Nucleotides, Dna Structure, Replication, Transcription, Translation

Front 1

How are the biological roles of DNA/RNA different from other classes of biological molecules like proteins and carbohydrates?

Back 1

DNA and RNA's function is the storage and transfer of information and the regulation of biochemical processes

Front 2

Osborn Avery experiment

Back 2

Treatment of R-form of penumococcus bacteria with pure DNA extracted from the S-form results in its transformation into the S-form that was inheritable.

Demonstrated that DNA was the transforming agent as well as the material responsible for transmitting genetic info from one generation to the next.

Front 3

Purines

Back 3

Consists of a pyrimidine ring fused to an imidazole ring

Includes adenine and guanine

Front 4

Pyrimidines

Back 4

Only consists of a six-membered nitrogen-containing ring

Includes Cytosine, Uracil (RNA), Thymine (DNA)

Front 5

What is the major form of DNA bases found?

Back 5

Major form of DNA bases are in amino-keto form

Front 6

What is the minor form of DNA bases found?

Back 6

Tautomeric form due to rearrangement of the double bonds

Front 7

Tautomeric form ratio

Back 7

A small fraction of each base exists in its tautomeric form

Front 8

Deoxynucleoside

Back 8

Deoxyribose + DNA base

Front 9

Nucleoside

Back 9

Ribse + DNA base

Front 10

Difference between Ribose and Deoxyribose sugars

Back 10

At the 2` position, the deoxyribose does not have a hydroxyl group.

Ribose is less stable because the 2` hydroxyl group is attacked, leading to degradation.

The deoxyribose has enhanced stability of ring structure because of 2` deoxy

Front 11

What is the linkage that is between the nucleotide base and the sugar?

Back 11

N-beta-Glycosidic bond joins the Nitrogen of the base to C1` on the sugar

Front 12

What are the phosphate of nucleosides derivatives of?

Back 12

Phosphoric acid - H3PO4

Front 13

What is the linkage that is between two different nucleosides?

Back 13

Phosphodiester bonds

Front 14

Deoxynucleotides

Back 14

DNA base + deoxyribose + phosphate
OR
deoxynucleoside + phosphate

Front 15

Where are phosphodiester bonds formed?

Back 15

Formed between the 3` OH position of one deoxynucleotide and 5` OH of the next

Front 16

What bonds create the backbone of DNA?

Back 16

repeating Phosphodiester bonds

Front 17

Oligonucleotides

Back 17

Nucleic acids less than 50 nucleotides

Front 18

Polynucleotides

Back 18

Nucleic acids that are greater than 50 nucleotides in length

Front 19

Chargoff's Rule

Back 19

The abundance of deoxyadenosine always equaled that of thymidine and the abundance of deoxyguanosine always equalted that of deoxycytidine

Front 20

How is the double helix stabilized?

Back 20

The electrons of the adjacent base pairs interact, generating stacking forces and stabilize the helix in addition to the hydrogen bonds between the base pairs.

Front 21

What are the different types of DNA conformations and which one is more prevalent?

Back 21

A, B, and Z

The right handed B form is the most prevalent

Front 22

What shape is the biological active form of DNA

Back 22

The form is superhelical created by either underwinding or overwinding the double helix.

Front 23

Histones

Back 23

Small basic proteins containing large amounts of positively charged arginine and lysine that strongly binds to negative charged phosphates on DNA to package and order the DNA into structural units called nucleosomes

Front 24

Chromatin

Back 24

The complex that includes DNA, histones, and other proteins that makes up chromosomes

Front 25

Nucleosomes

Back 25

Consist of a segment of DNA wound around a histone protein core

Front 26

Mitochondrial DNA

Back 26

A small portion of eukaryotic DNA that is located in the mitochondria.

It encodes some, but not all of the mitochondrial proteins.

Front 27

Structure of DNA

Back 27

RNA chains are single-stranded
Lack the continuous helical structure of double-stranded DNA but does make stem-loop structure

Uses uracil rather than thymine

Sugar is a ribose

Front 28

Small interfering RNA (siRNA)

Back 28

Form of RNA that is effective in reducing the expression or completely silencing specific genes

Front 29

What are the essential building blocks necessary for Purine synthesis?

Back 29

Glycine, Glutamine, Aspartate and Tetrahydrofolate.

