Cell bio 3

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1

least

Compounds that are the most oxidized have the _____ energy

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catabolism

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

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anabolsim

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

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multiple steps

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

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5

most

Compounds that are reduced have the _____ energy

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activation energy, we capture energy, step regulation

Animal cells do not combust because_____

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7

cAMP

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

<p>formed by ATP activation of epinephrine or glucagon, activates a PKA</p>
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8

PKA

Turns glycogen synthase off and phosphorylase on

<p>Turns glycogen synthase off and phosphorylase on</p>
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9

insulin

Bonds to its receptors to produce PDE, which deactivates cAMP

<p>Bonds to its receptors to produce PDE, which deactivates cAMP</p>
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10

glycolysis

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

<p>Occurs in cytoplasm, doesn’t require oxygen, starting pathway in all organisms, produces little ALP</p>
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glycolysis

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

<p>Is very thermodynamically favorable due to large negative G and [reactants] &gt;&gt;&gt; [products]</p>
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12

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

<p>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</p>
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13

TCA/Kreb’s/citric acid

Occurs in mitochondria, requires oxygen indirectly, ATP from GTP

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14

hexokinase

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

<p>uses ATP convert glucose and remove it from the reactant pool in the 1st step of glycolysis</p>
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15

NAD+

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

<p>Important cofactor/coenzyme that accepts electrons and becoms reduced, adds a 2nd phosphate in glycolysis</p>
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16

allosteric activator

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

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allosteric inhibitor

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

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pyruvate kinase

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

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anarobic metabolism

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

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20

High NAD+

_____ = low energy

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Low NAD+

____ = high energy

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22

electron transport chain

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glucose, pyruvate

Glycolysis starts with _____ and ends with ………

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24

outer

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

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inner

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

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water

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

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27

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

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oxygen

terminal electron acceptor (highest affinity) in aerobic respiration

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cytochrome c

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

<p>mobile carrier that is small and soluble, transport electrons to complex IV</p>
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complex II

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

<p>can shuttle electrons between complexes, gather electrons from FADH2 or NADH</p>
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31

complex IV

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

<p>collects 4 e- and then uses them to reduce oxygen and produce water</p>
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3 ways to contribute to gradient

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

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33

ATP synthases

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

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34

ADP

most important factor controlling respiration rate

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35

beta

catalytic domains that cause ADP to turn into ATP

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36

gamma

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

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37

open, loose, tight

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

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38

c

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

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39

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)

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40

rotenone

poison that blocks e- flow at complex 1

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41

antimycin

poison that blocks e- flow at complex 3

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42

cyanide

poison that blocks e- flow at complex 4

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43

CO

poison that blocks e- flow at complex 4

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uncouplers

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

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45

chloroplast

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

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light dependent

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

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47

calvin cycle

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

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48

NADP+

terminal electron acceptor (highest affinity) in photosynthesis

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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

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50

photosystem II

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

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51

photosystem I

system that makes NADPH from the e- transport

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52

rubisco

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

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53

stroma

where light independent rxn/Calvin cycle occurs

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54

thylakoid membrane

where light dependent rxn occurs

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55

regulated secretion

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

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56

constitutive secretion

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

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57

pathway of secreted proteins and IMPs

what is the picture?

<p>what is the picture?</p>
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58

rough ER

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

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smooth ER

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

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60

cytosolic ribosome

all translation starts in the ______

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61

cytosolic

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

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exocytosis

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

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endocytosis

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

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cisternae

part of the ribosome where proteins are synthesized

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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

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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

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pellet 1

contains: nuclei, mitochondria, and other big stuff

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pellet 2

contains: microsomes (ER and Golgi)

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69

lysate

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

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gel autoradiograph

using a SDS page, is labeled with a radiocactive ion

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71

sufficient

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

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72

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)

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73

SRP-receptor

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

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74

stop transfer sequence

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

<p>stretch of 20 hydrophobic AAS after a signal sequence, causes a cytosolic C terminus and a luminal N terminus</p>
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75

start transfer sequence

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

<p>stretch of ~20 hydrophobic AAs not at N terminus, causes a cytosolic N terminus and luminal C terminus</p>
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76

translocon

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

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77

binding protein

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

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78

signal peptidase

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

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79

NLS

sequence marking a protein for insertion into the nucleus

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80

motif of ML

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

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81

initial or core glycosylation of glycoproteins

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

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82

inside

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

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83

UGGT

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

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84

Calnexin

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

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85

ubiquination

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

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86

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)

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87

transmembrane proteins

have cytoplasmic sorting signals that bind to adapter proteins

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88

coat proteins

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

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89

adapter proteins

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

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90

COPII-coated vesicles

coat protein that move materials friom the RER to Golgi

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91

COPI-coated vesicles

coat protein that recycle materials back to precious Golgi

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92

Clathrin coated vesicles

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

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93

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

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94

CIS & CGN

modification in the Golgi: Sorting for RER retrievalPO4 addition on mannose, mannose removal

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medial

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

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96

trans

modification in the Golgi: Fucose, glucose and galactose addition

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97

TGN

modification in the Golgi: sialic acid addition, sorting

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98

asp-x-x-leu-leu

used for transport from the TGN to the lysosome via clathrin

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99

lys-lys-X-X (kkxx)

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

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100

DXE, or FF, FY, or YY

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

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