L4 - Transcription, Translation, & Protein Signaling

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is gene expression tightly regulated?

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1

is gene expression tightly regulated?

yes

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2

what does the central dogma of molecular biology describe?

making proteins

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3

what 3 polymerases involved in gene expression differ in template specificity, location w/i nucleus, and susceptibility to inhibitors?

RNA Polymerase I, II, & III

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4

what dos RNA polymerase I make?

18S, 5.8S, & 28S ribosomal RNA

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5

what does RNA polymerase II make?

makes pre-mRNA, & several small RNAs

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6

what does RNA polymerase III make?

makes 5.8S rRNA & tRNAs

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7

what is rRNA?

ribosomal RNA

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8

what is tRNA?

transfer RNA

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9

what is miRNA?

micro RNA

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10

what kind of RNA is translated into proteins?

mRNA

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11

what RNA can play roles in gene expression & protein synthesis?

all RNA (but only mRNA gets translated into proteins)

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12

how long due most human mRNAs exist for?

1-10 hours before they are cleaved by cellular nucleases

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13

how is RNA made?

made on a DNA template by RNA polymerases at transcriptional start sites

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14

what is a consensus sequence?

short sequence of nucleotides which is found several times in the genome & is thought to play same role in its different locations (protein binding site)

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15

what is the TATA box considered?

a non-coding DNA sequence (it contains consensus sequence characterized by repeating T & A base pairs)

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16

what do promoters contain?

contain consensus sequence to bind transcription factor (TF) & polymerase

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17

what are the gene regulatory elements?

promoters, enhancer, activators

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18

what is an enhancer?

DNA sequence that promotes transcription, each one is made up of short DNA sequences called distal control elements

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19

why do activators bind to distal control elements?

to interact w/ mediator proteins & TFs

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20

what protein complex regulates the amount of mRNA produced?

RNA Polymerase II

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21

does eukaryotic mRNA processing happen before or after the mRNA transcript is produced?

after, involves multiple steps

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22

why is capping important?

regulates nuclear export (cap needed to transport through nuclear pore), prevents degradation by exonucleases (capped mRNA look like 3’ end of RNA), promotes translation (translation initiation factor 4E binds to capped mRNA)

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23

what is the mRNA capping structure?

methylated guanine nucleotide that’s linked w/ triphosphates to the 5’ nucleotide instead of via phosphodiester bond

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24

what are the general steps of processing eukaryotic mRNA?

capping 5’ end, adding poly-A tail to 3’ end, splicing, mRNA decay

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25

what is splicing?

removal of introns & joining of exons

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26

what is the normal phosphodiester bond like?

linkage between the 3’ carbon atom of 1 sugar & the 5’ carbon atom of another

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27

what does the poly-A tail consist of?

multiple adenosine monophosphates (stretch of RNA that has only adenosine bases)

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28

what does the poly-A tail do to the RNA molecule?

makes it more stable, prevents its degradation, allows mature messenger RNA to be exported from nucleus & translated into a protein by ribosomes in cytoplasm

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29

what is alternative splicing?

form of transcriptional regulation, enables production of different mRNA isoforms from a single genes, mRNA is then translated to produce different proteins

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30

what are the 4 enzymes involved in the mRNA decay step of processing eukaryotic mRNA?

deadenylase, decapping enzyme, 5’ endonuclase, 3’ endonuclease (all are required for completed degradation of mRNA)

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31

what is the key process in the regulation of gene expression?

eliminate mRNA when there is enough protein

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32

what is RNA degradation crucial for?

elimination of defective RNAs

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33

what does translation require from tRNA?

to bring AAs to form a growing peptide chain

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34

how are mRNA codons read?

from 5’ to 3’

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35

how is a protein synthesized?

from N-terminus to C-terminus (extruded through a channel in the ribosome’s large subunit)

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36

what is the start codon?

AUG (encodes for methionine)

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37

what are the stop codons?

UGA, UAG, UAA (don’t encode for AAs)

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38

how many ribonucleotides make up 1 codon?

3

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39

what do codons dictate?

specific AAs or stop/start sequence

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40

is formation of charged tRNA required for protein translation?

yes

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41

what is the 1st step of mRNA translation to make a protein?

aminoacyl tRNA synthetase attaches AAs to their corresponding tRNA molecules using energy from ATP

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42

what kind of bonds are individual AAs linked w/ to make a protein?

peptide bonds

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43

what kind of free group does the N terminus have?

free amino group

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44

what kind of free group does the C terminus have?

free carboxyl group

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45

what is the difference between ribonucleotides & deoxyribonucleotides?

sugar component is ribose/deoxyribose (hydroxyl vs hydrogen at carbon 2)

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46

what are some ribonucleotides?

adenosine, guanosine, uridine, cytodine

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47

what are the purine molecules?

adenosine & guanosine

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48

how is 5-phosphoribosyl-1-pyrophosphate used?

