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Bio 300 Exam 1 > Exam 1 > Flashcards

Exam 1 Flashcards

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1
Q

DNA

What is a Pyrimidine

A

A sing ringed nucleotide base

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2
Q

DNA

What is a Purine

A

A double ringed nucleotide base

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3
Q

DNA

What is a dNTPS

A

Deoxyribonucleic Triphosphate

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4
Q

DNA vs. RNA Sugars

What is the diference between DNA and RNAs sugar?

A
  • DNA = Deoxyribsoe sugar
  • RNA = Ribose Sugar**
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5
Q

Bonds

What is a phosphodiester bond?

A
  • It is a bond between the 3rd carbon of a deoxyribose and the 5th carbon of a second deoxyribose
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6
Q

DNA

What is DNA?

A
  • Deoxyribose sugar
  • Phosphate
  • cyclic nitrogen base
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7
Q

DNA

Antiparallel Complimentary Base Pairing

A
  • Complementrary bases on both strands (5’ to 3’ one strand/3’ to 5’ on other strand)
  • Exact same code is found on both strands
  • Proteins always read DNA from 5’ -> 3’
  • A binds to T
  • C binds to G
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8
Q

DNA vs. RNA

What is the difference between DNA and RNA bases?

A
  • Thymine -> Uracil
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9
Q

DNA Replication

Describe the semi-conservative model of DNA Replication

A
  • Origonal Strands = Pink
  • Newley made strands = blue
    1. Double Helix opens, exposing bases
    2. Complementray bases are matched to template
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10
Q

DNA Replication

Describe the conservative model of DNA replication

A
  • Makes copies of each strand
  • Newley created strands anneal and parental strands close back up (Parental is conserved)
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11
Q

DNA Replication

Describe the dispersive model of DNA Replication

A
  • Double helix breaks and reforms
  • Parental is spread into two double helixes
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12
Q

Meselson-Stahl Experiment

What is the Meselson-Stahl Experiment?

A

Hypothesis = DNA Replication is Semi-Copnservative
* Ecoli was grown in N15 = heavy non-radioactive isotope of nitrogen
* DNA becomes Heavy
* Ecoli was added into an N14 media (normal Isotope)
1. The First Generation showed that an intermediate N15/N14 DNA was created disproving Conservative Replication
2. The second generation showed more N14 than N15 proving that Semi-conservative replication was the only possible replication model

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13
Q

DNA Replication Prokaryotes

Dna Replication Prokaryotes

A
  • In bacteria (E.Coli) experiments showed that their is only one orgin on their circular chromsome
  • Always starts at a location caled oriC
  • Replication is Bi-directional (Two replication forks moving away from oriC)
  • Until forks merge at a site called ter (terminiation of replication)
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14
Q

DNA Replication Eukaryotes

DNA Replication Eukaryotes

A
  • Linear rather than circular chromosomes
  • Much longer DNA strands
  • Have multiple orgin sites throughout each chromosome
  • Replication is bi-directional
  • Producing bubles (which merge later)
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15
Q

DNA Replication Enzymes

DNA Polymerase 1

A
  • First enzyme discoverd that built new strands of DNA
    Reaction Requires:
  • All four dNTPs (Nucleotides)
  • Template DNA
  • Can only attach a nucleotide to a 3’-OH group
  • This proves that DNA is built in a 5’ -> 3’ direction
  • This tells us that another enzyme must start the new strand before POl 1 can extend
  • Pol 1 is mostly involved in removing the primer and filling in gaps in the sequence
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15
Q

DNA Replication Enzymes

DNA Polymerase 1

A
  • First enzyme discoverd that built new strands of DNA
    Reaction Requires:
  • All four dNTPs (Nucleotides)
  • Template DNA
  • Can only attach a nucleotide to a 3’-OH group
  • This proves that DNA is built in a 5’ -> 3’ direction
  • This tells us that another enzyme must start the new strand before POl 1 can extend
  • Pol 1 is mostly involved in removing the primer and filling in gaps in the sequence
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16
Q

DNA Replication Enzymes: Primase

DNA Replication Enzymes: Primase

A
  • A type of RNA polymerase that can build RNA whithout a 3’ end to start from
  • RNA Polymerase builds a small sequence of RNA that is complementary to template DNA sequence
  • Hydrogen bonds hold primer to DNA
  • Then DNA polymerase can start building DNA sequence off the RNA Primer
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17
Q

