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Grade 12 Biology > DNA replication > Flashcards

DNA replication Flashcards

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1
Q

DNA Function

A

DNA carries the genetic instructions used in development, functioning and reproduction of all living things and some viruses.

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2
Q

RNA function

A

Ribonucleic acid there are three types that are involved in the converting DNA codes into polypeptides.

RNA may act as catalyst like enzymes, have complex regulatory roles in cells, such as regulating gene expression, modifying other RNA and regulate of bacterial growth.

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3
Q

Structure consist of

A

Sugar, nitrogen’s base, and phosphate group.

The phosphodiester bond links sugars to form backbone of DNA structure

Nitrogen containg bases from backbone linked to a carbon in the sugar by a glycoside ice bond

DNA is a huge polymer chromosome 1 in humans has 349 million base pairs.

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4
Q

The sugars

A

They are 5 carbon sugars
DNA has deoxyribose
RNA has ribose

> bonds to phosphate group at 3 prime-carbon and 5 prime carbon

> bond to nitrogenous base at 1 prime carbon

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5
Q

Nitrogenous bases

A

> DNA has 4 bases

> Adenine that binds to thymine
guanine that binds to cytosine

In RNA also 4 bases
> instead of thymine uracil binds with guanine

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6
Q

DNA Anti-parallel strands

A

One strand runs 5’ to 3’ and the other one 3’ to 5’

5’ sugars bond to phosphate
3’ hydroxyl group on sugar

DNA can be single stranded but it is more stable double stranded

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7
Q

Packaging DNA

A

In eukaryotes DNA is wrapped around proteins called histones this is a coiled form called chromatin

The structure is further compressed by supercooling this forms chromosomes

Most prokaryotes lack histones but have supercooled forms of DNA held together by special proteins

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8
Q

RNA structure

A

RNA is single stranded

It can form double stranded structures that are important to its function

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9
Q

Fredrick mischer

A

Isolated DNA from call nucleus

Named it nuclein
Determined it is composed of H,O,N,P

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10
Q

What every DNA polymerase needs

A
  • A template of DNA
    • Enzymes copy a single strand of DNA
    • Can’t work without something to copy from
  • A primer
    • A primer is a polynucleotide with a “free 3’ OH end”
    • In a normal DNA replication, this is RNA
  • A substrate
    • To make DNA, a polymer, monomers are needed
    • Nucleotide triphosphates (NTPs) are the monomers
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11
Q

DNA and replication

DNA structure

A
  • Rosalind Franklin took diffraction x-ray photographs of DNA crystals.
  • In the 1950’s, Watson & Crick built the first model of DNA using Franklin’s x-rays.
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12
Q

DNA and Replication(DNA)

A
  • Two strands coiled called a double helix.
  • Sides made of a pentose sugar Deoxyribose bonded to phosphate groups by phosphodiester bonds.
  • Center made of nitrogen bases bonded together by weak hydrogen bonds.
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13
Q

DNA and Replication (Helix)

A
  • Most DNA has a right-hand twist with 10 base pairs in a complete turn.
  • Left twisted DNA is called Z-DNA or southpaw DNA
  • Hot spots occur where right and left twisted DNA meet producing mutations
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14
Q

DNA and replication( nitrogenous bases)

A
  • Double Ring PURINES
    • Adenine (A)
    • Guanine (G)
  • Single Ring PYRIMIDINES
    • Thymine (T)
    • Cytosine (C)
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15
Q

DNA and Replication(base pairings)

A
  • Purines only pair with Pyrimidines
  • Three hydrogen bonds are required to bond Guanine & Cytosine.
  • Two hydrogen bonds are required to bond Adenine & Thymine.
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16
Q

DNA and replication( replication facts)

A
  • DNA has to be copied before a cell divides.
  • DNA is copied during the S or synthesis phase of interphase.
  • New cells will identical dna strands.
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17
Q

DNA replication (Semiconservative)

