Genetics Wxam 3

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The three modes of DNA replication

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1

The three modes of DNA replication

conservative, semiconservative, Dispersive

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2

Where does DNA replication begin?

Origin of Replication

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3

How many origins are in prokaryotes and eukaryotes

1 in Pro, many in Eu.

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4

Replication Initiation: proteins and function

Initiator protein: binds to origin and unwinds it

DNA helicase: further unwinds DNA

Single strand binding proteins: prevents DNA from winding back together

DNA Gyrase: lowers torsional strain by cutting DNA and join DNA back together

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5

Bidirectional

Replication of DNA in an origin occurs in opposite directions

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6

# of forks per origin

2

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7

Replication elongation: proteins and function

DNA polymerase: builds DNA by attaching nucleotides to free 3’ -OH

Primase: Adds complementary RNA primer made of ribonucleotides which generates 3’ OH

β-sliding clamp: keeps DNA polymerase in place

Clamp Loader: loads beta sliding clamp on DNA

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8

Direction of DNA polymerase

5’ to 3’

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9

Leading strand directions

Template: 3’ to 5’ and replicates 5’ to 3’

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10

Lagging strand directions

Template: 5’ to 3’ and replicates 5’ to 3’

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11

How does DNA polymerase ensure that DNA is replicated correctly

Nucleotide Selection: check if the added nucleotide has proper hydrogen bonding.

Proof Reading: Detects is base pair is mismatched then uses 3’ to 5’ exonuclease activity to replace the base pair.

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12

Termination of Replication

Eukaryotic: Two replication forks meet

Prokaryotic: Termination sequences that end replication Termination sequence

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13

Termination: proteins and function

RNAse H: Removes RNA primer

DNA ligase: bonds fragments of DNA

Topoisomerase: uncoils precatenase

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14

Precatenase

Newly synthesized DNA coils with parent

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15

Catenase

Interlocking of 2 DNA molecules

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16

Decatenation

The process of freeing up the daughter DNA molecules that are interlocked so that they can be distributed to daughter cells upon cell division

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17

Telomere

Repetitive sequences at the ends of DNA that are lost during replication in place of important genetic information.

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18

Enzyme that helps extend telomeres and how it does that

Telomerase: places a RNA template that extends DNA to which primers can attach and fill in a gap from the End Replication Problem

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19

Features of telomerase

RNA dependent DNA polymerase

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20

Centromere:

middle point where chromatids meet, Heterochromatin

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21

Telomere (the location):

ends of C’some, heterochromatin

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22

p arm

Short arm of C’some

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23

q arm

Long arm of C’some

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24

Non coding region def and examples

Do not code for RNA or proteins,

EX: intron, satellite DNA, regulatory sequence, repetitive DNA (telomeres, Interspersed repeats, Tandem repeats)

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25

Locus

Location of a gene

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26

Promoter

Sequence that aids in RNA synthesis

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27

Coding sequence

Sequence that codes for an RNA molecule

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28

Terminator

Signals the end of transcription

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29

Rules: +1

DNA sequence where transcription begins

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30

Rules: Negative numbers

sequence prior to start site

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Rules: Positive numbers

sequence after to start site

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32

Upstream

left of the sequence of interest, can be other things besides the coding sequence

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33

Downstream

right of the sequence of interest

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34

Central Dogma

D > D: Replication

D > R: Transcription

R > P: Translation

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35

Reverse Transcription means?

RNA > DNA

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36

Enzyme that mediates reverse transcription and when does reverse transcription occur?

Reversetransciptase, occurs when host cells are infected by viruses

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37

Bacterial RNA polymerase

Function:

Composition:

Special:

Function: Preforms transcription

Composition: β, α, β᾽, ω, σ

Special: holoenzyme without σ factor

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38

σ factor

allows RNA polymerase to identify promoter

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39

Initiation of Transcription: in Pro.

Sigma factor in RNA polymerase allows binding to promoter

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40

Coding Strand

Strand that is not the template for the RNA polymerase but is exactly like what it produces but DNA instead of RNA.

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41

Template Strand

Used as a template because its complementary strand is what we’re looking for.

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42

RNA polymerase direction

5’ to 3’

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43

Transcription elongation process in prokaryotes

occurs in transcription bubble with RNA continuously created in the 5’ to 3’ direction, DNA unwound at front rewound in back

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44

Elongation: what kind of nucleotides are added in transcription

Riboneucleotides

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45

Rho-dependant

Rho bind to rut site, RNA polymerase stalls at terminator sequence, rho catches up and uses helices activity or unwind the DNA RNA hybrid.

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46

Rho-independent

Inverted Repeat forms hairpin structure which destabilizes A-U pairing.

