w3 slides fc Flashcards
What is the best reason why genome size is not always correlated with organism complexity?
(A) Large genomes always contain more genes.
(B) Some genomes contain significant amounts of non-coding repetitive DNA.
(C) Prokaryotes have larger genomes than eukaryotes.
(D) Eukaryotic genomes lack regulation mechanisms.
Answer: (B) (Genome size variation is often due to non-coding DNA, not gene number.)
What is the primary function of repetitive DNA in the human genome?
(A) Encoding proteins that regulate gene expression
(B) Encoding tRNAs and rRNAs
(C) Acting as structural elements and regulating chromatin organization
(D) Preventing mutations in protein-coding genes
C (Repetitive DNA plays roles in chromatin structure, centromeres, and telomeres.)
What is the main challenge of DNA packaging in eukaryotic cells?
(A) DNA is negatively charged, and the nucleus is too small to contain it without compaction.
(B) Eukaryotic genomes contain too many genes to fit into a cell.
(C) DNA packaging prevents RNA polymerase from accessing genes.
(D) Prokaryotes have more efficient genome organization.
Answer: (A) (DNA is highly negative, requiring histones and chromatin structures to fit in the nucleus.)
How do histones contribute to DNA packaging?
(A) They bind DNA using positively charged lysine and arginine residues, neutralizing its negative charge.
(B) They attach covalently to the DNA backbone to form chromatin.
(C) They only function during mitosis.
(D) They prevent gene transcription permanently.
Answer: (A) (Histones neutralize DNA’s charge, allowing for chromatin compaction.)
How does prokaryotic DNA packaging differ from eukaryotic DNA packaging?
(A) Prokaryotic DNA is wrapped around histones.
(B) Prokaryotic DNA is compacted by supercoiling and nucleoid-associated proteins instead of histones.
(C) Eukaryotic genomes are circular, while prokaryotic genomes are linear.
(D) Prokaryotic genomes contain telomeres.
Answer: (B) (Prokaryotes compact DNA via supercoiling and DNA-binding proteins, not histones.)
Which of the following is true regarding nucleosomes?
(A) They are the most basic unit of DNA packaging in both prokaryotes and eukaryotes.
(B) They consist of DNA wrapped around histone proteins.
(C) They function exclusively during mitosis.
(D) They are found in mitochondria and chloroplasts.
Answer: (B) (Nucleosomes are composed of DNA wrapped around histone octamers.)
What is the primary function of chromatin remodeling complexes?
(A) They permanently silence genes.
(B) They use ATP to reposition nucleosomes, allowing access to DNA for transcription or replication.
(C) They digest histone proteins.
(D) They only function during cell division.
Answer: (B) (Chromatin remodeling complexes make DNA accessible by shifting nucleosomes.)
What distinguishes heterochromatin from euchromatin?
(A) Heterochromatin is transcriptionally inactive and highly condensed, while euchromatin is less condensed and active.
(B) Heterochromatin only exists during mitosis.
(C) Euchromatin contains more genes than heterochromatin.
(D) Euchromatin is permanently open.
Answer: (A) (Heterochromatin is compact and gene-silent, while euchromatin is more open and active.)
What is the purpose of FISH (Fluorescence In Situ Hybridization)?
(A) To sequence entire genomes
(B) To use fluorescent probes to detect specific DNA sequences on chromosomes
(C) To edit genes in living cells
(D) To study protein expression
Answer: (B) (FISH uses fluorescent DNA probes to visualize specific sequences in chromosomes.)
In what scenario would FISH be particularly useful?
(A) Diagnosing chromosomal abnormalities such as deletions or duplications
(B) Measuring mRNA expression
(C) Identifying proteins in cell membranes
(D) Detecting single nucleotide mutations
Answer: (A) (FISH is used in karyotyping to detect large chromosomal abnormalities.)
What is the major advantage of the semiconservative model of DNA replication?
(A) It allows one strand to be used as a template, reducing errors.
(B) It prevents DNA damage.
(C) It does not require enzymes.
(D) It is exclusive to eukaryotic cells.
Answer: (A) (Semiconservative replication ensures accuracy by using an existing strand as a template.)
How does bidirectional replication occur in both prokaryotic and eukaryotic cells?
(A) DNA replication begins at origins of replication, proceeding in two directions simultaneously.
(B) DNA is replicated continuously in one direction.
(C) Replication starts randomly at multiple points.
(D) Only eukaryotic cells use bidirectional replication.
Answer: (A) (Replication proceeds outward from replication origins in both directions.)
Why does DNA replication involve both a leading and lagging strand?
(A) DNA polymerase can only add nucleotides in the 5’ to 3’ direction, requiring discontinuous synthesis on one strand.