Front 30

How does Purine synthesis differ from Pyrimidine synthesis?

Back 30

Purines begin through the construct of the rings on a sugar while Pyrimidines do not.

Front 31

What is the central intermediate for Purine synthesis?

Back 31

Inosine Monophosphate (IMP)

Front 32

What is the role of glutamine in Purine synthesis?

Back 32

Glutamine donates its amine groups to make the central intermediate during Purine synthesis

Front 33

What is the role of Glycine in Purine synthesis?

Back 33

Glycine donates its carbon and nitrogen skeletons to make the central intermediate ring in Purine synthesis

Front 34

What is the role of Aspartate in Purine synthesis?

Back 34

Aspartate donates its carbon and nitrogen skeletons to make the central intermediate ring in Purine synthesis.

Front 35

What is the role of tetrahydrofolate in Purine synthesis?

Back 35

Tetrahydrofolate is a one carbon donor that participates in the formation of the central intermediate in Purine synthesis.

Front 36

What is used to make the 5 membered ring of Purines?

Back 36

Use glycine, glutamine and tetrahydrofolate and attach it to ribose

Front 37

What is used to make the 6 membered ring of Purines?

Back 37

Use aspartate's carbon skeleton and a carbon from tetrahydrofolate to finally make IMP.

Front 38

Why is the addition of glutamine to PRPP a committed step?

Back 38

PRPP has a pyrophosphate group at C1` which is an excellent leaving group, making the molecule high reactive, therefore, once the reaction occurs, the following molecules must be made.

Front 39

How many ATPs are needed to make IMP?

Back 39

4 ATPs

Front 40

How do you make NDPs from NMPs?

Back 40

Use kinases to add an additional phosphate at the 5` end

Front 41

How do you make NTPs from NDPs?

Back 41

Use nucleotide diphosphate kinases to add an additional phosphate at the 5` end

Front 42

How does chemotherapy block purine synthesis?

Back 42

Rapidly dividing cells, such as cancer cells, need purine synthesis to continue growing.

Use drugs which mimic the shape of a purine building block that can also inhibit an enzyme to block purine development

Front 43

Helicase

Back 43

Protein enzyme that separates the DNA strands and unwind the parental duplex

Front 44

Werner Syndrome

Back 44

Rare disorder characterized by premature aging

Due to deficient helicases

Front 45

Toposiosmerases

Back 45

Enzymes that wind/unwind DNA

Alter the linking number of DNA by three step process
1. Cleavage of one or both strands of DNA
2. Passage of segment of DNA through enzyme through this break
3. Resealing of DNA break

Front 46

Topoisomerase Type I

Back 46

Cleaves just one strand of DNA

Catalyzes the relaxation of a supercoiled DNA

Thermodynamically favorable

Front 47

Topoisomerase Type II

Back 47

Enzymes cleave both strands of DNA

Utilizes energy from ATP hydrolysis to add negative supercoils to DNA

Front 48

What is the rate of DNA replication?

Back 48

2000 bases are incorporated per second

Front 49

Primer used in DNA replication

Back 49

Short piece of RNA that is attached, usually to lagging strand of DNA, for DNA polymerase to catalyze replication

Front 50

Primase

Back 50

Primase catalyzes the synthesis of a short RNA segments, called a primer, complementary to a ssDNA template

Primase is activated by Helicase

Front 51

In what direction does synthesis go in DNA replication?

Back 51

Synthesis goes from 5` to 3`

Front 52

DNA polymerase III

Back 52

Holoenzyme

Primary enzyme complex involved in prokaryotic DNA replication

Catalytic prowess: 1000 nucleotides are added per second compared to 10nucleotides/sec for DNA polymerase I (It is 1000 times faster)

This is due to processivity

Has proofreading capabilities that correct replication mistakes by means of exonuclease activity (3` --> 5`)

Front 53

Processivity

Back 53

Measure of the average number of nucleotides added by DNA polymerase enzyme per association/disassociation with the template

Front 54

DNA polymerase I

Back 54

an enzyme that participates in the process of DNA replication in prokaryotes and also removes RNA primer

Possesses three enzymatic activities:
1. 5' -> 3' (forward) DNA polymerase activity, requiring 3' primer site and template strand
2. 3' -> 5' (reverse) exonuclease activity that mediates proofreading
3. 5' -> 3' (forward) exonuclease activity mediating nick translation during DNA repair

Front 55

Okazaki fragments

Back 55

Synthesis of DNA that is produced in a 5` to 3` direction away from the fork in pieces, that is eventually joined together

Front 56

DNA ligase

Back 56

Enzyme that catalyzes the formation of phosphodiester bonds between the 3` hydroxyl group at the end of one DNA chain and the 5`-phosphate group at the end of the other strand.