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47

Transcription in eukaryotes: How does DNA become accessible for transcription

Heterochromatin must be remodled to Euchromatin

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48

RNA poly II

creates pre-mRNA

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49

RNA polyermaerase II termination mechanism

uses protein like RAT1

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50

mRNA

Function:

Function: has information to make a polypeptide

In Eukaryotes: pre-RNA is modified into mature to RNA

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51

5’ cap def and what links it to the mRNA and what it does

Addition of 7-methyl guanine to 5’ end of mRNA, prevents degradation. triphosphate linkage. Increases mRNA stability

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52

Poly A tail

Strand of A’s added to 3’ end of mRNA

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53

Splicing

Removal of introns and joining of exons

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54

Alternate splicing

picking and closing which exons to express which forms a different protein for each combination

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Splicing is mediated by (protein)

spliceosome

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56

RNA that mediates splicing

snRNA

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57

structure formed by spliced introns

lariat

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58

RNA splicing steps order: Branch point, 5’ splice site, 3’ splice site

5’ splice site, Branch point, 3’ splice site

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59

Post transciptional processes for RNA

RNA splicing, 3’ cleavage and addition, addition of 5’ cap

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60

rRNA

Building blocks of ribosomes

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61

70s ribosomes are found in?

Prokaryotes

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62

80s ribosomes are found in?

Eukaryotes

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63

70s ribosome composition

Subunits: 50s and 30s, rRNA: 23s and 16s

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64

80s ribosome composition

Subunits: 60s and 40s, rRNA: 28s and 18s

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65

tRNA must be ____ to form ____________

processed, mature tRNA

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66

rRNA must be ______ to form _______

processed, mature rRNA

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67

rRNA is processed by ___________

snoRNA and snoRNP’s

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68

siRNA and miRNA length

21-25

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69

siRNA snd miRNA bind with proteins to form ____________

RNA-induced silencing complex (RISC)

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70

siRNA origin and creation

Foreign double stranded RNA which is cut into pieces by dicer making many siRNA

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71

siRNA function

Perfect binding to mRNA causing degradation

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72

miRNA origin and creation

RNA transcribed by a gene, pri-mRNA is cleaved forming hairpin structure, hairpin is cleaved by dicer

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73

miRNA processing

pre-miRNA transcribed from DNA which is cleaved to form hairpin structure and cleaved by dicer to form miRNA

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74

miRNA function

binds imperfectly to mRNA inhibiting translation or cleaves it

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75

crRNA production

pre-crRNA is transcribed from CRISPR array > it is then cleaved by CAS proteins and then processed and interacts with the CAS protein to from the effector complex

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CRISPR array composition

Palindromes and spacers (foreign DNA)

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77

crRNA function and mode of action:

Described as adaptive RNA defense system. Binds complementary to foreign DNA which signals CAS protein to cleave the DNA

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78

snRNA: location and function

In the nucleus and plays a role in splicing mRNA

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79

snoRNA: location and function

In the nucleosome and mRNA editing, genome imprinting, modifying tRNA and rRNA

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80

Long noncoding RNA

Long RNA molecule that do not encode for proteins but regulate gene expression by binding to proteins, modifying chromatin structure or interacting with mRNA

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81

One gene one enzyme hypothesis

Each gene codes for one unique enzyme

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82

One gene one protein hypothesis

Each gene codes for one unique polypeptide

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83

Codon nucleotide #

3

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84

start codon

AUG

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85

GENETIC CODE RULES

  1. Do not write stop

  2. include N and C terminus

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86

stop codons

UAA, UAG, UGA

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87

Degenerate

codon coded by more than 1 set of nucleotides

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88

wobble base paring

3rd codon anticodon interaction that is not conventional

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89

Eukaryotic: Core promoter

TATA box in which RNA polymerase will bind as well as accessory proteins

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90

Eukaryotic: Regulatory promoter

Upstream of core promoter and is where other proteins bind

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91

Binding site of ribosomes

A site: Aminoacyl

P site: peptydle site

E site: Exit site

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92

tRNA charging

adding an amino acid to a tRNA

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93

what adds amino acids to tRNA?

aminoacyl-tRNA synthetase

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94

aminoacyl-tRNA synthetase adding check

Active site: the active site has specific size and affinity to an amino acid.

Editing Site: the editing site will cleave a incorrect aa off

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95

Initiation of Translation in prokaryotes

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96

Initiation of Translation in Eukaryotes

+12 Initiation factor, no N-formal methionine, 5’ cap recognized by small ribosome 40s, no shine-dalgarno sequence but has Kozak instead

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97

Elongation of Translation in prokaryotes

EF-TU-GTP brings charged tRNA to A site, GTP is hydrolyzed and leaves, amino acid on tRNA at P-site transferred to amino acid on tRNA at A-site, a peptide bond is formed by 23s, EF-G-GTP is hydrolyzed moving the ribosome 5-3, then tRNA at P goes to E and the A goes to P.

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98

Termination of Translation in prokaryotes

Stop codon shows up causing release factors bind to A-site which causes hydrolysis of polypeptide and disassembly of 70s ribosome

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99

Draw a replication fork

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100

Draw the leaf clover model of tRNA

knowt flashcard image
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