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Molecular Biology Flashcards

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1
Q

The human genome contains ___ chromosomes

A

24 (22 autosomes plus 2 sex chromosomes)

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2
Q

The genome has multiple regions with high transcription rates, separated by long stretches of intergenic space.

What is intergenic space?

A

Intergenic space holds noncoding DNA regions that may direct the assembly of specific chromatin structure and can contribute to regulation of nearby genes though many have no known function.

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3
Q

2 major components of intergenic space

A

Tandem repeats and transposons

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4
Q

Gene

A

A DNA sequence that encodes a gene product

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5
Q

A gene includes two regions. What are they?

A

The regulatory region: promoters and transcription stop sites
The (non)coding region: codes for protein or non-coding for RNA

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6
Q

Single nucleotide polymorphisms

A

Single nucleotide changes once in every 1000 base pairs in the human genome

SNPs, pronounced “snips” are essentially mutations

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7
Q

Code Number Variation

A

Structural variations in the genome that lead to different copies of DNA sections.

Large regions of the genome can be duplicated (inc. copying number) or deleted (dec copying number) via this process

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8
Q

Repeated Sequences: Tandem Repeats

A

Short sequences of nucleotides are repeated one right after the other, from as little as three to over 100 times.

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9
Q

Repeated Sequences: Transposons

A

Mobile genetic elements that can jump around the genome and cause mutations and chromosome changes such as inversions, deletions and rearrangements.

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10
Q

DNA contains strands of nucleotides known as genes that serve as templates for the production of another nucleic acid known as:

A

RNA

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11
Q

Transcription

A

The process of reading DNA and writing the information as RNA generating mRNA or non-coding RNA

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12
Q

Messenger RNA (mRNA)

A

Read and used to construct proteins `

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13
Q

Translation

A

Synthesis of proteins using RNA as a template

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14
Q

Translation is accomplished by:

A

The ribosome

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15
Q

What is a ribosome?

A

Massive enzyme composed of many proteins and pieces of ribosomal RNA (rRNA)

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16
Q

Central Dogma

A

Inherited info is used to create objects via:

DNA –> RNA –> Protein

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17
Q

Genetic Code & Its Alphabet

A

Language used by DNA and RNA to specify the building blocks of proteins

Its alphabet contains only 4 letters (A, T, G, C)

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18
Q

Codon

A

3-letter nucleic word coding for a specific amino acid

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19
Q

Start Codon(s)

A

AUG

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20
Q

Stop Codon(s)

A

UAA: U Are Annoying
UGA: U Go Away
UAG: U Are Gone

Notifies ribosome that protein is complete and tells it to stop reading the mRNA

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21
Q

Nonsense Codons

A

Another words for stop codons because they don’t code for an amino acid

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22
Q

Often, all four of the codons with _________ encode the same amino acid.

A

Same first two nucleotides = same AA despite last nucleotide

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23
Q

If CCU is changed to CCC will the amino acid change?

A

No

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24
Q

Synonyms

A

2 or more codons encoding for the same amino acid

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25
Q

Degenerate

A

Genomic code is said to be degenerate because it has synonyms

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26
Q

An amino acid is specified by many codons, BUT

A

A codon only specifies a single amino acid

There is no code ambiguity

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27
Q

Mitosis produces two daughter cells with identical genomes, hence cell division requires:

A

DNA Replication

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28
Q

What phase does DNA replication occur during the cell cycle?

A

Replication occurs during the S phase (synthesis) in the interphase of the cell cycle.

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29
Q

Old DNA is called:

New DNA is called:

A

Prenatal DNA

Daughter DNA

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30
Q

Meselson & Stahl wanted to determine if DNA is semiconservative, conservative or dispersive.

Which was proven to be true?

What is semi-conservative replication?

What is conservative replication?

What is dispersive replication?

A

SC: After replication, one strand of the double helix is parental and one is newly synthesized daughter (old+new, old+new) (PROVEN TRUE)

CR: Parental DNA would remain as-is while an entirely new double stranded genome was created. (old+old, new+new)

DR: Both copies of the genomes were composed of scattered pieces of old and new DNA

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31
Q

DNA is semiconservative: this means

A

Individual strands of the double-stranded parent are pulled apart. A new daughter strand is synthesized using the prenatal DNA as a template to copy from. Each daughter chain is perfectly complementary to its parent.

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32
Q

DNA is usually tightly coiled. In the replication process:

A

The double helix is uncoiled and separated into two separate strands by an enzyme called Helicase.

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33
Q

Helicase

A

Uncoils and separates DNA for replication.

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34
Q

Origin of Replication (ORI)

A

Specific location (sequence of nucleotides) on the chromosome where the helices begins to unwind the DNA

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35
Q

When helicase unwinds the helix at the origin of replication, the helix gets wound more tightly above and below the ORI, like two ropes being unwound in the middle. How does the body prevent this from tearing the DNA?

A

Topoisomerases cut one or both of the strands and unwrap the helix, releasing the pressure from the helicase.

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36
Q

Topoisomerase:

A

Enzyme that cuts one or both strands of DNA to release excess pressure from the helicase unwinding the DNA in the center of the helix.

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37
Q

Single Stranded Binding Proteins (SSBP)

A

Protect DNA that has been unpackaged in preparation for replication and help keep the strands separated.

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38
Q

Another potential problem with replication of DNA is that the single strands are less stable than the double stranded DNA. How does the body account for this problem?

A

SSBPs (Single stranded binding proteins) protect the single strands and keep them separated.

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39
Q

Open complex

A

Separated single strands that allow replication to begin.

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40
Q

Primase

A

RNA polymerase that is the central component of primosome (RNA primer that synthesizes each template strand).

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41
Q

Primosome

A

RNA primer synthesizes each template strand

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42
Q

Why is primer synthesis important?

