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Biochem exam 3 > Chapter 35: DNA, RNA and Replication > Flashcards

Chapter 35: DNA, RNA and Replication Flashcards

1
Q

DNA vs RNA bases in a nucleotide

A

• DNA and RNA: adenine (A), guanine (G), and cytosine (C)
• DNA ONLY: thymine (T)
• RNA ONLY: Uracil (U)

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2
Q

Parts of a purine base?

A

2 rings
1. Pyrimidine ring
2. Imidazole ring

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3
Q

Parts of a pyrimidine base? What does the ring contain and where?

A

1 ring
1. Either a benzene of pyridine ring
2. The ring contains 2 nitrogen atoms at position 1 and 3

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4
Q

How are nucleotides connected to one another and what is the rxn type? Where is this connection?

A
  1. phosphodiester bond (dehydration rxn)
  2. Between 5’ phosphate group of 1 nucleotide and the 3’ OH group of a second nucleotide
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5
Q

Each phosphate in a nucleotide is connected to what? What is at either end of a polynucleotide?

A
  1. 2 sugar molecules
  2. One end of a polynucleotide will have a free 5’ phosphate (5’ end) and the other end will have an unbound 3’ OH group (3’ end)
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6
Q

How was the initial structure of DNA discovered? By who?

A

Who: Maurice Wilkins and Rosalind Franklin at King’s College (UK) (1952)

Discovered DNA is a polynucleotide that consists of many nucleotides. Also discovered the generic structure

X-ray diffraction: the crystalline structure is hit with x-rays which causes incident X-ray beams to diffract into many specific directions. This provides a diffraction pattern which gives info about the the atomic and molecular structure of the crystal

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7
Q

What did Watson, Crick, Franklin, and Wilkens discover?

A
  1. DNA is a double-stranded polynucleotide that adopts a right-handed helix
  2. Two strands are antiparallel (opposite directions): 5’ end of one interacts with 3’ of the other
  3. Bases lie flat in 3-D (perpendicular to axis)
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8
Q

What forms the inside of the DNA structure (backbone)? What lies outside the backbone?

A
  1. Backbone: bases form the hydrogen bonds with the bases from the opposite strand.
  2. Outside consists of sugar and phosphate groups attached to one another
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9
Q

In the backbone, what bases from hydrogen bonds with one another and how many between each?

A

Hydrogen bonds only form between:
A-T: 2 bonds
C-G: 3 bonds

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10
Q

In a DNA molecule, where is the common location of protein binding?

A

Within the alternating major and minor grooves (empty spaces in the 3-D structure of the double helix)

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11
Q

***What is the type (shape/form) of DNA found in MOST normal cells?

A

B-DNA

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12
Q

**What form of DNA is observed when water is removed via dehydration or high salt concentrations?

A

A-DNA

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13
Q

**What is more compact: A-DNA or B-DNA?

A

A-DNA

Characteristics (not HY):
1. 11-12 bases per turn
2. Still a right-handed helix
3. Bases are tilted upwards slightly (not flat)
4. Deeper/narrower grooves

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14
Q

What type of DNA is observed when the DNA consists of mostly C-G pairs?

A

Z-DNA

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15
Q

What type of DNA has a zig-zag shape, LEFT-handed helix and NO major grooves?

A

Z-DNA

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16
Q

**If a gram positive bacteria is exposed to harsh environments (heat, UV light, chemicals, drying, etc) what do they form and produce?

A
  1. They form protective endospores. This is done by removing water and forming a tough outer coat.
  2. They also produce SASPs (spores associated proteins) that bind to the DNA and convert it from B to **A-DNA. This tightens the DNA and protects it from damage
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17
Q

What type of DNA do scientists know less about? What have they discovered?

A

Z-DNA. They have discovered cellular and viral proteins that have the ability to bind tightly to Z DNA (but not A or B DNA)

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18
Q

What forms when sequences from the same single strand of nucleotides are inverted complements?

A

a hairpin structure

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19
Q

Where are hairpin structures most commonly found?

A

RNA

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20
Q

When the complementary sequences are contiguous in hairpin structures, what does NOT form?