R5P receives PPi using PRPP synthetase. PRPP reacts w/ glutamine via amidotransferase to build purine ring (for pyrimidines, orotate phosphoribosyl transferase adds PRPP to ring

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49

is methionine produced from one of the 5 starting families?

no

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50

which AA is produced from 3-phosphoglycerate?

makes serine

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51

does the synthesis of alanine require aminotransferase?

yes

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52

which alpha-keto acid receives an alpha amino group to generate alanine?

pyruvate receives an alpha-amino group, then this is paired w/ a second aminotransferase rxn

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53

what sites w/i ribosomes accept tRNA?

A & P sites

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54

what is the E site in ribosomes?

exit

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55

what is the P site in ribosomes?

peptidyl site for tRNA binding

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56

what is the A site in ribosomes?

aminoacyl/acceptor site for tRNA binding

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57

what are the parts of the subunits of ribosomes that accept tRNA?

large ribosomal unit consists of E/P/A sites, small ribosomal sububit consists of mRNA binding site

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58

what do the ribosomes help tRNA do?

bring in appropriate AAs for peptide synthesis

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59

how are proteins marked for degradation?

by adding 1 or more ubiquitin proteins to the degradation target

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60

what is the process of marking a protein for degradation called?

ubiquitination or ubiquitylation

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61

what molecules are proteins degraded by?

26S proteasome

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62

what are secondary ubiquitin molecules always linked to?

1 of the 7 lysine residues or the N terminal methionine of the previous ubiquitin molecule

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63

is ubiquitin recycled/reused in protein degradation?

yes

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64

what is ubiquitin?

small protein that exists in all eukaryotic cells

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65

what does ubiquitin consist of?

76 AAs & has molecular mass of about 8.6 kDA

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66

what is the function of ubiquitin?

to perform its myriad functions via conjugation to a large range of target proteins, a large variety of modifications can occur (degradation is an example)

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67

what does the 26S proteasome do?

protein complexes which degrade unneeded/damaged proteins by proteolysis

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68

what is proteolysis?

chemical rxn that breaks peptide bonds

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69

what kind of enzymes help proteolysis rxns?

proteases

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70

what are the 6 types of receptors that mediate in intracellular signaling?

G protein coupled receptor, receptor tyrosine kinase, receptor guanylyl cyclase, gated ion channel, nuclear receptor, adhesion receptor (integrin)

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71

explain G protein coupled receptor during signal transduction

external ligand binds to receptor & activates an intracellular GTP binding protein, which regulates an enzyme that generates an intracellular second messenger

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72

explain receptor tyrosine kinase during signal transduction

ligand binding activates tyrosine kinase activity via autophosphorylation

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73

explain receptor guanylyl cyclase during signal transduction

ligand binding to extracellular domain stimulates formation of 2nd messenger cyclic GMP

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74

explain adhesion receptor (integrin) during signal transduction

binds molecules in extracellular matrix, changes conformation, which alters its interactions w/ cytoskeleton

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75

explain gated ion channel during signal transduction

opens/closes in response to concentration of signal ligand or membrane potential

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76

explain nuclear receptor during signal transduction

steroid binding allows the receptor to regulate the expression of specific genes

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77

describe GPCR in detail

several transmembrane helices, extracellular binding site for ligand, intracellular binding site for GTPase (G protein trimer, aby subunits)

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78

what does GTP binding do to GPCRs?

induces a conformational change dissociating Gα (active) from Gβγ, GTP to GDP hydrolysis turns off G protein & causes reassociation, when on the G protein activates adenylyl/guanylyl cyclases

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79

describe receptor tyrosine kinases in detail

single transmembrane segment catalytic receptors, 1 transmembrane domain, has internal domain w/ a tyrosine kinase activity (catalyzes phosphorylation of select tyrosine residues in target proteins using ATP), signal is relayed to effectors of membrane transport/gene transcription/protein synthesis

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80

are G protein coupled receptor & G protein linked receptor the same?

yes

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81

are G protein & G protein coupled receptor the same?

no, 2 different proteins

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82

what are transducers?

second messengers, pass on the signal

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83

what second messengers does G protein activity produce?

cAMP, phospholipid derivatives, release of Ca2+ ions

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84

what is activated when phosphorylation cascades by receptor tyrosine kinases are activated?

other protein kinases, protein phosphatases

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85

what are some consequences of conformational changes and signal transduction?

open ion channels, form nuclear transcription complexes

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86

explain Ca2+ & calmodulin as second messengers

Ca2+ is second messenger & calmodulin is its modulating protein, that is a transducer in that it regulates

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87

what are the steps of Ca2+ & calmodulin as second messengers?

calcium channel open, calcium enters & binds to calmodulin & causes conformational change, change is required for binding to another protein

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88

does the cytosolic Ca2+ ion concentration increase or decrease when the calcium channel opens?

increases (in the opening of calcium channels in membranes of calciosomes, endoplasmic reticulum, & plasma membrane)

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89

how many calcium modulated proteins are known?

about 180

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90

how can cytoplasmic calcium ions be increased?

stimulated by cAMP, stimulated by inositol-1,4,5-P3 (IP3)

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91

are kinases catalytic receptors?

yes

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