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MCAT Biology Review > Chapter 4 - 4.4: Molecular Biology > Flashcards

Chapter 4 - 4.4: Molecular Biology Flashcards

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1
Q

Name the 2 nucleic Acids

A

DNA: Deoxyribonucleic Acid
RNA: Ribonucleic Acid

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2
Q

Define Nucleic Acid

A

Found in the nucleus
Possess many acidic phosphate groups

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3
Q

Define nucleosides

A

Glycosylamines that are essentially nucleotides without their phosphate group

Consist of a nucleobase and a 5 carbon sugar

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4
Q

What are the 3 components of nucleotides?

A

1) 5 carbon pentose sugar (deoxyribose/ ribose)

2) aromatic nitrogenous base

3) 1-3 phosphate groups

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5
Q

What are the two classes of Nucleotides?

A

Purines and Pyrimidines

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6
Q

What are purines?

A

Derived from precursors called purine

Include nucleotide Bases G and A

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7
Q

What are pyrimidines?

A

Aromatic heterocyclic organic compound similar to pyridine

Include nucleotide bases C, T and U

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8
Q

How does a nucleotide differ from a nucleoside ?

A

Nucleoside: 2 components, essentially nucleotide without its phosphate group (sugar with a nucleobase [purine or pyrimidine] linked at 1’ carbon)

Nucleotide: phosphate esters of nucleosides with 1, 2 or 3 phosphate groups joined

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9
Q

What is a nucleoside triphosphate (NTP)? If it has a deoxyribose sugar, it is then called dNTP.

A

Nucleotides with 3 phosphate groups

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10
Q

What do we call nucleotides with 3 phosphate groups?

A

Nucleoside triphosphate (NTP) or dNTP if deoxyribose sugar

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11
Q

Name the 3 pyrimidine nucleotide bases

A

Cytosine

Thymine (DNA)

Uracil (RNA)

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12
Q

Name 2 purine nucleotide bases

A

Adenine

Guanine

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13
Q

What part of the nucleotide is considered variable? Which two are invariable?

A

Variable: the base (A, T, C, U, G)

Invariable: Sugar and Phosphate groups (referred to as “backbone” of DNA)

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14
Q

Define polynucleotides

A

nucleotides linked together by phosphodiester bonds

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15
Q

How are nucleotides linked to form polynucleotides?

A

Phosphodiester bonds : 2 hydroxyl groups in phosphoric acid react with hydroxyl groups on other molecules to form 2 ester bonds

3’ hydroxy group of one deoxyribose and the 5’ phosphate group of the next link

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16
Q

Define Oligonucleotide

A

A polymer of several nucleotides linked together

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17
Q

Define polynucleotide

A

A polymer of many nucleotides

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18
Q

Which end of the chain is written first in a polynucleotide?

A

The end of the chain with a free 5’ phosphate group is written first

The other nucleotides are read in 5’ to 3’ direction

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19
Q

What is a product of the polymerization of nucleotides?

A

pyrophosphate

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20
Q

Which scientists developed a model of the structure of DNA in the cell?

A

James Watson and Francis Crick

Helped by Maurice Wilkins and Rosalind Franklin

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21
Q

What is the Watson Crick model?

A

Portrays cellular DNA as a right handed double helix held together by Hydrogen bonds between bases

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22
Q

Are the nucleotides in polynucleotide chains hydrogen bonded together in a parallel or antiparallel orientation ?

A

Antiparallel: the 5’ end of one chain is paired with the 3’ end of the other

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23
Q

Which nucleotide bases hydrogen bond with which?

A

H bonded pairs always consist of one purine and one pyrimidine

A is always bonded to T (U for RNA)
G is always bonded to C

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24
Q

How many H bonds does a G-C nucleotide pairing have?

A

3 H-bonds

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25
Q

How many H bonds does an A-T nucleotide pairing have?

A

2 H-bonds

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26
Q

What makes 2 chains of DNA complimentary?

A

If the bases in each strand match up and can Hbond when the strands are oriented in antiparallel

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27
Q

What is a kilobase pair (Kbp)?

A

dsDNA of 1000 nucleotides long

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28
Q

What is annealing or hybridization?

A

The binding of 2 complementary strands of DNA into a double helix

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29
Q

What do we call The binding of 2 complementary strands of DNA into a double helix ?

A

Annealing or hybridization

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30
Q

What do we call the separation of 2 strands of complementary DNA?