A

A loop —> ONLY a stem forms instead

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21
Q

DNA wraps around histone proteins and forms _____________. These condense into _____________ which then condenses further to form ______________.

A
  1. Nucleosomes
  2. Chromatin fibers
  3. Chromosomes
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22
Q

What is the basic unit of the chromatin which comprises 147 base pairs of DNA wrapped around an octamer of core histones?

A

nucleosome

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23
Q

Histone proteins are ______ charged proteins that stick to _________ charged DNA to form nucleosomes. They form an octamer made of two molecules of each _____, _______, ____, and _______.

A
  1. +
  2. -
  3. H2A, H2B, H3, and H4 histones
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24
Q

What type of chromatin in DNA is tightly packed and never gets transcribed or cleaved?

A

Heterochromatin

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25
Q

***What enzyme breaks the phosphodiester bond in DNA or RNA? What cleaves dsDNA vs ssRNA?

A
  1. Nucleases
  2. DNase (deoxyribonucleases)
  3. RNase (ribonucleases)
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26
Q

How do you detect places of high transcription? What about gene activity?

A
  1. nuclease activity = transcription
  2. DNase I sensitivity = gene activity
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27
Q

What protects the ends of DNA from degradation via exonucleases (from the “outside”: 5’ or 3’ end)?

A

Telomeres

28
Q

What are telomere sequences rich in? How do they stabilize the DNA and what shape do they form?

A
  1. Cs and Gs
  2. The G-rich single-stranded overhang inserts itself into the double helix and forms a triple- helix structure, stabilizing the DNA as if it had a circular shape. Forms a semi-circular shape called a T-loop
29
Q

What is linked to genetic diseases and aging?

A

Telomere stability

30
Q

What are nucleases that cut at the end of nucleotide chain?
What are nucleases that cut in the middle of nucleotide chain?

A
  1. exonucleases
  2. endonucleases
31
Q

What are nucleases typically used for (2 things)? What do they recognize and how do they cut DNA/RNA?

A
  1. DNA repair
  2. Molecular cloning
  3. They recognize specific sequences of nucleotides in DNA/RNA. They break the phosphodiester bond via hydrolysis to generate a 5’-phosphate and 3’ OH terminus. They can cut either with blunt ends or staggered.
32
Q

What is the optimum activity of nucleases dependent on?

A

pH

33
Q

What do nucleases also require to perform their action (2 things)

A
  1. metal ions, usually Ca2+ or Mg2+ or Mn2+
  2. Enzyme amino acids, usually histidine, lysine, aspartic acid, glutamic acid (the charged amino acids)
34
Q

**What enzyme participates in the overwinding or underwinding of DNA? What is the reason for this?

A
  1. Topoisomerases: when DNA starts to replicate, it prevents supercoiling on either side of the DNA thats pulling apart. It does this by cutting the phosphate backbone, unwinding it and joining it back together
  2. To allow transcription or replication to occur
35
Q

***What helps with replication fork movement and relaxes supercoils associated with transcription?

A

Topoisomerase I

36
Q

***What are motor proteins that move directionally along a nucleic acid phosphodiester backbone to separate two nucleic acid strands? How do they do this and what is needed?

A
  1. Helicases: “unzip”
  2. They break the hydrogen bonds between complementary bases and use ATP hydrolysis as their energy source
37
Q

**What type of helicase HELPS TO MAINTAIN STABILITY OF THE GENOME and suppress inappropriate recombination?

A

RecQ helicases (3’-5’)

38
Q

The ATRX gene of the Superfamily 2 subgroup (SF2), is involved in chromatin remodeling, gene regulation, and DNA methylation. It helps prevent apoptosis, resulting in cortical size regulation, as well as contribution to the survival of hippocampal and cortical structures, affecting memory and learning. If there is a problem with this gene, what is the result?

A

X-linked-alpha-thalassaemia-mental retardation

39
Q

What type of chromosomes do bacteria have?