(B) The lagging strand is made before the leading strand.
(C) The leading strand undergoes more proofreading.
(D) The lagging strand is unnecessary.
Answer: (A) (DNA polymerase synthesizes in the 5’ to 3’ direction, requiring Okazaki fragments on the lagging strand.)
What is the function of DNA ligase in DNA replication?
(A) It seals the nicks between Okazaki fragments on the lagging strand.
(B) It unwinds DNA at the replication fork.
(C) It synthesizes primers for DNA polymerase.
(D) It repairs base-pair mismatches.
Answer: (A) (DNA ligase joins discontinuous fragments in lagging strand synthesis.)
What is the primary role of helicase in DNA replication?
(A) Unwinding the DNA double helix at the replication fork
(B) Joining Okazaki fragments
(C) Synthesizing RNA primers
(D) Repairing mismatched bases
Answer: (A) (Helicase separates DNA strands, creating single-stranded templates for replication.)
Why is primase necessary for DNA replication?
(A) It synthesizes short RNA primers to provide a 3′-OH group for DNA polymerase
(B) It prevents supercoiling of DNA
(C) It extends the leading strand continuously
(D) It removes RNA primers from Okazaki fragments
Answer: (A) (DNA polymerase cannot start de novo; primase provides an RNA primer for initiation.)
What feature of DNA polymerase enhances replication fidelity?
(A) Requires ATP hydrolysis for every base pair added
(B) Ability to synthesize in both directions
(C) 3’ to 5’ exonuclease activity for proofreading
(D) Can work without a template strand
Answer: (C) (Proofreading ensures incorrect nucleotides are removed and replaced.)
What happens when an incorrect nucleotide is incorporated during replication?
(A) DNA polymerase detects the mismatch and removes it using exonuclease activity
(B) The error remains and is always passed to the next generation
(C) The lagging strand compensates for the mistake
(D) The replication fork collapses
Answer: (A) (DNA polymerase corrects errors using its proofreading function.)
Why is the end-replication problem an issue for eukaryotic chromosomes?
(A) DNA polymerase cannot completely replicate the 5′ ends of linear DNA
(B) Prokaryotic chromosomes face the same issue
(C) Primase cannot bind to the ends of DNA
(D) Ligase activity is disrupted at chromosome ends
Answer: (A) (The lagging strand is left incomplete, leading to chromosome shortening.)
What is the function of telomerase?
(A) It extends the ends of linear chromosomes by adding repetitive sequences
(B) It prevents DNA replication errors
(C) It replaces damaged nucleotides
(D) It facilitates RNA transcription
Answer: (A) (Telomerase maintains telomere length in dividing cells.)
How do histone modifications regulate gene expression?
(A) They alter chromatin structure, making DNA more or less accessible
(B) They permanently remove genes from the genome
(C) They prevent histones from interacting with DNA
(D) They stop DNA replication
Answer: (A) (Acetylation loosens chromatin; methylation can repress or activate genes.)
What is the effect of histone acetylation on transcription?
(A) It prevents RNA polymerase from binding
(B) It condenses chromatin and silences genes
(C) It removes nucleosomes from DNA
(D) It reduces histone-DNA interactions, leading to transcription activation
D - (Acetylation neutralizes histone charge, loosening chromatin for transcription.)
How does nucleotide excision repair (NER) fix DNA damage?
(A) It removes damaged bases and replaces the segment with new DNA
(B) It only works during replication
(C) It converts double-stranded DNA into single-stranded RNA
(D) It permanently deletes damaged genes
Answer: (A) (NER corrects bulky lesions like UV-induced thymine dimers.)
What is the key difference between base excision repair (BER) and mismatch repair (MMR)?
(A) BER fixes single damaged bases, while MMR corrects replication errors
(B) MMR is used for UV damage
(C) BER only occurs in prokaryotes
(D) MMR replaces entire DNA strands
Answer: (A) (BER removes chemically altered bases; MMR fixes mismatches.)
How are eukaryotic chromosomes organized within the nucleus?
(A) Chromosomes occupy distinct territories to prevent tangling
(B) They float randomly throughout the nucleoplasm
(C) They interact with the endoplasmic reticulum
(D) They move freely between the cytoplasm and nucleus
Answer: (A) (Chromosome territories help organize nuclear function.)
How does the nuclear envelope contribute to genome regulation?
(A) It contains nuclear pores that regulate the transport of RNA and proteins
(B) It isolates DNA completely from the cytoplasm
(C) It prevents all proteins from entering the nucleus
(D) It degrades excess mRNA
Answer: (A) (Nuclear pores control movement of molecules between the nucleus and cytoplasm.)
