Cell bio 3

least

Compounds that are the most oxidized have the _____ energy

catabolism

reactions which breakdown complex molecules into simpler ones, usually done to release energy for work (respiration)

anabolsim

reactions which use simpler molecules to build more complex ones, usually require an input of energy (photosythesis)

multiple steps

cells do not have an effective means of transforming and storing an explosive amount to energy, so metabolims is done in _____

most

Compounds that are reduced have the _____ energy

activation energy, we capture energy, step regulation

Animal cells do not combust because_____

cAMP

formed by ATP activation of epinephrine or glucagon, activates a PKA

PKA

Turns glycogen synthase off and phosphorylase on

insulin

Bonds to its receptors to produce PDE, which deactivates cAMP

glycolysis

Occurs in cytoplasm, doesn’t require oxygen, starting pathway in all organisms, produces little ALP

glycolysis

Is very thermodynamically favorable due to large negative G and \[reactants\] >>> \[products\]

phosphofructokinase

uses ATP to catalyze the conversion of fructose-6-phosphate to fructose-1,6-bisphosphate by adding a phosphate in step 3, ends energy investment phase

TCA/Kreb’s/citric acid

Occurs in mitochondria, requires oxygen indirectly, ATP from GTP

hexokinase

uses ATP convert glucose and remove it from the reactant pool in the 1st step of glycolysis

NAD+

Important cofactor/coenzyme that accepts electrons and becoms reduced, adds a 2nd phosphate in glycolysis

allosteric activator

binds to a site on an enzyme other than the active site, typically sensitive indicators of the cells needs.

allosteric inhibitor

binds to a site on an enzyme other than the active site, typically downstream products

pyruvate kinase

makes the product 2 ATP and 2 pyruvate in the 10th step of glycolysis

anarobic metabolism

another word for fermentation, occurs in the cytosol, returns NADH to NAD+ which is recycled in the glycolysis pathway

High NAD+

_____ = low energy

Low NAD+

____ = high energy

electron transport chain

glucose, pyruvate

Glycolysis starts with _____ and ends with ………

outer

the _____ membrane of the mitochondria is more permeable, a 1:1 protein:lipid ratio, and is homologous to bacterial membranes

inner

the _____ membrane of the mitochondria is less permeable, 3:1 protein:lipid ratio, and required special transport proteins

water

a pH gradient inside of the mitochondria is maintained by _____ and used to bring H+ ions inside to produce ATP

ubiquinone

small, mobile, carbon ring, e- transporter, lipid-soluble, travels by lateral diffusion in the lipid bilayer, accepts/donates 2 H+ and 2 e- from complex I or II

oxygen

terminal electron acceptor (highest affinity) in aerobic respiration

cytochrome c

mobile carrier that is small and soluble, transport electrons to complex IV

complex II

can shuttle electrons between complexes, gather electrons from FADH2 or NADH

complex IV

collects 4 e- and then uses them to reduce oxygen and produce water

3 ways to contribute to gradient

electron pumps (complexes 1, 3, 4), ubiquinone, Oxygen removing H+ from the solution

ATP synthases

enzyme consisting of F1 and F0, the F1 (orange has alpha/beta subunits) (bannana is stalk)

ADP

most important factor controlling respiration rate

beta

catalytic domains that cause ADP to turn into ATP

gamma

as _____ subunit turns, it interacts with the beta subunits differently

open, loose, tight

the three positions of the beta subunits which are caused by the gamma subunit

c

intermembrane subunit that acts as a water wheel for the H+ gradients

proton-motive force

energy provided by the H+ gradient, can:

1\.Make ATP via ATP synthase

2\.Exchange ADP for ATP  (antiport).

3\.Bring in Pi with H+ (symport)

4\.Bring in pyruvic acid with H+ (symport)

rotenone

poison that blocks e- flow at complex 1

antimycin

poison that blocks e- flow at complex 3

cyanide

poison that blocks e- flow at complex 4

CO

poison that blocks e- flow at complex 4

uncouplers

allow H+ ions to diffuse through membrane and never reach high concentrations of ATP

chloroplast

large organelle with 3 membranes (2 outer 1 inner) containing stacks (granum) of thylakoids (pennies)

light dependent

reactions that occur in thylakoid membranes, uses sunlight and water to make NADPH and ATP

calvin cycle

reaction that turns CO2 into a carbohydrate using energy from the light reactions, recycles ADP and NADP+ to begining of cycle

NADP+

terminal electron acceptor (highest affinity) in photosynthesis

chlorophyll

pigment within the membrane of thylakoid that is excited by light and releases energy by (a.) fluorescence (b.) resonance energy transfer (c.) e- transfer

photosystem II

system where light is absorbed by reaction center and starts e- transport through the plastoquinone

photosystem I

system that makes NADPH from the e- transport

rubisco

ribose biphosphate carboxylase (RuBP), fixes CO2 in the Calvin cycle to make carboxylkase intermediates, start with 6 of them

stroma

where light independent rxn/Calvin cycle occurs

thylakoid membrane

where light dependent rxn occurs

regulated secretion

Type of secretion where proteins are stored in secretory granules and released upon a specific signal. Examples include insulin and digestive enzymes.