A
  1. A single, circular chromosome that is typically supercoiled
40
Q

Bacterial DNA replication (Theta replication): Initiation

  1. how many origins of replication are there?
  2. Where does replication begin and what binds?
  3. What happens when the origin of replication binds the initiator protein?
A
  1. SINGLE origin of replication
  2. DNA replication starts at oriC (ONLY 1 place). OriC contain binding sites for a complex of initiator proteins (DnaA) to bind to the chromosome
  3. Once DnaA proteins bind, it causes a slight “bend” to be introduced.
41
Q

Bacterial DNA replication (Theta replication): Unwinding

  1. What forms due to the bending of the DNA? What binds to this formation?
A
  1. A replication “bubble”: serves as a binding site for 2 proteins (DnaB, DnaC)
42
Q

Bacterial DNA replication (Theta replication): Unwinding

  1. What do DnaB and DnaC do once they bind to the replication “bubble”? What type of proteins are they?
A
  1. They ATP to further break hydrogen bonds between the DNA strands and separate them.
  2. DnaB and C are types of helicases
43
Q

Bacterial DNA replication (Theta replication): Unwinding

Once the DNA is separated into single strands, what keeps the strands apart?

A
  1. single-strand-binding proteins (SSB proteins)
44
Q

Bacterial DNA replication (Theta replication): Unwinding

What enzyme binds to the chromosome “ahead” of the replication fork and relieves the tension by making small cuts in the strands, unwinding and resealing?

A

DNA gyrase (a type of topoisomerase)

45
Q

Bacterial DNA replication (Theta replication): Primer synthesis

  1. Once the DNA strands are separated, what enzyme creates the primer (a short 5-10 nucleotide RNA chain that is complimentary to the template)?
  2. AFTER A PRIMER IS CREATED, what enzyme creates a new strand by extending from the primer (elongation)?
A
  1. primase
  2. DNA polymerase III

**NO PRIMER = NO DNA REPLICATION

46
Q

Bacterial DNA replication (Theta replication): Synthesis of new DNA strands

**1. During elongation, which end does DNA polymerase III add new nucleotides?
**2. In what direction is a new DNA strand synthesized?

A
  1. onto the 3’ end of a growing strand
  2. 5’ -> 3’ direction
47
Q

Bacterial DNA replication (Theta replication): Synthesis of new DNA strands

  1. Steps of adding a nucleotide via DNA polymerase III:
  2. Complimentary nucleotides of DNA?
A
  1. dNTP (deoxynucleotide triphosphate) is brought in, pyrophosphate (P-P) is removed (1P left)
  2. DNA poly III reads the template strand and adds
    its complementary nucleotide
  3. Reads T, adds A; reads G, adds C and vice versa
48
Q

Bacterial DNA replication (Theta replication): Synthesis of new DNA strands

**1. How does DNA polymerase III correct any mistakes during elongation? What direction is this done?

**2. What is the sliding clamp (++++ charged) structure that locks the whole replication complex onto the ssDNA strands? Purpose?

A
  1. It will back up, cut it out, and put the correct one in, 3’->5’ exonuclease activity (via hydrolysis)
  2. β clamp, prevents DNA polymerase III from falling off the template strand. This increases the processivity of the alpha-subunit
49
Q

Bacterial DNA replication (Theta replication): Synthesis of new DNA strands

  1. What is the strand that is made continuously as DNA pol III moves towards the replication fork
  2. What strand is made discontinuously (moving away from the replication fork) and is initially composed of
    small fragments called Okazaki fragments?
A
  1. Leading strand
  2. Lagging strand
50
Q

Bacterial DNA replication (Theta replication): Primer removal and ligation

  1. What enzyme removes the RNA primers from both the leading and lagging strands and fills in the gaps with DNA?
  2. Where does the above enzyme start?
  3. What enzyme then seals the spaces between each Okazaki fragment on the lagging strand and creates the last phosphodiester bond?
A
  1. DNA polymerase I: it has 5’->3’ exonuclease activity and 5’->3’ polymerization
  2. At the end of each Okazaki fragment!!
  3. DNA ligase (gLue)
51
Q

**What is the shape and number of bacterial vs human chromosomes?

A

Bacteria: Single, circular chromosome (Avg size: 4.6 x 106 base pairs)

Humans: Multiple, linear chromosomes (Total size: 3.3 x 109 base pairs)

52
Q

***Compared to prokaryotic chromosomes, eukaryotic chromosomes have _____ origins of replications? How are these origins approved for replication?

