bio h fall final

What is a nucleotide?

The monomer (building block) of DNA and RNA. Composed of three parts: a phosphate group, a 5-carbon sugar (deoxyribose in DNA, ribose in RNA), and a nitrogenous base.

What are the three parts of a nucleotide?

1. Phosphate group 2. 5-carbon sugar 3. Nitrogenous base

What is the function of DNA?

To store and transmit genetic information.

What sugar is found in DNA?

Deoxyribose (lacks an oxygen on the 2' carbon).

What sugar is found in RNA?

Ribose (has a hydroxyl –OH group on the 2' carbon).

What are the four nitrogenous bases in DNA?

Adenine (A), Thymine (T), Guanine (G), Cytosine (C)

Which base is found ONLY in DNA (not RNA)?

Thymine (T) — replaced by Uracil in RNA.

Which base is found ONLY in RNA (not DNA)?

Uracil (U) — replaces Thymine.

What are the four nitrogenous bases in RNA?

Adenine (A), Uracil (U), Guanine (G), Cytosine (C)

Base pairing rule: Adenine pairs with…

Thymine (in DNA) or Uracil (in RNA); held by 2 hydrogen bonds.

Base pairing rule: Guanine pairs with…

Cytosine; held by 3 hydrogen bonds.

What type of bond holds complementary bases together?

Hydrogen bonds (weak individually, but strong collectively).

What are purines? Which bases are purines?

Purines have a double-ring structure. Adenine (A) and Guanine (G) are purines.

What are pyrimidines? Which bases are pyrimidines?

Pyrimidines have a single-ring structure. Cytosine (C), Thymine (T), and Uracil (U) are pyrimidines.

What are the two backbone components of DNA?

Alternating phosphate groups and deoxyribose sugars (the sugar-phosphate backbone). Bases are found in the center.

What does "antiparallel" mean in DNA structure?

The two strands of DNA run in opposite directions — one runs 5'→3' and the other runs 3'→5'.

What is the 5' end of a DNA strand?

The end where a free phosphate group is attached to the 5' carbon of the sugar.

What is the 3' end of a DNA strand?

The end where a free hydroxyl (–OH) group is attached to the 3' carbon of the sugar.

What does "semi-conservative replication" mean?

Each new DNA molecule consists of one original (parental) strand and one newly synthesized strand.

What is the role of DNA helicase?

Unzips (unwinds) the DNA double helix by breaking hydrogen bonds between base pairs.

What is the role of DNA polymerase?

Adds new DNA nucleotides to the growing strand in the 5'→3' direction during replication.

What direction does DNA polymerase add nucleotides?

5' to 3' direction (adds to the 3' end of the growing strand).

Where does DNA replication occur?

In the nucleus (of eukaryotic cells).

What are Okazaki fragments?

Short segments of DNA synthesized on the lagging strand during replication, because DNA polymerase can only work 5'→3' and the lagging strand runs in the opposite direction.

What is the main structural difference between DNA and RNA?

DNA is double-stranded with deoxyribose sugar and thymine; RNA is single-stranded with ribose sugar and uracil.

If a DNA sample contains 30% Thymine, what % is Adenine? What % is Guanine?

Adenine = 30% (A pairs with T). Guanine = 20% (since A+T = 60%, the remaining 40% is split equally between G and C).

What is a micropipette used for?

To measure and transfer very small, precise volumes of liquid (in microliters, µL).

What is the volume range of a P20 micropipette?

2 µL to 20 µL

What is the volume range of a P200 micropipette?

20 µL to 200 µL

Which stop do you use when taking up liquid with a micropipette?

The first stop (press to first stop before entering liquid, then release slowly to draw up).

Which stop do you use when dispensing liquid with a micropipette?

The second stop (push past first stop to fully expel liquid).

What is a centrifuge used for?

To spin samples at high speed, separating substances by density (denser materials pellet at the bottom).

Why must a centrifuge be balanced?

Unbalanced loads can damage the rotor and cause dangerous vibration. Balance tubes of equal mass are added opposite uneven samples.

What is gel electrophoresis used for?

To separate DNA (or protein) fragments by size using an electric current through an agarose gel.