DNA Replication Enzymes: Polymerase 3

Dna Replication Enzymes: Polymerase 3

A
  • Turns out Pol 3 is the enzyme responsible for DNA Replication in vivo (in living organisms)
  • 5’ -> 3’ only starting from a primer sequence
  • pol 3 can also proofread the sequence as it synthesizes
  • 3’ -> 5 exonuclease activity (goes back and removes bases that are not complementary, re-synthesizes correctly)
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17
Q

DNA Replication Enzymes: Polymerase 3

Dna Replication Enzymes: Polymerase 3

A
  • Turns out Pol 3 is the enzyme responsible for DNA Replication in vivo (in living organisms)
  • 5’ -> 3’ only starting from a primer sequence
  • pol 3 can also proofread the sequence as it synthesizes
  • 3’ -> 5 exonuclease activity (goes back and removes bases that are not complementary, re-synthesizes correctly)
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18
Q

DNA Replication Enzymes: Helicase

DNA Replication Enzymes: Helicase

A
  • Enzymes that Unwinds the helix and breaks hydrogen bonds
  • Denaturing double stranded DNA into two single strands
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19
Q

DNA Replication Enzymes: Single Stranded Binding Proteins

DNA Replcation Enzymes: Single Stranded Binding Proteins

A
  • Coat the denatured starnds of DNA and prtoect them so that they are not degraded
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20
Q

DNA Replication Enzymes: Helicase

DNA Replication Enzymes: Helicase

A
  • Helicase: Introduces increasing tension in the helix behind the replication forl
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21
Q

DNA Replication Enzymes: Topoisomerases

DNA Replication Enzymes: Topoisomerases

A
  • Topoisomerases: Relax the tension in the strand by undoing twists and knots
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22
Q

DNA Replication Enzymes: Ligase

DNA Replication Enzymes: Ligase

A
  • Ligase: Forms phosphodiester bond that seals the sugar-phosphate backbone
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23
Q

DNA Replication Enzymes: Ligase

DNA Replication Enzymes: Ligase

A
  • Ligase: Forms phosphodiester bond that seals the sugar-phosphate backbone
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24
Q

DNA Replication

DNA Replication Summary

A

DNA Replication Enzymes order:
1. Helicase
2. Topoisomerase
3. Primase
4. Single Stranded binding Proteins
5. DNA POL 3
6. DNA POL 1
7. Ligase

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25
Q

DNA Replication Leading vs. Lagging

DNA Replication Leading vs. Lagging Strand

A

Only one strand can be used to synthesize new DNA continuosly
* Template stranbd that is 3’ -> 5’ (Leading strand)
* Newley formed strand is therefore 5’ -> 3’

Other template strand must synthesize new DNA backwards from replication fork

  • Known as lagging strand = 5’ -> 3’
  • Newley formed strand is therefore 3’ -> 5’
  • Built in small pieces 5’ -> 3’ and then jumps
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26
Q

DNA Replication: Eukaryotes

DNA Replication: Eukaryotes and Chromatin

A
  • Eukaryotes must remove histones to allow replication protiens to bind DNA
  • Chromatin remodeling is occurring during S phase just like during gene expression
  • Histones are displaced ahead of replication fork and reassembled imeaditly
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27
Q

DNA Replication: Eukaryotes

DNA Replication: Eukaryotes Linear Ends

A
  • Because eukaryotic chromsomes are linear, replication at the ends is tricky
  • Linear ends look the same as (DSB) double strand breaks in DNA

Two Problems can occur to DSBs:

  1. Ends can fuse to other blunt ends
  2. Ends can be degraded
    * Loosing a bit of sequence with each s-phase (telomeres)
28
Q

DNA Transcription

DNA Transcription: Flow of Information

A

DNA:

  • Template strand (3’ -> 5’) Vs. Coding Strand (5’ to 3’)

mRNA:

  • Always transcribed (5’ -> 3’)
29
Q

Definitions

Transcription vs. Translation

A

Transcription: To copy down, within the same language

  • Lanuguage = nucleic acids
  • DNA to RNA

Translation: To translate from one language to another

  • From nucleic acids to amino Acids
  • RNA to protein
29
Q

Definitions

Transcription vs. Translation

A

Transcription: To copy down, within the same language

  • Lanuguage = nucleic acids
  • DNA to RNA

Translation: To translate from one language to another

  • From nucleic acids to amino Acids
  • RNA to protein
30
Q

Transcription: Enzymes

Transcription Enzymes: RNA Polymerase

A

Very similar to DNA Polymerase

  • Reads DNA template 3’ to 5’
  • Builds new strand complementary 5’ to 3’

