DNA and Gene Expression

1. What is DNA?

DNA (deoxyribonucleic acid) is a molecule that carries genetic information and instructions for growth, development, functioning, and reproduction of all living organism

2. What is DNA made up of?

DNA is made up of nucleotides, which consist of a sugar (deoxyribose), a phosphate group, and a nitrogenous base.

3. What shape is DNA?

DNA has a double helix shape, resembling a twisted ladder.

4. What is each nucleotide made up of?

Each nucleotide is made up of three components: a deoxyribose sugar, a phosphate group, and a nitrogenous base

5. What is the backbone of DNA?

The backbone of DNA consists of alternating sugar (deoxyribose) and phosphate groups.

6. How are the rungs of the ladder connected together?

The rungs of the ladder are connected by hydrogen bonds between complementary nitrogenous bases.

7. What are the four nitrogen bases?

The four nitrogen bases are adenine (A), thymine (T), guanine (G), and cytosine (C).

8. How do the nitrogenous bases of DNA pair?

The nitrogenous bases pair according to complementary base pairing rules: adenine pairs with thymine (A-T), and guanine pairs with cytosine (G-C).

9. What do the sequence of bases code?

The sequence of bases codes for genetic information that determines traits and directs protein synthesis.

10. How does Biotechnology use DNA's stability and reproducibility?

Biotechnology uses DNA's stability to store genetic information reliably and its reproducibility through replication to clone genes, create genetically modified organisms, and produce proteins.

What does understanding the structure of dna allow

Understanding the structure of DNA allows scientists to manipulate genes, diagnose genetic diseases, develop treatments, create GMOs, and conduct forensic analysis.

When does DNA replication occur

DNA replication occurs during the S phase of the cell cycle, before cell division.

What is semiconservative replication

Semiconservative replication is when each new DNA molecule contains one original strand and one newly synthesized strand.

14. How does the DNA double helix unwind?

The DNA double helix unwinds when the enzyme helicase breaks the hydrogen bonds between base pairs, separating the two strands.

15. What is the replication fork?

The replication fork is the Y-shaped region where the DNA double helix is unwound and new strands are synthesized.

16. What is the leading strand?

The leading strand is the DNA strand that is synthesized continuously in the 5' to 3' direction toward the replication fork.

17. What is the lagging strand?

The lagging strand is the DNA strand that is synthesized discontinuously in short fragments (Okazaki fragments) away from the replication fork.

18. What type of DNA does bacteria have?

Bacteria have circular, double-stranded DNA located in the nucleoid region, plus smaller circular DNA molecules called plasmids.

19. What is DNA polymerase?

DNA polymerase is an enzyme that synthesizes new DNA strands by adding nucleotides complementary to the template strand during replication.

20. What is the Origin Recognition Complex?

The Origin Recognition Complex (ORC) is a protein complex that binds to origins of replication and initiates DNA replication in eukaryotic cells.

21. What is Helicase?

Helicase is an enzyme that unwinds the DNA double helix by breaking hydrogen bonds between base pairs at the replication fork.

22. What is the purpose of the template DNA?

The template DNA serves as a pattern for synthesizing a new complementary DNA strand during replication.

What is the the replication bubble

The replication bubble is a region where DNA replication is occurring, with two replication forks moving in opposite directions from an origin of replication.

24. What is the replication fork?

The replication fork is the Y-shaped structure formed when DNA unwinds during replication, where new DNA strands are synthesized.

25. What are topoisomerases?

Topoisomerases are enzymes that relieve tension and prevent supercoiling ahead of the replication fork by cutting and rejoining DNA strands.

What are single strand binding proteins

Single-strand binding proteins (SSBPs) bind to separated DNA strands during replication to prevent them from reannealing or forming secondary structures.

27. What are RNA primers?

RNA primers are short RNA sequences synthesized by primase that provide a 3'-OH group for DNA polymerase to begin DNA synthesis.

28. What is primase?

Primase is an enzyme that synthesizes short RNA primers needed to initiate DNA replication.

29. What are Okazaki fragments?

Okazaki fragments are short DNA segments synthesized discontinuously on the lagging strand during DNA replication.

30. What is DNA ligase?

DNA ligase is an enzyme that joins Okazaki fragments together by forming phosphodiester bonds between adjacent nucleotides on the lagging strand.

31. What are histone proteins?

Histone proteins are proteins around which DNA wraps to form nucleosomes, helping to package and organize DNA in eukaryotic cells.

32. What are histones?

Histones are positively charged proteins that DNA coils around to form chromatin structure in eukaryotes.

33. What are nucleosomes?

Nucleosomes are the basic units of DNA packaging, consisting of DNA wrapped around a core of eight histone proteins.

34. What is chromatin?

Chromatin is the complex of DNA and proteins (mainly histones) that makes up chromosomes in eukaryotic cells.

35. What are euchromatin?

Euchromatin is loosely packed chromatin that is transcriptionally active and accessible for gene expression.

36. What are heterochromatin?

Heterochromatin is tightly packed chromatin that is transcriptionally inactive and not readily accessible for gene expression.

