Nucleic Acids and Protein Synthesis - Review Flashcards

A comprehensive set of Q&A flashcards covering nucleic acids, DNA/RNA structure, transcription/translation, genetic code, regulation, CRISPR-Cas9, PCR, gel electrophoresis, cloning, GMOs, and ethics.

What are nucleotides and what are their three components?

A phosphate group, a nitrogenous base, and a pentose (five-carbon) sugar.

Name the two main types of nucleic acids and their general roles.

DNA stores genetic information; RNA transmits and expresses that information to synthesize proteins (mRNA, tRNA, rRNA).

Where is DNA located in prokaryotes versus eukaryotes?

Prokaryotes: single circular chromosome (nucleoid) and plasmids; Eukaryotes: linear DNA in nucleus; mitochondria have circular mtDNA; chloroplasts contain plastid DNA.

What is meant by the term ‘antiparallel’ in DNA structure?

The two DNA strands run in opposite directions (5' to 3' on one strand aligns with 3' to 5' on the other).

What is the DNA backbone made of?

A sugar-phosphate backbone linked by phosphodiester bonds.

Which bases pair in DNA and what are their classifications?

A pairs with T; G pairs with C. Purines: A and G; Pyrimidines: C and T (U in RNA).

Why are DNA base pairs complementary?

To form hydrogen bonds and maintain a uniform width; two purines would create too much space, preventing proper pairing.

What are the three main forms of RNA?

mRNA, rRNA, and tRNA.

Where does transcription occur and what is produced?

In the nucleus; produces pre-mRNA (a precursor to mRNA).

What is RNA processing and what does it involve?

Modification of pre-mRNA in the nucleus: 5' cap, 3' poly-A tail, and intron splicing with possible alternative splicing.

What is translation and where does it occur?

Synthesis of a polypeptide from mRNA at ribosomes; tRNA delivers amino acids during this process.

What is a codon and what is an anticodon?

Codon: a three-nucleotide unit on mRNA; anticodon: a three-nucleotide unit on tRNA that pairs with the codon (start codon AUG; anticodon UAC carries Met).

What does the genetic code mean when described as universal and degenerate?

Universal triplet code: same codons code for the same amino acids across organisms; degenerate means multiple codons can code for the same amino acid.

What is a gene and what is gene expression?

A gene is a DNA segment that codes for a protein; gene expression is transcription of DNA to mRNA and translation to a protein.

What is a promoter region and what is the TATA box?

Promoter: region upstream where RNA polymerase binds; TATA box is a DNA sequence (A/T-rich) ~25–35 bp upstream that helps identify the promoter.

What is an operon and what is the Trp operon?

Operon: cluster of adjacent structural genes with a common promoter and operator transcribed as a single mRNA; Trp operon regulates enzymes for tryptophan production in prokaryotes.

What is the transcription initiation complex?

A group of transcription factors together with RNA polymerase that binds to the promoter to initiate transcription.

What is attenuation in the Trp operon and when does it occur?

A regulatory mechanism in prokaryotes where transcription is terminated prematurely via formation of mRNA hairpins during translation of a leader sequence; requires simultaneous transcription and translation (occurs in prokaryotes, not in eukaryotes).

What are amino acids and their basic structure?

Amino group (NH2), carboxyl group (COOH), and a variable R group; joined by peptide (covalent) bonds with loss of water.

How many different amino acids are there and what distinguishes them?

20 standard amino acids; they differ by their variable R group, giving each its properties.

What are the four levels of protein structure?

Primary: amino acid sequence; Secondary: alpha helix and beta-pleated sheet; Tertiary: 3D folding; Quaternary: assembly of multiple polypeptide chains.

What role do chaperone proteins play in protein folding?

Assist in folding polypeptide chains into their correct three-dimensional structure.

What is the proteome?

The complete set of proteins expressed by a genome, tissue, or organism; often larger than the genome.

What is the secretory pathway and which organelles are involved?

Rough ER (protein synthesis and some post-translational modification), Golgi apparatus (modification and packaging), secretory vesicles and exocytosis to export proteins.

