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Biology 111 > Nucleic Acids (9) > Flashcards

Nucleic Acids (9) Flashcards

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1
Q

Is a polymer of nucleotides

A

DNA

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2
Q

nucleotides contain

A
  1. A pentose sugar
  2. A phosphate group
  3. A nitrogen containing base
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3
Q

Pentose sugars

A

ribose in RNA

deoxyribose in DNA

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4
Q

nitrogen containing bases and their pairing

A

Adenine base pairs Thymine (Uracil in RNA)

Guanine base pairs with Cytosine.

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5
Q

dNTP

A

deoxy (aNy base) Tri Phosphate

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6
Q

hybridizing

A

Bases are attached to one another through hydrogen bonds. RNA can also attach to DNA through hydrogen bonds.

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7
Q

The phosphodiester linkage

A

The phosphate group links the 5’ carbon of one sugar to the 3’ carbon of the next sugar to produce a strand with a sugar-phosphate backbone.

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8
Q

Structural Aspects of Strands of DNA

A
  • The DNA is double stranded
  • Each strand is held together by the hydrogen bonds that form between the bases of opposite strands
  • The two strands run anti-parallel ( 5’ carbon of one strand is attached to a 3’ carbon of the other strand)
  • The strands are twisted to form a double helix
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9
Q

Gene

A

A unit of genetic function which carries the information for a single protein or RNA (although some encode more than one protein). It is a sequence of nucleotides.

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10
Q

Genetic Information

A

Genes are a sequence of nucleotides and the genetic information is contained in the sequencing of the nucleotides.

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11
Q

Methionine

A

The start codon AUG.

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12
Q

Stop Codons

A

UAA
UAG
UGA

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13
Q

Replication

A

DNA makes a copy of itself.

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14
Q

Transcription

A

DNA makes an RNA copy.

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15
Q

Translation

A

The process in which genetic information (sequence of nucleotides) is translated into a sequence of amino acids (protein synthesis).

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16
Q

When a cell divides…

A

DNA must replicate before cell division. There is only one copy of DNA in the cell so the existing DNA serves as a template for the new DNA.

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17
Q

Semiconservative Replication

A

DNA replication that uses each parent strand of DNA as a template for a new strand. Since base pairings are always the same, knowing the sequence of one strand means that you automatically know the sequence of the second strand. Each molecule of DNA contains an “old” and “new” strand.

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18
Q

Two Basic Steps of DNA Replication

A
  1. The hydrogen bonds between the strands are broken. This opens the double helix and makes each strand available for base pairing to new nucleotides.
  2. The new nucleotides are covalently bonded to each growing strand.
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19
Q

Polymerase

A

In DNA replication, nucleotides are always added to the 3’ carbon end of the growing strand by an enzyme called polymerase.

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20
Q

Types of Polymerases

A

There are several different types of polymerases but all of them add nucleotides to the 3’ end of the strand.

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21
Q

ATP, GTP, CTP, and TTP

A

Base pair with the existing strand and polymerase will covalently attach the nucleotide to the new strand.

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22
Q

Where energy for the synthesis of nucleotides to the growing chain comes from

A

Energy for synthesis of nucleotides to the growing chain comes from breaking the bonds between terminal 2 phosphates.

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23
Q

DNA Replication Complex

A
  1. DNA helicase
  2. Single strand binding proteins
  3. Primase
  4. DNA polymerase III
  5. DNA polymerase I
  6. DNA ligase
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24
Q

DNA Helicase

A

An enzyme that unwinds DNA, exposing the single strands. Each strand serves as a template for the new strand being made.

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25
Q

Single Strand Binding Proteins

A

Bind to the single strand of DNA to keep it open and unwound during replication.

26
Q

DNA Polymerase III

A

An enzyme that adds nucleotides to the 3’ carbon end of a new DNA strand. It cannot start a new strand.

27
Q

Primase

A

An enzyme that starts the new strand during DNA replication. However, it starts the new strand with an RNA primer. The direction of synthesis of a new strand is from 5’ to 3’.

28
Q

RNA Primer

A

The segment of RNA that is started by the enzyme primase.

29
Q

DNA Polymerase I

A

An enzyme that removes the RNA primer and replaces it with DNA by adding nucleotides to the 3’ end of a growing strand.

30
Q

DNA Ligase

A

An enzyme that links fragments of DNA together.

31
Q

Replication Fork

A

The area in a DNA molecule where the unwinding is occurring.

32
Q

Process of DNA Replication (Step-By-Step)

A
  1. DNA helicase unwinds the DNA to expose the single strands.
  2. Single stranded binding proteins bind to the DNA to keep it unwound.
  3. Primase begins synthesis of the complementary strand with an RNA primer. The direction of the synthesis is from 5’ to 3’ for the new strand.
  4. The primase dissociates.
  5. DNA polymerase III attaches to the strands.
  6. DNA polymerase III extends the RNA primer, adding nucleotides to the 3’
  7. DNA polymerase III proofreads the newly added nucleotide to check for an error. If there is an error polymerase III replaces the incorrect nucleotide with the correct one.
  8. The leading strand completes the segment.
  9. On the lagging strand, DNA polymerase III completes its segment and dissociates.
  10. Helicase unwinds another segment.
  11. On the leading strand, DNA polymerase III continues to add nucleotides and on the lagging strand, primase adds another RNA primer.
  12. Primase dissociates.
  13. DNA polymerase III adds nucleotides to the 3’ end of the RNA primer
  14. The process is repeated until the end of the existing DNA
  15. DNA polymerase I removes the RNA primers and replaces them with DNA on the 3’ end, leaving gaps in the DNA backbone.
  16. Ligase makes the phosphodiester bond that DNA could not do and the DNA replication is complete.
33
Q

Lagging Strand

A

The strand during DNA replication when polymerase III is adding nucleotides that does not have new nucleotides added as quickly. This strand is built in segments. Primase adds several RNA primers along this strand.

