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Biochemistry Exam #4 > Genetics/Molecular Biology Basics > Flashcards

Genetics/Molecular Biology Basics Flashcards

1
Q

Define gene

A

Gene: functional unit of DNA on a chromosome

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2
Q

What do coding regions contain? What do non-coding regions contain (2)?

A

Coding region contain…
- Exons: DNA sequence that encodes the final protein product

Non-coding regions contain…

  • Introns: spliced out because do not contain DNA sequence
  • Regulatory information: promoter or terminator sequence
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3
Q

What is the start and end of a gene? Which of the regulatory information is found on each end?

A

Start: 5’ end
- Promoter sequence found

End: 3’ end
- Terminator sequence found

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4
Q

Define allele

A

Variant form of a gene that is created by a mutation in the DNA sequence (ex. considered alleles if genes are NOT 100% identical from mother and father)

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5
Q

What is the difference between a polymorphism and a mutation?

A

Polymorphism: common variants in DNA sequence - occur in over 1% of population

Mutation: very rare change in DNA sequence of an individual

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6
Q

What are the two types of polymorphisms?

A
  • SNPs (Single Nucleotide Polymorphisms): single base change; reason for much of the variation found between individuals (i.e. height, skin color, etc)
  • Repeat Polymorphism: repeat segments of a sequence that are common and inherited; vary in the number of repeats of a specific sequence
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7
Q

What are the three classifications of Repeat Polymorphisms, and how many base pairs are typically repeated with each?

A
  • STRPs (Short Tandem Repeat Polymorphisms: 2-5 base pairs repeated
  • VNTRs (Variable Number Tandem Repeats): 14-500 base pairs repeated
  • CNVs (Copy Number Variations): over 1000-2 million base pairs repeated
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8
Q

What can examination of Repeat Polymorphisms be used for? Which classification of Repeat Polymorphisms is most often used?

A

Molecular Fingerprinting can be used to examine the number of repeats of a sequence, then use this information for identification
- Examples are paternity testing and CODIS

Variable Number Tandem Repeats are often used (4-500 base pairs repeated)

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9
Q

What are the three primary types of mutations? Describe each

A
  • Point mutation: base substitution
  • Insertion mutation: 1+ base pairs added
  • Deletion mutation: 1+ base pairs removed
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10
Q

What are the two cell types that mutations can be found in? Which can be passed onto future generations?

A
  • Germline cells (gametes): CAN be passed on to next generation
  • Somatic cells (all other cells): can NOT be passed on
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11
Q

What are the three types of point mutations? Describe each

A
  • Missense mutation: wrong amino acid added
  • Nonsense mutation: new stop codon added (early termination)
  • Silent mutation: base change that does not change the amino acid
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12
Q

What are the two types of insertion/deletion mutations? Describe each and the affect this may have on codon reading

A
  • Frameshift mutation: insertion/deletion of 1-2 base pairs; all codons past the insertion/deletion point are read in the wrong frame
  • In-frame mutation: insertion/deletion of 3 base pairs; extra AAs are added/deleted but remaining codons are read correctly
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13
Q

What are the five effects of mutations? Describe each

A
  • Lethal mutations: death during development of before reaching reproductive age
  • Conditional mutations: disease symptoms only manifest under specific environmental conditions
  • Loss-of-function mutations: partial or complete loss of gene function
  • Gain-of-function mutations: increased protein activity, new protein function OR a protein being expressed in new cellular location (often negative)
  • Dominant negative mutations: mutant gene allele produces a protein that interferes with the activity of the normal protein produced by the other allele
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14
Q

What is the central dogma of biology?

A

DNA to RNA via transcription

RNA to protein via translation

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15
Q

Describe the five features of double-stranded DNA

A
  • 5’ end (contains a free terminal phosphate group)
  • 3’ end (contains an -OH group)
  • Antiparallel arrangement: 2 strands that run in opposite directions
  • Phosphodiester backbone
  • Hydrogen bonds between base pairs
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16
Q

What is complementary base pairing and what two things does it ensure?

A

Complementary base pairing is hydrogen bonding between specific nucleic acid pairs

  • Ensures double-stranded DNA can be duplicated during cell division
  • Ensures that each strand of DNA can be used as a template for transcription of DNA to RNA
17
Q

What are the complementary base pairs found in DNA? What are the complementary base pairs found in RNA?

A
  • DNA: A-T and C-G

- RNA: A-U and C-G

18
Q

How do restriction enzymes play a role in cloning genes?

A

Restriction enzymes are used to cleave specific sections of double-stranded DNA at specific sites, as well as use those same restriction enzymes to cleave specific sites of a DNA strand from another organism

19
Q

What are the three steps of making recombinant DNA? Describe each in detail

A
  1. Digest: plasmid vector is digested with two different restriction enzymes to open it up and create 2 sticky ends; a foreign piece of DNA is also digested by the same two restriction enzymes to provide the same sticky ends on that DNA
  2. Ligate: gene of interest is inserted into same spot on vector using sticky ends - Ligase seals the breaks in the phosphodiester bonds
  3. Transform: introduce (transform) the recombinant plasmid into bacteria
20
Q

What is Gel Electrophoresis and how does this occur?

A
  • Agarose is used to create gels, and an electrical field is added
  • DNA is drawn to the positive end due to their negative phosphate backbone – DNA stops/separates depending on size as it goes down the field
21
Q

What does PCR stand for and what is this technique used for? Describe the process in four steps

A

PCR is Polymerase Chain Reaction and it is used to create more copies of a specific DNA segment

  1. Denature: heat is used to denature (separate) double-stranded DNA
  2. Anneal: complementary primers (forward and reverse) bind to their target regions in the denatured DNA
  3. Elongate: heat-stable DNA polymerase is added to elongate the primers and complete new strands
  4. Repeat for 20-35 cycles
22
Q

What does Reverse Transcriptase PCR measure?

A

Levels of mRNA transcription

23
Q

What is Next Generation Sequencing? What are the two types of structures evaluated? Describe this process in three steps (hint: be sure to differentiate the process depending on the structure being sequenced)

A

Next Generation Sequencing: collection of sequencing methods that can be performed simultaneously (high volume)

  1. Fragmented genomic DNA or isolated mRNA are ligated to adapters
  2. Undergo PCR (or Reverse Transcriptase PCR for mRNA) to create libraries
  3. Libraries are sequenced (genomic DNA is reassembled to obtain the sequence of entire genome) and (mRNA can be quantitated to see what genes are transcribed, and how much of each gene)
24
Q

What are the three types of blotting tests, and what does each evaluate?

A
  • Southern Blot: detects and quantitates DNA
  • Northern Blot: detects and quantitates RNA (gene expression)
  • Western Blot: detects and quantitates proteins
25
Q

How exactly does Western Blotting evaluate proteins?

A

Detects the presence of proteins based on antibody binding

26
Q

What is ELISA and what is it often used to evaluate/diagnose clinically (and how)?

A

ELISA: quantitates protein analytes (such as hormones, peptides, antibodies, etc)
- Used to evaluate HIV by detecting anti-viral antibodies

Biochemistry Exam #4 (10 decks)

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