Differences

  • Uses ribonucleotides (rNTPS and U) rather than deoxynucleotides (dNTPS and T) to build an RNA strand
  • Dosent require a primer to initiate synthesis
  • mRNA is released single stranded
31
Q

Transcription: Promoter

Transcription: Promoter

A
  • Sigma subunit of RNA polymerase binds a sequence of DNA known as the promoter
  • Recognizes consensus sequence of Promoter region (TATAAT known as “TATA Box”
  • Promoters are located upstream of the gene sequence
  • Regulatory regions because they control how much gene transcription occurs
32
Q

Transcription: Termination

Transcription: Termination

A
  • Like a promoter sequence, a termination sequence contains consensus sequences that the RNA Polymerase recgonizes

These consenses sequences signal:

  • Single stranded mRNA to be released
  • RNA Polymerase subunits dissociate
  • In prokaryotes termination sequences are transcribed and form secondary structure (hairpin loop) within the mRNA
33
Q

Transcription

Transcription Summary

A
34
Q

Transcription: Eukaryotes

Transcription in Eukaryotes

A

General mechanism of transcription is the same, but with more complexity

  1. Chromatin remodiling must open tightly packed DNA to allow RNA Pol access
  2. Transcription occurs in nucleus, mRNA is then translocated to cytoplasm before translation to proteins
  3. Three diferent RNA Pol
  4. Initation and regulation of transcription is more tightly controled
    * In addition to promoters also have enhancer and repressor sequences
    * Trancription factors (proteins)
  5. mRNA is processed post-transcriptionally
    * 5’ cap and 3’ tail
    * Splicing removes large sections of mRNA that will never be translated
35
Q

Transcription

Promoter Sites

A

TATA box: found in all, or almost all eukaryotic genes

  • Core-promoter region
  • siter where double helix of DNA denatures (H-Bonds open allowing RNA pol acess)

CAAT Box: is a common enhancer site

  • Most genes have more than one type of promoter and enhancer in combination
36
Q

Transcription

Transcription facotrs

A
  • Proteins that bind to promoter sites and influence efficiency of transcription
  • Often TFs recruit RNA Pol to promoter site (some are necessary for RNA pol to bind)
  • Others inhibit or block DNA acess
  • This allows eukaryotes very tight control over gene expression
37
Q

mRNA Processing

mRNA Processing: Caps and Tails

A

Methyl cap added to 5’ end

  • Protects mRNA from nuclease
  • Helps tag mRNA for transport to cytoplasm
  • May help recognize start of translation

String of A’s added to 3’ end (Poly-A-tail)

  • Protects mRNA from nuclease

Inton sequences are spliced out

  • Only exons are translated into protein
37
Q

mRNA Processing

mRNA Processing: Caps and Tails

A

Methyl cap added to 5’ end

  • Protects mRNA from nuclease
  • Helps tag mRNA for transport to cytoplasm
  • May help recognize start of translation

String of A’s added to 3’ end (Poly-A-tail)

  • Protects mRNA from nuclease

Inton sequences are spliced out

  • Only exons are translated into protein
38
Q

mRNA Processing

mRNA Processing: Splicing

A

Amazingly rRNAs can splice out their own introns without help

  • Known as Ribozymes

Majority of mRNAs use a spliceosome

  • Small nuclear RNAs (snRNAs)
  • Complexed with proteins (snRNPs or snurps)

Snurps loop out introns and ligate exons

39
Q

Translation

Translation: Reading Frame

A
  • Reading frame is how the sentence is read starting at a specific start site
  • DNA/RNA sequences can have different reading frames depending on start site
  • if you change the start site all the word will change
40
Q

Translation

Translation: Frame Shift Mutation

A
  • Mutation produced by adding one, two, three, or four bases into the middle of DNA
  • only the addition or deletion of three bases does not affect the reading frame
  • Addition of anything other than three bases caused a frame shift mutation (Changes the reading frame)
41
Q

Translation

Translation: Anticodons`

A
  • During translation transfer RNA (tRNA) complimentary base pairs with mRNA to translate mRNA into protein
  • tRNA holds different amino acids depending on anticodon sequence
42
Q

Translation

Termination Message

A
  • certin combinations produced only short peptide sequences
  • Someting must be signaling translation to end and release peptide
  • Nothing exsits in RNA polymer, must be termination codons signal the end of translation of the mRNA
  • “Stop codons” were discoverd (UAA, UAG, UGA)
43
Q

