BIS 2A Midterm 3

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What are the three constituent molecules of a nucleotide?

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Britt 2022

107 Terms

1

What are the three constituent molecules of a nucleotide?

Phosphate group, ribose or deoxyribose sugar, nitrogenous base

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2

Which carbon atom is attached to the nitrogenous base?

1' carbon

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3

Which carbon atom is attached to the phosphate group?

5' carbon

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4

What is the purpose of DNA?

Storing genetic information Stored in the nitrogenous base

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5

What are the four nitrogenous bases in DNA?

Adenine, guanine, cytosine, thymine

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6

What are the four nitrogenous base sin RNA?

Adenine, guanine, cytosine, uracil

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7

What is the difference between the 5' end and the 3' end?

3' carbon in the pentose sugar with hydroxyl group while 5' carbon is attached to the phosphate group

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8

DNA is a

double stranded molecule runs anti parallel

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9

What is the name of the bond that connects two nucleotides?

phosphodiester bond (polar)

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10

What is the function of DNA Polymerase I?

removes RNA primer and replaces them with DNA nucleotide

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11

What is the function of DNA polymerase III?

Synthesizes daughter strands

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12

Function of Helicase ?

separates parent DNA strands

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13

Function of Ligase?

connects Okazaki fragments

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14

Function of primase?

generates RNA primer

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15

Function of telomeres?

lengthens telomeres

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16

Function of single stranded binding proteins?

Reduces super-coiling of DNA, which allows helicase to operate Keep the strand separated by holding them in place

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17

Where does DNA replication take place?

Origin of replication

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18

How does Helicase operate?

Breaks down hydrogen bonds between nucleotides which allows double-helix to separate

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19

What direction does the DNA Polymerase III move along the template strand?

3' - 5'

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20

What direction does the DNA polymerase III move along the daughter strand?

5' - 3'

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21

mismatched proteins

detect mismatches and excise patch of nucleotides

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22

What reduces spontaneous mismatches?

mismatch repair and proofreading by DNA polymerase

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23

Another source of mutation?

UV induces crosslinks between adjacent primidines (C and/or T)

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24

Why do UV induce mutation need to be repaired?

Because neither DNA polymerase nor RNA polymerase can get past them.

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25

What allows repair on damaged base pairs?

the double stranded nature of DNA

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26

mutation

new allele crick base pairing

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27

damaged nucleotide

example include accidentally methylated base It will be detected and the methyl group will be removed by O6methylguanine methyltransferase

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28

DNA damage can be

mutagenic (can cause mutations)

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29

mutation can not be

repaired

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30

Error-free repair of a degraded double strand break

homologous recombination unbroken sister chromatid is used as a template

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31

What if a double strand break occurs but no sister chromatid is available?

the broken ends may simply be rejoined- which might result in a deletion mutation, if any bases were damaged or lost.

This is called a nonhomologous end joining

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32

In eukaryotes...

there are 3 different RNA polymerases

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33

In eubacteria and Archeans...

there are one RNA polymerases

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34

rRNA

Ribosomal

  • transcribes from ribosomal RNA genes

  • makes up most of the ribosome

  • stable

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35

mRNA

  • transcribed from protein-coding genes -carries copy of coding region of gene

  • translated to protein

  • unstable

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36

tRNA

  • transcribed from tRNA genes

  • an adaptor that recognizes sequences of nucleic acids on mRNA and pairs them with the correct amino acids

  • stable, recycled

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37

RNA is like DNA, but

ribose instead of deoxyribose (NTPs vs dNTPS) Uracil instead of Thymine

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38

Requirements for Transcription

DNA template, the appropriate RNA polymerase, Ribonucleotide triphosphate: ATP, UTP, CTP, GTP

Steps include:

  1. Initiation

  2. Elongation

  3. Termination

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39

Initiation and Promoter

Promoter is a DNA sequence that binds and directs RNA polymerase to initiate transcription

Specifies location, orientation, and fréquence of initiation

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40

1st step of Initiation

RNA polymerase binds to DNA at the promoter

RNA polymerase unwinds and separates the DNA

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41

2nd step of initiation

The 2nd strands of DNA separate within RNA polymerase, transcription begins (upstream)

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42

RNA synthesis (elongation)

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43

Synthesis is anti-parallel to the

template strand

RNA sequence matches that of the "coding strand"

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44

Rules of RNA Transcription

  • RNA polymerase moves toward the 5' end of the template strand

  • mRNA is built antiparallel to the DNA, in the 5' to 3' direction

  • new nucleotides are added to the 3' end of the strand

  • RNA Pol. does not need a primer to start synthesis

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45

Polymerase moves which way on the template strand

3' to 5'

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46

termination =

dissociation of RNA polymerase from the DNA

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47

Eukrayotic mRNAs must be processed from preRNA to mRNA in 3 steps

  1. Capping of the 5' end

  2. Polydenylation (adding many A's to the polyadenylation site)

  3. Splicing which removes introns - noncoding sequences - from pre-mRNA

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48

codons

sixty four - three letter 'words' spelled by RNA basses sense = correspond to an amino acid

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49

How is the information from the genetic code converted into the language of amino acids?

There must be an adapter molecule (tRNA)

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50

Where do tRNAs come from?

They are encoded by genes, transcribed by RNA Polymerase III (in eukaryotes)

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51

More tRNA facts

They are recycled - amino acid carriers enzyme double checks that the correct amino acid is attached to the tRNA

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52

A charged tRNA has

had the correct amino acid attached to its 3' end

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53

Animoacylation of tRNA

adding an amino acid to the 3' end of a tRNA = "charging"

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54

What do adapter molecules do?