A

DNA polymerase cannot start a new DNA chain from scratch. It can only add nucleotides to an existing nucleotide chain. RNA primer is usually 8-12 nucleotides long and is replaced by DNA

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43
Q

Daughter DNA is created as a:

A

Growing polymer

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44
Q

DNA polymerase

A

Catalyzes the elongation of the daughter strand using the parental template. Elongates the primer by adding NTPs to its 3’ end.

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45
Q

What direction is the template strand read in?

A

5’-3’

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46
Q

DNA polymerase is part of a large complex of proteins known as the:

Other proteins in this complex help DNA poly to:

Prokaryotic vs Eukaryotic replisome:

A

Replisome

Polymerize DNA quickly

P: 13 components & E: 27 proteins (more complexity in E needed because replication machinery must unwind DNA from histone proteins)

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47
Q

Since the two template strands are _____ , the two primers will elongate towards ______ of the chromosome.

A

antiparallel

opposite ends

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48
Q

Before each base pair is incorporated into the growing polymer,

A

DNA poly checks each nucleotide to make sure it forms the correct base pair

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49
Q

Thermodynamic driving force for the polymerization reaction is the:

A

Removal and hydrolysis of pyrophosphate (P2O7)^-4 from each double NTP added to the chain.

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50
Q

Polymerization occurs in the _____ direction, with or without exception?

A

5-3’

Lengthened by addition of a nucleotide to the 3’ end of the chain. No exceptions

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51
Q

DNA polymerization requires a: t____

A

Template

Can’t make DNA from scratch–must copy an old chain.

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52
Q

DNA polymerization requires a: p_____–

A

Primer

Cannot start a new nucleotide chain… RNA primer has to do so.

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53
Q

Both template strands are read from _____ while daughter strands are elongated _____

A

Read from 3’-5’

Elongated from 5’-3’ **

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54
Q

Replication forks

A

Areas where the parental double helix continues to unwind

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55
Q

Leading strand

A

Replication is continuous into the widening of the fork

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56
Q

Lagging strand

A

Discontinuous… A lagging strand is dropped down behind the end of the leading strand as the fork widens this results in Okazaki fragments

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57
Q

Okazaki fragments

A

Fragments result of the lagging strand being dropped down behind the end of the leading strand

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58
Q

Eventually, all the RNA primers _____ and all the fragments are _______

A

are replaced by DNA

joined by an enzyme called DNA Ligase

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59
Q

DNA Ligase

A

Connects the Okazaki Fragments.

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60
Q

DNA polymerase is said to be processive. This means:

A

DNA poly is able to add thousands of nucleotides before falling off the template

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61
Q

Prokaryotes have ____ different DNA polymerases

A

5

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62
Q

DNA polymerase I (prokaryotes)

A

Starts adding nucleotides as the RNA primer.

5’-3’ activity

Can only add about 15-20 nucleotides/second, so DNA poly III usually takes over about 400 pairs downstream of the ORI

Capable of 3’-5’ exonuclease activity (proofreading) and removes primer via 5’-3’ exonuclease activity while simultaneously leaving behind new DNA in 5-3’ activity

DNA poly I is important in excision repair

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63
Q

DNA poly III (prokaryotes)

A

Super fast, super accurate elongation of the leading strand. 5-3 polymerase function and 3-5 exonuclease activity (enzyme moves backward to chop off nucleotide it just added if incorrect: proofreading function)

Replicative enzyme

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64
Q

Proofreading Function aka (_______) is:

A

Exonuclease activity

Enzyme moves backward to chop off nucleotides if it was added incorrect (3-5’)

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65
Q

Theta replication and theta mechanism

A

Prokaryotes one circular chromosome has only one origin, as the replication proceeds the chromosome is duplicating and begins to look like the greek letter theta.

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66
Q

Eukaryotic Replication has ____ ORI’s because:

A

Several ORIs because the chromosomes are so large that a single origin would be too slow.

“replication bubbles” along the DNA strand meet and the daughter strands are litigated together.

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67
Q

DNA replication machinery is unable to replicate sequences at the very end of the chromosomes because the DNA ligase cannot lay a primer on the end and then replace it with DNA because there is no DNA on the other side of the primer.

To compensate for this:

A

After each round of the cell cycle and DNA replication, the ends of chromosomes shorten.

Ends are known as telomeres

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68
Q

Telomeres

A

Disposable regions at the end of the chromosome

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69
Q

When telomeres become too short:

A

Critical length can be reached where the chromosome can no longer replicate and cells activate DNA repair pathways as a result while they go into a senescent state (not dividing just alive) or undergo apoptosis (pre-programmed death)

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70
Q

Hayflick limit

A

Number of times a normal human cell type can divide until telomere length stops cell division

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71
Q

Telomere shortening is linked to many:

A

Age related diseases

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72
Q

Telomerase: function?

A

Enzyme that adds repetitive nucleotide sequences to the ends of chromosomes and therefore lengthens telomeres

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73
Q

Telomerase is a _____ complex, containing ____ and ______

Transcriptase enzyme is:

A

RNA primer and reverse transcriptase enzyme (read DNA templates and generate DNA)

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74
Q

RNA template is:

A

3’-CCCAATCCC-5’ allowing for chromosome extension

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75
Q

RNA template allows for chromosome extension one DNA repeat at a time. The DNA repeat codon is:

A

5’-GGGTTAGGG-3’ (complement to template: CCCAATCCC)

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76
Q

The telomerase complex continuously polymerizes, then translocates, allowing:

A

Extension of six-nucleotide telomere repeats

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77
Q

In most organisms, telomerase is only present in the germ line, embryonic stem cells and some white blood cells. However, _____ can also express telomerase, which can help the cells ______

Telomere extension allows the cells to bypass _____ and ______ , and can therefore contribute to ________

A

Cancer cells

Immortalize

Senescence (existence without replication)
Apoptosis (Self-programmed death)

Transformation to a precancerous state

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78
Q

Genetic Mutation

A

Any alteration of the DNA sequence of the organisms genome

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79
Q

Germ-line mutations

A

Can be passed to the offspring, because they occur in the germ cells which give rise to gametes

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80
Q

Somatic mutations

A

Occur in somatic (non-gametic) cells and are not passed onto offspring

Only effect individual, not next generation

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81
Q

Point mutations

A

Single base substitutions (A in place of G)

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82
Q

Point mutations can be transitions or transversions.