34
Q

Leading Strand

A

The strand during DNA replication when polymerase III is adding nucleotides that has nucleotides added to the strand faster than the other strand.

35
Q

On the Leading Strand:

A
  1. Primase binds to the DNA and makes a small sequence of RNA complementary to the DNA
  2. DNA polymerase III adds nucleotide triphosphates to the 3’ end of the new strand
36
Q

Pyrophosphate

A

When DNA polymerase III adds a nucleotide to the new DNA strand the bond between the first phosphates is broken releasing pyrophosphate (2 phosphate groups covalently bonded). The bond in the pyrophosphate is also broken to supply additional energy.

37
Q

Initiates Replication…

A

Primase is necessary to initiate replication because DNA polymerase III cannot start the process, only add nucleotides.

38
Q

Okazaki Fragments

A

DNA polymerase III adds DNA nucleotides complementary to the template strand in a 5’ to 3’ direction, filling in the gaps between RNA primers on the lagging strand. These DNA fragments synthesized by DNA polymerase III are called Okazaki fragments.

39
Q

Direction of Building of the Lagging Strand

A

Overall it is built in a 3’ to 5’ direction but it is done by creating small fragments in a 5’ to 3’ direction and linking them together.

40
Q

Direction of Building of the Leading Strand

A

The DNA builds it in the 5’ to 3’ direction as one continuous strand.

41
Q

Origin of Replication

A

A sequence of DNA recognized by the replication complex. The DNA replication complex binds to the origin of replication on the chromosome. Several origins of replication exist on each chromosome so several complexes replicate the DNA at that same time.

42
Q

Mutations

A

Any change in the DNA sequence. The change in the amino acids causes a change in the protein. DNA polymerase III is involved in the change.

43
Q

Telomeres

A

A region of repetitive nucleotide sequences at the end of a chromosome, which protects the end of the chromosome from deterioration or from fusion with neighboring chromosomes.

44
Q

How mutations occur

A

Mutations can result from DNA copying mistakes made during cell division (replication), exposure to ionizing radiation, exposure to chemicals called mutagens, or infection by viruses.

45
Q

Germ-Line Mutations

A

Occur in the eggs and sperm and can be passed on to the offspring. Mutations that occur in cells that give rise to gametes.

46
Q

Somatic Mutations

A

Occur in the body cells and are not passed on. Are passed on during mitosis, but not to subsequent generations.

47
Q

DNA Repair Mechanisms

A
  1. Proofreading
  2. Mismatch Repair
  3. Excision Repair
48
Q

Proofreading

A

As new bases are added to a growing strand DNA polymerases checks for errors. When DNA polymerase recognizes an error it removes the wrong nucleotide and tries again.

49
Q

Mismatch Repair

A

The mismatch repair mechanism occurs after the DNA is replicated, proteins scan new DNA for mismatched base pairs.

50
Q

DNA Methylation

A

Occurs after DNA replication. The mismatched repair mechanism operates before the new DNA strand is methylated. This mechanism can distinguish between the methylated (old) template strand and the unmethylated (new) strand. Mythlatoin determines which base is correct (the base on the template strand) and which base needs to be replaced (the base on the new strand)

51
Q

Excision Repair

A

Excision repair enzymes “inspect” the cell’s DNA for damage, then cut the damaged strand and remove it. DNA polymerase and DNA ligase fill in and seal up the resulting gap. If the mutation occurs after the strands are methylated then there is a 50:50 chance that the mutation will be corrected.

52
Q

Two Types of Mutations

A

All mutations are altrations of the DNA nucleotides sequence and are of two types:

  1. point mutations
  2. chromosomal mutations
53
Q

Point Mutations

A

Are mutations of single genes. Result from the addition or subtraction of a base or the substituion of one base for another. Result of mistakes during DNA replication or can be caused by environmental mutagens.

54
Q

Chromosomal Mutations

A

Are changes in the arrangements of chromosomal DNA segments. Different types of mutations that can result from this type of repair mechanism:

  1. Deletions
  2. Duplications
  3. Inversions
  4. Translocations
55
Q

Missense Mutations

A

Cause amino acid substitution. May reduce the functioning of a protein or disable it completely.

56
Q

Silent Mutations

A

Result in no change in the amino acid sequence of the protein.

57
Q

Nonsense Mutations

A

Base substitutions that change an amino acid codon into a stop codon. Shortened proteins are usually not functional.

58
Q

Frame-Shift Mutations

A

Consists of the insertion or deletion of a single base. This shifts the code, changing many of the codons to different codons. These shifts almost always lead to the production of nonfunctional proteins.

59
Q

DNA Polymorphisms

A

Differences in nucleotide sequence among individuals.

60
Q

Deletions

A

Result from the chromosomal mutations repair mechanism. Deletions are a loss of a chromosomal segment.

Biology 111 (2 decks)

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