Who discovered transformation

Frederick Griffith discovered transformation in 1928 through his experiments with Streptococcus pneumoniae bacteria.

38. When was transformation discovered?

Transformation was discovered in 1928 by Frederick Griffith.

39. What was the end conclusion of DNA transformation?

The conclusion was that DNA is the hereditary material responsible for transformation, as DNA from dead pathogenic bacteria could transform living non-pathogenic bacteria.

40. What is transcription?

Transcription is the process of copying genetic information from DNA to RNA, specifically producing messenger RNA (mRNA).

41. What is mRNA?

mRNA (messenger RNA) is a type of RNA that carries genetic information from DNA to ribosomes for protein synthesis.

42. What is a ribose phosphate backbone?

A ribose phosphate backbone is the structural framework of RNA, consisting of alternating ribose sugars and phosphate groups.

43. What is a codon?

A codon is a three-nucleotide sequence on mRNA that codes for a specific amino acid or a stop signal during translation.

44. What is a polypeptide?

A polypeptide is a chain of amino acids linked by peptide bonds that will fold to form a protein.

45. What is an enzyme?

An enzyme is a biological catalyst, usually a protein, that speeds up chemical reactions in living organisms.

46. What is the central dogma of molecular biology?

The central dogma of molecular biology states that genetic information flows from DNA to RNA to protein (DNA → RNA → Protein).

47. Why is it important to understand the structure of RNA in biotechnology?

Understanding RNA structure is important because RNA is involved in gene expression, can be used for gene therapy, RNA interference, vaccine development (mRNA vaccines), and developing treatments for genetic diseases.

48. How are RNA used to treat disease and create new therapies?

RNA can be used in therapies such as mRNA vaccines, antisense oligonucleotides to block disease-causing genes, siRNA for gene silencing, and CRISPR guide RNAs for gene editing.

49. What makes RNA unstable?

RNA is unstable due to the presence of a 2'-OH group on the ribose sugar, which makes it more susceptible to hydrolysis, and because it is usually single-stranded.

50. What is the ribose-phosphate backbone?

The ribose-phosphate backbone is the structural framework of RNA consisting of alternating ribose sugars and phosphate groups connected by phosphodiester bonds.

51. What makes DNA more stable?

DNA is more stable because it lacks the 2'-OH group on the sugar (has deoxyribose instead), is double-stranded which protects bases, and forms a more stable double helix structure.

52. When does uracil pair with thymine?

Uracil does not pair with thymine. Uracil replaces thymine in RNA and pairs with adenine (A-U pairing in RNA).

53. What are the three key differences between RNA and DNA?

The three key differences are: (1) RNA has ribose sugar while DNA has deoxyribose, (2) RNA contains uracil instead of thymine, (3) RNA is usually single-stranded while DNA is double-stranded.

54. What is messenger RNA?

Messenger RNA (mRNA) is RNA that carries genetic information from DNA in the nucleus to ribosomes in the cytoplasm for protein synthesis.

55. What is a codon?

A codon is a sequence of three nucleotides on mRNA that specifies which amino acid will be added during protein synthesis or signals start/stop.

56. What are amino acids?

Amino acids are the building blocks of proteins, consisting of an amino group, a carboxyl group, and a variable side chain.

57. What is an anticodon?

An anticodon is a three-nucleotide sequence on tRNA that is complementary to a specific codon on mRNA.

58. What do tRNA molecules do?

tRNA (transfer RNA) molecules transport specific amino acids to the ribosome during translation and match them to the appropriate codons on mRNA.

59. What does the cloverleaf shape of tRNA allow?

The cloverleaf shape of tRNA allows it to have both an anticodon region to bind to mRNA and an amino acid attachment site, enabling it to function as an adaptor molecule.

60. What is the small ribosomal subunit?

The small ribosomal subunit is the smaller of two ribosomal components that binds to mRNA and helps decode the genetic message.

61. What is the large ribosomal subunit?

The large ribosomal subunit is the larger ribosomal component that catalyzes peptide bond formation between amino acids.

62. What do ribosomes do?

Ribosomes are cellular structures that facilitate protein synthesis by reading mRNA and assembling amino acids into polypeptide chains.

63. Why is it important to understand transcription?

Understanding transcription is important because it's the first step in gene expression, helps explain how genes are regulated, is crucial for understanding genetic diseases, and is a target for therapeutic interventions.

64. What is RNA polymerase?

RNA polymerase is an enzyme that synthesizes RNA by reading a DNA template strand and assembling complementary RNA nucleotides.

65. What is mRNA?

mRNA (messenger RNA) is the RNA molecule that carries protein-coding information from DNA to ribosomes.

66. What are exons?

Exons are the coding sequences of a gene that remain in the mature mRNA after splicing and are translated into protein.

67. What are introns?

Introns are non-coding sequences of a gene that are removed from the primary RNA transcript during splicing before translation.

What is the 5 cap

The 5' cap is a modified guanosine nucleotide added to the 5' end of eukaryotic mRNA that protects it from degradation and aids in ribosome binding.