A

Melting or Denaturation

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31
Q

What is melting or denaturation ?

A

The separation of 2 complementary DNA strands

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32
Q

Which are true about dsDNA?

i) If the fraction of purines and total molecular weight of a double helix are known, the amount of cytosine can be calculated

ii) If the amount of G in a ds is known, the amount of C can be calculated

iii) The oligonucleotide ATGTAT is complementary to the oligonucleotide ATACAT

iv) The 2 chains in a piece of dsDNA containing mostly purines will be bonded together more tightly than the 2 chains containing mostly pyrimidines

A

ii and iii are correct

i) Incorrect: the ratio of purines to pyrimidines is always the same (50:50) since each purine (A G) is paired with a pyrimidine (C U T)

ii) Correct: for every G theres a C, for every A theres a T

iii) Correct: strands are antiparallel. A and T pair, G and C pair, and the 5’ end is always written first

iv) Incorrect: ratio is always 50:50. However, 2 chains containing mostly GC pairs will bond more tightly than 2 chains containing mostly AT pairs (3 H-bonds vs 2)

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33
Q

What is Chargoff’s Rule?

A

Concept that tells us how to calculate the # of purines if we know the # of pyrimidines or vice versa

[A] = [T] and [G] = [C]

and [A] + [G] = [T] + [C]

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34
Q

What does it mean when we say that DNA is coiled?

A

It corkscrews in a clockwise motion

Bases are interior

Ribose/ phosphate backbone are exterior

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35
Q

What stabilizes the DNA double helix?

A

Van der Waals interactions between the bases stacked upon each other

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36
Q

Define genome

A

The sum total of al an organisms genetic info

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37
Q

Define a Eukaryote

A

An organism composed of one or more cells containing visibly evident nuclei and organelles

Nucleus enclosed within a nuclear envelope

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38
Q

What do we call pieces of eukaryotic genomes composed of several large pieces of dsDNA?

A

Chromosomes

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39
Q

How many chromosomes do humans have? How many come from each parent?

A

46 chromosomes total
23 from each parent

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40
Q

Define prokaryote

A

bacterial, single celled organism lackign a nucleus and other membrane bound organelles

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41
Q

How are prokaryotic genomes stored?

A

prokaryotic genomes are composed of a single circular chromosome

Viral genomes may be linear or circular DNA or RNA

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42
Q

How many base pairs approximately do human genomes have? Bacterial genomes?

A

Human: over 10^9 base pairs

Bacterial: only 10^6

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43
Q

Is there correlation between genome size and evolutionary sophistication?

A

No. The organisms with largest known genomes are amphibians

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44
Q

Why cant DNA remain as a simple double helix free floating in the cell?

A

It would be bulky and fragile

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45
Q

Define Supercoil.

A

A DNA double helix that has undergone additional twisting since DNA cannot remain as a simple double helix free floating in the cell

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46
Q

What act in prokaryotes is the equivalent to supercoiling in DNA double helixes?

A

prokaryotes have a mechanism to make their single circular chromosome more compact and sturdy

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47
Q

Why would active exonucleases be floating free in the cell?

A

2 potential reasons

1) mRNA has a very short lifespan: degraded rapidly and more is made if protein is still needed.

This is consistent with the idea that regulation of gene expression occurs primarily at the transcriptional level since this is more efficient.

2) Viruses may inject RNA into the cell. If it does not have the correct cap and tail modifications, exonucleases will destroy it

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48
Q

One piece of RNA isolated from a human cell is found to produce two different polypeptides when added to a cell free protein synthesis system containing all the enzymes necessary for eukaryotic gene expression. When the two polypeptides are separated and digested with trypsin, they produce fragments of the following molecular weights:

Polypeptide 1: 5 kD, 8 kD, 12 kD, and 14 kD
Polypeptide 2: 3 kD, 5 kD, 8 kD, 10 kD, 12 kD, and
14 kD

How can we explain the synthesis of two different polypeptides from one piece of RNA?

A

This is an example of the use of splicing for the regulation of gene expression

The piece of RNA must have been hnRNA. In the cell free system it underwent “differential splicing” to produce one of two different mRNA molecules

It appears that polypeptide 1 came from an mRNA which had more material spliced out than the mRNA coding for polypeptide 2.

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49
Q

What is DNA gyrase?

Explain its function.

