DNA Structure, Replication, Transcription, Translation & Sequence Practice

[W1 DNA] What are the three parts of a DNA nucleotide?

Phosphate, deoxyribose sugar, and a nitrogenous base. [L1 pp. 15-25]

[W1 DNA] What bonds form a DNA strand's backbone?

Covalent phosphodiester bonds connect adjacent nucleotides through their sugars and phosphates. [L1 pp. 15-25]

[W1 DNA] What holds complementary DNA bases together?

Hydrogen bonds between A-T and G-C pairs. [L1 pp. 15-25]

[W1 DNA] What does antiparallel mean?

The two paired DNA strands run in opposite directions: one 5′→3′ and the other 3′→5′. [L1 pp. 15-25]

[W1 DNA] What do 5′ and 3′ refer to?

Numbered carbon positions in the nucleotide sugar that establish strand direction. [L1 pp. 15-25]

[W1 DNA] Where is DNA found in a eukaryotic cell?

Mainly in the nucleus, also in mitochondria, and in chloroplasts in plants/algae. The organelle locations clarify the basic nuclear model. [L1 pp. 15-25]

[W1 DNA] Where is prokaryotic DNA found?

In a nucleoid region, not a membrane-bound nucleus, some DNA is also carried on plasmids. Supporting comparison. [L1 pp. 15-25]

[W1 DNA] How do DNA and RNA differ in sugar and bases?

DNA: deoxyribose and A/T/C/G. RNA: ribose and A/U/C/G. [L1 pp. 15-25]

[W1 DNA] How do DNA and RNA usually differ in strand structure?

Cellular DNA is usually double-stranded, RNA is usually single-stranded but can fold. Viral genomes have exceptions. [L1 pp. 15-25]

[W1 DNA] What do DNA and RNA have in common?

Both are nucleotide polymers with sugar-phosphate backbones, base sequences, and 5′/3′ directionality. [L1 pp. 15-25]

[W1 DNA] Why does a cell have DNA?

To store inherited information that can be copied and expressed as functional RNA and proteins. [L1 pp. 15-25]

[W1 DNA] Why can different cell types have similar DNA but different functions?

They express different sets of genes. [L1 pp. 15-25]

[W1 DNA] What is the main contrast between replication and gene expression?

Replication copies DNA, gene expression uses information in DNA to make functional RNA and, for protein-coding genes, protein. [L1 pp. 15-25]

[W1 Society] What was Rosalind Franklin's contribution to DNA structure research?

Her X-ray diffraction research, including Photo 51 made with Raymond Gosling, supplied crucial evidence for DNA's helical structure used in developing the double-helix model. [L1 pp. 7-12, 18-20, guide source A]

[W1 Society] How does Franklin's story connect science and society?

Scientific credit and historical recognition are affected by gender, institutional power, collaboration, and whose work narratives emphasize. [L1 pp. 7-12, 18-20, guide source A]

[W1 Society] Does the social nature of science mean all claims are equally supported?

No. People shape questions and institutions, but controls, evidence quality, and comparison across studies still distinguish stronger claims. [L1 pp. 7-12, 18-20, guide source A]

[W1 Society] Why consider the weight of evidence rather than one striking study?

A single study can have bias, confounding, or chance findings, consistency across well-designed studies strengthens inference. [L1 pp. 7-12, 18-20, guide source A]

[W1 Society] Which DNA details did the instructor explicitly exclude from memorization?

Drawing chemical structures of bases/nucleotides and distinguishing purines from pyrimidines. [L1 pp. 7-12, 18-20, guide source A]

[W1 Toolkit] What is the highlighted DNA replication toolkit?

Template DNA, helicase, RNA primers, DNA-dependent DNA polymerase, and DNA nucleotides A/C/G/T. [L1 pp. 26-39, L2 pp. 1-5]

[W1 Toolkit] What does helicase do in DNA replication?

Separates the paired strands so they can serve as templates. [L1 pp. 26-39, L2 pp. 1-5]

[W1 Toolkit] Why does DNA polymerase need a primer?

