genetics 2 exam study guide

What is the main structural difference between DNA and RNA?

DNA is double-stranded and contains deoxyribose and thymine, while RNA is single-stranded and contains ribose and uracil.

How does DNA's structure benefit its function?

Its double-stranded, complementary base pairing ensures stability and accurate replication.

What advantage does RNA's structure provide?

RNA's single-stranded, flexible structure allows it to fold into complex shapes and perform catalytic and regulatory functions.

What are the exceptions to DNA being the universal genetic material?

Some viruses, like retroviruses (e.g., HIV) and many plant viruses, use RNA as their genetic material.

What are the three components of a nucleotide?

A phosphate group, a five-carbon sugar (deoxyribose or ribose), and a nitrogenous base.

What atoms are removed when nucleotides form linkages?

A hydroxyl group (-OH) from the sugar and a hydrogen (H) from the phosphate, releasing water (H₂O).

How are the carbons in a nucleotide sugar numbered?

They are numbered from the oxygen in the ring clockwise: 1′ (attached to base), 2′ (differs in RNA/DNA), 3′ (OH for polymerization), 4′, and 5′ (attached to phosphate).

How are purine and pyrimidine atoms numbered?

Purines (A, G) are numbered 1-9 around the double ring; pyrimidines (C, T, U) are numbered 1-6 around the single ring.

What is base complementarity?

Adenine pairs with thymine (or uracil) via two hydrogen bonds, while guanine pairs with cytosine via three hydrogen bonds.

What are the key features of the Watson-Crick DNA model?

Two antiparallel strands, right-handed helix, complementary base pairing, sugar-phosphate backbone on the outside, 10 base pairs per turn.

How do covalent and hydrogen bonds differ in DNA?

Covalent bonds form the strong sugar-phosphate backbone, while hydrogen bonds weakly join complementary bases, allowing strand separation during replication.

List three differences between DNA and RNA.

1) Sugar: deoxyribose vs. ribose. 2) Base: thymine vs. uracil. 3) Structure: double vs. single strand.

What are the three major types of RNA?

mRNA (messenger RNA), tRNA (transfer RNA), and rRNA (ribosomal RNA).

How does each type of RNA contribute to information flow?

mRNA carries the code, tRNA brings amino acids, and rRNA catalyzes peptide bond formation in the ribosome.

How is UV absorption used to study nucleic acids?

Both DNA and RNA absorb UV light at 260 nm; increases in absorbance (hyperchromic shift) indicate strand separation or denaturation.

What happens to DNA when it is heated and denatured?

The strands separate but remain intact; hydrogen bonds break, but covalent bonds do not.

Why is Tₘ related to base composition?

Higher G-C content increases Tₘ because G-C pairs form three hydrogen bonds versus two in A-T pairs.

What is molecular hybridization?

The process where complementary DNA or RNA strands from different sources anneal to form hybrid double strands.

What does the Watson-Crick model suggest about DNA replication?

DNA replicates semiconservatively, with each new molecule containing one old and one new strand.

What happens if cytosine is converted to uracil by deamination?

Uracil pairs with adenine instead of guanine, causing a potential point mutation.

What base results if 5-methylcytosine undergoes deamination?

Thymine.

How does FISH work?

Fluorescent DNA probes bind to specific chromosome regions in cells to detect abnormalities such as aneuploidy.

Why are chromosomes 13, 18, 21, X, and Y used in FISH screening?

Abnormalities in these chromosomes cause common viable aneuploidies like Down, Patau, and Edwards syndromes.

What structure might a molecule have if it contains both ribose and deoxyribose?

A hybrid nucleic acid, possibly double-stranded but irregular, partly DNA-like and partly RNA-like.

Would RNA migrate the same as DNA in gel electrophoresis?

No, RNA folds into complex shapes and is single-stranded, so its migration depends on structure, not just size.

Why do cells use deoxyribose for DNA and ribose for RNA?

DNA's missing 2′-OH increases stability for long-term storage, while RNA's 2′-OH makes it more reactive for short-term use.

What are the requirements for in vitro DNA synthesis under DNA polymerase I?

A DNA template, a primer with a free 3′-OH, and dNTPs.