A

DNA gyrase is an enzyme that uses energy of ATP to twist DNA

Gyrase functions by breaking DNA and twisting the two sides of the circle around each other. This results in a twisted circle like structure composed of dsDNA

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50
Q

Do eukaryotes or prokaryotes have more DNA in their genome?

What does this imply for packing?

A

Eukaryotes do

Therefore requires denser packaging to fit within the cell

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51
Q

What are histones?

A

Globular proteins that eukaryotic DNA is wrapped around for storage

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52
Q

What are the globular proteins that eukaryotes wrap their DNA around for storage called?

A

histones

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53
Q

What are nucleosomes?

A

Bead-looking, composed of DNA wrapped around an octamer of histones (8)

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54
Q

Appearing bead-looking, these are composed of DNA wrapped around an octamer of histones (8).

A

Nucleosomes

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55
Q

What is the name of the space between nucleosomes?

It is a length of double helical DNA

A

Linker DNA

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56
Q

What is Linker DNA

A

It is a length of double helical DNA that makes up the space between nucleosomes

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57
Q

Define Chromatin

A

Fully packed DNA, but not condensed

DNA wrapped around histone proteins or DNA and histone proteins

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58
Q

What do we call fully packed, but not yet condensed DNA?

A

Chromatin

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59
Q

Which bonds make up nucleotides into oligo/polynucleotides ?

A

phosphodiester bonds

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60
Q

Which bonds make up complimentary polynucleotides into DNA double helix?

A

H bonds

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61
Q

DNA double helix + DNA gyrase = ?

A

super coils

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62
Q

Super coils + ____ = nucleosomes

A

8 histones

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63
Q

DNA double helix + _____= super coils

A

DNA gyrase

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64
Q

____ + DNA gyrase = super coils

A

DNA double helix

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65
Q

Super coils + 8 histones = ?

A

nucleosomes

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66
Q

_______ + 8 histones = nucleosomes

A

super coils

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67
Q

Describe the process of compacting DNA double helix to Chomosomes?

A

DNA double helix + DNA gyrase = supercoils

Supercoils + 8 histones= nucleosomes

nucleosomes —> chromatin —> Chromosome

68
Q

What are the differences between chromatin, chromosome, and chromatid?

A

Chromatin: fully packed DNA, not yet condensed

Chromosome: chromatin after it has been condensed

Chromatid: Duplicated chromosome attached at centromere

69
Q

Define centromere

A

The region of the chromosome to which the spindle fibres attach during cell division

70
Q

The region of the chromosome to which the spindle fibres attach during cell division

A

The centromere

71
Q

Define Kinetochores

A

Multi-protein complexes that act as attachment sites for spindle fibres during cell division

72
Q

Multi-protein complexes that act as attachment sites for spindle fibres during cell division

A

Kinetochores

73
Q

Define Spindle Fibres

A

They form a protein structure that divides the genetic material in a cell

These are necessary to equally divide the chromosome in a parental cell into 2 daughter cells during mitosis and meiosis

74
Q

They form a protein structure that divides the genetic material in a cell

These are necessary to equally divide the chromosome in a parental cell into 2 daughter cells during mitosis and meiosis

A

Spindle Fibres

75
Q

What are the 2 main components of centromeres?

A

Heterochromatin and repetitive DNA sequences

76
Q

What is heterochromatin?

A

Chromosome material of different density from normal (usually greater), in which the activity of the genes is modified or suppressed

Compare with euchromatin.

77
Q

What is Euchromatin ?

A

Chromosome material which does not stain strongly except during cell division. It represents the major genes and is involved in transcription.

Compare with heterochromatin.

78
Q

What are the 2 types of “arms” that chromosomes have?

A

p (short) and q (long) arms

79
Q

Describe the metacentric chromosome

A

Even p and q arm distribution

80
Q

Describe the submetacentric chromosome

A

approx 1/3 is p arm

2/3 q arm

81
Q

Describe acrocentric chromosome

A

approx 1/4 is p arm

3/4 is q arm

82
Q

Describe Telocentric chromosome

A

all q arm, no p arm

83
Q

Define telomeres

A

The ends of linear chromosomes

At DNA level these regions are distinguished by a distinct nucleotide sequence repeat 50 to hundreds of times

84
Q

The ends of linear chromosomes

At DNA level these regions are distinguished by a distinct nucleotide sequence repeat 50 to hundreds of times

A

Telomeres

85
Q

a) How long are repeated units in telomeres usually?

b) Which nucleotide are they rich in?

c) What repeated sequence is common in many vertebrates (humans, mice, etc)

A

a) 6-8 bps long, repeated

b) usually Guanine rich

c) 5’ - TTAGGG - 3’

86
Q

Are telomeres composed of single or double stranded DNA? Explain why.