Uses ATP in eukaryotes

Uses NAD+ in bacteria

Front 57

What is the error rate of base-pairing?

Back 57

Error rate is about 10^6

If proofreading activity is removed, the error rate increases to about 10^3

Front 58

What are some of the differences between bacterial and eukaryotic DNA replication?

Back 58

Replication is continuous in bacterial cells.
In eukaryotic cells it is done in phases.

Bacterial chromosomes have a single point of origin.
Eukaryotic chromosomes have multiple points of oritins at which replications begins.

Front 59

Poymerase δ

Back 59

The major eukaryotic enzyme involved in DNA replication on leading and lagging strands

Exonuclease Activity goes 3` to 5`

Front 60

Single stranded binding proteins

Back 60

Prevents the single strands of DNA from reassociating during replication

Front 61

Telomerase

Back 61

Enzyme that adds DNA sequence repeats ("TTAGGG") to the 3' end overhang of DNA strands in the telomere regions

Acts as a RNA-dependent DNA polymerase (like reverse transcriptase) because it contains both proteins and RNA

Once long, the primase enzyme can bind and synthesize the complementary strand

Front 62

Xeroderma pigmentosum

Back 62

Genetic disorder of DNA repair in which the ability to repair damage caused by ultraviolet (UV) light is deficient

Front 63

Mismatch repair

Back 63

Parental DNA strands contain methyl groups on adenine bases in specific sequences

During replication, the newly synthesized strands are not immediately methylated

Unmethylated strand is repaired

Front 64

Benzo[a]pyrne

Back 64

Not carcinogenic until it is oxidized

Covalently binds to guanine residues in DNA, interrupting hydrogen bonding in G-C base pairs

Produced distortions of the helix

Front 65

Thymine dimer

Back 65

UV light can cause two adjacent pyrimidines to form a covalent dimer

Front 66

Translocation

Back 66

When the free ends of DNA at break points reseal with free ends of a different chromosome

Front 67

Transposons

Back 67

Segments of DNA that can move from their original position in the genome to a new location

Found in all organisms

Front 68

Reverse Transcriptase

Back 68

An enzyme that uses a single-stranded RNA template to make a DNA copy

Found in retroviruses

Front 69

cDNA

Back 69

Complementary DNA

The DNA copy of the RNA produced by reverse transcriptase

Front 70

Transcription

Back 70

Synthesis of RNA from a DNA template

Catalyzed by a large enzyme called RNA polymerase

Front 71

RNA polymerase

Back 71

Catalyzes the initiation and elongation of RNA chains

Front 72

Which strand of DNA is used for transcription?

Back 72

Copying takes placed from complementary (template/antisense) strand.

Therefore the mRNA has the same sequence of genes as the coding (sense) strand

Front 73

Why type of bonds are created by DNA polymerases and RNA polymerases

Back 73

Forms ester bonds between nucleotides that base-pair with the complementary nucleotides on the DNA template

Front 74

Difference between RNA and DNA polymerase

Back 74

Unlike DNA polymerase, RNA polymerase can initiate the synthesis of new chains in the absence of primers

RNA polymerase also lacks 3` to 5` exonuclease proofreading activity

Front 75

Bacterial RNA polymerase

Back 75

Single RNA polymerase transcribes DNA to generate all forms of RNA (mRNA, rRNA, and tRNA)

Front 76

Eukaryotic RNA polymerase

Back 76

Three different RNA polymerases involved in transcription.

Front 77

RNA Polymerase I

Back 77

Eykaryotic RNA polymerase that produces most of the rRNA.

