Chapter 9: DNA and Its Role in Heredity

Merged flashcards from Chapter 9 of Principles of Life, 3rd Edition.

Early evidence for DNA

Included:

1. DNA is present in the nucleus and in condensed chromosomes

2. DNA doubles in abundance during the S phase of the cell cycle

3. DNA is twice as abundant in the diploid than in the haploid cells of an organism

These were discovered through staining and extraction of DNA

Experimental evidence for DNA

Included:

1. DNA affected the development of organisms that take it up

2. DNA encodes information that affects cell responses

These were discovered through experiments with bacteria transformation and bacteriophages (viruses), using selective degradation and radioactive marking to determine effects respectively

Chargaff’s rules

States that:

• The abundance of adenine is equivalent to the amount of thymine (A = T)

• The abundance of guanine is equivalent to the amount of cytosine (G = C)

• The relative abundances of the two groups to each other are not all equal

Rosalind Franklin

An English chemist who successfully imaged the shape and structure of DNA using X-ray crystallography, most importantly highlighting its helical, thin, and consistently thick shape

James Watson and Francis Crick

An American geneticist and English physicist pair that described the structure of DNA using chemical models, developing a structure that explained all its known properties

Sugar-phosphate backbone

The structure comprising the hydroxyl group on the 3’ carbon and phosphate group on the 5’ carbon, linking nucleotides together

• Forms antiparallel with the other strand, building the 3’ and 5’ groups in opposite directions

• Twists to form a clockwise (right-handed) helix every 10 nucleotides

Major and minor grooves

The wider and narrower sides of the helix, respectively, due to differences in sugar-phosphate backbone distance on each side

• Combined with chemical differences in base pair orientations, these allow molecules to differentiate and bind to sequences, particularly from the wider side

Complimentary base pairs

The specific pairings of nucleotides with each other, explaining Chargaff’s rules and Franklin’s observed thickness

• Adenine to thymine (A-T) with 2 hydrogen bonds

• Guanine to cytosine (G-C) with 3 hydrogen bonds

Proposed replication methods

Included:

• Semiconservative replication (each strand is used as a template for a new strand)

• Conservative replication (strands remain together while two new strands are created separately)

• Dispersive replication (strands are dispersed in the new daughter molecules)

Semiconservative replication

A proposed method of replication where each parental molecule strand serves as a template for a new strand

Conservative replication

A proposed method of replication where the parental molecule remains intact with two newly created strands

Dispersive replication

A proposed method of replication where daughter molecules are composed of new and original parental DNA

Meselson-Stahl experiment

An experiment performed by Matthew Meselson and Franklin Stahl that demonstrated the semiconservative replication of DNA, where:

1. Bacteria was grown in a ¹⁵N medium, and then transferred to a ¹⁴N medium

2. DNA was collected at different periods in time to allow for replication

3. DNA densities were measured in a salt gradient, finding that:

   1. DNA was dense at first

   2. The two DNA strands after replication were then intermediately dense

   3. The four DNA strands after replication were then two intermediately and two light strands

DNA replication steps

Include:

1. Initiation (denaturation and separation of DNA molecules, synthesis of RNA primers)

2. Elongation (synthesis of new DNA molecules starting from RNA primers, using strands as templates)

3. Termination (stoppage of replication after completion)

Elongation

The second step of DNA replication, involving the synthesis of new DNA molecules starting from RNA primers, using strands as templates

Termination

The final step of DNA replication, involving stoppage of replication after completion

Initiation

The first step of DNA replication, involving denaturation and separation of DNA molecules and the synthesis of RNA primers

Origin of replication (ori)

Where DNA synthesis is initiated, as two DNA helicase enzymes unwind the parent molecule and create an exposed replication fork for access to replication proteins

• Additional twisting after unwinding is relieved by topoisomerase, which break and rejoin the backbone

• Prokaryotes have one of these, eukaryotes have many due to large number of base pairs

RNA primer

A RNA signal synthesized by RNA primase after denaturation, complimentary to the template strand

• Used by DNA polymerase to initiate DNA synthesis due to the need for a double-stranded molecule

DNA polymerase

An enzyme that catalyzes the synthesis of DNA, initiated by an RNA primer and energized by a released pyrophosphate ion

• Synthesizes DNA in the 5’ to 3’ direction, reading DNA in the 3’ to 5’ direction