Hold amino acids and interact with mRNA codons

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55

What happens when RNA polymerase hits a nonsense mutation?

Transcription continues until a transcription termination site is reached.

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56

Circular DNA is found in which type of cell?

Both prokaryotic and eukaryotic cells

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57

Strong Promoter means

RNA Polymerase binds very tightly, so the transcription rate is high

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58

In what type of cells doe genes contain exons, which are interrupted by introns, which are spliced after transcription?

Eukaryotic cells

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59

Which of the following represents a change that CANNOT be passed on to the next generation? A. Changes in gene expression due to increased production of a hormone. B. Changes in DNA packaging leading to gene silencing. C. Changes in DNA sequence due to exposure to radiation. D. None of the above, as they are all heritable changes.

A. Changes in gene expression due to increased production of a hormone.

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60

Eukaryotic DNA is packed into nucleosomes due to the action of:

Histones

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61

Does RNA polymerase require help to bind to weak promoters?

Yes

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62

The role of ligase is to

seal nicks (single strand breaks in the backbone) in DNA

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63

What is the role of DNA Pol I in DNA replication?

Replaces primers required for DNA synthesis with DNA

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64

DNA double strands breaks are intentionally generated by the cell during ... and are repaired via ...

Meiosis, homologous recombination

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65

The promoter tells RNA polymerase:

where to begin transcription How often to being transcription Which strand to transcribe

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66

RNA splicing

eliminate internal noncoding sequences from mRNA

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67

Horiztontal gene transfer includes

Examples: Insertion of a gene from a jellyfish into a mouse The generation of the first eukaryotes from a bacterium and an archean

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68

Positive regulation

Transcription factor increases transcription by binding to a regulatory element (activation)

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69

Negative regulation

Transcription factor blocks transcription by binding to a regulatory element (repression)

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70

What are the layers of gene regulation?

  1. Promoter strength: weak or strong

  2. transcription factor: activator or repressor

  3. regulation of the transcription factor

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71

What are regulatory sequences?

Regions of DNA with specific sequences that can, when bound by a transcription factor, help increase or decrease gene expression

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72

What is an enhancer?

Regulatory sequence that helps enhance (increase) gene expression

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73

silencer

regulatory sequence that helps inhibit (decrease) gene expression

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74

effector

a molecule that binds transcription factors to change transcription

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75

inducer

a molecule that binds to repressors to deactivate them (prevent binding to DNA) or binds to activators to activate them (allow binding to DNA)

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76

inhibitor

a molecule that binds to activators and prevents from binding to DNA (opposite of inducer)

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77

operator

a regulatory sequence to which a repressor can bind These are found in Prokaryotic cells

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78

The majority of DNA in bacterial cells is synthesized from:

DNA polymerase

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79

Without primase...

Replication would be unable to start

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80

DNA FACT

DNA is negatively-charged and migrates from the negative end to the positive end

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81

Which of the RNA molecules can be described as a copy of the gene that codes for a protein?

mRNA (carries the genetic information necessary to build a protein)

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82

Hydrogen bonds between nitrogenous bases

A and T = 2 G and C = 3 A and U = 2

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83

Where does DNA replication and transcription occur in eukaryotes?

The nucleus

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84

Where does translation occur in eukaryotes?

The ribosome

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85

Where does DNA replication occur in prokaryotes?

Cytoplasm

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86

Where does transcription and translation occur in prokaryotes?

Cytoplasm

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87

What sites must be present in DNA so that RNA polymerase can transcribe the DNA to RNA?

RNA binding site transcription start site transcription stop site

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88

What two things does the promoter determine?

where RNA polymerase binds to DNA

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89

What is the -10 sequence in the promoter known as?

TATA box

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90

How does a base-pair change in the promoter affect transcription?

Base-pair changes affect the ability of RNA polymerase to recognize and bind to the promoter

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91

Transcription: Elongation

Double stranded DNA that enters from the front of the enzyme is unwound and the template strand is made available for complementary base pairing

Two DNA strands reunite at the trailing end of the transcription bubble while the single-stranded RNA emerges alone

The bubble generated by RNA polymerase is small

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92

In transcription elongation, when joining nucleotides together, what is the exergonic reaction?

Breaking of the phosphoanhydride bond

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93

What is the purpose of the 5' cap?

Regulation of nuclear export prevention of degradation by exonucleases promotion of translation promotion of 5' proximal intron excision

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94

What is splicing?

Splicing removes introns and splices exon together Multiple proteins can be obtained from one gene Exon exit the nucleus, whereas the introns stay

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95

initiation summary

the ribosome assembles around the mRNA. The first tRNA is attached at the start codon

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96

Elongation Overview

The tRNA transfers an amino acid to the tRNA corresponding to the codon. The ribosome then moves to the next mRNA codon to continue the process, creating an amino acid

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97

termination overview

When a peptidyl tRNA encounters a stop codon, the ribosome folds the polypeptide into its final structure

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98

Which direction does tRNA attach to mRNA?

Antiparallel IF mRNA is read 5'-3', the tRNA will be 3'-5-

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99

What enzyme attaches amino acid to tRNA molecules?

Aminoacyl tRNA syntestases attach amino acids to the tRNA molecules

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100

Missense Mutation

A mutation that results in a different amino acid in the peptide chain

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