A

Telomeres are composed of both

Single stranded is found at the very end of the chromosome and is approx 300 bp long

It loops to form a knot, held together with many telomere associated proteins

This stabilizes the end of the chromosome.

Specialized telomere cap proteins distinguish telomeres from double stranded breaks so to prevent activation of repair pathways

87
Q

What is the ultimate function of telomeres?

A

To prevent chromosome deterioration and prevent fusion with neighbouring chromosomes

Function as “disposable buffers”, blocking the ends of chromosomes

88
Q

Would prokaryotic DNA have telomeres?

A

No. Many prokaryotes have circular genomes so their DNA does not have telomeres

89
Q

How many autosomes does the human genome have?

A

22

90
Q

How many sex chromosomes do humans have?

A

2 different sex chromosomes

91
Q

How many base pairs does the human genome have?

How many genes does the human genome code for?

A

a) 3.2 billion bps

b) 21, 000 genes

92
Q

What are Intergenic regions? What are they largely composed of?

A

Separate the regions of the human genome with high transcription rates.

Composed of noncoding DNA with no clear function (contains some direction and regulation for genes)

Tandem repeats and Transposons

93
Q

Define Gene

A

A DNA sequence that encodes a gene product

94
Q

What are Single nucleotide Polymorphisms (SNPs or “snips”) ?

A

Single nucleotide variations

Occur once in ever 1,000 bps

Essentially small mutations

95
Q

Single nucleotide variations

Occur once in ever 1,000 bps

Essentially small mutations

A

Single Nucleotide Polymorphisms (SNPs or “snips”)

96
Q

If the size of the human genome is just over 3 billion bps and Single Nucleotide Polymorphisms (SNPs) occur ever 1,000 bps, how many human SNPs are there?

A

3 x 10^9 bps x 1 SNP / 1000bps= 3 x 10^6 SNPs or approx 3 million human SNPs

97
Q

Where do SNPs most often occur?

What happens if an SNP occurs in a coding region of the genome?

A

a) In non coding regions of genome

b) Can lead to specific traits and phenotypes ex. PTC sensitivity

70% of people taste PTC as bitter and 30% dont taste it at all

98
Q

Define Copy Number Variations

A

Structural variations in the genome that lead to different copies of DNA sections

Large regions of genome can be duplicated or deleted

Specific mechanism isnt clear but potentially d/t misalignment of repetitive DNA sequences during synapsis of homologous chromosomes in meiosis

99
Q

How do SNPs (Single Nucleotide Polymorphisms) differ from CNVs (Copy number variation) ?

A

compared to SNPs, CNVs apply to much larger regions of the genome

100
Q

What are the effects of CNVs (copy number variation) ?

A

CNVs are a normal part of our genome but also can be associated with cancer and diseases

Genes involved in immune system function and brain development activity are often enriched in CNVs

101
Q

Define Haploid

Give examples

A

The presence of a single set of chromosomes in an organisms cell

Only the egg and sperm cells in humans are haploid

102
Q

Define Diploid

Give examples

A

The presence of 2 complete sets of chromosomes in an organisms cells, with each parent contributing a chromosome to each set

Humans are diploid. Most of the body’s cells contain 23 chromosome pairs

103
Q

a) What are Tandem Repeats?

b) In which situations are they considered irregular?

c) In which 4 situations do they serve functional purpose?

A

a) Short sequences of nucleotides are repeated one after the other from 3 to over 100 times

b) Repeats can be unstable if the repeating unit is short (di or trinucleotides) or if it is very long. Unstable tandem repeats can lead to chromosome breaks and some are implicated in disease

c) (1) Heterochromatin, (2) centromeres, and (3) telomeres are all rich in repeats

(4) DNA fingerprinting: Tandem repeats vary in length between individuals

104
Q

What is considered, the “template” for production of another nucleic acid: RNA?

A

Genes : sequences of nucleotides

105
Q

What is the difference between transcription and translation of the genetic code?