Genetic Code

Degeneracy

A
  • Almost all amino acids are specified by more than one codon

Exceptions

  • Methionine (AUG Only)
  • Tryptophan (UGG Only)

Degeneracy allows for mutations in the DNA and/or mRNA sequence to be completley silent in the protein sequence

  • Mutations in the 3rd base of the codon are the least likley to affect protein sequence
  • Multiple tRNAs exsist for the same amino acid
44
Q

Genetic Code

Wobble Hypothesis

A
  • Hydrogen bonding between complementary base pairs is also more flexible at the third position
  • tRNAs anticodon does not have to match the mRNA codon perfectly
  • First two bases must be complementary
  • But the third base of codon can make less than ideal hydrogen bonding, still atach
  • Same tRNA can be used for diferent codon
45
Q

Genetic Code

Orderd Genetic Code

A
  • Chemically similar amino acids often have similar codon sequences

For Example:

  • AAA and AAG = Lysine
  • AGA and AGG = Arginine
  • Lysine and Arginine are both positivley charged amino acids
  • Potential effects of mutation on protein is minimized - less dramatic change in protein
46
Q

Translation

Initiation Codon

A

Translation of the mRNA doesnt start at the first nucleotide in the mRNA sequence:
1. Reading frame must be established
* Out of three options, only one is used
2. Translation always begins at a start codon
* AUG = Methionine
* Establsihes Reading Frzme
* Sometimes removed post-translationally

47
Q

Translation

Termination Codon

A
  • Three codons do not encode for amino acids
  • There is no tRNA complementary to these three codons
  • Insted they terminate trnslation: Ribosome breaks apart and peptide is released

Stop Codons:
* UAA
* UAG
* UGA

48
Q

Translation

Ribosomal Structure

A

Made of two subunits
* One large subunit
* One small subunit

Both subunits made of proteins and rRNA
* rRNAs are enzymes that catalyze all the necessary reactions to translate and build new proteins

49
Q

Translation

Charging tRNAs

A
  • After tRNA is transcribed and folded
  • Appropriate amino acid must be linked
  • Enzyme: Aminoacyl tRNA Synthetase
  • Must be incredibaly acurate at matching the correct amino acid to the correct tRNAs
  • Using energy from ATP, Amino acid is attached to 3’ end of tRNA
  • Aminoacyl tRNA Synthetase charges the tRNA based on structure of tRNA NOT based on anticodon sequence
50
Q

Translation

Anticodon

A
  • 3rd base of mRNAs codon binds to 1st base of tRNAs codon
  • Bases 1 and 2 of the mRNA codon must be exactly complemntary to bases 2 and 3 of the tRNA
  • Hydrogen Bonding holds tRNA in place
  • Wobble base allows less specific hydrogen bonding to occur
51
Q

Translation: Eukaryotes

Translation in Eukaryotes

A

Important Differences
* mRNA lasta much longer allowing for more protein product to be made
* Transcription occurs within nucleus and translation occurs in cytoplams
* Specifically in the Rough endoplasmic reticulum (Rough ER)
* More proteins in tightly controlled process

52
Q

Protein Folding

Protein Misfolding Causes Disease

A
  1. Misfolded Proteins are non-functiona;
    * Active site does not fit substrate
    * Enzyme cant do reaction
  2. Misfolded proteins are ddestroyed
    * By ubiquitin and proteasome
  3. Misfolded proteins can acumulate
    * Forma large plaue (Huntington/Alzheimer)
    * Destory the cell (Degenerative diseases)
53
Q

Definition

Mutation

A

Changes in the DNA sequence that may consist of:
* Single Nucleotide changes: complementary base changes acordinagly
* Deletion or insertion of one or more bases
* Major alteration in chromosome structure or abnormality: known as chromosomal abnormality

54
Q

Mutations

Spontaneous vs. Induced Mutations

A

Spontaneous mutations: arise during S-phase - During DNA replication
* Arise because the DNA polymerase made an accidental mistake while copying
* Inserting wrong base, skipping over sequence

Induced Mutations: when a mutagen changes the DNA sequence directly
* Different mutagens induce different. and specific, changes to the sequence

55
Q

Mutations

Somcatic vs. Germline Mutations

A

Somatic mutations occur in somatic cells
* Any cell in body that is not a gamate
* Why dpes it matter to differentiate
* How do somatic mutant affect phenotype