It extends an existing strand's free 3′ end rather than beginning a new strand from nothing. [L1 pp. 26-39, L2 pp. 1-5]

[W1 Toolkit] In what direction is new DNA synthesized?

5′→3′, while the template is read 3′→5′. [L1 pp. 26-39, L2 pp. 1-5]

[W1 Toolkit] What does semiconservative replication mean?

Each daughter DNA double helix contains one parental strand and one newly made strand. Supporting clarification. [L1 pp. 26-39, L2 pp. 1-5]

[W1 Toolkit] What is the transcription toolkit?

Template DNA, DNA-opening activity, DNA-dependent RNA polymerase, and RNA nucleotides A/C/G/U. [L1 pp. 26-39, L2 pp. 1-5]

[W1 Toolkit] What does DNA-dependent RNA polymerase make?

RNA from a DNA template. [L1 pp. 26-39, L2 pp. 1-5]

[W1 Toolkit] Which DNA strand is complementary to mRNA?

The template or antisense strand. [L1 pp. 26-39, L2 pp. 1-5]

[W1 Toolkit] Which DNA strand resembles mRNA?

The coding or sense strand when both are written 5′→3′, except mRNA has U instead of T. [L1 pp. 26-39, L2 pp. 1-5]

[W1 Toolkit] What is the translation toolkit?

mRNA, ribosomes, tRNAs, and amino acids, ribosomes read codons and tRNAs deliver amino acids. [L1 pp. 26-39, L2 pp. 1-5]

[W1 Toolkit] What is a codon?

A three-nucleotide sequence in mRNA specifying an amino acid or termination signal. [L1 pp. 26-39, L2 pp. 1-5]

[W1 Toolkit] What is the usual start codon and its amino acid?

AUG, methionine (Met). [L1 pp. 26-39, L2 pp. 1-5]

[W1 Toolkit] What are the three stop codons?

UAA, UAG, and UGA. They do not add an amino acid. [L1 pp. 26-39, L2 pp. 1-5]

[W1 Toolkit] What does tRNA do?

Pairs its anticodon with an mRNA codon and delivers the corresponding amino acid. [L1 pp. 26-39, L2 pp. 1-5]

[W1 Toolkit] Where do nuclear transcription and translation occur in eukaryotes?

Nuclear transcription occurs in the nucleus, translation occurs at ribosomes in the cytoplasm, including rough-ER-associated ribosomes. [L1 pp. 26-39, L2 pp. 1-5]

[W1 Toolkit] Are all parts of an exon translated?

No. Exons are retained after splicing and can contain untranslated regions. "Exons = coding" in the slide is shorthand. [L1 pp. 26-39, L2 pp. 1-5]

[W1 Toolkit] Is the promoter part of the resulting mRNA?

The promoter is a DNA region involved in initiating transcription, not a segment of the mRNA. Supporting clarification. [L1 pp. 26-39, L2 pp. 1-5]

[W1 Toolkit] What is PCR's basic purpose?

Amplify a DNA sequence using polymerase, primers, and nucleotides, heating separates strands. [L1 pp. 26-39, L2 pp. 1-5]

[W1 Toolkit] What extra step is needed before PCR amplification of viral RNA?

Reverse transcription converts RNA into DNA. Supporting clarification. [L1 pp. 26-39, L2 pp. 1-5]

[W1 Toolkit] An antigen test detects a viral protein. Which process made that target?

Translation. [L1 pp. 26-39, L2 pp. 1-5]

[W1 Sequence practice] What is the 5′→3′ complement of DNA 5′-ACGGAT-3′?

5′-ATCCGT-3′. First pair it as 3′-TGCCTA-5′, then reverse the written order. [L1 pp. 21, 23, 33-38, worked exercises]

[W1 Sequence practice] What is the 5′→3′ complement of DNA 5′-TTAAGCT-3′?