A

Transcription: the process of reading DNA and writing info as RNA (occurs in the nucleus)
- this CAN produce a final gene product (non coding RNAs) or a messenger molecule (mRNA)
- mRNA is used to construct proteins

Translation: The synthesis of proteins using RNA as template
- accomplished in the cytoplasm (E and P) by the ribosome, a massive enzyme composed of proteins and pieces of rRNA ( ribosomal RNA)

106
Q

What is known as the Central Dogma (Fundamental Law) of molecular biology?

A

DNA –> RNA –> protein

107
Q

What is the smallest codon size that would allow the 4 letter nucleotide alphabet to encode 20 different amino acids?

A

4^1= 4 X
4^2= 16 X
4^3= 64 Correct

3 nucleotides is the minimum codon size

108
Q

Define codon

A

A 3 letter nucleic acid word that codes for a particular amino acid

109
Q

Why is uracil shown on the genetic code chart and why is Thiamine absent?

A

RNA is the nucleic acid that actually encodes protein (for amino acids) during translation and Uracil is only in RNA.

110
Q

Using the Genetic Code Chart:

The codon GTG in DNA is transcribed in RNA as _____, that ribosome translates into which amino acid?

A

the transcribed RNA codon is CAC (complimentary to GTG) which if you look at the chart codes for histidine

111
Q

Using the Genetic Code Chart:

The genetic code was studied by experimenters using a cell free protein synthesis system. All the materials necessary for protein synthesis (Ribosomes, amino acids, tRNA, GTP, ATP) were purified and placed in a beaker. Then synthetic RNA was added and protein was translated from this template. For ex. When synthetic RNA containing only cytosine (CCC…) was added, polypeptides containing only proline (polyproline) resulted. What kind of synthetic RNA would give rise to a mixture of polyproline, polyhistidine, and polythreonine?

A

The RNA would have to be CCACCACCACCACCA…

This yields polyproline if read as CCA CCA CCA CCA

But if read as CAC CAC CAC it would give rise to polyhistidine

If read as ACC ACC ACC ACC it would encode to polythreonine

112
Q

How many codons total are there? How many of them specify amino acids? What do the rest of them do?

A

64 total

61 specify amino acids

The rest (3) are stop codons.

113
Q

Using the Genetic Code:

If the last nucleotide in the codon CUU is changed in a gene that codes for protein, will the protein be affected?

What is the name of this phenomenon?

A

No because CU_ codes for leucine no matter what the 3rd nucleotide is

These 2+ codons that code for the same amino acid are known as synonyms

114
Q

These are 2+ codons that code for the same amino acid.

A

Synonyms

115
Q

What are three aspects of molecular biology that arent explicitly stated in the Central Dogma?

A
  1. Some viruses (retroviruses) make DNA from RNA using the enzyme reverse transcriptae
  2. Info can be transferred other ways (ex. DNA methylation + Post translational modification of proteins can alter gene expression and convey info even though neither is included in the central dogma )
  3. Many final gene products are not proteins but are RNAs instead
116
Q

What is known as the control centre of the cell?

A

The DNA genome

117
Q

What is Replication of DNA?

A

Mitosis produces 2 identical daughter cells from one parental cell

Each daughter must have the same genome as the parent

This is an enzymatic process (much like the Krebs cycle or glycolysis )

118
Q

What is old DNA called in the replication process? New DNA?

A

old: parental DNA
new: Daughter DNA

119
Q

Which scientists did experiments to determine if DNA replication is semiconservative, conservative, or dispersive?

A

Meselson and Stahl

120
Q

Is DNA replication Conservative, Dispresive or Semiconservative?

A

Semiconservative

Individual strands of the double stranded parent are pulled apart then a new daughter strand is synthesized using parental DNA as a template to copy

121
Q

What is Conservative DNA replication?

A

Parental dsDNA remains as is and an entirely new double stranded genome is created

122
Q

What is Dispersive DNA Replication?

A

Both copies of the genomes composed of scattered pieces of new and old DNA.

123
Q

What is semiconservative DNA replication?

A

AFter replication, one strand of the new double helix is parental (old) and one strand is newly synthesized daughter DNA

124
Q

What is helicase?

A

An enzyme that unwinds the double helix and separates the strands of DNA to be replicated

125
Q

What needs to be done to DNA before it can be replicated?

A

Replication cannot occur unless the double helix is uncoiled and separated into 2 single strands by helicase

126
Q

How does helicase know where to begin unwind DNA for replication?