How does DNA move in gel electrophoresis?

DNA is negatively charged, so it migrates toward the positive electrode (anode). Smaller fragments move faster and farther.

What is a restriction enzyme?

A protein that cuts DNA at a specific recognition sequence (restriction site). Each enzyme recognizes a unique sequence.

What is a sticky end (in restriction enzyme cuts)?

A staggered cut that leaves single-stranded overhangs, which can base-pair with complementary sticky ends for ligation.

What is a blunt end (in restriction enzyme cuts)?

A straight cut through both strands, leaving no overhangs.

What is a plasmid?

A small, circular, double-stranded DNA molecule found in bacteria that replicates independently of the chromosome. Used as a vector in biotechnology.

What is a recombinant plasmid?

A plasmid that has been cut with restriction enzymes and had foreign DNA (a gene of interest) inserted and ligated in.

What is a competent cell?

A bacterial cell that has been treated (e.g., with calcium chloride + heat shock) to make its membrane permeable and able to take up foreign DNA/plasmids.

What is a transformed cell?

A cell that has successfully taken up and incorporated foreign DNA (e.g., a plasmid).

What is the ampR gene in the pARA-R plasmid?

A gene that codes for ampicillin resistance — it allows transformed bacteria to survive on ampicillin-containing plates.

What is the araC gene in the pARA-R plasmid?

A regulatory gene that produces a protein activating the pBAD promoter when arabinose is present.

What is the pBAD promoter?

A regulatory DNA sequence (not a gene) that controls expression of the rfp gene — it switches on when arabinose is present.

What is the rfp gene?

A gene that encodes red fluorescent protein (RFP), causing bacteria to appear red/pink when expressed.

What can grow on an LB plate?

All bacteria (both transformed and untransformed), since LB is just nutrient agar.

What can grow on an LB/AMP plate?

Only bacteria that contain the ampR gene (i.e., successfully transformed bacteria).

What can grow as red colonies on an LB/AMP/ARA plate?

Only transformed bacteria that express the rfp gene in the presence of arabinose — producing red fluorescent protein.

In the transformation lab, how should plate P− (no plasmid, LB/AMP) appear if the experiment worked?

No colonies — bacteria without the plasmid have no ampicillin resistance and cannot survive.

What is an agar plate?

A petri dish filled with a nutrient gel (agar) used to grow and culture bacteria.

What is the Central Dogma of molecular biology?

The flow of genetic information: DNA → (transcription) → RNA → (translation) → Protein.

What is transcription?

The process of copying information from DNA into messenger RNA (mRNA), carried out in the nucleus by RNA polymerase.

What is translation?

The process of decoding mRNA to synthesize a specific sequence of amino acids (a protein), carried out at ribosomes.

What enzyme carries out transcription?

RNA polymerase (it both unzips DNA and adds RNA nucleotides).

Where does transcription occur?

In the nucleus.

Where does translation occur?

At the ribosomes (in the cytoplasm or on the rough ER).

What is the result of transcription?

A single-stranded mRNA molecule.

What is the result of translation?

A polypeptide (chain of amino acids) / protein.

What are the three types of RNA and their functions?

1. mRNA (messenger RNA) — carries the genetic code from DNA to the ribosome. 2. rRNA (ribosomal RNA) — structural/functional component of ribosomes. 3. tRNA (transfer RNA) — carries amino acids to the ribosome, matching anticodon to mRNA codon.

What is a codon?

A sequence of three consecutive nucleotides on mRNA that codes for a specific amino acid (or a stop/start signal).

How many bases make up one codon?

3 bases (a triplet).

What is the universal start codon?

AUG — codes for the amino acid methionine (Met).

What is an anticodon?

A sequence of three bases on a tRNA molecule that is complementary to a specific mRNA codon.

If the mRNA codon is GUC, what is the tRNA anticodon?

CAG (complementary and antiparallel: G→C, U→A, C→G).

During transcription, if the DNA template has thymine (T), what base goes in the mRNA?

Adenine (A). (T on DNA → A on mRNA)

During transcription, if the DNA template has adenine (A), what base goes in the mRNA?