How does an exposed 3′-OH participate in strand elongation?

It attacks the α-phosphate of the incoming dNTP, forming a phosphodiester bond and extending the chain.

Compare DNA polymerase I, II, and III.

DNA Pol I removes RNA primers and fills gaps; Pol II is involved in repair; Pol III is the main replicative polymerase.

Define unidirectional vs. bidirectional DNA synthesis.

Unidirectional: replication fork moves in one direction; bidirectional: forks move outward in both directions from the origin.

Define continuous vs. discontinuous DNA synthesis.

Continuous: leading strand synthesized 5′→3′ without interruption; discontinuous: lagging strand synthesized in Okazaki fragments.

Name proteins that unwind DNA in vivo.

Helicase unwinds DNA; single-strand binding proteins stabilize it; topoisomerase relieves supercoiling.

Define Okazaki fragments, DNA ligase, and RNA primers.

Okazaki fragments are short DNA pieces on the lagging strand; DNA ligase joins fragments; RNA primer initiates DNA synthesis.

Outline the current model for DNA synthesis.

Replication is bidirectional; leading strand synthesized continuously, lagging strand discontinuously; primers are replaced and fragments ligated.

Why is eukaryotic DNA synthesis more complex than bacterial?

Eukaryotic chromosomes are linear and much larger; multiple origins and chromatin structure complicate replication.

What is the effect of a dnaE mutation?

It causes a defect in the Pol III alpha subunit, leading to replication stops and requiring special growth conditions.

What happens when there is a dnaQ mutation?

It results in a defective Pol III epsilon subunit, causing loss of proofreading and an increased mutation rate.

How does telomerase function in humans?

Telomerase extends telomeres in germ cells and stem cells, preventing loss of essential sequences during replication.

What factors determine the number of bidirectional origins needed to replicate the D. melanogaster genome?

It depends on genome size, replication rate, and the time window available for replication.

What is the role of RNA primers at the replication fork?

RNA primers are complementary to the DNA template and provide a free 3′ OH end for elongation.

What did Okazaki discover about short DNA fragments?

He observed that short fragments are produced on the lagging strand and are later joined to form continuous DNA.

How can you identify DNA vs RNA dinucleotides?

Identification depends on the sugar: ribose indicates RNA, while deoxyribose indicates DNA.

Describe the DNA organization in viruses, bacteria, and eukaryotes.

Viruses have compact, often circular DNA; bacteria have a single circular chromosome; eukaryotes have multiple linear chromosomes with chromatin and histones.

Compare the chromosome sizes of bacteriophages and E. coli.

Bacteriophages have a few thousand base pairs and are small and simple, while E. coli has millions of base pairs and is larger and more complex.

Why is eukaryotic DNA considered more complex than that of viruses or bacteria?

Eukaryotic DNA has a larger genome, chromatin structure, introns, regulatory sequences, and repetitive elements.

What is the composition and arrangement of nucleosomes?

Nucleosomes consist of DNA wrapped around a histone octamer (two each of H2A, H2B, H3, H4), with H1 binding linker DNA.

How do nucleosomes fold into chromatids?

Nucleosomes form a 30 nm fiber, which loops to create the chromatid structure during mitosis.

Define heterochromatin and provide examples.

Heterochromatin is dense and transcriptionally inactive; examples include centromeres, telomeres, and Barr bodies.

Contrast SINE and LINE sequences.

SINEs are short interspersed nuclear elements, while LINEs are long retrotransposons with reverse transcriptase activity.

Why are VNTRs important in forensics?

Variable number tandem repeats (VNTRs) are highly variable between individuals, allowing for DNA fingerprinting.

What occurs to nucleosome positioning at the replication fork?

New nucleosomes assemble rapidly, and their distribution can be tested by labeling old and new histones.

How do bacteriophage chromosomes form closed rings?

This can occur through circularization via complementary ends or ligation after injection.

How are microsatellites used in paternity testing?

By comparing repeat numbers at multiple loci, matching alleles can indicate potential parentage.

What is the relationship between genes near telomeres and disease?

Proximity to telomeres may affect gene regulation, requiring further information on gene expression.