A
  • Theoretically, 3 ways a DNA molecule could give rise to 2 new DNA molecules:
  • Semi-conservative means that each time DNA is replicated, the new double stranded molecules consist of one old strand and one new strand.
    • Conservative would result in a molecule with 2 old strands and one with 2 new ones.
    • each new DNA molecule would be a combination of old and new pieces.
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18
Q

DNA replication (Meselson and Stahl (1957)

A
  • DNA was produced in cells grown with N-15, a “heavy” isotope of nitrogen. (normal is N-15)
  • When DNA was placed into an ultracentrifuge, it migrated closer to the bottom because of its greater density.
  • What happened when N-15 labelled cells were allowed to keep growing in presence of N-14?
  • After one generation, all of the DNA molecules of intermediate density.
  • After two generations, half of them were intermediate, and the other half were light.
  • These results are consistent with semi-conservative replication.
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19
Q

DNA replication (origin of DNA)

A
  • Origin of DNA replication: particular site on DNA where copying of the DNA always starts.
    • Replication is bidirectional,
    • In each direction, there is a replication fork (Enzyme,DNA Helicase),
    • Most bacterial DNA is circular, so there is one Origin and and one terminus
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20
Q

DNA replication ( replicon)

A
  • Replicon: a length of DNA molecule replicated after initiation from one origin. Examples:
    • Bacterial DNA, plasmids, segments of eukaryotic chromosomes.
    • In linear DNA, origins occur at various places within the DNA molecule. The DNA replicated from one origin is a replicon.
  • In circular bacterial genomes, replication proceeds from a single origin, the entire molecule is a replicon.
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21
Q

how long does DNA replication take

A
  • DNA replication is a complicated process involving a variety of enzymes and other proteins, so it takes a while.
  • Speed of replication:
    • Bacteria: 1500 bp per second,
    • Eukaryotes: 10-100 bp per second.
  • In fruit flies, only 15-30 minutes to replicate all the DNA, similar to E.coli. How? Multiple origins (replication bubble).
  • E.Coli takes 30 minutes to replicate all its DNA, yet it can double every 20 minutes. How does it do this?
    • Starts a round of DNA replication before finishing the previous round.
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22
Q

DNA polymerases (bacteria): Enzymes that synthesize DNA

A
  • Kornberg dicovers DNA pol I (1956)
    • Demonstrates enzyme faithfully copies DNA (1960)
  • DNA pol II and III discovered
    • Pol I: cleaves out Okazaki fragments
      • Most abundant of the 3.
    • Pol II: repairs DNA damage,
    • Pol III: main DNA replicating enyzme
      • Pol III is a complex, multi-component enzyme complex (has a quaternary structure)
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23
Q

Adding and Removing Bases: Directionality

A
  • DNA synthesis is always in a 5’ to 3’ direction.
  • All 3 DNA pols have 3’ to 5’ exonuclease activity
    • Nuclease: enzyme activity that cuts nucleic acids,
    • Exo- means cuts from an end
    • 3’ to 5’ means the opposite direction from synthesis
      • proofreading ability; polymerase can “backspace” to remove a base put it by mistake.
  • DNA pol I have a 5’ to 3’ exonuclease activity
    • cuts off DNA bases in the same direction as synthesis.
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24
Q

The Need for Ligase

A

A new nucleoside triphosphate could be added onto the 3’ end but there is no way a polymerase can join a 3’ end to an existing 5’ end of a DNA strand that has a single phosphate group. This is the job of the enzyme ligase. It makes a covalent bond to connect ends after Okazaki fragments are replaced and are used as a tool in recombinant DNA technology.

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25
Q

Proofreading New DNA

A
  • DNA polymerase initially makes about 1 in 10,000 base-pairing errors
  • Enzymes proofread and correct these mistakes.
  • The new error rate for DNA that has been proofread is 1 in a billion base-pairing errors.
26
Q

DNA Damage and Repairs

A
  • Chemicals & ultraviolet radiation damage the DNA in our body cells,
  • Cells must continuously repair damaged DNA
  • Excision repair occurs when any of over 50 repair enzymes remove damaged parts of DNA
  • DNA polymerase and DNA ligase replace and bond the new nucleotides together
27
Q

protein synthesis (DNA)