5′-AGCTTAA-3′. [L1 pp. 21, 23, 33-38, worked exercises]

[W1 Sequence practice] Why is simply swapping A/T and C/G sometimes insufficient?

The complement is antiparallel. If both answers must be written 5′→3′, you must reverse the complemented sequence too. [L1 pp. 21, 23, 33-38, worked exercises]

[W1 Sequence practice] Template DNA is 3′-TAC TGG AGG ATT-5′. What is the mRNA?

5′-AUG ACC UCC UAA-3′. [L1 pp. 21, 23, 33-38, worked exercises]

[W1 Sequence practice] Template DNA is 5′-TTA GGA GGT CAT-3′. What is the mRNA in 5′→3′ order?

5′-AUG ACC UCC UAA-3′. Reverse-complement the supplied template and use U. [L1 pp. 21, 23, 33-38, worked exercises]

[W1 Sequence practice] Coding DNA is 5′-ATG ACC TCC TAA-3′. What is the mRNA?

5′-AUG ACC UCC UAA-3′. Keep the order and change T to U. [L1 pp. 21, 23, 33-38, worked exercises]

[W1 Sequence practice] Translate 5′-AUG ACC UCC UAA-3′.

Met-Thr-Ser, followed by termination, the peptide has three amino acids. [L1 pp. 21, 23, 33-38, worked exercises]

[W1 Sequence practice] Template DNA is 3′-TAC AAA CCG ACT-5′. Give mRNA and peptide.

mRNA: 5′-AUG UUU GGC UGA-3′. Peptide: Met-Phe-Gly, then stop. [L1 pp. 21, 23, 33-38, worked exercises]

[W1 Sequence practice] Coding DNA is 5′-ATG GAA TGC TGA-3′. Give mRNA and peptide.

mRNA: 5′-AUG GAA UGC UGA-3′. Peptide: Met-Glu-Cys, then stop. [L1 pp. 21, 23, 33-38, worked exercises]

[W1 Sequence practice] Which sequence do you look up in an amino acid table?

The mRNA codon read 5′→3′, not template DNA or a tRNA anticodon. [L1 pp. 21, 23, 33-38, worked exercises]

[W1 Sequence practice] Does a stop codon count toward peptide length?

No, it signals termination without adding an amino acid. [L1 pp. 21, 23, 33-38, worked exercises]

[W2 Viruses] What is a virion?

A virus particle containing a viral genome and protective viral proteins, sometimes with a lipid envelope. [L2 pp. 8-29]

[W2 Viruses] Why are viruses often called not living?

They are acellular and cannot independently grow, metabolize, or reproduce, they require host cells. [L2 pp. 8-29]

[W2 Viruses] What are the two main production goals of an infecting virus?

Copy its genome and make viral proteins, then package them into new virions. [L2 pp. 8-29]

[W2 Viruses] Which crucial protein-making structure do viruses lack?

Ribosomes, viral protein synthesis uses host ribosomes. [L2 pp. 8-29]

[W2 Viruses] What are the five lecture stages of a viral life cycle?

Attachment, entry, genome replication and gene expression, assembly, release. [L2 pp. 8-29]

[W2 Viruses] What happens in attachment?

A viral surface component binds an appropriate host-cell receptor. [L2 pp. 8-29]

[W2 Viruses] What happens in entry and uncoating?

The virus/genome gets inside and the genome becomes available for replication or expression. [L2 pp. 8-29]

[W2 Viruses] What happens in assembly?

New genomes and viral structural components are packaged into virions. [L2 pp. 8-29]

[W2 Viruses] What happens in release?

New virions leave the host cell through a virus-specific exit process. [L2 pp. 8-29]

[W2 Viruses] Which stage does an antibody blocking spike-receptor binding interrupt?

Attachment, stage 1. [L2 pp. 8-29]

[W2 Viruses] Which stage does a membrane-fusion inhibitor interrupt?

Entry, stage 2. [L2 pp. 8-29]

[W2 Viruses] Which enzyme and stage does remdesivir target in the lecture?