5’ to 3’

The direction of DNA synthesis, requiring a reading of DNA in the 3’ to 5’ direction

• Bases in the new strand are complimentary to the template strand

• Phosphodiester bonds are added to form this link, releasing a pyrophosphate ion for energy

Leading strand

The template strand that can be synthesized continuously by DNA polymerase

Lagging strand

The template strand that is synthesized discontinuously, as replication must proceed in the opposite direction of the replication fork, leaving emptiness without the continuous addition of primers to make Okazaki fragments

• These RNA primers must later be removed and replaced with DNA to complete replication, which is then joined by DNA ligase

DNA ligase

An enzyme that joins two DNA fragments on a lagging strand following the replacement of RNA primers with an unjoined DNA fragment

Okazaki fragments

Short strands of DNA that are synthesized discontinuously on the lagging strand, stopping before the next RNA primer

Terminal site (ter)

This is created when two replication forks meet, or when termination sequences occur (in prokaryotes)

• Proteins prevent the further replication of DNA

End-replication problem

A problem present at the end of the lagging strand of DNA where, after removal of the RNA primer, no DNA can be synthesized by DNA polymerase due to the lack of a 3’ end to extend

• Mitigated by the repeated addition of telomeres (which do not code for proteins) that can be replaced by telomerase, which synthesizes DNA using RNA as a template to allow DNA polymerase to finish

Telomeres

Non-coding end sections of DNA that protect coding sections of DNA from being lost to the end-replication problem and protect chromosome ends from being treated as chromosome breaks that need to be joined

• Replaced by telomerase after loss due to DNA replication and repair

Incorporation error rate

The probability that an incorrect base will be inserted into a new strand of DNA, creating a mismatch

• These are mitigated by proofreading (immediate removal and replacement) and mismatch repair (scanning by a complex for removal and replacement by cellular processes)

Proofreading

A function of DNA polymerases where mismatched nucleotides are removed immediately after being placed down

Mismatch repair

A function of a specialized complex where newly replicated molecules are scanned for helix irregularities, removing and replacing incorrect fragments when found

Point mutation

A mutation that substitutes, deletes, or inserts a single base pair in a DNA molecule

Base-pair substitution

A type of point mutation that leads to a change of a single base pair (A-T to G-C), created through:

• Erroneous replacing of the original instead of the new strand

• Lack of repair before the next round of DNA replication

Tautomers

The two structural isomeric forms of a base; having a rarer form present can result in the incorrect pairing of another base

Deamination

The removal of an amino group in a base, resulting in a different base form; this can result in mispairing that is passed down after replication

Spontaneous mutations

Mutations caused by polymerase errors or spontaneous chemical change in bases

Mutagens

Substances that chemically alter DNA and lead to induced mutations (unlike spontaneous mutations)

• Commonly related to cigarette smoking, certain dietary components, and radiation; these can often be mitigated

Excision repair

The repair of damaged nucleotides with their replacement by normal ones

• Involves proteins that remove the fragment for repair by DNA polymerase and ligase

Silent mutations

Mutations that do not change the amino acid sequence or function of the protein

Loss-of-function mutations

Mutations that occur due to low expression or nonfunctional protein production

• Often recessively inherited, as a wild-type allele usually results in sufficient functional protein

Gain-of-function mutations

Mutations that lead to proteins with altered function

• Often dominantly inherited, as the mutant allele results in a still functioning protein

Conditional mutations

Mutations that affect the phenotype only under certain environmental conditions

• Often seen with temperature-sensitive traits, such as coat color in rabbits

Nonhomologous end joining

The joining of two broken ends without regard for homology, potentially joining separate pieces of DNA to cause chromosomal mutations

Deletion

The loss of a chromosome segment, typically with severe consequences due to gene absences

Duplication

The repetition of a chromosome segment, resulting in multiple copies of that segment

• Occur due to crossing-over errors between homologous chromosomes, producing a deletion in the other chromosome

• Typically have mild effects on phenotype due to over-expression of genes

Inversions

Mutations where a chromosome segment is reversed in sequence

• Occur due to cutting out and rotation, resulting in a reversed sequence in the chromosome

Translocations

Mutations where non-homologous chromosomes exchange segments

• Can potentially be harmless if break points do not interrupt genes, but otherwise can cause erroneous expression