Transitions are:
Transversions are:

A

Transitions: substitution of a pyramide for another pyramide or substitution of a purine for another purine)

Transversions: substitution of a pyramide for a purine, or vice versa

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83
Q

3 Types of Point Mutations

A

Missense, Nonsense, Silent

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84
Q

Missense Mutations

A

Causes one amino acid to be replaced with another amino acid… May not be serious if the AA are similar

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85
Q

Nonsense Mutations

A

A stop codon replaces a regular codon and prematurely shortens the protein

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86
Q

Silent Mutations

A

A codon is changed into a new codon for the same amino acid, there is no change in the proteins amino acid sequence

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87
Q

Insertion Mutation

A

Adding one or more extra nucleotides into the DNA sequence

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88
Q

Deletion Mutation

A

Deletion/removal of one or more nucleotides

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89
Q

Insertion and Deletion Mutations can cause

A

A shift in the reading frame

All AA in the gene will be changed and the whole gene will be read differently

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90
Q

Frameshift mutations

A

Cause a change in the reading frame of the gene

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91
Q

Frameshift can lead to:

A

Premature termination of translation (yielding an incomplete polypeptide) if an abnormal stop codon results

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92
Q

Insertions and deletions can also involve

A

Thousands of bases

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93
Q

Inversion Mutation

A

Segment of a chromosome is reversed end to end

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94
Q

For inversion to occur the chromosome undergoes:

A

Breakage and rearrangement within itself

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95
Q

Chromosome Amplification Mutation

A

Segment of a chromosome is duplicated

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96
Q

Translocation Mutation

A

Recombination occurs between non-homologous chromosomes creating a gene fusion where a new gene product is made from parts of two genes that were not previously connected.

Common in many cancer types

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97
Q

Translocation can be balanced or unbalanced meaning:

A

Balanced: no genetic information is lost

Unbalanced: genetic information is lost or gained

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98
Q

Tranposase

A

Cut and paste function that catalyzes mobility

Excision from donor and integration into a new genetic acceptor site (sometimes it is completely removed and then moved, other times it is duplicated and moved, while still maintained at the original location)

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99
Q

When transposons are mobilized they can insert in any part of the genome, and this can affect gene expression/mutation. They can jump into a protein-coding region and disrupt or mutate the sequence. They can also jump into:

A

Regulatory parts of the genome and ramp up gene expression at a nearby site

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100
Q

Loss of Heterozygosity Mutation

A

Diploid organism when one allele of a certain gene is lost, due to deletion or recombination

This makes the locus homozygous: there is only one gene copy in a diploid organism. If the remaining alley is mutated or defective, all normal expression oft he gene product is lost

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101
Q

Direct Reversal DNA Repair

A

Some types of mutation are reversible.

For ex, UV radiation can be reversed by normal light via photoreactivation (cal induce another type of mutation leading to myeloma)

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102
Q

Homology-Dependent Repair

A

Mutations on one strand can be repaired by the other undamaged strand.

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103
Q

Two types of homology dependent repair

A

Excision repair: divided into repair that happens before DNA replication

Post-replication repair: repair during and after NDA replication

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104
Q

Excision Repair

A

Removing defective bases or nucleotides and replacing them. If these bases aren’t repaired, could induce mutations during replication since replication machinery cannot pair them properly.

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105
Q

Post-Replication Repair to subtypes:

How is the newly synthesized strand recognized?

A

Mismatch Repair and Genome Methlyation

Gene methylation or 3’ terminus ID / DNA gaps

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106
Q

Mismatch Repair Pathway

A

Targets mismatched base pairs that were not repaired by DNA polymerase proofreading during replication

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107
Q

Genome Methylation

A

Help differentiate between the older and daughter DNA

Parental template strand will be labeled with methylated bases so bacterial machinery can read these methyl tags and known which base is the correct one (older stand) and which needs to be replaced (newer strand)

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108
Q

Double strand break repair:

Two types of pathways are Homologous recombination and Non-homologous end joining

The goal of both is to:

A

Reattach and fuse chromosomes that have come apart because of DSB

Can lead to deletions or translocations if done incorrectly

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109
Q

Homologous Recombination

A

Process where one sister chromatid can help repair a DSB in the other sister chromatid.

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110
Q

How does homologous recombination work?

A
  1. DSB identified and trimmed to single stranded DNA by helicase and nuclease
  2. Find complementary sister chromatid and form joint molecule (intertwined kinda)
  3. DNA poly and ligase build new DNA
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111
Q

Non-homologous End Joining

A

Accomplish repair in cells not in the cell cycle because these cells do not have a sister chromatid to function as a complementary template

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112
Q

Non-homologous End Joining Process

A
  1. Broken ends are stabilized and processed
  2. DNA ligase connects the fragments

None of this requires specificity. The goal is just to reconnect broken chromosomes which can result in base pairs being lost or chromosomes being constructed in an abnormal way. This is all still better than DSB.

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113
Q

Gene expression

A

Process whereby the information contained in genes begins to have effects in the cell

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114
Q

RNA is distinct from DNA in three ways:

As a result of these differences, RNA is:

A

RNA is single stranded (except some viruses)
RNA contains uracil instead of thymine (U not T)
The pentose ring in RNA is ribose rather than 2’ deoxyribose

Less Stable because can hydrolysis itself

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115
Q

Coding RNA

A

mRNA

Carries genetic information to the ribsomone for translation into protein

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116
Q

A strand of mRNA has several regions:

5’ region (5’UTR)

Open Reading Frame (ORF)

A

5’ region is not translated into protein (untranslated region) but is important to initiation and regulation

ORF is the region that codes for a protein; starts at start codon and ends at end codon.

