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Nuclear structures
  • Chromosomes
    • 46 in humans (23 pairs)
      • 22 pairs of autosomes, 1 pair of sex chromosomes
    • contains DNA and RNA
  • Deoxyribonucleic acid (DNA)
    • Thymine, adenine, guanine, and cytosine
      • adenine linked to thymine (A-T)
      • guanine linked to cytosine (G-C)
    • double stranded
    • strands linked together by phosphate groups
    • 2' hydrogen group
    • regulates cell division
    • mRNA is produced from DNA
      • an exon is portion of gene that codes for mRNA
      • exon is expressed
  • Gene
    • segment of DNA that contains the information needed to synthesize a protein
    • determines the unique biologic qualities of a cell
    • exon
      • coding information 
    • intron
      • does not code for mRNA
  • Ribonucleic acid (RNA)   
    • usually single stranded but can be double stranded
      • double stranded RNA found in some viruses
      • certain interactions between single stranded RNA in human cells can form double stranded RNA
    • has ribose sugar
    • Uracil, adenine, guanine, and cytosine (no thymine)
    • less stable than DNA
    • 2' hydroxyl group
    • can be located in either the nucleus or cytoplasm
    • messenger RNA (mRNA)
      • translates DNA information into protein
    • ribosomal RNA (rRNA)
      • major part of ribosome, which helps synthesize a protein
    • transfer RNA (tRNA)
      • transfers amino acids to mRNA
Genetic Terms
  • Nucleotides
    • thymine, adenine, guanine, and cytosine
  • Codon
    • sequence of three nucleotides
    • each codon correlates to one of the 20 amino acids
    • linking of the amino acids create a protein
  • Gene promotor
    • regulatory portion of DNA that controls initiation of transcription
  • Gene enhancers
    • site on DNA that transcription factors bind to
    • regulate transcription
  • Transcription 
    • DNA => mRNA
  • Translation 
    • mRNA => protein
  • Haploid
    • Haploid is the amount of DNA in a human egg or sperm cell (half the amount of DNA in a normal cell)
Cell Cycle
  • Phases 
    • G0
      • represents a "stable" phase
      • cells are diploid (2N) in the G0 and G1 phases
    • G1
      • initial growth phase
      • cells are diploid (2N) in the G0 and G1 phases
    • S
      • DNA replication/synthesis phase 
      • cells become tetraploid (4N) at the end of S and for the entire G2 phases
    • G2
      • gap phase
      • cells become tetraploid (4N) at the end of S and for the entire G2 phases
    • M
      • mitosis phase
Apoptosis
  • Defined as programmed cell death
  • Requires a series of intracellular signaling events
  • Different from cell lysis - where a cell releases its contents into the surrounding area
  • One hallmark of cancer is the cell's loss of apoptosis 
Research techniques
  • Agarose gel electrophoresis
    • separates DNA based on size
    • DNA is negatively charged
    • gel exposed to electric field
    • smaller pieces moves through gel faster
  • Southern blotting
    • restriction enzymes cut up DNA
    • separate on agarose gel
    • identifies DNA sequence
  • Northern blotting
    • restriction enzymes cut up RNA
    • separate on agarose gel
    • identifies RNA sequence
  • Western blotting
    • SDS-PAGE gel
    • identifies protein
  • DNA ligation
    • combining different DNA fragments not found together naturally to create recombinant DNA
  • Plasmid vector
    • an extrachromosomal element, often circular, that can replicate and be transferred independently of the host chromosome 
    • one example of the function of a plasmid is antibiotic resistance
    • can be introduced into bacteria in the process of transformation
  • Polymerase chain reaction (PCR)
    • DNA => DNA
    • a molecular biology tool used to generate many copies of a DNA sequence 
    • uses "primers" specific to a segment of DNA
    • requires temperature-mediated enzyme DNA polymerase
  • Reverse transcription polymerase chain reaction (RT-PCR) 
    • RNA => DNA
    • variant of polymerase chain reaction (PCR) used in molecular biology to generate many copies of a DNA sequence from fragments of RNA
    • RNA strand is first reverse transcribed into its DNA complement
    • amplification of the resulting DNA proceeds using polymerase chain reaction
 

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(OBQ07.157) What is the post-amplification product of reverse transcription polymerase chain reaction (RT-PCR)? Review Topic

QID:818
1

RNA

34%

(452/1326)

2

DNA

58%

(771/1326)

3

Protein

6%

(84/1326)

4

Mitochondria

0%

(6/1326)

5

Immunoglobulins

1%

(11/1326)

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PREFERRED RESPONSE 2

Reverse transcription polymerase chain reaction (RT-PCR) is a variant of polymerase chain reaction (PCR) used in molecular biology to generate many copies of a DNA sequence from fragments of RNA. The RNA strand is first reverse transcribed into its DNA complement, followed by amplification of the resulting DNA using polymerase chain reaction. Polymerase chain reaction amplifies short segments of DNA by using the temperature stable DNA polymerase enzyme.


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(OBQ07.178) DNA replication occurs during which phase of the cell cycle? Review Topic

QID:839
1

M

15%

(90/593)

2

S

56%

(331/593)

3

R

11%

(68/593)

4

G1

11%

(66/593)

5

G2

6%

(33/593)

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PREFERRED RESPONSE 2

The cell cycle consists of four distinct phases: initial growth (G1), DNA replication/synthesis (S), a gap (G2), and mitosis (M) (see illustration).