A

IT begins to unwind at a specific location (sequence of nucleotides) on the chromosome called the origin of replication (ORI)

This sequence is found by proteins with tertiary structure to specifically recognize a particular pattern of nucleotides. These scan along chromosomes until they find the ORI and then call in helicase and other enzymes for DNA replication initiation

127
Q

What is the ORI (Origin of replication)?

How is it found in DNA replication?

How does this differ between Eukaryotes and Prokaryotes

A

A sequence of nucleotides on the chromosome that tells helicase where to start unwinding for replication

This sequence is found by proteins with tertiary structure to specifically recognize a particular pattern of nucleotides. These scan along chromosomes until they find the ORI and then call in helicase and other enzymes for DNA replication initiation

Prokaryotes use a protein called DnaA to find the ORI
Eukaryotes have 3 proteins cooperate to find the ORI

128
Q

How is the ORI found in Eukaryotes?

A

3 proteins cooperate to find the ORI

2 of these proteins are synthesized during M and G phases of the cell cycle

These proteins link DNA replication to the cell cycle, ensuring DNA replication doesnt initiate during other phases of the cell cycle

129
Q

What is responsible for replication initiation in prokaryotes?

A

DnaA

130
Q

What are the 2 top problems that helicase create?

What are the structures that resolve these problems?

A

1: When helicase unwinds at ORI, the helix winds tighter up and downstream from the ORI. Without topoisomerase (to unwrap the helix to relieve tension), the chromosome would tangle and eventually break.

131
Q

What is known as an open complex in the replication process?

A

Separated strands ready for replication!

132
Q

What is the role of topoisomerases?

A

Enzymes that cut one or both strands and unwrap the helix, releasing tension created by helicase

133
Q

What is the role of Single stranded binding proteins? (SSBPs)

A

These protect DNA thats been unpackaged in prep for replication and keeps strands separated in an open complex

134
Q

What is the primosome?

A

a protein complex responsible for creating RNA primers for DNA replication

Its central component is RNA polymerase

135
Q

What is RNA polymerase?

A

Enzymes that catalyze the synthesis of DNA/RNA polymers whose sequence is complementary to the original template

136
Q

What is primase ?

A

A type of RNA polymerase: plays role in synthesis of RNA primer

137
Q

Why is primer synthesis by RNA polymerase important for DNA replication?

A

Because the next enzyme, DNA polymerase, cannot start a new DNA chain from nothing, it can only add nucleotides to an existing nucleotide chain

138
Q

What is DNA polymerase and what does it do?

A

DNA pol catalyzes elongation of daughter strand using the parental template

It elongates the primer made by RNA polymerase by adding dNTPs to its 3’ end

139
Q

What direction is the template strand READ in for DNA replication?

A

If the daughter strand must be made 5’ to 3’, and the opposite strand must be read for it to be complementary and antiparallel, the template must be read 3’ to 5’

140
Q

What is the replisome? What are its three main components?

A

This is a large complex of proteins
It carries out replication of DNA

  1. helicase
  2. DNA polymerase
  3. Primase
141
Q

Does prokaryotic or Eukaryotic replisome contain more components? Why?

A

Eukaryotic has more proteins

Additional complexity in eukaryotic system required because replication machinery must also unwind DNA from histone proteins

142
Q

In the process of replication, do primers on both sides elongate strands towards the same direction? or opposite? why?

A

The primers will elongate towards opposite ends of the chromosome because the template strands are antiparallel

143
Q

Which structure in replication checks each new nucleotide to make sure the correct base pair has been formed before incorporating into the growing polymer?

A

DNA polymerase

144
Q

What process is the thermodynamic driving force for the polymerization reaction in DNA replication?

A

The removal and hydrolysis of pyrophosphate from each dNTP added to the chain

145
Q

List the 7 replication rules to remember

A
  1. DNA replication is semiconservative
  2. Polymerization occurs in the 5’ to 3’ direction without exception
  3. DNA pol requires a template
  4. DNA pol requires a primer
  5. Replication forks grow away from the origin in both directions
  6. Leading strand replication is continuous. Lagging strand replication is discontinuous
  7. All RNA primers are eventually replaced by DNA
146
Q

What direction does polymerization occur in?

A

5’ to 3’

147
Q

Does replication proceed away or towards the origin of replication?

A

Away from the ORI

148
Q

Define Replication forks

A

The areas where the parental double helix continues to unwind

149
Q

Which strand must wait for the replication fork to widen before continuing to polymerize?

Which strand grows leading into the replication fork?

A

Lagging strands

Leading strand

150
Q

What are Okazaki Fragments?