Why do eukaryotic genomes require multiple origins of replication?
(A) Their genomes are much larger and replication must occur efficiently
(B) They have circular chromosomes
(C) Their DNA polymerase is slower than prokaryotic enzymes
(D) They only replicate their genomes once per cell cycle
a
How does prokaryotic DNA replication differ from eukaryotic replication?
(A) Prokaryotic replication requires telomerase
(B) Prokaryotic DNA is linear
(C) Eukaryotic replication occurs in the cytoplasm
(D) Prokaryotes have a single origin of replication, while eukaryotes have multiple origins
D
What is the primary function of chromatin immunoprecipitation (ChIP)?
(A) To identify proteins bound to specific DNA regions in living cells
(B) To measure mRNA levels
(C) To separate DNA by size
(D) To sequence entire genomes
a
Why is next-generation sequencing (NGS) useful in genome analysis?
(A) It only detects mutations
(B) It allows high-throughput sequencing of entire genomes quickly and accurately
(C) It measures protein activity
(D) It does not require DNA polymerase
B
histones
-histones are small proteins- rich in lysine and arginine
-positive charge neutralizes negative charge of DNA (wrapping DNA around histone helps with neutralization)
linker histone structure and function
Structure:
H1 is not part of the histone octamer but is a separate histone protein.
It has a globular central domain and long N- and C-terminal tails, which interact with DNA.
Function:
Stabilizes nucleosome structure by binding where DNA enters and exits the nucleosome core.
Compacts chromatin by promoting the formation of higher-order chromatin structures (30-nm fiber).
Regulates gene expression by influencing DNA accessibility to transcription factors and polymerases.
Key Concept: H1 acts as a “clamp” to secure DNA around nucleosomes and facilitates chromatin compaction.
packaging of nucleosomes
-sequence-specific clamp proteins and cohesins are involved in forming chromatin loops
-as cells enter mitosis, condensins replace most cohesins to form double loops of chromatin to generate compact chromosomes
structure and function of cohesins
Structure:
Cohesins are ring-shaped protein complexes composed of SMC (Structural Maintenance of Chromosomes) proteins and accessory subunits.
The core complex includes SMC1, SMC3, SCC1 (RAD21), and SCC3.
Function:
Chromatid Cohesion: Holds sister chromatids together from S-phase until anaphase to ensure accurate chromosome segregation.
DNA Repair: Helps facilitate homologous recombination by keeping sister chromatids close.
Gene Regulation & Chromatin Structure: Contributes to chromatin looping, regulating transcription.
Separation During Anaphase: Cleaved by separase enzyme, allowing sister chromatids to separate during mitosis/meiosis.
Key Concept: Cohesins act as molecular “glue” holding sister chromatids together until they are properly aligned for separation.
heterochromatin
Highly condensed chromatin
-meiotic and mitotic chromosomes
-centromeres and telomeres
-time spent highly condensed varies
-heterochromatic regions of interphase chromosomes are areas where gene expression is SURPRESSED
euchromatin
relatively non-condensed chromatin
-degree of condensation varies
-level of activity varies
active euchromatic regions of interphase chromosomes are areas where genes tend to be expressed
What is the structure and function of condensins in chromosome organization?
Structure:
Condensins are multi-subunit protein complexes belonging to the SMC (Structural Maintenance of Chromosomes) family.
Core subunits include SMC2 and SMC4, along with regulatory subunits (CAP-D2, CAP-G, CAP-H in condensin I; CAP-D3, CAP-G2, CAP-H2 in condensin II).
Function:
Chromosome Condensation: Compacts DNA during mitosis and meiosis, facilitating chromosome segregation.
Loop Extrusion: Helps create and stabilize chromatin loops, essential for higher-order chromosome structure.
Regulation of Gene Expression: Influences chromatin architecture, impacting transcriptional activity.
Chromosome Segregation: Ensures proper chromosome alignment and prevents tangling during cell division.
Key Concept: Condensins drive chromosome compaction, ensuring proper segregation during mitosis and meiosis by organizing DNA into higher-order structures.
how does a gene being expressed reorient chromatin?
gene OFF: genes in the middle of compact chromatin, homologous chromosomes detected by hybridization techniques
gene ON: genes move around from condensed(compact) area
what is the direction of dna replication?
there are 3 main models but focusing on…
Bidirectional growth from one starting point in the 5’ to 3’ direction
where does DNA rep start?
Always starts from the same location on DNA
-What are some of the characteristics of the sequences at replication origins?
–easy to open, A-T rich
–recognized by initiator proteins that bind
to the DNA
how does DNA replication proceed in bacteria?
this style of replication only applies to:
-circular genomes
what happens at the DNA replication forks?
