive transport?

electrochemical gradient is gradient of electrochemical potential an ion can move across a membrane. chemcial gradient=difference in solute concentration across a memrane and electrical gradient (difference in charge across a membrane)

difference between electrochemical gradient and electron motive force

electrochemical proton gradient is used to drive formation of ATP and transport of selected metabolites across inner mitochondrial membrane

endosymbiont therory

emdosymboisis of cyanobacterium gave rise to chloroplast and photosynthetic eucaryoic cells

why are membranes manufactured asymmetrically in the smooth ER?

enzyme inserts new phospholipids into cytosolic monolayer.

what is tay-sachs disease?

genetic disorder caused by insufficient activity of enzyme that breaks down sphingolipids. Sphingolipids then build up and destroy brain and nerve function

what is the basic structure of a glycolipid

glycolipids (glycosylated lipids) are derivatives of phospholipids that contain a carbohydrate head group. this carbohydrate head group may contain anywhere from one to six sugars

define glycolysis. is o2 involved? is co2 released? by what method is ATP produced during glycolysis? what happens during steps 6 and 7 of glycolysis and why these steps are the central reactions of glycolysis? what are the end products of glycolysis? what are the energy requirements and energy yields of glycolysis? why is glucose phosphorylated during the energy investment phase of glycolysis?

glycolyysis is partial oxidation of glucose and producion of ATP in the absense of oxygen (anaerobic reactions). net gain of 2 ATP molecules and 2 NADH molecules for every molecule of glucose broken down. ATP investementis 2 molecules of ATP are initally consumed in first three reactions to provide energy neeed to drive the reaction. steps 6-7 are the energy-generation phase, aldehyde is converted int a carboxylic acid. this reaction releases enough free energy to syntehsiE a molecule from ADP+Pi. no molecular oxygen is involved but oxidation occurs becuase 2 hydrogen atoms are removed 2 ATP and 2 NADH step 6: energy released during C-H bond oxidation drives formation of high-energy phosphate bond step 7: hydrolysis drives ATP formation

how does the amphipathic nature of transmembrane proteins allow them to span ?

hydrophobic interior region by hydrophilic exterior region on the sides of the membrane

what are the primary functions of sphingolipids?

important roles in signal transmission, cell recognition, cell surface protection

in what ways can proteins associate with a membrane?

transporters, anchors, receptors, and enzymes. most membrane functions are carried out by proteins

citric cycle does not use oxygen

it requies oxygen to procceed becuase oxygen is a lectron acceptor

what are lipid rafts and what are their characteristics and functions?

localized regions of plasma membrane where there are elevated levels of cholesterol, protein, and sphingolipids. sphingolipids and cholesterol self assemble to form lipid rafts, they are basic building blocks). lipid rafters are more ordered and tightly packed that the surrounding bilayer and can float freely. lipid rafts are ticker and more viscus. they serve as organizing centers for assembly of signaling molecules-influenceing membrane fluidity and membrane protein movement.

how does the length and saturation of the fatty acid tails affect membrane fluidity?

longer fatty acid tails, makes the membrane less fluid (more stable). saturated fatty acids allows for closer packing, so there is less fluidity

what are the primary functions of phospholipids?

major component of animal cell membranes. protects and determines what goes in/out of a cell

which part of mitochondria does citirc acid cycle occur

matrix

what is redox pair? how does redox poteintial affect movement of eectrons?

measure of the tendency of a given system to acquire electrons and thereby be reduced is defined as he redox potential molecule that loses electron is eelctron donor, molecule taht takes electrons is acceptor. together, this forms a redox pair nadh and nad+ is a redox pair

non-cyclic and cyclic photosynthesis

non-cyclic photosynthesis is a 2 stage process forming ATP and NADPH. this is found in plants, cynanobacteria and algae cyclic photosynthesis: shut of PSII, allowing the production of ATP only using PS I. organism that has no need for reductive power in NADPH to fix power but still needs ATP

FRET and how it relates to photosystems

mechanism of energy transfer between two ight sensitive molecules (chromophores). donor transfer energy to acceptor

structure and function of mitochondira. important charachteristics of inner and outer mitochonrial membrane

mitochondria contains enzymes required for he oxidation of pyruvate and fatty acids to acetyl-coA and enzymes for citric acid cycle, channel forming protein called porin. outer membrane: has many copies of porin, which forms wide aqueous channels through a lipid bilayer, which makes the intermembrane space of mitochondria chemcialy equivalent to the cytosol inner membrane: impermeable to the passage of ions and small molecules.

where does the reaction of conversion of pyruvate ito acetyl coA take place? what enzyme catalyzes this reacction

mitochondrial matrix, and the enzyme is pyruvate dehydrogenase complex

What role do transfer RNAs play in translation?

molecular adaptors that match amino acids with codons

how do the different components move throughout the membrane?

most components are in constant motion. held by weak hydrophobic and van der waal's forces. there is lateral diffusion, rotation, felxion, and transverse diffusion.