Germline mutations occur in gametes
* Organism with mutation is normal
* Offspring produced will have this mutation in every cell of their body

56
Q

Mutations

Phenotypic Effects

A
  1. No change in protein
  2. Chnages protein(s): Structure, function, location, amount, and/or destory it completley
  3. Provide variation: (Neither harmful or helpful)
    * Loss of function: the protein is either not made, destroyed immediatley or cannot do its normal job
    * Gain of Function: Protein gains a new activity that it did not normally do or more protein is made or made unexprectedly
    * Regulatory Mutations: affect amount of protein or when/where gene is expressed.
57
Q

Mutations

Exact Molecular Changes

A
  1. Point Mutation - alters a single base
    * Missense: encodes a diferent amino acid
    * Nonsense: changes codon to stop codon
    * Silent: Encodes the same amino acid
  2. Deletions or insertions - one or more base pairs
    * Frameshift: Changes the reading frame
  3. Duplication or expanisons
  4. Chromosomal Rearrangments: Genes end up on wrong chromsome
58
Q

Mutagens

Spontaneous Mutagens

A

What exact mechanisms cause sponatious mutations?
* Mistakes during DNA replication
* Strand Slippage: Polymerase slips or stutters along the strand (In/del or Duplications)
* Different version of Nucleotide used: Tautomeric Shift
* Transposable Elements: Moving through genome disrupts sequence

59
Q

Mutations

Deamination

A
  • Randomly an amino group is removed from nucleotide and converted to carbonyl
  • When this happens the complementary base pair changes
  • Point mutaion is complementary strand
60
Q

Induced Mutations

Free Radicals

A
  • Reactive oxygen species
  • Contain unpaired electrons (Desperately want to form a pair)

In order to make a pair, they will react with almost anything either:
* Steel an electron (Starting a chain reaction of free radicals)
* Or bind in middle of a compound (can modify DNA or protien)

61
Q

Induced Mutations

Alkylating Agents

A

Chemicals that donate an akyl group
* Carbon Chain (CH3- or CH3CH2-)
* usually small chains

Once again, mutated nucleotide makes wrong complementary pair

62
Q

Induced Mutations

UV Light

A

DNA damage caused by exposure to UV light (ultraviolet radiation)
* Covalently bonds two thymines

DNA Replication can not work throgh thymine dimers
* Either DNA repair machinery
* Or cell undergoes apoptosis

63
Q

Induced Mutations

Radiation

A

Radiation that is even more powerful than UV can penetrate even deeper into tissues
* X-Rays from X-Ray machines
* Gamma Irradiation - from radioactive ions

Can introduce:
* Free radicals
* Point mutations
* Break Phosphodiester bonds
* Chromosomal breaks and rearrangments

64
Q

DNA Repair

Proofreading

A
  • DNA POL 3 in bacteria has an error rate of around 1 in (100,000)
  • Rember that polymerase contains ability to reverse direction, exonuclease wrong bases and replace with correct
  • This improves acuracy of DNA replication to 1 in (10,000,000)
65
Q

DNA Repair

Mismatch Repair

A
  • Daughter strand cut, degraded and remade, using the template strand
  • How does organim differentiate between daughter and template strabnd?
  • MMR can only be done during S phase
  • Bacteria: Daughter strand is not yet methylated - unmethylated strand cut
  • Eukaryotes: Daughter stand is not fully ligated - looks for nicks
66
Q

DNA Repair

Homologus Recombination

A
  • After S-phase is completed, DNA can still be repaired, through other mechanisms:
  • Error is recgonized - by DNA repair proteins scanning DNA
  • Region of bubble/lesion is cut
  • leaving a gap
  • Gap is filled in using undamaged template strand from homologus chromsome
67
Q

DNA Repair

DSB Repair

A
  • Ionzing radiation , along with other things, causes double stranded breaks
  • DSB Repair proteins recgonize the break in both strands
  • Endonuclease back both strands, leaving both strands with single strand over hang
  • Overhang searches the homologus chromosome for complementary sequence
  • Homologus recombination
68
Q

DNA Repair

Excision Repair

A

Excision repair is also post-replication (done by all pro- and eukaryotes)
* Error is recgonized and cut out (leaving a gap on one strand)
* DNA Polymerase fills in the gap by reading the template strand
* DNA Ligase seals the remaining nicks in the phosphodiester bonds

Bio 300 Exam 1 (1 decks)

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