Cell Bio Exam 3 Alcedo

Front 1

Actin Filament Locations

Back 1

- Microvili (intestines)

- Contractile Bundles in cytoplasm (muscles)

- Leading edge of migrating cell (like filipodia)

- Contractile ring in dividing cell

Front 2

Actin Monomers Leave after ATP dissociates

Back 2

False

Front 3

Treadmilling

Back 3

In actin filaments, at intermediate levels of free monomers, filament stays same size, monomers are added at + end more quickly than leaving, and at - end they leave more quickly than arriving, leads to moement toward plus end from minus end

Front 4

Phalloidin

Back 4

actin drug: bonds and stabilizes filament

Front 5

Cytochalasin

Back 5

actin drug: caps filament plus end, prevents polymerization there

Front 6

Latrunculin

Back 6

actin drug: binds actin monomers, prevents polymerization

Front 7

Taxol

Back 7

Microtubule drug: binds and stabilizes microtubules

Front 8

Colchicine (colcemid) & Vinblastine (vincristine)

Back 8

microtuble drug: binds tubulin dimers, prevents polymerization

Front 9

Monomer sequestering protein

Back 9

abp: prevents polymerization

Ex: profilin

Front 10

Nucleating proteins

Back 10

abp: bind to + end, allow adding of new monomers (forming nonbranched filaments)

Ex: formin

Front 11

actin-related proteins

Back 11

abp binds to sides of existing filaments, making branched one (important in lamellipodium of migrating cell)

ex: arp2-arp3

Front 12

Capping protein

Back 12

abp stabilizes actin. Prevents new monomers from binding, but also prevent disassembly

Front 13

severing proteins

Back 13

abp cuts proteins, makes the cell cortex more fluid, less gel like

Front 14

Cross linking proteins

Back 14

apb mechanical support for cell membrane, makes cell cortex less fluid, more gel like

Front 15

bundling proteins

Back 15

fillipodia or microvilli of cells

Front 16

Myosin motor proteins

Back 16

tracks for organelle transport, contraction in muscles

Front 17

Lamellipodia

Back 17

bigger ones, attach to ECM or to proteins on another cell due to integrins. Ones that dont attach are swept backward over cells upper surface, doing ruffling

Front 18

Rho-GTPase Protein Family

Back 18

Actin interaction with actin binding proteins involves the activation of these (there are three of them) Rac, CDC 42, and Rho

Front 19

Rac

Back 19

Rho-GTPase Protein Family

Lamellipodia formation

Front 20

CDC 42

Back 20

Rho-GTPase Protein Family

Fillopodia formation

Front 21

Rho

Back 21

Rho-GTPase Protein Family

Bundles of Contractile Actin

Front 22

Myosin I

Back 22

- Present in all cells

- Single head domain binds/hydrolyzes ATP, allows it to move along actin filament (head determines cargo)

- Only move toward + end

- Can bind to plasma membrane, moves actin filament, like during migration and cell shape change

Front 23

Myosin II

Back 23

- only in muscles

- Dimer: 2 heads and coiled coil tail of 2 heavy chains

- (-) end of actin filaments overlap myosin filaments

- Myosin filaments slide actin filament in opposite directions

Front 24

Myofibrils

Back 24

- Make up the bulk of muscle cytoplasm

- Made of a chain of sarcomeres (the contractile unit)

- Actin filaments are anchored to Z-disk structures (on either end with actin, myosin is in the middle)

Front 25

Tropomyosin and Troponin

Back 25

Tropomyosin (on Myosin II) Normally blocks myosin II binding side on actin. Troponin is attached and can bind Ca2+, causing conformational change, exposing myosin II binding site

Front 26

Which carbon does DNA have an H instead of an OH like RNA?

Back 26

Carbon 2'

Front 27

Purines

Back 27

- A and G

Front 28

Pyrimidines

Back 28

- C and T

Front 29

A and T

Back 29

form 2 H bonds

Front 30

C and G

Back 30

form 3 H bonds

Front 31

RNA Polymerase

Back 31

- adds ribonucleotides one by one to active site

- RNA goes in through the Ribonucleoside Triphosphate Tunnel

Front 32

Messenger RNA

Back 32

encode protein sequence

Front 33

Ribosomal RNAs

Back 33

- form core of ribosome

- catalytic roles in ribosome for protein synthesis

- catalyze peptide bond formation between amino acids

Front 34

Transfer RNAs

Back 34

adaptor between mRNA and Amino Acids

Front 35

Micro RNA

Back 35

regulates gene expression

Front 36

Other Noncoding RNAs (ncRNA)

Back 36

splicing, regulation of gene expression, telomere maintenance, other processes

Front 37

Promoter Region in Bacterial DNA

Back 37

Induces RNA polymerase to bind tightly to it

Front 38

Sigma Factor Subunit

Back 38

Attached to bacterial RNA Polymerase, recognizes promoter sequence and allows RNA polymerase to tightly bind to it