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117
Q

Eukaryotic mRNA is usually monocistronic meaning

A

One gene, one protein principle meaning that each piece of mRNA encodes only one polypeptide (one ORF) hence there are as many mRNAs as there are proteins.

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118
Q

Because each mRNA can be read many times:

A

Each transcript can be used to make many copies of its polypeptide.

119
Q

Prokaryotic mRNA is usually polyistronic meaning

A

mRNA codes for more than one polypeptide

120
Q

mRNA is constantly produced and degraded based on the

A

Cells need for proteins encoded by each piece of mRNA

Allows cells to regulate amount of protein they synthesize

121
Q

Heterogeneous nuclear RNA (hnRNA)

A

First RNA transcribed from DNA is an immature or precursor to mRNA in eukaryotes

Processing events are required for hnRNA to become mature mRNA

122
Q

Since prokaryotes do not process their primary transcripts,

A

hnRNA is only found in eukaryotes

123
Q

Non-coding RNA (ncRNA)

A

Functional RNA that is not translated into protein

124
Q

Human genome codes for thousands of ncRNAs and there are several types… The two major types are:

A

Transfer RNA (tRNA) and ribosomal RNA (rRNA)

125
Q

Transfer RNA (tRNA)

A

Responsible for translating the genetic code

Carries amino acids from the cytoplasm to the ribosome to be added to a growing protein

126
Q

Ribosomal RNA (rRNA): how many types?

All serve as:

A

Human have four types of rRNA molecules

All serve as components of the ribosome and polypeptide chains

127
Q

Although most enzymes are made from polypeptides, one rRNA has a catalytic function of the ribosome, this is called a:

A

Ribozyme

128
Q

What is transcription and how does it relate to replication?

A

Process of making RNA from DNA as a template

Transcription is reading and writing, without changing the language… For this reason transcription is similar to replication in a lot of ways.

129
Q

Both replication and transcription involve:

A

Template-driven Polymerization

130
Q

Template-Driven Polymerization is:

A

RNA transcript is complementary to the DNA template just as the daughter strand is complementary to the parental strand

131
Q

Driving force for replication and transcription:

A

Removal and subsequent hydrolysis of pyrophosphate from each nucleotide added to the chain, with the existing chain acting as a nucleophile.

132
Q

Like replication, transcription only occurs in the:

A

5-3’ direction

133
Q

Unlike replication, transcription does or doesn’t require a primer? Why?

A

Transcription does not require a primer because the primer in replication is a piece of mRNA made by the RNA polymerase

134
Q

Another important difference between transcription and replication is the RNA polymerase lacks:

A

Exonuclease function, so it cannot correct its error/proofread

Therefore, replication is a higher fidelity process

135
Q

Transcription, like replication, begins at:

A

A specific location on the chromosome called the start site (different name than the ORI for replication)

136
Q

Sequence of nucleotides on a chromosome that activates RNA polymerase to begin the process of transcription is called a:

A

Promoter

137
Q

Point where RNA polymerization actually starts is called the:

A

Start Site

138
Q

Template aka non-coding, transcribed, or antisense strand

A

Strand that is actually transcribed and complementary to the transcript (only one of the DNA strands encodes for a particular mRNA molecule)

139
Q

Coding/Sense Strand

A

Same sequence as the transcript (except for a T in the place of U)

140
Q

Transcription starts at a point and then proceeds ________ which is:

What does upstream mean?

A

Downstream: toward the 3’ end of the coding strand) (referred to with positive numbers)

Toward the 5’ end of the coding strand (referred to with negative numbers)

141
Q

Start site

A

First nucleotide that is actually transcribed on the template strand

142
Q

Which nucleotide is given the number +1?

A

The nucleotide on the coding site corresponding to the start site nucleotide on the template strand

143
Q

In Prokaryotes, all types of RNA are made by the same:

A

RNA polymerase

Large enzyme complex with five subunits

144
Q

What is the core enzyme in prokaryotes responsible for rapid elongation of the transcript?

A

RNA polymerase

145
Q

The RNA polymerase is the core enzyme responsible for rapid elongation of the transcript, however this enzyme along cannot initiate transcript. An addition subunit termed: _____ is required to form what is called the ____, which is responsible for:

A

Sigma factor (sigma) is required to form the holoenzyme which is responsible for initiation

146
Q

Three stages of transcription in prokaryotes

A

initiation, elongation, termination

147
Q

Initiation of transcription in prokaryotes occurs when

A

RNA poly holoenzyme binds to a promoter

148
Q

To initiation transcription, RNA poly holoenzyme binds to a promoter that contains two primary sequences called:

A

Pribnow box at -10

The -35 sequence

149
Q

The holoenzyme scans across a chromosome like a train on a railroad until:

A

It finds a promoter and then it stops to form a closed complex

150
Q

The RNA polymerase must ______ before it can synthesize RNA

A

Unwind the double helix DNA

151
Q

A RNA polymerase bound at the promoter with a region of single stranded DNA is termed the ____

Once formed, it allows _____

A

Open complex

Transcription can now occur.

152
Q

The sigma factor plats two roles in helping the polymerase find promoters:

A
  1. Increase the ability of RNA poly to find promoters

2. Make holoenzyme more specific

153
Q

The core enzyme elongates the RNA chain processively, meaning

A

One polymerase complex synthesizes an entire RNA molecule

154
Q

As the core enzyme elongates the RNA, it moves down the DNA in a ____ direction in a _____, in which a region of the DNA double helix is unwound to allow the polymerase to access the complementary DNA template

A

Downstream direction

Transcription bubble

155
Q

When a termination signal is detected, in some cases with the help of the protein called “rho”, the:

A

Polymerase falls off of the DNA, releases the RNA and the transcription bubble closes

156
Q

In eukaryotes, translation and transcription occur in the:

In prokaryotes, translation and transcription occur in the:

A

For eukaryotes, transcription occurs in the nucleus and then it is modified and transported across the cell membrane to be translated in the cytoplasm

