Cell biology basics

Nucleus

Cell’s central organelle; contains the cell’s DNA

Nucleolus

Small region of the nucleus that functions in ribosome synthesis

Ribosomes

An organelle that serves as the site of protein synthesis. It is composed of two ribosomal RNA subunits that wrap around mRNA to start the process of translation, followed by protein synthesis.

Rough Endoplasmic Reticulum

• Its membrane is dotted with embedded granules—organelles called ribosomes, giving it a bumpy appearance.

• Primary job is the synthesis and modification of proteins destined for the cell membrane or for export from the cell.

Smooth Endoplasmic Reticulum

• Lacks ribosomes

• Synthesis of lipids; synthesizes phospholipids, the main component of biological membranes, as well as steroid hormones.

• Sequesters (i.e., stores) and regulates the concentration of cellular Ca⁺⁺

• Metabolizes some carbohydrates and performs a detoxification role, breaking down certain toxins.

Golgi Apparatus

• Looks like stacked flattened discs

• Responsible for sorting, modifying, and shipping off the products that come from the rough ER

Lysosomes

• An organelle that contains enzymes that break down and digest unneeded cellular components, such as a damaged organelle.

• Originate from Golgi vesicles

Peroxisome

• A membrane-bound cellular organelle that contains mostly enzymes

• lipid metabolism and chemical detoxification.

• enzymes within this organelle serve to transfer hydrogen atoms from various molecules to oxygen, producing hydrogen peroxide (H₂O₂). Combat reactive oxygen species

Proteasome

• It breaks down proteins, the building blocks and mini-machines that make up many cell parts

• The barrel-shaped organelle disassembles damaged or unwanted proteins, breaking them into bits that the cell can reuse to make new proteins

Transcription

RNA polymerase transcribes a gene’s DNA into an RNA transcript with a complimentary sequence

Where does transcription take place in a cell?

The nucleus

The 3 stages of transcription

Initiation, Elongation, Termination

Transcription (initiation)

• An enzyme called RNA polymerase attaches to a specific DNA sequence called a promoter, which marks the start of a gene.

• Proteins called transcription factors help the RNA polymerase bind to the promoter and open up the DNA double helix.

• The two DNA strands separate so the enzyme can read the bases on the template/non-coding strand

Transcription (Elongation)

• RNA polymerase moves along the DNA template strand and builds a new messenger RNA (mRNA) strand.

• The enzyme adds matching RNA nucleotides using base pair rules (adenine pairs with uracil, and cytosine pairs with guanine).

• The mRNA strand grows in the 5' to 3' direction.

Transcription (Termination)

• The RNA polymerase reaches a special DNA sequence called a terminator.

• Transcription stops, and the completed RNA strand detaches from the DNA.

• The DNA strands zip back together into a double helix

RNA splicing

A molecular biology process that edits a newly made precursor messenger RNA (pre-mRNA) into a mature messenger RNA (mRNA) by removing non-coding regions called introns and joining coding regions called exons

Translation

• The ribosome translates the mRNA code into amino acids.

• Special RNAs called transfer RNA (tRNA) bring amino acids to the ribosome, and the ribosome assembles them into a growing polypeptide chain.

Juxtacrine signaling

A type of cell-to-cell communication that requires direct physical contact between adjacent cells

Paracrine signaling

A type of local cell communication where a cell releases chemical signals to affect nearby target cells (short distance).

Endocrine signaling

A long-distance form of cell communication where specialized endocrine cells release hormones into the bloodstream to regulate distant target cells

Fat-soluble receptors are located….

Inside the cell membrane

Water-soluble receptors are located…..

Outer cell membrane

The signal is a

Ligand

Ion channel

• Ligand binds causing the channel to open

• Ions move in or out → intracellular electrical signal → cell responds

• Common in nervous system

Enzyme (Receptor Tyrosine kinases)

• Ligand Binding: A signaling molecule (like a growth factor or insulin) binds to the outside part of the receptor monomer

• Dimerization: The binding causes two receptor units to come together and form a pair, known as a dimer

• Autophosphorylation (Cross-Phosphorylation): The joined tyrosine kinase domains activate each other and add phosphate groups to specific tyrosine amino acids on the tail of the opposing receptor

• Signaling Complex Assembly: These newly phosphorylated tyrosine sites act as docking platforms. Intracellular relay and adapter proteins with specialized domains (like SH2 domains) bind to these sites.

• Signal Transduction Cascade: Signaling cascades relayed by activated signaling proteins into the cell’s interior which lead to cell growth and proliferation

G-protein-coupled

• Epinephrine binds to GCPR, which activates the G-protein in the cell.

• Activated G-protein then activates adenylyl cyclase, the enzyme that converts ATP into cAMP.