What is the poly a tail

A Poly-A tail is a string of adenine nucleotides added to the 3' end of eukaryotic mRNA that protects it from degradation and aids in translation.

70. What percent of human genetic diseases is due to improper RNA splicing?

Approximately 15-60% of human genetic diseases are caused by mutations affecting RNA splicing.

71. What is the ribosomal complex?

The ribosomal complex is the structure formed by the large and small ribosomal subunits that come together to translate mRNA into protein.

72. During translation, what happens at initiation?

During initiation, the small ribosomal subunit binds to mRNA at the start codon (AUG), the initiator tRNA carrying methionine binds to the start codon, and the large ribosomal subunit joins to form the complete ribosome.

73. During translation, what happens at elongation?

During elongation, tRNA molecules bring amino acids to the ribosome, the ribosome moves along mRNA reading codons, and peptide bonds form between amino acids to build the polypeptide chain.

74. During translation, what happens at termination?

During termination, the ribosome reaches a stop codon (UAA, UAG, or UGA), release factors bind to the stop codon, the completed polypeptide is released, and the ribosomal subunits dissociate from mRNA.

75. Why is gene regulation important?

Gene regulation is important because it controls when and how much protein is produced, allows cells to respond to environmental changes, enables cell differentiation, and conserves cellular energy and resources.

What is the regulator gene

The regulator gene is a gene that codes for a regulatory protein (repressor or activator) that controls the expression of other genes.

What is the promoter region

The promoter region is a DNA sequence where RNA polymerase binds to initiate transcription of a gene.

78. What is the operator region?

The operator region is a DNA sequence where regulatory proteins (repressors) bind to block or allow transcription of adjacent genes.

79. What is an inducer?

An inducer is a molecule that triggers gene expression by inactivating a repressor protein, allowing transcription to occur.

80. What is the repressor protein?

The repressor protein is a regulatory protein that binds to the operator region to prevent transcription of genes.

87. What is polymerase chain reaction?

Polymerase chain reaction (PCR) is a laboratory technique used to amplify specific DNA sequences, making millions of copies from a small sample.

88. How did PCR revolutionize medicine?

PCR revolutionized medicine by enabling rapid disease diagnosis, genetic testing, forensic analysis, paternity testing, detection of infectious agents, and personalized medicine approaches.

What is the starting material for PCR

The starting material for PCR is a DNA sample containing the target sequence to be amplified, along with primers, nucleotides (dNTPs), DNA polymerase, and buffer solution.

90. What are PCR tubes?

PCR tubes are small plastic tubes designed to withstand rapid temperature changes and hold the reaction mixture during PCR amplification.

91. What are primers?

Primers are short single-stranded DNA sequences (15-30 nucleotides) that are complementary to the target DNA and provide a starting point for DNA polymerase.

92. Where does the forward primer bind?

The forward primer binds to the 3' end of the template strand (antisense strand) in the 5' to 3' direction.

93. Where does the reverse primer bind?

The reverse primer binds to the 3' end of the complementary strand (sense strand) in the 5' to 3' direction.

94. What are dNTPs?

dNTPs (deoxynucleotide triphosphates) are the building blocks of DNA, including dATP, dTTP, dGTP, and dCTP, used by DNA polymerase to synthesize new DNA strands.

95. What is Taq polymerase?

Taq polymerase is a heat-stable DNA polymerase enzyme isolated from the bacterium Thermus aquaticus that can withstand the high temperatures used in PCR.

96. Where is Taq polymerase isolated from?

Taq polymerase is isolated from Thermus aquaticus, a thermophilic bacterium found in hot springs.

97. What does thermostable mean?

Thermostable means able to remain stable and functional at high temperatures without denaturing or losing activity.

98. What are the three steps of PCR?

The three steps of PCR are: (1) Denaturation - heating to separate DNA strands, (2) Annealing - cooling to allow primers to bind, (3) Elongation - DNA polymerase synthesizes new strands.

99. What temperature does denaturation happen at?

Denaturation happens at approximately 94-96°C (201-205°F).

What happens during denaturization

During denaturation, the double-stranded DNA is heated to break hydrogen bonds between base pairs, separating the DNA into two single strands.

101. What temperature does annealing happen at?

Annealing happens at approximately 50-65°C (122-149°F), depending on the primer sequences.

102. What happens during annealing?

During annealing, the temperature is lowered to allow primers to bind (hybridize) to their complementary sequences on the single-stranded DNA template.

103. What temperature is elongation at?

Elongation occurs at approximately 72°C (162°F), the optimal temperature for Taq polymerase activity.

104. What happens during elongation?

During elongation, Taq polymerase synthesizes new DNA strands by adding dNTPs complementary to the template strand, extending from the primers.

105. How does PCR exponentially amplify DNA?

PCR exponentially amplifies DNA because each cycle doubles the number of DNA copies, resulting in 2^n copies after n cycles (e.g., 30 cycles produce over 1 billion copies).

106. What is the importance of recombinant DNA technology?

Recombinant DNA technology is important for producing insulin and other medicines, creating genetically modified organisms, gene therapy, studying gene function, and developing vaccines.