Front 39

A terminator sequence signals RNA polymerase to stop synthesizing, and the terminator sequence is transcribed into the RNA

Back 39

True true true

Front 40

RNA Polymerase 1

Back 40

transcribes rRNA genes

Front 41

RNA Polymerase 2

Back 41

transcribes all protein genes, miRNA gnes, ncRNA genes (eg. spliceosomes)

Front 42

RNA Polymerase 3

Back 42

transcribes tRNA genes, 5S rRNA genes, and other small RNAs

Front 43

TATA box

Back 43

Present on Eukaryotic promoter, upstream of +1

Front 44

TFIID

Back 44

Initiating transcription factor. Includes TBP (TATA binding protein)

Front 45

TBP

Back 45

TATA Binding Protein, present on TFIID, recognizes the TATA Box and distorts the DNA there, acting as a signal for other transcription factors and RNA polymerase to assemble for transcription initiation complex

Front 46

TFIIH

Back 46

- Unwinds DNA helix (ATP dependent) to expose template

- Phophorylates RNA Polymerase 2 tail, releasing it from transcription initiation complex, beginning transcription. After transcription is done, the tail is dephosphorylated

- Phosphorylation of tail also leads to assembly of RNA processing proteins on its tail

Front 47

5' Capping

Back 47

mRNA processing in Eukaryotes. Methylated guanine is added to 5' cap after ~25 bp are made

Front 48

Polyadenylation

Back 48

mRNA processing in Eukaryotes. Poly A tail (100-600 adenines) is added near 3' end. Polyadnylation signal recruits the protein complex that cleaves the mRNA near the signal, after which poly A tail is added

Front 49

Poly A Polymerase

Back 49

Adds the Poly A tail after the mRNA is cleaved near the signal

Front 50

The distance between 5' end and branched sequence is usually shorter than between the 3' end and the branched sequence

Back 50

FALSE!

Front 51

How are introns spliced out during processing?

Back 51

In eukaryotes, the 2' OH group of Adenine cleaves RNA at splice juntion. 5' Splice junction of intron covalently links to 2'OH of A, and 5' exon is release. Then 5' phosphate of exon 2 reacts with 3' OH, splices both exons and release the intron in the form of a lariat rope

Front 52

small nuclear ribonculeoprotiens (snRNPs)

Back 52

recognize special intronic sequences that will be cut out

Front 53

U1 snRNP

Back 53

recognizes 5' end of intron

Front 54

U2 snRNP

Back 54

recognizes 3' branch point junction

Front 55

Amino Acyl- tRNA synthetase

Back 55

One per amino acid that links amino acid to tRNA

Front 56

Charging

Back 56

When tRNA is bound to amino acid,, this bond is high energy, will be hydrolzyes during peptide bond formation, the energy of this bond gives energy to bind amino acids together

Front 57

translation initiation factor

Back 57

replaces the 5' cap protein in the cytosol, this can be recognized by small ribosome subunit

Front 58

Peptidyl Transferase

Back 58

rRNA acts as this, it directs tRNA to growing polypeptide

Front 59

Ribozymes

Back 59

RNA molecules with catalytic functions (ribosomes)

Front 60

Initiator methionine tRNA

Back 60

slightly different than regulat tRNA< initiates protein synthesis

Front 61

formyl-methionine

Back 61

prokaryotic translation initiator

Front 62

Tetracyclene

Back 62

antibiotic against bacterial RNA synthesis: blocks binding of aminoacyl-tRNA to A site of ribosome

Front 63

Streptomyocin

Back 63

antibiotic for bacterial RNA synthesis: prevents transition from initiation complex to chain elongation

Front 64

Deamination

Back 64

removes amino group from cytosine to produce abberant uracil

Front 65

semiconservative replication model

Back 65

each strand is replicated and bound to new one, one new strand, one original in each double helix

Front 66

dispersive replication model

Back 66

parts cross, no unwinding necessary

Front 67

conservative replication model

Back 67

original helix unwinds, copies, and rewinds

Front 68

Nucleoside

Back 68

base and sugar

Front 69

nucleotide

Back 69

nucleoside triphsophate (so before nucleoside is hydrolyzed and bound)

Front 70

RNA polymerase primase

Back 70

intiates synthesis on DNA, makes an RNA primer

Front 71

RNA Primer

Back 71

About 10 nucleotides long, make by RNA polymerase primase, DNA polymerase can now add nucleotides to 3' end of primer

Front 72

RNAse H

Back 72

recognizes RNA bound to DNA (an RNA prime) RNAse then digests it

Front 73

Repair DNA polymerase

Back 73

replaces RNA primer after RNAse H recognizes it and RNAse digests it

Front 74

DNA ligase

Back 74

seals nicks between replicated fragments

Front 75

Single-stranded DNA binding protein

Back 75

keeps DNA helix unzipped

Front 76

Primase

Back 76

synthesizes RNA prime

Front 77

Sliding clamp

Back 77

keeps DNA polymerase on DNA strand

Front 78

Clamp Loader

Back 78

Loads sliding clamp onto DNA polymerase

Front 79

DNA topoisomerase

Back 79

nicks helix on single strand to relieve torsional stress from helicase unwinding strand while it is attached to proteins in the nucleus

Front 80

Depurination

Back 80

Removes base from phosphate and sugar, but leaves backbone. If left unrepaired, you may have a deletion in the sequence. Doesn't cause strand break, though

Front 81

Dimer Formation

Back 81

Thymine forms a dimer, which is bulky. Caused by UV radiation usually?