A

Small chunks of DNA comprising the lagging strand

151
Q

As the replication forks grow, does helicase have to continue to unwind the double helix and separate the strands?

A

Yes

152
Q

What joins Okazaki Fragments ?

A

DNA Ligase

153
Q

How many DNA polymerase enzymes do eukaryotes have?

How many do Prokaryotes have? What are they?

A

a) several different DNA polymerase enzymes

b) 5: DNA Polymerase I, II, III, IV, and V

(only really need to know functions of I and III

154
Q

DNA pol III function in prokaryotes

What special function does it have?

A

Responsible for the super fast, super accurate elongation of the leading strand

Has 5’ to 3’ polymerase activity but also 3’ to 5’ exonuclease activity

155
Q

What is exonuclease?

What are the 2 important types ? How do they differ?

A

A function of Prokaryotic DNA pol I and III

Can cut a polynucleotide chain in the middle of the chain, usually a particular sequence. Means “to cut a nucleic acid chain”

Two important types are repair enzymes and restriction enzymes:
- Repair enzymes: remove chemically damaged DNA from the chain
- Restriction enzymes: Endonucleases found in bacteria. Destroy DNA of infecting viruses, restricting the host range of the virus

156
Q

Proofreading function

A

3 to 5 exonuclease activity in which the enzyme moves backwards to chop off the nucleotide it just added if incorrect

The ability to correct mistakes in this way

157
Q

Prokaryotic DNA pol III is most known as ____

Prokaryotic DNA pol I is important for ____

A

Replicative enzyme. Has no known function in repair

Excision repair `=

158
Q

Roles of prokaryotic DNA pol II, IV, and V

A

II: Has 5’ to 3’ activity and 3’ to 5’ proofreading function. Participates in DNA repair pathways and backup for DNA pol III

IV and V: Both are error prone in 5’ to 3’ polymerase activity. These function to stall other polymerase enzymes at replication forks when DNA repair pathways have been activated, an important part of prokaryotic checkpoint pathway

159
Q

If a bacterium has a mutation in the gene for DNA pol III resulting in an enzyme without the 3’ to 5’ exonuclease activity, will mutations occur more often than in bacteria with a normal DNA pol gene

A

Yes: the 3’ to 5’ exonuclease functions to edit polymerase’s work

without editing, many more point mutations would occur due to incorporation of the wrong nucleotides. Normal polymerase is very adept at sensing correct bps and removing bases that dont belong

160
Q

What do we call prokaryotic replication, based on the shape its chromosome takes on?

A

Replication of prokaryotes is said to proceed by the theta mechanism and is called theta replication

Prokaryotes have 1 chromosome which is circular and so as replication proceeds, the partially duplicated genome starts looking like the greek letter theta

161
Q

In Eukaryotic Replication, when many replicating forks continue to widen, they create the appearance of bubbles along the DNA strand referred to as ______

A

replication bubbles

Eventually replication forks meet and the separate daughter strands are ligated together

162
Q

Replication Bubbles in Eukaryotic Replication

A

when many replicating forks continue to widen, they create the appearance of bubbles along the DNA strand

This is because Eukaryotic Chromosomes are large and so they have many origins to start the replication process

163
Q

What are telomeres and how do they function?

A

Telomeres are disposable repeats at the ends of chromosomes

These are consumed and shorten during cell division. When they become too short, the chromosome can no longer replicate —-> result: cells can activate DNA repair pathways, enter a senescent state, or activate apoptosis

164
Q

What does it mean if a cell enters a senescent state?

A

Biological aging, the gradual deterioration of functional characteristics in living organisms: alive but not dividing

Something that can happen when telomeres at the ends of chromosomes become too short to a critical length where the chromosome can no longer replicate. Many age related diseases are linked to telomere shortening

165
Q

What is the Hayflick limit ?

A

The number of times a normal human cell type can divide until telomere length stops cell division

166
Q

Telomerase

A

An enzyme that adds repetitive nucleotide sequences to the ends of chromosomes thus lengthening telomeres

Is a robinucleoprotein complex, contains an RNA primer, and reverse transcriptase enzymes (generates complimentary DNA from RNA template)

167
Q

In most organisms, telomerase is only expressed in what types of cells?

A

embryonic stem cells (germ line)

some WBCs

Cancer cells: helps cells immortalize, allowing the bypass of senescence and apoptosis

MCAT Biology Review (3 decks)

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