A
  • DNA containing genes, sequences of nucleotide bases
  • These genes code for polypeptides (proteins)
  • Proteins are used to build cells and do much of the work inside cells
28
Q

proteins synthesis ( genes and proteins)

A
  • Proteins are made of amino acids linked together by peptide bonds
  • 20 different amino acids exist
29
Q

genes and proteins (polypeptides)

A

Amino acid chains are called polypeptides

30
Q

genes and protiens (DNA begins the process)

A
  • DNA is found inside the nucleus
  • Proteins, however, are made in the cytoplasm of cells by organelles called ribosomes
  • Ribosomes may be free in the cytosol or attached to the surface of rough ER
31
Q

genes and proteins(Rules of RNA and DNA)

A
  • DNA is the master plan

- RNA is the blueprint of the master plan

32
Q

genes and proteins(RNA Differs from DNA)

A
  • RNA has a sugar ribose, whereas DNA has sugar deoxyribose.
  • RNA contains the base uracil (U)
  • DNA has thymine (T)
  • RNA molecule is single-stranded
  • DNA is double-stranded.
33
Q

protein synthesis ( Three Types of RNA)

A
  • Messenger RNA (mRNA) copies DNA’s code &carries the genetic information to the ribosomes
  • Ribosomal RNA (rRNA), along with protein, makes up the ribosomes
  • Transfer RNA (tRNA) transfers amino acids to the ribosomes where proteins are synthesized.
34
Q

protein synthesis( Messenger RNA)

A
  • Long straight chain of nucleotides
  • Made in the nucleus
  • Copies DNA & leaves through nuclear pores
  • Contains the nitrogen bases A, G, C, U (no T)
  • Carries the information for a specific protein
  • Made up of 500 to 1000 nucleotides ling
  • Sequence of 3 bases called codon
  • AUG- methionine or start codon
  • UAA, UAG, or UGA - stop codon
35
Q

protein synthesis ( Ribosomal RNA)

A
  • rRNA is a single strand 100 to 3000 nucleotides long.
  • Globular in shape
  • Made inside the nucleus of a cell
  • Associates with proteins to form ribosomes
  • Site of protein synthesis
36
Q

protein synthesis ( the genetic code )

A
  • A codon designates an amino
  • An amino acid may have more than one codon
  • There are 20 amino acids, but 64 possible codons
  • Some codons tell the ribosome to stop translating
  • Use the code by reading from the center to the outside
  • Example: AUG codes for Methionine
37
Q

protein synthesis ( Transfer RNA )

A
  • Clover-leaf shape
  • Single-stranded molecule with attachment site at one end for an amino acid
  • Opposite end has three nucleotide bases called the anticodon
38
Q

protein synthesis (Codons and Anticodons)

A
  • The 3 bases of an anticodon are complementary to the 3 bases of a codon
    • Example: Codon ACU and Anticodon UGA
39
Q

protein synthesis(Pathway to Making a Protein)

A

💡 DNA ⇒ mRNA ⇒ tRNA (ribosomes)⇒ Protein

40
Q

Protein Synthesis

A
  • The production or synthesis of polypeptide chains (proteins)
  • Two phases:
    • Transcription and Translation
  • mRNA must be processed before it leaves the nucleus of eukaryotic cells
41
Q

protein synthesis(Transcription)

A
  • The process of copying the sequence of one strand of DNA, the template strand
  • mRNA copies the template strand
  • Requires the enzyme RNA polymerase.
  • During transcription, RNA polymerase binds to DNA and separates the DNA strands
  • RNA polymerase then uses one strand of DNA as a template to assemble nucleotides into RNA.
  • Promoters are regions on DNA that show where RNA polymerase must bind to begin the transcription of NA
  • Called the TATA box
  • Specific base sequences act as signals to stop, called the termination signal
42
Q

protein synthesis (mRNA Processing)

A
  • After the DNA is transcribed into RNA, editing must be done to the nucleotide chain to make the RNA functional
  • Introns, non-functional segments of DNA are snipped out of the chain.
43
Q

protein synthesis (mRNA Editing)