Transcription and translation for prokaryotes occurs together in cytoplasm because the cell has no nucleus

157
Q

Translation and transcription occur _____ in prokaryotes and _____ in eukaryotes

A

Simultaneously in P

Non-simultaneously in E

158
Q

Primary transcript in prokaryotes is:

Primary transcript in eukaryotes is:

A

mRNA (ready to be translated)

hnRNA (modified extensively before translation)

159
Q

Splicing

A

Eukaryotic DNA has non-coding sequences intervening between segments that code for proteins

These intervening sequences contain enhancers or other regulatory sequences and can be quite long

160
Q

Introns

A

Intervening sequences in the RNA

INtrons INtervene

161
Q

Extrons

A

Protein coding regions of the RNA actually expressed

EXtrons are EXpressed

162
Q

Before the RNA in eukaryotes can be translated:

A

The introns must be removed and the extrons connected via splicing

163
Q

Spliceosome

A

Contains proteins and snRNA (small nuclear RNA)

Proteins bind to the snRNA forming snRNPs (small nucleic ribonucleic proteins)

164
Q

The spliceosome assembles around each ____ that needs to be removed via a series of steps in which ________ as the reaction proceeds. This complex undergoes many _________

A

Introns

Different snRNPs are recruited and released

Conformational changes to attain catalytic activity

165
Q

Two splicing reactions are catalyzed by the spliceosome

A
  1. Intron forms a looped structure

2. Joins two externs and releases loop

166
Q

Alternative splicing

A

For a given gene, there are different options for splicing patterns leading to different mRNAs (in length and sequence) being made from one DNA gene sequence

This increases the complexity in gene expression

167
Q

hnRNA must be modified in two more ways (in addition to splicing) before translation can occur:

A

A tag is added to each end of the molecule (5’ cap and a 3’ poly-A tail)

168
Q

Before translation, the hnRNA must be modified by adding a tag to each end of the molecule…

A 5’ cap is:

A 3’ poly-A tail is:

A

5’ cap: methylated guanine nucleotides on the 5’ side (made first)

3’ poly-A tail: string of adenine nucleotides

169
Q

The 5’ cap is essential for _____ , while both the cap and the poly-A tail are important in:

A

Translation

Preventing digestion of the mRNA by the exonucleases that are free in the cell

170
Q

In eukaryotes there are several types of RNA polymerases:
1.
2.
3.

A

RNA poly I, II and III

171
Q

RNA poly I in eukaryotes:

A

Transcribes most rRNA

172
Q

RNA poly II in eukaryotes:

A

Transcribed hnRNA (ultimately mRNA), snRNA and some miRNA

173
Q

RNA poly III in eukaryotes:

A

Transcribes tRNA, siRNA, some miRNA and a subset of rRNA

174
Q

Translation

A

Synthesis of polypeptides according to the amino acid sequence dictated by mRNA codons

175
Q

During translation, the mRNA molecule attaches to a ribosome at a specific codon and the appropriate amino acid is delivered by a ___ molecule.

Then the: _____

The process is repeated until the _____, at which point the ribosome _____

A

tRNA

Ribosome binds the two amino acids together, creating a dipeptide

Polypeptide is complete at which point the ribosome drops the mRNA and the new polypeptide departs

176
Q

Each tRNA is composed of a single transcript produced by

A

RNA poly III

177
Q

The ____ structure of every tRNA molecule is ____

A

tertiary; similar

178
Q

tRNA molecules have a ___ structure that is stabilized by ______

A

Stem-and-loop structure

H-bonding between bases on neighboring segments of the RNA chain

179
Q

One end of tRNA is known as the anti-codon segment and is responsible for:

Anticodon:

A

Organizing the mRNA codon to be translated.

Three ribosome sequence that is complementary to the mRNA codon to be translated by the tRNA

180
Q

A key step in translation is the:

It is this specificity that dictates:

A

Specific base pairing between the tRNA anticodon and the mRNA codon

Which amino acid will be added to a growing polypeptide chain by the ribosome

181
Q

The other end of the tRNA molecule has the amino acid acceptor site which is responsible for:

A

Amino acid attachment to the tRNA (the same for all tRNA molecules)

182
Q

The two ends of the tRNA molecule are:

A

Amino acid acceptor site and anticodon segment

183
Q

Each tRNA molecule can be named based on the amino acid it is specific for… for example a tRNA molecule responsible for valine can be written as:

When the valine attaches it can be written as:

A

tRNAval

Val-tRNAval

184
Q

The Wobble Hypothesis

A

First two codon-anticodon pairs obey normal base pairing rules, but the third position is more flexible

Explains that there are less tRNA molecules than AA codon combinations

185
Q

There are 61 amino acid codons, so are there 61 tRNA molecule types?

A

No there are fewer than 45 so each tRNA must encode for more than one AA

186
Q

I is especially wobbly in the third base pair and can bond to which different codon bases?

A

A U or C

187
Q

5’ Base in tRNA is:

  • G
  • U
  • I

List the wobble 3’ Base in Codons (mRNA)

A

G: U (wobble base)
U: G (wabble base)
I: A, U or C (all wobble bases)

188
Q

tRNA loading (aka amino acid activation)

A

Reaction coupling of two-high energy phosphate bonds hydrolyzed to provide enough energy to overcome G>0 and high Ea to attach an AA to its tRNA molecule

189
Q

Why is tRNA loading useful?