What is the function of ribosomes and their subunits?

Ribosomes translate mRNA into polypeptides; small subunit reads mRNA, large subunit catalyzes peptide bond formation.

What is CRISPR-Cas9 and what is the PAM?

CRISPR-Cas9 is a gene-editing tool using a Cas9 endonuclease guided by gRNA; PAM (Protospacer Adjacent Motif) is a short DNA sequence that must flank the target site for Cas9 binding.

What are spacer and protospacer in CRISPR?

Protospacer: viral DNA fragment captured and inserted into CRISPR loci; spacer is the memory sequence used to recognize future infections.

What is guide RNA (gRNA) and how does it function with Cas9?

gRNA (from crRNA and tracrRNA) guides Cas9 to the complementary target DNA sequence for cleavage.

Why is the PAM site important in CRISPR editing?

Cas9 requires a PAM adjacent to the target to bind and cut; this prevents self-targeting of the organism’s own CRISPR loci.

What are knockouts and knockins in genome editing?

Knockout: disruption of a gene to stop its function; knockin: insertion of a new gene or sequence at a specific site.

What is the donor DNA in CRISPR knockin edits?

A DNA fragment with compatible ends that is inserted at the cut site to create a desired modification.

What is PCR and what are its three steps with approximate temperatures?

Denaturation (~90–95°C), Annealing (~50–60°C, ~55°C typical), Extension (~72°C).

Why is Taq polymerase used in PCR instead of human polymerase?

Taq is stable at high temperatures and can withstand denaturation steps without denaturation itself.

What is the role of primers in PCR?

Short DNA sequences that provide starting points for DNA synthesis by DNA polymerase.

What is gel electrophoresis used for in DNA analysis?

To separate DNA fragments by size using an electric field; smaller fragments move faster and farther.

What are STRs and how is mtDNA different for profiling?

Nuclear STRs are highly polymorphic short tandem repeats; mtDNA is maternally inherited, present in many copies and useful when nuclear DNA is degraded.

What features make a plasmid a good cloning vector?

Origin of replication, selectable marker (e.g., antibiotic resistance), multiple cloning site (MCS), promoter for gene expression.

How is recombinant plasmid identified using lacZ screening (blue-white screening)?

If lacZ is disrupted by the insert, colonies remain white; intact lacZ yields blue colonies with X-gal.

How is recombinant DNA used to produce insulin in GMOs?

Insulin gene segments are inserted into plasmids, transformed into bacteria, cultured, and the insulin chains are produced and assembled.

What are GMOs and transgenic organisms?

GMOs have genomes altered by genetic engineering; transgenic organisms contain foreign genes from another species.

Give examples of GM crops and one key ethical/social/biological issue for each.

Bt cotton: pest resistance, reduced pesticides but possible resistance and gene flow; Golden Rice: enhanced vitamin A, concerns about biodiversity and safety perceptions.

What are the three ethical approaches in biology described in the notes?

Consequence-based (utilitarian), duty/rules-based (deontology), virtues-based (character/ethics).

What are the four ethical principles listed (beneficence, non-maleficence, respect, justice) and their meanings?

Beneficence: maximize benefits; Non-maleficence: avoid harm; Respect: autonomy and welfare; Justice: fair distribution of benefits and burdens.

What is meant by the term ‘origin of replication’ in plasmids?

A DNA sequence where DNA replication initiates inside the plasmid.

What is the role of the Golgi apparatus in the protein secretory pathway?

Modifies, packages, and transports proteins and lipids for export; vesicles bud from Golgi to secretion or other destinations.

What is transcription versus translation directionality in terms of strand orientation?

Transcription uses the DNA template strand (3' to 5'), producing mRNA in a 5' to 3' direction; translation reads mRNA in codons to build polypeptides.

What is the difference between nuclear DNA and mtDNA in terms of inheritance and recombination?

Nuclear DNA recombines and is inherited from both parents; mtDNA is maternally inherited, does not recombine, and exists in high copy numbers.