Biology Exam #4: DNA, Protein Synthesis, and Cell Division

Comprehensive vocabulary flashcards covering DNA structure, transcription, translation, protein structure, the cell cycle, mitosis, and oncogenesis based on biology lecture notes.

Purines

Double-ring nitrogenous bases found in DNA, specifically adenine and guanine.

Pyrimidines

Single-ring nitrogenous bases found in DNA, specifically thymine and cytosine.

Phosphodiester bond

The C-O-P-O-C linkage connecting two adjacent nucleotides by linking one nucleotide to the phosphate group of another.

Base stacking

The arrangement where the flat, nonpolar (hydrophobic) surfaces of DNA bases stack on top of each other along the same strand, contributing to double helix stability.

Van der Waals forces

Weak attractions between neighboring nonpolar atoms caused by transient positive and negative charges as electrons move, helping stabilize stacked DNA bases.

DNA polymerization directionality

The process by which DNA is synthesized exclusively in the $5' \rightarrow 3'$ direction because DNA polymerase can only attach the incoming phosphate group to a free $3'\text{-OH}$ group.

Promoter

A specific sequence of double-stranded DNA, commonly consisting of the sequence TATAAA, where transcription factors and RNA polymerase bind to initiate transcription.

Transcription bubble

The unwound region of DNA created by RNA polymerase that exposes the template strand for RNA synthesis.

Prokaryotic transcription

Transcription that occurs in the cytoplasm without a nucleus, allowing mRNA to be translated immediately while transcription is still occurring.

Eukaryotic transcription

Transcription occurring within the nucleus, requiring the primary mRNA transcript to undergo processing before exiting to the cytoplasm.

5′ cap

A protective modification added to the beginning ($5'$ end) of eukaryotic mRNA that protects it from degradation and aids ribosome recognition.

Poly-A tail

A modification added to the end ($3'$ end) of eukaryotic mRNA that protects it against degradation and facilitates transport to the cytoplasm.

RNA splicing

The post-transcriptional process in which noncoding introns are excised and protein-coding exons are spliced together to form a mature mRNA transcript.

Alternative splicing

The differential joining of exons in diverse combinations, enabling a single gene to encode multiple distinct but related proteins.

Amino acid core structure

A fundamental structure consisting of a central $\alpha$-carbon bonded to four distinct chemical entities: a carboxyl group, an amino group, a hydrogen atom, and a variable R-group (side chain).

Polypeptide R-group arrangement

The alternating orientation of side chains (boxed in black) on opposite sides along the amino acid backbone, which directly dictates protein folding and side-chain interactions.

Hydrophobic amino acids

Nonpolar amino acids that aggregate in the central core/interior of folded proteins to stay shielded from the aqueous cellular environment.

Hydrophilic amino acids

Strongly polar, basic (positively charged), or acidic (negatively charged) amino acids that typically locate to the outer surface of folded proteins.

Peptide bond

A covalent linkage formed between adjacent amino acids to assemble a polypeptide chain.

Primary structure

The linear sequence of amino acids within a polypeptide chain, conventionally denoted using three-letter abbreviations (e.g., Ala-Met-Ala-Met).

Secondary structure

Localized conformational patterns (alpha helices or beta sheets) stabilized by hydrogen bonding between functional groups of the polypeptide backbone, independent of R-groups.

Alpha helix

A tightly coiled right-handed helical protein motif containing $3.6$ amino acids per turn, maintained by hydrogen bonds between each residue's carboxyl group and the amide group four positions ahead.

Beta sheet

A secondary protein structure characterized by polypeptide segments folding back and forth in parallel or antiparallel alignments, stabilized by backbone hydrogen bonds.

Tertiary structure

The overarching three-dimensional conformation of an individual protein, governed by interactions among variable R-groups, secondary motifs, and hydrophobic/hydrophilic effects.

Quaternary structure

The multi-subunit protein arrangement formed when two or more distinct polypeptide subunits assemble into a single functional complex.

Denaturation

The unfolding and loss of functional three-dimensional structure of a protein caused by exposure to elevated temperatures or chemical treatments.