A

Because breaking the aminoacyl-tRNA bond will drive peptide bond formation forward

190
Q

Amino acid activation/tRNA loading occurs in many steps…

  1. An amino acid is attached to ____ to form ____ . In this reaction, the nucleophile is the acidic ____ of the amino acid and the leaving group is ___
  2. The pyrophosphate leaving group is ____ to 2 orthophosphates. This reaction is ______
  3. tRNA loading, an unfavorable reaction, is driven forward by the _______.
A
  1. An amino acid is attached to AMP to form aminoacyl AMP . In this reaction, the nucleophile is the acidic oxygen of the amino acid and the leaving group is PPi
  2. The pyrophosphate leaving group is hydrolyzed to 2 orthophosphates. This reaction is exothermic and spontaneous G<0
  3. tRNA loading, an unfavorable reaction, is driven forward by the destruction of the high energy aminoacyl-AMP bond created in step one.
191
Q

Overall, amino acid activation requires ______ because it uses two high energy bonds

An ATP equivalent is a single high-energy phosphate bond

You can get 2 ATP equivalent by:

A

2 ATP equivalents

Hydrolysizing 2 ATP to 2ADP + 2 Pi or by hydrolysizing 1 ATP to 1 AMP + 2 Pi

192
Q

How is the attachment of the amino acid to each tRNA accomplished?

A

Aminoacyl-tRNA synthetase enzymes

193
Q

Aminoacyl-tRNA synthetase enzymes are specific to:

A

Each AA. There is at least one aminoacyl-tRNA synthetase for every amino acid

194
Q

The Aminoacyl-tRNA synthetase enzymes recognizes the tRNA and amino acids based on:

A

Their three-dimensional structures

195
Q

Aminoacyl-tRNA synthetase enzymes function with ______ and ______

A

High specificity and low error rate

196
Q

Amino acid activation serves two functions:

A

Specific and accurate amino acid delivery

Thermodynamic activation of the amino acid

197
Q

Ribosomes are located in the ____

A

Cytoplasm

198
Q

Each ribosome has a ___ and a ___

A

Small subunit and a large subunit

199
Q

The unit of measurement used for ribosomes is the Svedberg (S). Svedbergs are a ______, meaning __________

A

Sedimentation rate

How quickly something will sink in a gradient during centrifugation–units aren’t additive

200
Q

The prokaryotic ribosome sediments in a gradient at a rate of 70S, so it is referred to as the ____

A

70S ribosome

201
Q

Eukaryotes have an ______ ribosome

A

80S

202
Q

In both E and P ribosomes, the complete ribosome has ____ special binding sites. Name them

A

3

A site, P site & E site

203
Q

A site:

P site:

E site:

A

A: new tRNA delivers its amino acid

P: growing polypeptide chain still attached to the tRNA is located during translation

E: now-empty tRNA sits prior to its release from the ribosome

204
Q

During translation, the next codon to be translated is exposed in the:

A

A site

205
Q

tRNAs move through the sites from

A

A-P-E (Ape)

206
Q

Basic pairing:
A with ___
G with ___

A

A with T

G with C

207
Q

On prokaryotes, as transcription is occurring, several ribosomes attach and start transcribing the DNA, so the transcription and translation occur in the ____

A

Same direction (5-3’)

208
Q

Because prokaryotes often have polycistronic mRNAs their ribosomes can also start translation in the middle of the chain. This means that

A

Termination and initiation sequences are found between each ORF

209
Q

An upstream regulatory sequence is essential for initiation, just as in :

A

transcription

210
Q

Shine-Dalgarno sequence

A

A ribosome binding site (Instead of a promoter)

211
Q

Like transcription, translation has three distinct stages:

Many antibiotics function by:

A

Initiation, elongation and termination

Inhibiting a particular stage

212
Q

Initiation of translation begins with the small ribosomal subunit binding to two initiation proteins called
IF1 & IF3

This complex then binds to the mRNA transcript

Next, the first aminoacyl-tRNA joins, along with a third initiation factor called IF2 which is also bound to one GTP molecule

Finally, the 50S subunit completes the complex. This process is powered by ____

A

The hydrolysis of one GTP molecule

213
Q

The first aminoacyl-tRNA is also called the

A

Initiator tRNA aka fMet-tRNA(f-met)

214
Q

The fMet stands for formylmethionine which is used as:

A

The first amino acid in all prokaryotic proteins

215
Q

The P initiator tRNA sits in the __ site of the 70S ribosome , ____ bonded to the start codon

A

P site

Hydrogen bonded to the start codon

216
Q

Before P elongation, all the initiation factors

A

Dissociate from the complex

217
Q

P Elongation, a three step cycle, begins once the initiation factors dissociate from the complex.

In the first step, the second amino-acyl tRNA enters the ___ and ___ bonds with the second codon

A

A site and hydrogen

218
Q

In the first step of P elongation, the second amino-acyl tRNA enters the A site and hydrogen bonds with the second codon.

In the second step, the peptidyal transferase activity of the large ribosomal subunit (23S rRNA) catalyzes the formation of a peptide bond between fMet and the second amino acid.

The amino acid #2 acts as the nucleotide and the tRNA fMet acts as the LG . A new dipeptide is now attached to ____

A

tRNA #2

219
Q

The third step of elongation during translation in prokaryotes is:

A

translocation

220
Q

Translocation (3rd step of elongation in translocation of P) is:

A

tRNA #1 (empty) moves to the E site, tRNA #2 (holding growing peptide) moves to the P site and the next codon to be translated moves to the A site

221
Q

Translocation process: tRNA #1 (empty) moves to the E site, tRNA #2 (holding growing peptide) moves to the P site and the next codon to be translated moves to the A site

Costs how much energy?

A

One GTP molecule

222
Q

The new dipeptide is still attached to tRNA #2 and tRNA 3 is still H-bonded to codon #2. The presence of tRNA #1 is the E site is thought to:

A

Help maintain the reading frame of the mRNA (disruption of tRNA binding to the E site results in an increase in the number of frameshift mutations in the resulting protein)

223
Q

Termination (3rd step of prokaryotes translation) occurs when the:

A

Stop codon occurs in the A site

224
Q

During termination, (3rd step of prokaryotes translation) instead of tRNA,

A

A release factor enters the A site

225
Q

During termination, (3rd step of prokaryotes translation) instead of tRNA, a release factor enters the A site. Instead of the tRNA, a release factor enters the A site.