A
  1. MULTIPLE
  2. approved for replication by origin recognition complexes (ORCs)

ORCs recruit helicase, SSB protein, DNA pols, etc. and come off after replication (NO ORCs = NO REPLICATION)

53
Q

**In eukaryotic cells (humans), unreplicated DNA is coated with ____________? Following replication, they come off the DNA and are prevented from going back on

A

MCM proteins (helicases)

**No MCM proteins, no replication

54
Q

Do bacteria or eukaryotes have more DNA polymerases?

A

Eukaryotes!! Have 13 different ones

Prokaryotes only have 5 different DNA polymerases

55
Q
  1. In eukaryotic DNA replication, what subunit function as the primase to add primer to leading/lagging strand templates and begin extending them? This enzyme has LOW processivity and falls off quickly.
  2. What subunits replace this enzyme and finishes the job on the lagging strand vs leading strand? They have HIGH processivity and 3’-> 5’ exonuclease activity
A
  1. Polymerase alpha (pol α): LOW processivity, NO 3’-5’ exonuclease acitivty
  2. Polymerase delta (Pol δ): lagging strand
    Polymerase epsilon: leading strand
56
Q

Unlike bacterial DNA, eukaryotic DNA is tightly coiled around proteins called __________.

A

Histones

57
Q

Eukaryotic DNA replication differences:

  1. How are histones altered to make DNA accessible for replication? Purpose?
A
  1. acetylation: adding an acetyl group (COCH3). This NEUTRALIZES the POSITIVE charge of the histone causing them to lose attraction to DNA (- charge)
58
Q

What enzyme adds >1,000 copies of a repeated sequence (e.g. TTAGGG) onto the ends of each chromosome at the end of replication? Where is this enzyme active? Purpose?

A
  1. Telomerase: contains an RNA template to bind to chromosome end
  2. ONLY active in gametes, embryos, and stem cells
  3. It modifies the end of our chromosomes (telomeres) to
    prevent the loss of important genes
59
Q

Replication of WHAT cell organelle ONLY happens in eukaryotes? Shape of genome? What does the DNA contain?

A
  1. Mitochondrial replication***
  2. Circular genome (derived from bacteria)
  3. DNA contains genes required for life (Most function in oxidative phosphorylation: Cytochrome b, Cytochrome c oxidase, NADH dehydrogenase, )ATP synthase
60
Q

Mitochondrial replication characteristics:

A
61
Q

How do drugs that “look like” nucleotides affect DNA replication?

A

They compete with nucleotides to bind to DNA polymerase but are NOT incorporated (stuck to DNA polymerase)

62
Q

How do drugs that are nucleoside analogs (look like a nucleotide) affect DNA replication?

A

They are incorporated into the DNA but lack a 3’ OH. Therefore, once incorporated you can’t add more nucleotides to the strand

63
Q

How are drugs that compete with DNA polymerase affect DNA replication?

A

They compete with DNA pol for their binding site on DNA (looks like the phosphate group on nucleotides). Therefore they inhibit DNA pol from binding —> stops replication

64
Q

Alternative splicing is when ALL _________ are removed, but ________ are variably cut out. What is the result?

A
  1. introns
  2. exons
  3. Yields different proteins from the SAME mRNA (isoforms)
    more exons = more isoforms

In general, one gene provides instructions for a single protein. BUT, after a gene is transcribed and goes through mRNA processing, it can produce many different mRNA products from alternative splicing. These different mRNA products will all code for different proteins

65
Q

**What are most inhibitors of transcription?

A

nucleoside analogs: stop phosphodiester bonds or hydrogen bonds from forming, act as premature transcription chain terminators (no leaving group, no hydroxyl in the right configuration)

66
Q

Types of nucleoside analogs:

A
  1. Actinomycin: derived from bacterium streptomyces, VERY TOXIC, First antibiotic shown to have anti-cancer
    properties.
  2. Actinomycin D: NOT as toxic.

**3. Alpha-amanitin: cyclic peptide of 8 amino acids, DEADLIEST (“alpha”) of all the amatoxins, found in mushrooms (ex: death cap)
• Selective inhibitor of RNA polymerase II and III (BUT NOT I)

Biochem exam 3 (11 decks)

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