Viral RdRp, RNA synthesis during stage 3, genome replication/gene expression. [L2 pp. 8-29]

[W2 Viruses] Would a drug preventing viral protein translation also affect stage 3?

Yes, stage 3 includes both genome replication and gene expression, although its target differs from remdesivir's. [L2 pp. 8-29]

[W2 Viruses] What distinguishes public-health stages from intracellular viral stages?

Exposure, infection, illness, and spread describe population/person-level events, attachment through release describes events in a host-cell infection cycle. [L2 pp. 8-29]

[W2 Viruses] What are four ways to classify viruses in the lecture?

Symptoms, structure, genome sequences, and replication strategy. [L2 pp. 8-29]

[W2 Viruses] What is a limitation of classifying viruses only by symptoms?

Unrelated viruses can cause similar symptoms, symptoms alone do not establish genome type or relatedness. [L2 pp. 8-29]

[W2 Viruses] What does Baltimore classification emphasize?

Genome type and how a virus produces mRNA: DNA/RNA, strand number, sense, and reverse-transcription routes. [L2 pp. 8-29]

[W2 Viruses] Must you memorize all seven Baltimore groups for this lecture?

The slide says no, learn the classification logic and predict replication from clues. [L2 pp. 8-29]

[W2 Viruses] What does positive-sense RNA mean?

RNA that can function as a message for translation by ribosomes. [L2 pp. 8-29]

[W2 Viruses] What does negative-sense RNA mean?

RNA complementary to the positive-sense message, it must be copied into positive RNA before translation. [L2 pp. 8-29]

[W2 Replication] What is the replication/gene-expression path for a dsDNA virus?

Viral DNA → more DNA via DNA-dependent DNA polymerase, DNA → mRNA via DNA-dependent RNA polymerase, mRNA → protein at host ribosomes. [L2 pp. 11, 21-34, L7 pp. 17-22]

[W2 Replication] Must all DNA viruses use host polymerases?

No. Depending on the virus, polymerases may be supplied by the host or encoded by the virus. [L2 pp. 11, 21-34, L7 pp. 17-22]

[W2 Replication] What is the basic replication path of SARS-CoV-2?

Incoming positive RNA is translated to make replication proteins, RdRp makes negative templates and then new positive RNAs, proteins and genomes assemble into virions. [L2 pp. 11, 21-34, L7 pp. 17-22]

[W2 Replication] Why does a negative-sense RNA virion need to bring RdRp?

Its genome cannot directly be translated, and human cells do not supply the needed RNA-copying enzyme, it must make positive RNA first. [L2 pp. 11, 21-34, L7 pp. 17-22]

[W2 Replication] What is the genome type of measles virus in the synthesis lecture?

Negative-sense single-stranded RNA, it is enveloped. [L2 pp. 11, 21-34, L7 pp. 17-22]

[W2 Replication] What does a negative-sense RNA virus use as a template for new negative genomes?

A full-length positive-sense RNA intermediate. [L2 pp. 11, 21-34, L7 pp. 17-22]

[W2 Replication] Does SARS-CoV-2 need to convert its genome into DNA?

No. Its normal replication strategy uses RNA intermediates. [L2 pp. 11, 21-34, L7 pp. 17-22]

[W2 Replication] What does RNA-dependent RNA polymerase do?

Makes RNA using an RNA template, it does not make proteins. [L2 pp. 11, 21-34, L7 pp. 17-22]

[W2 Replication] How can you decode a polymerase's name?

The "dependent" part identifies the template, the nucleic acid before "polymerase" identifies the product. [L2 pp. 11, 21-34, L7 pp. 17-22]

[W2 Replication] What kind of genome does SARS-CoV-2 have?

Positive-sense single-stranded RNA, approximately 30,000 nucleotides long. [L2 pp. 11, 21-34, L7 pp. 17-22]

[W2 Replication] What is the distinction between SARS-CoV-2 and COVID-19?