• The increase in cAMP activates PKA

• PKA activates glycogen phosphorylase which breaks down glycogen and eventually yielding glucose.

Signal transduction

Second messengers

RTK and insulin

• Insulin binds to RTK receptor on muscle or fat cell

• Activated RTK phosphorylates other proteins → translocation of glucose transporters to cell surface

• Glucose enters cell

• Blood glucose decreases

Stopping cell signaling

• Stop the signal at the receptor (Remove or degrade the signal molecule, Internalize or sequester the receptor, Inactivate or down regulate the receptor)

• Stop the signal inside the cell (Break down second messengers, Inactivate signaling proteins, Remove phosphate groups, Degrade or inactivate key proteins)

Cell cycle

Each time the cell divides into two, it goes through a sequence of events that may include growth, DNA replication, preparation to divide, and finally division.

Interphase

• the longest phase of the cell cycle where a cell grows, performs its normal functions, and copies its DNA to prepare for cell division

• Includes G1, S, and G2 phases

G1 (First Gap phase)

The cell increases in size and prepares to replicate its DNA.

G1 checkpoint

Toward the end of G1, the cell has to be sufficiently healthy to replicate its DNA. If the DNA is undamaged and enough resources are available for the cell to keep growing and divide, growth signals will stimulate the cell to proceed to the DNA synthesis, or S, phase. Otherwise, either the cell dies or it enters a resting state, also referred to as G0 phase.

G0 phase

• Toward the end of the G1 phase, a cell can "exit" the cell cycle when it receives a signal to differentiate, or when resources are insufficient to grow and divide. Whether or not a cell exits the cell cycle depends on the organism’s stage in development, the type of cell, and the resources available.

• a resting, or nondividing, stage.

S (Synthesis phase)

The cell replicates its DNA. At the end of this phase, the cell has two complete sets of chromosomes.

S phase checkpoint

Throughout the S phase, DNA is continuously monitored for replication errors. If DNA synthesis progresses without errors, growth signals will stimulate the cell to proceed to G2, during which the cell matures.

G2 (second gap phase)

The cell continues to grow and prepares for division.

G2 Checkpoint

To proceed to the next phase, all chromosomes have to be fully replicated and contain no other types of damage. Only then can it enter mitosis, or M phase, and divide.

M phase (mitosis)

In this last phase of the cell cycle, the cell stops growing and divides into two daughter cells, each with the same number of chromosomes

M checkpoint

For mitosis to proceed correctly, the two copies in a duplicated chromosome (each called a sister chromatid) should both be attached to the mitotic spindle. If they are, mitosis continues: The two sister chromatids separate, becoming two chromosomes. The two identical sets of chromosomes move to opposite ends of the dividing cell.

Mitosis

A type of cell division where a single cell divides into two genetically identical daughter cells

Prophase and Prophase II

Chromosomes, which contain genetic information, condense and prepare to attach to the spindle—a cellular machine that moves chromosomes during cell division.

Metaphase and Metaphase II

Chromosomes align along the spindle’s center

Anaphase and Anaphase II

Chromosomes pull apart and move toward the spindle’s poles, which also move apart

Telophase and Telophase II

New nuclear envelopes form around the two separated sets of chromosomes (creates 2 and 4 cells respectively)

Cytokinesis

Cells divide

Meiosis

A specialized type of cell division that reduces the chromosome number by half, producing four genetically distinct haploid gametes (sperm and egg cells) from a single diploid cell

Prophase I

• As the chromosomes condense, they form groups of four chromatids called tetrads or bivalents. Close inspection reveals that each chromosome is replicated and consists of two sister chromatids.

• Crossing over

Metaphase I

The tetrads (homologous chromosomes) are at the center of the cell

Anaphase I

The chromosomes that make up each tetrad separate

Telophase I

The cell divides into two cells

Haploid (n)

A cell with one complete set of unique chromosomes. Examples include human sperm and egg cells, where (n = 23)

Diploid (2n)

A cell with two complete sets of chromosomes—one set from each parent. Regular body cells (somatic cells) are diploid. For humans, (2n = 46) (23 pairs)

Nondisjunction

The failure of chromosomes or chromatids to separate properly during cell division, leading to daughter cells with an abnormal number of chromosomes

Apoptosis

• Programmed cell death

• Occurs more often

• Releases anti-inflammatory signals, preventing tissue inflammation

• Blebs from dying cell are eaten by phagocytes

Necrosis

• Cells die due to injury or disease

• Occurs less frequently

• Causes oncosis (cell swelling)

• Cell bursts and and releases damage-associated molecular patterns. This triggers inflammatory response and attracts immune cells

• Another thing that can cause necrosis is that there are no phagocytes around