A
  • Exons, segments of DNA that code for proteins, are then joined by the enzyme ligase
  • A guanine triphosphate cap is added to the 5’ end of the newly copied mRNA
  • A poly-A tail is added to the 3’ end of the RNA
  • The newly processed mRNA can then leave the nucleus.
44
Q

protein synthesis( mRNA Transcript)

A
  • mRNA leaves the nucleus through its pores and goes to the ribosomes.
45
Q

protein synthesis( Translation)

A
  • Translation is the process of decoding the mRNA into a polypeptide chain
  • Ribosomes read mRNA three bases or 1 codon at a time and construct the protein
46
Q

protein synthesis( Ribosomes)

A
  • Made of a large and small subunit
  • Composed of rRNA (40%) and proteins (60%)
  • Have two sites for tRNA attachment P and A
47
Q

Step 1- Initiation

A
  • mRNA transcript start codon AUG attaches to the small ribosomal subunit
  • Small subunit attaches to large ribosomal subunit
48
Q

Mutations

A
  • Mutations are simply changes in the DNA
  • Classes of DNA
    • Small Mutations
    • Large Mutations
49
Q

mutations (small mutations)

A
  • Point Mutations - Single Base Changes
  • Change of small group of base pairs
  • Types;
    • Substitution - replacement of one base by another
    • Insertion - placement of one or more extra nucleotides in the sequence
    • Deletion - removal of one or more nucleotides in the sequence
    • Inversion - two adjacent bases trading places
  • Deletion and Insertions can cause changes to the reading frame of codons.
50
Q

small mutations effects

A
  1. Silent - does not change amino acid coded for thus has no effect
  2. Nonsense- converts a codon into a stop signal
  3. Missense - result in the single substitution of amino acid
51
Q

small mutation (frameshift)

A

Insertion or Deletion of one or more base pairs causes the reading frame to shift in one direction

Result in multiple missense and/or nonsense effects

52
Q

large scale

A

May Involve:

  • Large chunks of DNA inserted, lost, or repeated (10,000 - 5,000,000 bases long)
  • Duplication or loss of genes
  • Whole regions of chromosomes
53
Q

large scale causes

A
  1. Spontaneous mutations - errors during DNA copying, damages to bases not caused by factors from the external environment
  2. Induced mutation - damage caused exposure to mutagenic agents, such as, UV radiation, X-rays, certain chemicals
54
Q

large scale effects

A

Alteration of a single nucleotide result in sixth amino acid being valine instead of glutamic acid

Changes shape of protein hemoglobin cause them to form rigid rods that stick to one another

This can interrupt blood flow.

55
Q

lac operon

A

Lac Operon produces 3 proteins

  1. B-galactosidase - splits bond in lactose
  2. Galactoside Permease- a transport protein that embeds in the cell membrane and pumps lactose into the cell
  3. Transacetylase
56
Q

Trp Operon

A
  • Genes are normally “on” and will produce tryptophan.

- If tryptophan is present, it binds to the repressor and prevents more tryptophan from being made.

57
Q

4 Categories of Gene Regulation in Eukaryotes

1) Transcriptional Regulation (as mRNA is synthesized)

A
  • Regulates which genes are transcribed or rate of transcription
  • Access to promoters is enhanced or decreased
  • Example: Methylation of genes, transcription factors can’t bind
58
Q

4 Categories of Gene Regulation in Eukaryotes 2) Post Transcriptional (as mRNA is being processed)

A
  • Controls availability of mRNA to ribosomes.

- Example: Alternative splicing, perhaps 74% of human genes undergo this.

59
Q

4 Categories of Gene Regulation in Eukaryotes

3) Translational (as protein is being synthesized)

A
  • Controls how often and how rapidly mRNA is translated to a protein.
    • Example: Variation of the length of poly(A) tail
60
Q

4 Categories of Gene Regulation in Eukaryotes

4) Post-translational (after the protein has been synthesized)

A
  • Controls when proteins become functional, how long are functional, and when degraded
    • Example: activation of p53, a tumor suppressor protein by phosphorylation.

Grade 12 Biology (5 decks)

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