SARS-CoV-2 is the virus, COVID-19 is the disease it causes. [L2 pp. 11, 21-34, L7 pp. 17-22]

[W2 Replication] What do SARS-CoV-2 S, N, M, and E stand for?

Spike, nucleocapsid, membrane, and envelope proteins. [L2 pp. 11, 21-34, L7 pp. 17-22]

[W2 Replication] Which SARS-CoV-2 protein is central to attachment?

Spike, it binds the host receptor ACE2. [L2 pp. 11, 21-34, L7 pp. 17-22]

[W2 Replication] What does SARS-CoV-2 nucleocapsid protein do?

Associates with and helps package the RNA genome. [L2 pp. 11, 21-34, L7 pp. 17-22]

[W2 Replication] What does the SARS-CoV-2 nsp12 region encode?

RNA-dependent RNA polymerase (RdRp). [L2 pp. 11, 21-34, L7 pp. 17-22]

[W2 Replication] Does the human central dogma ordinarily use viral RdRp?

No. Human transcription uses DNA-dependent RNA polymerase. Do not generalize this to every organism in nature. [L2 pp. 11, 21-34, L7 pp. 17-22]

[W2 Replication] Why must a positive-RNA virus still replicate RNA even though it can translate immediately?

Translation produces protein, not new genome copies. [L2 pp. 11, 21-34, L7 pp. 17-22]

[W2 Replication] Are all SARS-CoV-2 proteins translated directly from the full incoming genome?

No. Initial translation produces replication machinery, structural proteins are made from subgenomic mRNAs. Clarification of the lecture diagram. [L2 pp. 11, 21-34, L7 pp. 17-22]

[W2 Immunity] How do innate and adaptive immunity differ in speed and specificity?

Innate defenses respond rapidly and broadly, adaptive responses are antigen-specific and slower on first exposure. [L3 pp. 7-18]

[W2 Immunity] What changes during a later exposure in adaptive immunity?

Memory cells support a faster response to the previously encountered antigen. [L3 pp. 7-18]

[W2 Immunity] What is the basic role of B cells?

They recognize specific antigens and can form antibody-secreting plasma cells and memory B cells. [L3 pp. 7-18]

[W2 Immunity] What is the difference between a plasma cell and a memory B cell?

A plasma cell secretes antibodies, a memory B cell supports a response to a later encounter. [L3 pp. 7-18]

[W2 Immunity] What is an antigen?

A molecular target recognized by adaptive immune receptors or antibodies. [L3 pp. 7-18]

[W2 Immunity] How do neutralizing and non-neutralizing antibodies differ?

Neutralizing antibodies directly interfere with infection. Non-neutralizing antibodies bind without directly blocking infection and may recruit other immune functions. [L3 pp. 7-18]

[W2 Immunity] Which exposure does vaccination try to mimic?

A controlled first antigen exposure, preparing adaptive memory for a later real encounter. [L3 pp. 7-18]

[W2 Immunity] Why is self versus nonself only an introductory immune model?

Beneficial microbes, allergies, and autoimmunity show that foreignness and harmfulness do not map perfectly onto one another. [L3 pp. 7-18]

[W2 Immunity] What do war versus ecological pandemic metaphors emphasize?

War emphasizes enemies and conflict, ecology emphasizes interdependence, environments, and social connections. [L3 pp. 7-18]

[W2 Vaccines] How does a live attenuated vaccine work?

It supplies a weakened living pathogen whose limited replication stimulates immunity. [L3 pp. 19-29, guide sources B-C]

[W2 Vaccines] What is a major benefit and limitation of live attenuated vaccines?

Often strong, durable immunity, may be unsuitable for certain immunocompromised people and require careful storage. [L3 pp. 19-29, guide sources B-C]

[W2 Vaccines] What type of vaccine is MMR?

Live attenuated. [L3 pp. 19-29, guide sources B-C]

[W2 Vaccines] What is an inactivated vaccine?

A killed/inactivated pathogen that cannot replicate, often requiring repeat doses or boosters. [L3 pp. 19-29, guide sources B-C]