It is insensitive to the effects of alpha-amanitin

Front 78

RNA Polymerase II

Back 78

Eukaryotic RNA polymerase that produces mRNA

Strongly inhibited by alpha-amanitin, even under low concentrations of poison

Front 79

RNA Polymerase III

Back 79

Eukaryotic RNA polymerase that produces small RNAs like tRNA and 5S rRNA

Inhibited by alpha-amanitin only under high concentrations

Front 80

alpha-amanitin

Back 80

Poison that binds tightly to RNA polymerase II.

Blocks the elongation phase of RNA synthesis

Higher concentrations of the poison also inhibits RNA polymerase III

Front 81

Cis acting activating regions

Back 81

The promotor region is on the same strand of DNA that is being transcribed

Front 82

Trans acting proteins

Back 82

Proteins that bind to promotor DNA sequences. They are not on the same strand.

Front 83

Promotor region

Back 83

Areas that are on the DNA that shows which genes to transcribe and where RNA polymerase should start transcribing them

Front 84

Two basic markers for where transcription should start in Prokaryotes

Back 84

TATA/Pribnow box (-10)

-35 base pair consensus sequence

Front 85

How is frequency of transcription controlled

Back 85

Controlled by regulatory sequences within the promotor and enhancers

Front 86

Promotor-proximal elements

Back 86

Interact with proteins that stabilize RNA polymerase binding to the promotor to help with rapid transcription

Front 87

Eukaryotic promotors

Back 87

TATA box present, but is more downstream (-20 to -30)

G-C rich sequence found at -40

CAAT box at -110

Front 88

General Transcription Factors

Back 88

AKA Basal factors

Bind to TATA box and facilitate the binding of RNA polymerase II to transcribe mRNA

Front 89

TFIIH

Back 89

Unwinds DNA for either transcription or DNA repair

Acts as an ATP-dependent DNA helicase

Front 90

Transcription factors that act in the site of promotion

Back 90

These generally work on many genes

Front 91

Transcription factors that act at specific genes

Back 91

Are gene specific transcription factors

Front 92

What signals terminate transcription

Back 92

Formation of hairpin loop on RNA preceding a number of Uracil residues

Rho factors associate with RNA polymerase and leads to termination

Front 93

Rho factors

Back 93

Rho factors are ATP-dependent helicases that associate with RNA polymerase and leads to termination

It pulls RNA away from the RNA polymerase

Front 94

What leads to the formation of hairpin loops?

Back 94

Palindrome sequences cause the RNA to fold back on itself forming the loop

Front 95

Operon

Back 95

A region of DNA that controls the process of transcription

Front 96

Lac Operon

Back 96

Repressor protein, encoded by promotor, blocks the promotion of genes to be transcribed. It prevents RNA polymerase from transcribing these genes

An inducer binds to the repressor protein, causing it to dissociate.

RNA polymerase can now recognize the promotor for genes.

Front 97

Cistron

Back 97

A region of DNA that encodes a single polypeptide chain

Front 98

Repressor Protein

Back 98

Repressor protein, encoded by promotor, blocks the promotion of genes to be transcribed. It prevents RNA polymerase from transcribing these genes

Front 99

Inducer

Back 99

A stimulator that binds to the repressor protein of lac operons, causing it to dissociate

Front 100

Capping modification

Back 100

Synthesized by RNA polymerase II

5` terminal end is modified such that a GTP is attached in a 5` to 5` linkage and methylation occurs at guanine and 2`C of ribose

It decreases the rate of degradation and serves as a recognition site for the binding of mature mRNA to ribosomes for translation

Front 101

Poly(A) Tail

Back 101

Modification of RNA where 250 adenine nucleotides are added to the 3` end by poly(A) polymerase

Front 102

Removal of Introns

Back 102

Modification of pre-mRNA where large regions are excised and the exons are spliced together.

It is carried out by spliceosomes

Front 103

Spliceosomes

Back 103

Assemblies of proteins and small RNA molecules (Ribozyme) that carry out splicing of Exons

Front 104

Stop Codons

Back 104

UAA, UAG, UGA

Front 105

Degenerative genetic code

Back 105

More than one codon can code for the same amino acid

Front 106

Synonyms

Back 106

Codons that specify the same amino acid

Front 107

Point mutation

Back 107

A single base change

Front 108

Silent mutation

Back 108

A change that specifies the same amino acid

Front 109

Missense mutation

Back 109

A change that specifies a different amino acid

Front 110

Nonsense mutation

Back 110

A change that produces a stop codon

Front 111

Insertion mutation

Back 111

An addition of one or more bases

Front 112

Deletion mutation

Back 112

A lost of one or more bases

Front 113

Frame-shift mutations

Back 113

Subclass of insertion/deletion mutation

When bases are added or removed, it causes a shift in the reading frame, therefore all the codons will be shifted