Uracil (U). (A on DNA → U on mRNA)

What is a missense mutation?

A point mutation where one base change results in a codon that codes for a DIFFERENT amino acid, potentially altering protein function.

What is a silent mutation?

A point mutation where a base change results in a codon that still codes for the SAME amino acid — no change in protein.

What is a nonsense mutation?

A point mutation that changes an amino-acid codon into a STOP codon, causing premature termination of the protein.

What is a frameshift mutation?

An insertion or deletion of bases that shifts the reading frame of the mRNA, altering all codons downstream — usually catastrophic to protein function.

What is the template strand of DNA?

The strand of DNA that RNA polymerase reads (3'→5') to produce a complementary mRNA strand.

What is a stem cell?

An undifferentiated cell capable of self-renewal and differentiation into specialized cell types.

What is differentiation?

The process by which an unspecialized (undifferentiated) cell becomes a specialized cell with a specific function.

What is a totipotent stem cell?

Can give rise to ALL cell types, including placenta. Example: a fertilized egg (zygote).

What is a pluripotent stem cell?

Can give rise to almost any cell type in the body EXCEPT placental cells. Example: embryonic stem cells; planarian stem cells.

What is a multipotent stem cell?

Can differentiate into a limited range of related cell types. Example: adult human stem cells (e.g., bone marrow stem cells → blood cells only).

What are the phases of the cell cycle in order?

G1 → S → G2 → M (Mitosis) → Cytokinesis (then back to G1 or G0).

What happens in G1 phase?

The cell grows, synthesizes proteins, and carries out normal functions. First growth phase; prepares for DNA replication.

What happens in S phase?

DNA is replicated (synthesized) — each chromosome is duplicated.

What happens in G2 phase?

The cell continues to grow, produces additional proteins and organelles, and prepares for cell division.

What happens in M phase (mitosis)?

The replicated chromosomes are separated into two new nuclei; followed by cytokinesis (division of cytoplasm).

What is G0?

A resting/quiescent state where the cell is neither dividing nor preparing to divide (exits the cell cycle).

What are the stages of mitosis in order?

Prophase → Metaphase → Anaphase → Telophase (+ Cytokinesis)

What happens during Prophase?

Chromosomes condense and become visible; mitotic spindle forms; nuclear envelope breaks down.

What happens during Metaphase?

Chromosomes line up at the cell's equator (metaphase plate); spindle fibers attach to centromeres.

What happens during Anaphase?

Sister chromatids are pulled apart to opposite poles of the cell by spindle fibers.

What happens during Telophase?

Nuclear envelopes reform around each set of chromosomes; chromosomes begin to decondense; cell begins to pinch.

What is cytokinesis?

The division of the cytoplasm following mitosis, producing two separate daughter cells.

What does mitosis produce?

Two genetically identical diploid daughter cells (somatic/body cells).

What is a cell cycle checkpoint?

A regulatory point in the cell cycle where the cell's progress is monitored and errors are detected before proceeding.

What is checked at the G1 checkpoint?

Is the cell large enough? Is the DNA undamaged? Are growth signals present?

What is checked at the G2 checkpoint?

Was DNA replicated correctly and completely? Is the cell large enough to divide?

What is checked at the Metaphase (spindle assembly) checkpoint?

Are all chromosomes properly attached to spindle fibers at the metaphase plate?

What is apoptosis?

Programmed cell death — a controlled process where a damaged or unneeded cell destroys itself to protect the organism.

What is a proto-oncogene?

A normal gene that promotes cell growth and division (like a gas pedal). Mutation can turn it into an oncogene.

What is an oncogene?

A mutated proto-oncogene that is permanently "on," causing uncontrolled cell division — acts like a stuck gas pedal.

What is a tumor suppressor gene?

A gene that inhibits cell division and promotes apoptosis (like a brake pedal). Example: p53.

What does the p53 gene do?

Detects DNA damage and either halts the cell cycle for repair or triggers apoptosis. Often called the "guardian of the genome."

How does a tumor suppressor gene mutation lead to cancer?

When mutated (inactivated), the "brake" is removed — cells with damaged DNA are not stopped or destroyed, allowing uncontrolled division.