This causes the peptidyl transferase to hydrolyze the bond between the last tRNA, and the completed polypeptide

Finally, the ribosome

A

Separates into its subunits and releases both the mRNA and the polypeptide

226
Q

List the differences between eukaryotic and prokaryotic translation

A
  1. Ribosome is larger in E and has different components
  2. mRNA must be processed before translation in E
  3. N-terminal amino acid is different in E (Met not fMet)
  4. E mRNA must be spliced, capped, tailed and transported from the nucleus to the cytoplasm (can’t proceed simultaneously)
227
Q

Eukaryotes do not use the ____ sequence to initiation translation

A

Shine-Dalgarno

228
Q

In E translation, there are 5’ ___ sequences that start translation: a common one is called the _____, which is a consensus sequence typically located a few nucleotides before the start codon

A

UTR

Kozak Sequence

229
Q

First, a 43S pre-initation complex forms, composed of the 40S small ribosomal subunit, the Met-tRNA(Met) and several proteins called eukaryotic initiation factors or eIFs.

Next, the assembled complex is recruited to the ____ of the transcript, by an initiation complex of ____

Additional proteins are recruited and the initiation complex stars ____ the mRNA from the 5’ end, looking for a _____

Once the start codon is found, the ____ is recuited and ____

A

5’ capped end

proteins (including other eIF proteins)

scanning

start codon

large ribosomal subunit

translation can begin

230
Q

Cap-Dependent Translation

A

States that E translation starts at the 5’ end of the mRNA and encodes for only one polypeptide chain

231
Q

However, despite cap-dependent translation, E are also sometimes capable of:

A

Starting translating in the middle of an mRNA molecule

232
Q

When a E starts translating in the middle of a mRNA molecule it is called

A

Cap-independent translation

233
Q

To accomplish cap-independent translation, the transcript must:

A

Have an internal ribosome entry site (IRES) a specialized nucleotide sequence

234
Q

Most IRES found in E:

A

Help the cell deal with stress or activate apoptosis

AKA help the cell make proteins under sub-optimal conditions

235
Q

IRES help the cell make proteins under sub-optimal conditions why is this important?

A

Cell-independent translation allows the cell to make proteins when it is crucial for survival or pre-programmed death even though cell-dependent translation usually ceases during this time

236
Q

Activation of translation using an IRES requires _____ than normal initiation

A

different proteins

237
Q

Epigenetics

A

Focuses on changes in gene expression that are not due to changes in the DNA sequences, but. are either heritage or have long-term effect

238
Q

Principle site of regulation of gene expression in both E and P

A

Transcription

More mRNA made, more protein

239
Q

Both E and P DNA can be covalently modified by ______ .

In E: Bacteria methylation of new DNA occurs shortly after synthesis.

Why is there a delay?

A

Adding a methyl group

The delay is useful in mismatch repairs in E

240
Q

In P: methylation can control gene expression by

A

Promoting or inhibiting transcription

241
Q

In E: methylation turns off gene expression in two different ways

A
  1. Methylation physically blocks the gene from transcriptional proteins
  2. Certain proteins bind methylated CpG groups and recruit chromatin remolding proteins that change the winding of DNA around histones
242
Q

One way to increase gene expression is to increase the copy number of a gene by ____

Increasing gene dose allows:

Similarly, ___ can cause a decrease in gene expression

A

Amplification

Cell to make large quantities of the corresponding protein

Gene deletion

243
Q

Geonomic Imprinting is when:

A

Only one allele is of a gene is expressed

244
Q

Gene imprinting is generational meaning

A

That a gene imprinted in an adult may be “unimprinted” and expressed in offspring

245
Q

Silencing of a gene involves three things

A

GNA methylation, histone modification and binding of long non-coding RNAs

246
Q

X chromosome inactivation

A

Females have two sex chromosomes, Xi (inactive) and Xa (active)

247
Q

X chromosome inactivation implies that: every cell derived from each cell in the inner cell mass has _____, however, because each cell makes its own decision, ______

A

Same X chromosome inactivated

An adult can have different X chromosomes in different cells and tissues

248
Q

Xi is very condensed and packaged _____, it also has _____

A

Heterochromatin

High levels of DNA methylation

249
Q

What is the problem with transcription as the primary method of regulation for P?

A

That it is “pre-set” and cannot respond to changing conditions in the cell

250
Q

The transcription of enzymes involved in biosynthesis should be inhibited by:

The transcription of enzymes involved in catabolic pathways should be inhibited by:

And activated by:

A

The product

The absence of the substrate

The presence of the substrate

251
Q

Repressible enzymes

A

Anabolic enzymes whose transcription is inhibited in the presence of excessive product

252
Q

Inducible enzymes

A

Catabolic enzymes whose transcriptions can be stimulated by the abundance of a substrate

253
Q

Lac operon: kind of enzyme and codes for

A

Inducible enzyme

Codes for lactose catabolism

254
Q

Trp operon: kind of enzyme and codes for

A

Repressible and codes for biosynthesis/anabolism

255
Q

An operon has two components, a coding sequence for enzymes and ______ or _____

A

upstream regulatory sequences or control sites

256
Q

Operons may also include genes for ___, but ___ .

These genes can be located elsewhere in the genome and typically have their own __

A

Regulatory proteins (repressors or activators) but don’t have to

Promoters

257
Q

The lac operon contains several components:

P region is

A

promoter site on DNA to which RNA polymerase binds to initiation transcription of Y, Z and A genes

258
Q

The lac operon contains several components:

O region is

A

Operator site to which the Lac repressor binds

259
Q

The lac operon contains several components:

Z gene is

A

Codes for enzyme beta-galactosidase, which cleaves lactose into glucose and galactose

260
Q

The lac operon contains several components:

Y gene is

A

Codes for permeate, a protein which transports lactose into the cell

261
Q

The lac operon contains several components:

A gene is

A

codes for transacetylase, an enzyme which transfers an acetyl group from acetyl-coA to beta-galactoside (not requires for lactose metabolism)

262
Q

Genes with own promoter coding for proteins important in the regulation of the lac operon:

crp gebe

I gene

A

Crp gene: located at the distant site, this gene codes for a catabolite activator protein (CAP) and helps couple the lac operon to glucose levels in the cell

I gene located at a distant site, this gene codes for the Lac repressor protein

263
Q

Protein products of crp and I

A

Control gene expression of Z,Y & Z

264
Q

Bacterial cells preferentially uses ___ as an energy source

This means that in the presence of glucose:

In low glucose conditions, adenylyl cyclase is activated and cAMP levels are high. CAP binds cAMP and this complex binds the promoter of the lac operon to activate RNA poly at the operon and contributes to the operon being turned ______.