Front 82

DNA Glycosylases

Back 82

recognizes mismatches, removes thei nccorect base and leaves apurinic/apyrimidinc site.

Front 83

AP endonuclease

Back 83

recruited by absence of base, cuts phophate backbone so the repair DNA polymerase can fill in the missing nucelotide(s) using good strand as a template

Front 84

Nonhomologous End Joining

Back 84

accidental DNA breaks. Nuclease eats some of DNA around break, and DNa ligase reseals it. (loses some of info- some nucleotides)

Front 85

Homologous Recombination

Back 85

Strand invasion occurs, when homologous pairs are together and can use the other as a template

Front 86

Finn Dorset Sheep

Back 86

Where the mammory cell came from

Front 87

Scottish Blackface Sheep

Back 87

What the cell was grown inside of

Front 88

Major Groove

Back 88

Where transcription factors that recognize regulatory DNA sequences bind to. They also bind as dimers

Front 89

Operon

Back 89

sequence of bacterial DNA used to regulate synthesis of different proteins.

Front 90

Operator

Back 90

DNA sequence bound by a repressor. Inside of an operon

Front 91

Eukaryotic Transcription is regulated by enhancer sequences that act from a distance

Back 91

blah yes

Front 92

Eukaryotic Activator Protein

Back 92

binds to enhancer on Eukaryotic DNA, can fold DNA in loop to react with mediator, promotes assembly of transcription complex

Front 93

Mediator

Back 93

Aids in transcription regulation, is connected to general transcription gactors (TATA bp, TFIID, TFIIH)

Front 94

Repressor elements

Back 94

Prevent assembly of transcription complex

Front 95

Histone H1

Back 95

Binds to linker DNA losely

Front 96

Histone Acetyltransferase

Back 96

acetylates histone tails, taking away the lysine's positive charge, weakens attraction between histone tails and DNA

Front 97

Chromatic Remodeling Complex

Back 97

Can remodel chromatin for easier access to TATA box, also weakens interactions of DNA and histones

Front 98

Histone Deacetylases

Back 98

Deacetylates the histone tails, increases attraction of histones and DNA, makes transcription more difficult

Front 99

Bicoid

Back 99

Activator for EVE

Front 100

Hunchback

Back 100

Activator for EVE

Front 101

Giant

Back 101

Repressor for EVE (anterior end)

Front 102

Kruppel

Back 102

Repressor for EVE (posterior end)

Front 103

Heterochromatin

Back 103

inactive chromatin, not really transcribed

Front 104

Euchromatin

Back 104

expressed, active part of chromatin

Front 105

"Master" transcription regulator

Back 105

Can trigger several genes at once for transcription of all genes to produce full organ! ex: Eyeless

Front 106

Maintenance Methyltransferase

Back 106

Recognizes methylated cytosine on one side of DNA, will methylate cytosine on other side to match

Front 107

De Novo Methyltransferase

Back 107

methylates DNA from scratch, until maintenance one

Front 108

Activating Marks

Back 108

acetylation of lysine residues to weaken attraction to histones or methylation of certain lysine residues (can be inherited from mother cell)

Front 109

Represeive Marks

Back 109

Methylation of other lysine residues to tighten interactions (can be inherited from mother cell)

Front 110

Induced Pluripotent Stem Cell (iPSC)

Back 110

reprogrammed somatic cells to embryonic stem cells (with genes Sox2, Oct4, Nanog, Klf4 (Kruppel-Like Factor)

Front 111

Dicer

Back 111

cleaves precurose miRNA to form double stranded mRNA intermediate (~22 nucleotide pair) RISC protein complex now recognizes mature miRNA, and will attach to one strand of it and make it search for complementary target mRNA sequences

Front 112

RISC

Back 112

protein complex that recognizes the mature miRNA and will attach to the single strand of the miRNA, to search for complementary target mRNA sequences.

Front 113

siRNAs

Back 113

small interfering RNAs, act as a cellular defense against double stranded RNA viruses

Front 114

Autocrine Signaling

Back 114

Signal acts on the same cell it came from (eg. stem cells)

Front 115

Synaptic Signaling

Back 115

Can be over long distances if the axon in long, but it only really travels across a synapse

Front 116

Contact- Dependent Signaling

Back 116

direct contact between cells is needed. A cell will have a surface protein recognized by receptors on adjacent cells (leads to Lateral Inhibition/ Lateral Specification)