Codon

A triplet of consecutive nucleotides on an mRNA strand that codes for a specific amino acid or acts as a stop signal during translation.

Anticodon

A sequence of three nucleotides on a tRNA molecule that base-pairs complementarily with an mRNA codon during translation.

Aminoacyl-tRNA synthetase

The enzyme responsible for attaching the correct cognate amino acid onto its corresponding tRNA molecule, thereby charging it.

A site

The aminoacyl site of the ribosome, which receives and binds the incoming charged aminoacyl-tRNA.

P site

The peptidyl site of the ribosome where the forming peptide bond is synthesized between adjacent amino acids.

E site

The exit site of the ribosome where deacylated tRNA molecules are released following peptide bond formation.

Binary fission

The mechanism of asexual cell division in prokaryotes where the circular genome is duplicated, the cell elongates, and divides into two identical daughter cells.

M phase

The stage of the cell cycle during which the parent cell divides into two daughter cells via nuclear division (mitosis) and cytoplasmic division (cytokinesis).

Interphase

The interval separating two successive M phases, comprising the $G_1$, S, and $G_2$ phases.

G1 phase

The phase of interphase dedicated to cell growth, expression of regulatory proteins, and cytoplasm duplication.

S phase

The phase of interphase during which DNA synthesis and chromosome replication take place.

G2 phase

The interphase period during which the cell completes final preparations for mitosis and cytokinesis.

G0 phase

A resting state entered by cells that are not actively dividing or cycling.

Helicase

The replication enzyme that unwinds and separates the two complementary parental strands of the DNA double helix.

Single-stranded binding proteins

Proteins that coat and stabilize unwound single strands of DNA to prevent premature reannealing during replication.

Topoisomerase II

The enzyme that relieves torsional strain and torsional stress caused by the unwinding of the DNA double helix.

RNA primase

The enzyme that initiates synthesis of a new DNA strand by laying down a short complementary RNA primer.

DNA ligase

The enzyme that covalently seals nicks and joins Okazaki fragments together into a continuous DNA strand.

Okazaki fragments

Short, discontinuous segments of DNA synthesized along the lagging strand during DNA replication.

Telomeres

Repetitive noncoding DNA sequences capping the ends of linear eukaryotic chromosomes that protect against chromosome degradation and shortening.

Telomerase

The enzyme that elongates the terminal sequences of linear eukaryotic chromosomes to counteract shortening during replication cycles.

Sister chromatids

Two identical copies of a chromosome generated during replication that are joined together at a shared centromere.

Centromere

The central constricted chromosomal region where sister chromatids are held together.

Kinetochore

Protein complexes situated on chromosomes that serve as the anchor attachment points for spindle microtubules.

Prophase

The first phase of mitosis, characterized by chromosome condensation, initiation of nuclear envelope breakdown, and centrosome migration to opposite cellular poles.

Prometaphase

The second phase of mitosis during which the nuclear membrane completely dismantles and mitotic spindle microtubules attach to chromosome kinetochores.

Metaphase

The third phase of mitosis wherein condensed chromosomes align along the middle (equatorial plate) of the cell.

Anaphase

The fourth phase of mitosis wherein spindle fibers contract repeatedly, separating sister chromatids and pulling them apart toward opposite poles.

Telophase

The fifth phase of mitosis wherein spindle microtubules disassemble and new nuclear envelopes reform around each set of separated chromosomes.

Apoptosis

Programmed cell death that eliminates damaged cells to prevent aberrant division and facilitates proper tissue morphogenesis, such as the separation of digits.

p53

A tumor suppressor protein activated by DNA damage that upregulates the Bax gene, forming Bax/Bax dimers to trigger apoptosis.

Oncogene

A mutated, cancer-causing gene that drives unchecked cellular proliferation.

Proto-oncogenes

Normal cellular genes governing regular cell division that can mutate into cancer-promoting oncogenes, metaphorically functioning as the cell cycle's 'gas pedal'.

Tumor suppressors

Normal regulatory genes that signal cells to halt division (acting like 'brakes'); their loss of function or mutation permits malignant cellular growth.