constitutive secretion

Type of secretion by cells where secretory products are continuously released into the extracellular space without any specific stimulus.

pathway of secreted proteins and IMPs

what is the picture?

rough ER

functions: production, folding, quality control and secretion of some proteins

smooth ER

functions: synthesis of steroid hormones, detoxification, and sequestration of calcium ions

cytosolic ribosome

all translation starts in the ______

cytosolic

cytoplasmic proteins imported mitochondrial proteins , and nuclear proteins are made by _____ ribosomes

exocytosis

vesicle fusion for secretion outside the cells (e.g. RER to cis Golgi at PM)

endocytosis

vesicle formation for intake of molecules at the plasma membrane (also called budding at organelles)

cisternae

part of the ribosome where proteins are synthesized

golgi complex

stack of flattened cisternae divided into functional groups, including a cis and trans face

functions: process proteins from the RER for secretion or the lysosome

signal hypothesis

signal codons in the mRNA cause a signal peptide, which causes insertion into the RER, where it is cleaved off. allows for certain proteins to be secreted

pellet 1

contains: nuclei, mitochondria, and other big stuff

pellet 2

contains: microsomes (ER and Golgi)

lysate

in vitro translation: the supernatant containing soluble proteins, ribosomes, tRNA, initiation & elongation factors (all the good stuff for protein synthesis)

gel autoradiograph

using a SDS page, is labeled with a radiocactive ion

sufficient

adding a 28 aa signal pathway is _____ to turning a regular protein into a secretory one

signal recognition particle (SRP)

G protein that (regulated by GTP or GDP) binds to the signal peptide, binds ribosome (stopping translation) and binds SRP receptor (docking station)

SRP-receptor

an IMP resident in RER membrane. cytoplasmic domain binds to SRP-GTP

stop transfer sequence

stretch of 20 hydrophobic AAS after a signal sequence, causes a cytosolic C terminus and a luminal N terminus

start transfer sequence

stretch of \~20 hydrophobic AAs not at N terminus, causes a cytosolic N terminus and luminal C terminus

translocon

protein complex that forms pore for passage of nascent polypeptide. Sec61 = main protein compenent

binding protein

\
an RER lumenal protein that helps seal the translocon and functions as a chaperone.

signal peptidase

will cut peptide bind connecting signal sequence to the remainder of the protein

NLS

sequence marking a protein for insertion into the nucleus

motif of ML

K (K/L) X (K/L)

initial or core glycosylation of glycoproteins

addition of oligosaccharides onto asp, 3 of which are cut off to help with folding

inside

proteins stay _____ the RER during folding in order to esure proper function

UGGT

functions as a folding sensor in the RER, if improperly folded, UGGT adds a glucose onto a protein

Calnexin

in the RER, modifies folding proteins by removing a glucose molecule

ubiquination

in the RER, addition of ubiquinone to a protein that fails to fold, marks for destruction in the cytoplasm

co-immunoprecipitation

determins if and how proteins interact by observint the pellet in an SDS page and immunoblotting the protein of interest (not the target of the antibody)

transmembrane proteins

have cytoplasmic sorting signals that bind to adapter proteins

coat proteins

assemble onto adapters, forming a sphere and making a pinch-off bud

adapter proteins

binds to transmembrane proteins with sorting signals and allows for binding of coat proteins

COPII-coated vesicles

coat protein that move materials friom the RER to Golgi

COPI-coated vesicles

coat protein that recycle materials back to precious Golgi

Clathrin coated vesicles

coat protein that uses AP2 for plasma membrane and AP1 for golgi

SNARE

(1) Tethering: Rab G-proteins on the vesicle and target surface each bind to tethering proteins that \n mediate the first connection between vesicle and target. \n (2) Docking: v-SNARES on the vesicle and t-SNARES on the target surface interact in a specific \n manner to allow docking of the vesicle at the target surface. \n (3) Fusion: the v- and t-SNARES are helical and they coil around one another and twist which \n physically pulls on the vesicle and target membranes and allows them to become one

CIS & CGN

modification in the Golgi: __Sorting for RER retrieval__, __PO4 addition on mannose,__ mannose removal

medial

modification in the Golgi: further mannose removal, N-acetylglucosamine addition,

trans

modification in the Golgi: Fucose, glucose and galactose addition

TGN

modification in the Golgi: sialic acid addition, __sorting__

asp-x-x-leu-leu

used for transport from the TGN to the lysosome via clathrin

lys-lys-X-X (kkxx)

used for transport back to the RER through Arf 1by COP I

DXE, or FF, FY, or YY

used for transport from RER to the golgi by COP II through Sar 1