** Review **

A

Glucose

Lac operon will be off or expressed in low amounts

On when glucose is low

265
Q

The I gene codes for a repressor protein which binds the operator of the lac operon. This:

A

Prevents RNA poly from binding the promoter and transcribing Z, Y and A genes

Blocks transcription when lactose is absent

Causes conformational change to make the operon fall off the DNA

266
Q

I gene is allosteric meaning

A

Happens at a distant site from the operator binding

267
Q

Therefore, high transcription of Z, Y and A genes occurs when ____ is absent and ____ is present

A

Glucose is absent and lactose is present

268
Q

Low glucose results in an increased amount of _____, which binds to CAP and helps activate the ______ activity at the lac operon.

Lactose presence means the _____ is unable to bind the lac operator and negatively regulation transcription, thus the polycistornic mRNA is transcribed at ____

A

cAMP
RNA poly

Lac repressor protein

High levels

269
Q

When lactose supply is scarce, there isn’t enough to _____ and most of the repressor proteins return to their ______. They now ___ to the operator, ____ transcription levels

A

Bind to the repressots

Original Structure

Rebind to the operator, decreasing transcription

270
Q

High Trp Operon Process

A

https://www.google.com/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&ved=2ahUKEwj23eW80unfAhWrVN8KHXJSC3oQjRx6BAgBEAU&url=https%3A%2F%2Fwww.khanacademy.org%2Fscience%2Fbiology%2Fgene-regulation%2Fgene-regulation-in-bacteria%2Fv%2Ftrp-operon&psig=AOvVaw0p8bpUUHAzJBNd_hwVOPEY&ust=1547430578454183

271
Q

Low Trp: Operon

A

https://www.google.com/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&ved=2ahUKEwjs6fDT0unfAhWhd98KHbNKBVUQjRx6BAgBEAU&url=https%3A%2F%2Fwww.khanacademy.org%2Fscience%2Fbiology%2Fgene-regulation%2Fgene-regulation-in-bacteria%2Fv%2Ftrp-operon&psig=AOvVaw0p8bpUUHAzJBNd_hwVOPEY&ust=1547430578454183

272
Q

Upstream control elements

A

Code promoter containing binding sites for the basal transcription complex and RNA poly II and TATA box

Binding of the TBP to the TATA box initiations transcription complex assembly at the promoter

273
Q

Another kind of transcriptional regulation occurs when enhancer sequences are bound by

A

Activator protiens

274
Q

Activator proteins can make effects when the enhance is located thousands of base pairs away from a promoter

This is accomplished by

A

DNA looping so the enhancer and activator proteins can get close to transcriptional machinery

275
Q

Gene repressor proteins

A

Inhibit transcription

276
Q

_______ have DNA binding domains and are crucial in transcription regulation

A

Transcription factors

277
Q

RNA Translocation

A

mRNA transcripts aren’t translated into proteins until they are localized properly in the cell

278
Q

mRNA Survelliance

A

Cells closely monitor mRNA to ensure that only high-quality transcripts are read by the ribosome

Defective transcripts and stalled transcripts are degraded

279
Q

Defective transcripts

A

Premature stop codons or no stop codons

280
Q

Stalled transcripts

A

Ribosome is stalled in translation

281
Q

RNA Interference

A

A way to silence gene expression after a transcript has been made

miRNA and siRNA mediated

siRNA bind to mRNA and degrades them

Amount of transcript decreases and gene expression is negatively regulated

282
Q

Newly synthesized proteins from the ribosome cannot function–they need to be correctly folded, modified or processed and then transported to the right location

These modifications are called

Proteins can also be covalently modified

A

Post-translational modifications (occur after protein synthesis)

283
Q

Chaperons

A

Proteins that fold new proteins (and other macromolecules) into the correct 3D structure

284
Q

Zymogens (aka Proenzymes)

A

cleave proteins that may be dangerous

285
Q

Signal to get ready

DNA Rep
DNA Transcription
DNA Translation

A

R: ORI

Transcription: promoter

Translation: sine-dolgarno (P) and kozak (E) found in 5’ untranslated region

286
Q

Signal to start

DNA Rep
DNA Transcription
DNA Translation

A

R: ORI

Transcription: start site

Translation: AUG codon

287
Q

Key synthesis enzyme

DNA Rep
DNA Transcription
DNA Translation

A

R: DNA poly

T: RNA poly

T: Ribosome (rRNA and peptides)

288
Q

Template molecule

DNA Rep
DNA Transcription
DNA Translation

A

DNA

DNA

mRNA

289
Q

Read direction

DNA Rep
DNA Transcription
DNA Translation

A

3-5 on DNA template

3-5 on DNA template

5-3 on RNA template

290
Q

Molecule synthesized

DNA Rep
DNA Transcription
DNA Translation

A

R: DNA

T: RNA (mRNA in P. hnRNA in E.)

T: Peptides

291
Q

Prokaryotic location

DNA Rep
DNA Transcription
DNA Translation

A

Cytoplasm

Cytoplasm

Cytoplasm

292
Q

Eukaryotic location

DNA Rep
DNA Transcription
DNA Translation

A

Nucleus

Nucleus

Cytoplasm

293
Q

Signal to stop

DNA Rep
DNA Transcription
DNA Translation

A

R: Replication bubbles ligated together

T: Stop sequence or poly-A sequence

T: Stop codon (UAA, UGA, UAG)

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