What is required for an mRNA to be considered export ready?

must be bound to a specific set of proteins: Poly-A-Binding Proteins, A cap-binding complex, proteins that mark completed RNA splices, nuclear transport receptor

what kinds of tissues are sphingolipids primarily found in?

neural tissues, brain tissue extracts

What is the mRNA-binding site?

one binding site.

structure of chloroplats stroma, inner/outer membranes, thylakoids, grana, thylakoid space

outer membrane is hgihly permeabe and inner membranes (thylakoid) is barely permeable

difference between substrate-level phosphoryoation and oxidative phosphorylation. stages of oxidative phosphorylation

oxidatie phosphorylation: process of ATP synthesis involves consumption of o2 sage 1: energy of electron transport is used to pump protons across membrane stage 2: energy in proton gradient is harndessed by atp synthase to make atp

what types of membrane transport require transporters or channel proteins?

passive (facilitated transport) and active transport

explain how patch clamping allows us to understand ion channel behavior

patch clamping is method of studying ion channels. invoves recording ion channel behavior, glass pipette with small tip is pressed on cell membrane, forming a seal. suction is applied, plasma membrane remaines attached or is detached. ionic flow through a channel can be measured

what is ph in mitochondrial maattrix andinnermembrane space?

ph is higher in the matrix compared to intermembrane

what type of enzymes insert new phospholipids into the cytosolic monolayer?

phospholipid syntheses

what occurs during light reactions?

photosynthetic electron-transfer reactions in thylakoid membrane. chlorophyll obtains electrons from water, and generates o2 via water splitting enzyme. electron flow pumps H+ across thylakoid membrane from stroma into thlakoid space. this creates an electrochemical proton gradient across the thylakoid membrane and the proton gradient is used to produce ATP in the stroma. high energy electrons reduce NADP+ to NADPH in stroma

where are most ion channels found?

plasma membranes

what determines ion channel slectivity

pore size and distribution of charged amino acids in pore

What role do ribosomes (rRNA) play in translation?

responsible for reading the order of amino acids and linking amino acids together

What happens to misfolded and unwanted proteins?

proteasome acts on proteins marked for destruction by ubiquitin. Proteasome cap recognizes the marking and translocates it into the proteasome core where it is digested.

what are the primary functions of glycolipids?

protection- strengthen and protect the plasma membrane cell recognition- attacks pathogen, organ/graft compatibility, blood transfusion, embryonic development

how can the lateral movement of proteins in the plasma membrane be restricted?

protein protein interaction, proteins teathered to ECM molecules outside of the cell, proteins tethered to cell cortex inside the cell, proteins tethered to other proteins in adjacent cell

What are nuclear pore complexes (NPCs) and what do they do?

provide access to the nucleus and regulate the transport of proteins and RNA across the nuclear envelope.

what are transmembrane proteins?

single pass, multipass, amphipathetic, hydrophobic region of interior membrane. 1. single pass- polypeptide chain cross bilayer as an alpha helix 2. multipass-transmembrane alpha helix with an aqueous pore

What role does ubiquitin (polyubiquitin) play in this process?

small protein that marks proteins for destruction by covalent attachment to the proteins

what kinds of molecules can undergo simple diffusion and which cannot?

small, uncharged, nonpolar (hydrophobic) molecues can go through via simple diffusion (gases and steroid-based hormones). the smaller the molecule and the less strongly its association with water, the more rapidly it will diffuse across a bilayer. hydrophobic interior creates a barrior to most hydrophillic molecules and ions. ions are lectrically attracted to water

How is the genetic code redundant?

some amino acids are specified by more than one codon

what is the primary type of (oligo)glycolipid found in most animal cells?

sphingoglycolipid

mechaincally gated ion channels

stretch-activated (sound strikes auditory hair cells, vibrations stretch ion channels, ions follow into hair cells, electrical signal sent to brain and perceive as sound

which area is ATP produced?

stroma

how is the energy released during oxidation temporariily stored?

temporarily stored as high energy chemical bonds in activated carrier models

what is membrane transport?

the ability to move ions and molecules across membrnes seletivly

What is proteolysis?

the breakdown of proteins or peptides into amino acids by the action of enzymes.

What is the E Site?

the tRNA that just gave up its amino acid, now empty, exit the ribosome to go restock their amino acid.

Why is translation not a direct one to one correspondence between a single nucleotide on the mRNA and single amino acid in a protein?

there are only 4 different nucleotides in mRNA and 20 different types of amino acids in a protein

how do sterols affect membrane fluidity?

they act as a dynamic glue. More sterol=less fluid membrane

how are sphingolipds different from other phospholipids?

they are derived from sphingosine and not glycerol like other phospholipids. Usually found in neural tissues

are integral membrane proteins easy or difficult to isolate for biochemical studies?

they are difficult to isolate because they are directly associated with the membrane

what are liposomes and micelles and why are they important?

they are essential for the absorption of fat-soluble vitamins and complicated lipids. this is used in targeted drug therapy

how are glycolipids different from other phospholipids or sphingolipids?

they contain a carbohydrate head group

How do tRNAs function as adaptor molecules?

they recognize and bind codon at one site on their surface and to the amino acid on the other site

what is the process of transporting glucose from the gut to the bloodstream and know all of the different transporters and pumps used

this is an example of coupled transport. transport of glucose into gut epithelial cells. gut epithelial cells have a glucose/Na+ symport located on the top cell surface. glucose uniport on posterior cell curface and na-k pump on posterior cell surface. the unipmort and symport are functionally coupled to a na/k pump

How many consecutive nucleotides in an in an mRNA make up a codon?

three

which membrane is H+ gradient set up and used to produce ATP

thylakoid membrane