Replication fork is ASYMMETRICAL
-strands get duplicated differently
Leading strand replicated continuously
-lagging strand replicated discontinuously
dna replication procedure
1) separate DNA strands
2) synthesize DNA
3) proofread newly synthesized dna
ingredients for synthesis
origin of replication
primers
dNTPs (building blocks for dna)
ATP (energy source)
DNA polymerase
Accessory proteins
Chromatin Structure (Eukaryotes)
Chromatin = DNA + Proteins (like a coiled telephone wire)
🟢 Euchromatin → Loose, active, genes ON 🟢
🔴 Heterochromatin → Tightly packed, genes OFF 🔴
🚨 Exam Tip: Heterochromatin is found at centromeres & telomeres (stays permanently off).
Which protein helps DNA remain compact during mitosis?
condensin
The Replication Fork – How DNA is Copied
Imagine unzipping a zipper. That’s what helicase does!
🔹 Leading strand – Copied continuously
🔹 Lagging strand – Copied in fragments (Okazaki fragments)
💡 Key Concept: DNA polymerase can’t start on its own – it needs an RNA primer!
🚨 Exam Tip: Primase makes RNA primers to help start DNA replication.
Key Players in DNA Replication
🚀 Helicase → Unzips DNA (breaks hydrogen bonds)
🧷 Single-Strand Binding Proteins (SSBs) → Keep strands apart
🔗 Primase → Lays down RNA primer
🛠 DNA Polymerase → Adds new DNA (5’ → 3’ only!)
✂️ DNA Ligase → Seals Okazaki fragments
bacterial dna replication
1️⃣ Origin of Replication (oriC) – The starting point where replication begins.
2️⃣ Binding of Initiator Proteins – These proteins recognize oriC and prepare DNA for copying.
3️⃣ Unwinding by Helicase – The “unzipping” enzyme breaks hydrogen bonds between bases.
4️⃣ Single-Strand Binding Proteins (SSBs) – These keep the strands apart so they don’t reattach.
5️⃣ RNA Primers Made by Primase – DNA polymerase needs a starting point, so primase lays down short RNA primers.
6️⃣ DNA Polymerase – The builder enzyme adds new DNA nucleotides in the 5’ → 3’ direction.
7️⃣ Sliding Clamp – Holds DNA polymerase in place so it doesn’t fall off the DNA strand.
8️⃣ Nick Sealing by DNA Ligase – DNA ligase glues Okazaki fragments together on the lagging strand
main concepts
✅ DNA replication is semi-conservative (1 old + 1 new strand).
✅ Helicase unwinds DNA; SSBs keep strands apart; DNA polymerase builds new DNA.
✅ Leading strand = continuous; lagging strand = Okazaki fragments.
✅ Telomerase prevents chromosome shortening.
✅ DNA polymerase has proofreading (3’ → 5’ exonuclease activity).
✅ Mismatch repair corrects replication errors that proofreading misses.
✅ NER removes bulky DNA damage like thymine dimers.
Transcription Step 1: Initiation – Finding the Start Line
📌 RNA polymerase must find the right place to start transcribing DNA into RNA. This start point is called the promoter.
🛠 Key Players in Bacterial Transcription Initiation:
✅ RNA Polymerase → The enzyme that builds RNA
✅ Sigma Factor (σ factor) → Helps RNA polymerase find the promoter
✅ Promoter Sequences (-10 and -35 regions) → Specific DNA sequences that signal RNA polymerase where to bind
💡 Easy Analogy:
RNA polymerase is like a car, and the sigma factor is like GPS guiding it to the correct starting location (promoter).
Transcription Step 2: Elongation – Making the RNA Chain
Once RNA polymerase starts, sigma factor leaves and RNA polymerase moves forward, adding RNA nucleotides.
📌 Key Points:
✅ RNA is made 5’ → 3’ (just like DNA replication!)
✅ RNA polymerase does not need a primer
✅ The RNA strand is complementary to the DNA template strand
💡 Easy Analogy:
Think of RNA polymerase like a train, and DNA is the track. The train moves forward, laying down new RNA “tracks” behind it.
🚨 Exam Tip: RNA polymerase does NOT proofread like DNA polymerase!
Types of Mutations:
1️⃣ Silent Mutation – No change in the amino acid (due to redundancy)
2️⃣ Missense Mutation – One amino acid is changed (can be harmless or harmful)
3️⃣ Nonsense Mutation – Creates a STOP codon → Protein is too short!
4️⃣ Frameshift Mutation – Insertion/deletion shifts the reading frame → Disastrous!