What is the role of TSH2B in sperm DNA compaction?

TSH2B-containing nucleosomes are less stable, allowing for histone replacement by protamines.

Summarize the genetic code and transcription process.

The genetic code is a triplet code that is degenerate and non-overlapping; DNA is transcribed to RNA, which is then translated to protein.

What is the effect of adding or losing nucleotides on the reading frame?

Adding or removing 1-2 nucleotides causes a frameshift, while adding or removing multiples of three preserves the reading frame.

How do repeating tetranucleotides affect amino acids?

Patterns of repeating tetranucleotides determine codon assignments, allowing for the incorporation of more amino acids.

How did copolymer experiments help assign the threonine codon?

The AC... copolymer indicated that ACN codes for threonine.

What is the impact of single-base changes on amino acid substitutions?

Single-nucleotide substitutions can change a codon, leading to specific amino acid replacements.

What happens when synthetic RNA poly U + poly A is used in protein incorporation?

Only codons matching amino acids in the system are translated; incompatible sequences do not yield proteins.

How does deletion of one nucleotide affect predicted amino acid sequences?

It causes a frameshift, while three-nucleotide deletions maintain the reading frame.

What is the significance of glycine codon substitutions?

GGA allows for 8 substitutions causing amino acid changes, while GGU allows for 6 substitutions.

How does codon number correlate with amino acid frequency?

More codons lead to more frequent amino acids (e.g., leucine), while fewer codons correspond to less frequent amino acids (e.g., tryptophan).

Define transcription in the context of the central dogma.

Transcription is the process of producing RNA from a DNA template, following the central dogma: DNA → RNA → Protein.

What is the structure of bacterial RNA polymerase?

It consists of a core enzyme and a sigma factor; the core catalyzes elongation while the sigma factor recognizes promoters.

What are the steps of posttranscriptional RNA processing in eukaryotes?

Capping, polyadenylation, and splicing ensure RNA stability, export, and correct translation.

What is the function of 3′ poly-A sequences in mRNA?

They stabilize mRNA in eukaryotes and promote degradation in bacteria.

How did the triplet code evolve from a doublet?

The early amino acids were likely specified by the first two bases, with degeneracy increasing as more amino acids evolved.

What challenges arise from DNA directly templating protein in eukaryotes?

Spatial separation, processing requirements, and the need for ribosomes argue against direct translation from DNA.

What are the steps of translation and the role of the ribosome?

The ribosome reads mRNA codons, recruits tRNAs, and catalyzes peptide bonds, which is central to translating the genetic code.

What are the roles of tRNA and mRNA in protein synthesis?

mRNA carries codons, while tRNA carries anticodons and amino acids to the ribosome.

What is the Francis Crick adaptor hypothesis?

It states that tRNA acts as an adaptor between codons and amino acids.

Which molecule bears the codon and which bears the anticodon?

mRNA bears the codon, while tRNA bears the anticodon.

How many nucleotides are needed for a 141-amino acid hemoglobin chain?

141 amino acids require 423 nucleotides (141 × 3).

What are the steps involved in charging tRNA?

Aminoacyl-tRNA synthetase attaches an amino acid to the 3′ end of tRNA.

What are the four recognition sites in tRNA?

The four sites are the acceptor stem, anticodon loop, D loop, and TΨC loop.

What are isoaccepting tRNAs?

They are multiple tRNAs that can accept the same amino acid but have different anticodons, with specificity ensured by synthetases.

Why might a codon in the A site not be recognized by tRNA?

It requires matching aminoacyl-tRNA and elongation factors; the ribosome ensures fidelity.

How can hemoglobin amino acid substitutions occur?

They can occur through single-nucleotide changes using the codon table.

What are the four levels of protein organization?

Primary (sequence), secondary (α-helix, β-sheet), tertiary (3D fold), and quaternary (multiple subunits).

What are two common secondary structures in proteins?

The α-helix (spiral) and β-sheet (pleated), both stabilized by hydrogen bonds.

How do antibiotics inhibit translation?

Antibiotics can inhibit initiation, elongation, or termination by targeting ribosome components, blocking protein synthesis.

Still learning (15)

You've started learning these terms. Keep it up!