Front 114

Anticodon

Back 114

Loop on tRNA that is complementary to mRNA

Front 115

5` end of tRNA

Back 115

Phosphorylated area

Has an activated amino acid

Front 116

3` end of tRNA

Back 116

Activated amino acid is attached to the -OH group of 3`` end

Front 117

Wobble Hypothesis

Back 117

Some tRNA molecules can recognize more than one codon

Front 118

Hypoxanthine

Back 118

Base found in anticodon (it is the first base of anticodon to match last base in codon)

Allows wobble base-pairs to form

It can bind to adenine, cytosine or uracil

Therefore, one tRNA molecule can base pair with three different codons

Front 119

Aminoacyl-tRNA synthetases

Back 119

Enzymes that attach amino acids to their tRNA

Twenty different enzymes exist, one for each amino acid

Front 120

dHow does aminoacyl-tRNA synthetases chose tRNA partners?

Back 120

Anticodons
Acceptor stem - position that contains amino acid at the end of the loop
Other Unique features like unusual bases and placement of bases

Front 121

Ribosomal subunit

Back 121

Large subunit (50S)
Small subunit (30S)
Together form 70S

Front 122

Initiation of Translation

Back 122

Involves the formation of a complex composed of methionyl-tRNAiMet, mRNA and a ribosome

Initiator tRNA binds to 30S part of ribosome. GTP and initiation factors are attached to activate this.

mRNA binds

Front 123

P Site

Back 123

Peptidyl site on ribosome

Front 124

A site

Back 124

Aminoacyl site on the ribosome

Front 125

Shine-Delgarno sequence

Back 125

Protein synthesis begins with the interaction of 30S subunit and mRNA through this sequence.

Front 126

Differences between Eukaryotic and Prokaryotic Initiation of Protein Synthesis

Back 126

Eukaryotic
1. Binding of mRNA to small ribosomal subunit is through 5` cap of mRNA
2. First amino acid is methionine
3. Initiation factors are elFs
4. Ribosomes are 80S (40S and 60S)

Prokaryotes
1. Binding of mRNA to small ribosomal subunits is through Shine-Dalgarno sequence
2. First amino acid is formyl-methionine
3. Initiation factors are IFs
4. Ribosomes are 70S (30S and 50S)

Front 127

Peptidyltransferase

Back 127

rRNA of large ribosomal subunit catalyzes the formation of the peptide bond in translation of mRNA

Front 128

Translocation

Back 128

Uncharged tRNA moves from the P site and is release from the ribosome

Front 129

Ribosomal release factor

Back 129

A protein that resembles tRNA that recognizes stop codons and terminates translation

Front 130

Polysomes

Back 130

A group of Ribosomes that simultaneously translate a single mRNA

Front 131

Chaperones

Back 131

Bind to Nascent Polypeptide chains that protect against misfolding.

Front 132

Post-translation modification

Back 132

Initial methionine is removed by protease

Cleavages of proteins to activate (proinsulin to insulin)

Modified through phosphorylations, methylations, carboxylations, etc to change the behavior of the protein

Front 133

Proteins synthesized on polysomes in the cytosol

Back 133

After they are release from ribosomes, they remain in the cytosol, they they carry out their functions

Front 134

Proteins synthesized on cytosolic ribosomes

Back 134

Enter organelles, such as mitochondria or nuclei

Front 135

Proteins synthesized on ribosomes bound to RER

Back 135

Proteins are destined for secretion or for incorporation in organelles or cellular membranes

Front 136

Chromatin Remodeling

Back 136

Positive charge from amino group of lysine is acetylated, removing its charge, thereby reducing the electrostatic forces between histones and DNA.

Makes it easier for DNA to unwind

Front 137

Methylation of 5` cytosine

Back 137

Means of regulation of DNA to turn transcription and therefor translation off.

Front 138

Chloramphenicol

Back 138

Antiobiotic that inhibits the peptidyl transferase activity of the 50S ribosomal subunit in prokaryotes