The G1 and G2 phases of the cell cycle represent the “gaps” or growth phases in the cell cycle that occur between DNA synthesis and mitosis. G0 cells are in a stable state and have not entered the cell cycle. During the S phase, the DNA is synthesized and replicated. During the M phase or mitosis, all genetic material divides into two daughter cells.

The cells are diploid (2N) in the G0 and G1 phases. The cells become tetraploid (4N) at the end of S and for the entire G2 phases. There is no R phase in the cell cycle.

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(OBQ05.122) All of the following statements regarding RNA are true EXCEPT? Review Topic

QID:1008
1

RNA uses thymine while DNA uses uracil

65%

(190/292)

2

RNA may be either single or double-stranded

12%

(34/292)

3

RNA has a hydroxyl group at the 2' position in the ribose

9%

(26/292)

4

DNA has a hydrogen group at the 2' position in the deoxyribose

7%

(21/292)

5

RNA helix is of A-Form

7%

(19/292)

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PREFERRED RESPONSE 1

All of the statement listed are true EXCEPT for "RNA uses thymine while DNA uses uracil" which is a false statement.

There are two types of nucleic acids: Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The DNA contains the genetic codes to make RNA and the RNA in turn then contains the codes for the primary sequence of amino acids to make proteins. The DNA bases are thymine, adenine, guanine, and cytosine (TAGC). RNA bases are uracil, adenine, guanine, and cytosine (UAGC). DNA is double-stranded, whereas RNA may be either single or double-stranded. DNA has a hydrogen group instead of a hydroxyl group at the 2’ position in the ribose. DNA is only located in the nucleus, whereas RNA is found in the nucleus and the cytoplasm in the form of mRNA. RNA helix geometry is of A-Form whereas DNA helix is of B-Form.

Musgrave et al discuss important gene therapy and tissue engineering issues in orthopaedic surgery. Specific areas of musculoskeletal medicine where gene therapy and tissue engineering have shown promise and early treatment success include the areas of bone healing, cartilage repair, intervertebral disk pathology, and skeletal muscle injuries.

Incorrect Answers:
Answer 1: False - DNA uses thymine while RNA uses uracil.
Answer 2: True - RNA may be either single or double-stranded
Answer 3: True - RNA has a hydroxyl group instead of hydrogen group at the 2' position in the ribose
Answer 4: True - DNA has a hydrogen group at the 2' position in the deoxyribose
Answer 5: True - RNA helix is of A-Form


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(OBQ04.195) Tumor necrosis factor receptor 1 is involved in which of the following cellular events? Review Topic

QID:1300
1

Replication

4%

(25/623)

2

Agenesis

1%

(6/623)

3

Apoptosis

93%

(577/623)

4

Senescence

2%

(10/623)

5

Ectopy

0%

(3/623)

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PREFERRED RESPONSE 3

Apoptosis is defined as a sequence of events leading to programmed cell death. A cell undergoing apoptosis goes through a series of signaling events in which the cell disposes of itself in a neat and orderly manner. This is in contrast to cell lysis where the cell is destroyed, releasing its contents (including harmful enzymes) and DNA material which is toxic to neighboring cells.

Ashkenazi et al present a review of apoptosis, including the biochemical mechanism behind the programming. They note that the death receptors Fas and tumor necrosis factor receptor 1 (TNFR1) trigger apoptosis upon engagement by their cognate death ligands.

Illustration A shows a diagram of apoptosis, including the cellular mechanisms.

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(OBQ04.199) Which of the following statements best describes a plasmid? Review Topic

QID:1304
1

An extrachromosomal, circular piece of DNA that replicates independently of host DNA

87%

(283/326)

2

An extrachromosomal, linear piece of RNA which replicates independently of host DNA

8%

(26/326)

3

A protein which promotes transcription of DNA to RNA

5%

(15/326)

4

A gene which leads to cancerous cell transformation

0%

(1/326)

5

A gene which suppresses cancerous cell transformation

0%

(1/326)

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PREFERRED RESPONSE 1

A plasmid is an extrachromosomal circular piece of DNA that replicates independently of host DNA.

In nature, plasmids frequently carry genes that may benefit the survival of the organism, such as antibiotic resistance genes. Artificially, plasmids are frequently used as vectors to introduce genes into a cell and change genetic expression. This has potential therapeutic benefits for the treatment of arthritis and bone healing.

Whalen et al. discuss various methods for transferring therapeutic genes into an arthritic joint. These include gene transfer through a vector inserted directly into a joint, and indirect transfer where synovial cells are isolated and genetically modified using vectors, then transplanted back into the joint.

Lieberman et al. present a review discussing the potential future benefits of gene transfer in bone healing, spine fusion, and articular cartilage repair.

Illustration A shows a visual representation of a plasmid. Note how the plasmid is extrachromosomal and the structure is identical to that of the host DNA. Video V is an educational video that gives an overview on plasmids.

Incorrect Answers:
Answer 2: A plasmid is a small piece of DNA, not RNA.
Answer 3: This defines a trancription factor.
Answer 4: This defines an oncogene.
Answer 5: This defines a tumor suppressor gene.

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