cell bio 1

week 1-2

Nucleus

Stores DNA, controls gene expression

Mitochondria

Powerhouse of the cell, produces ATP

Rough ER

Synthesizes proteins.

Smooth ER

Synthesizes lipids and detoxifies substances

Golgi Apparatus

Modifies, sorts, and packages proteins and lipids

Lysosomes

Breaks down waste and cellular debris

Ribosomes

Synthesize proteins

Peroxisomes

Breaks down fatty acids and detoxifies harmful substances

Cytoskeleton

Provides structure and facilitates cell movement

Chloroplasts (in plant cells)

Conduct photosynthesis

Vacuoles

Stores nutrients, waste, and provides structural support

Eukaryotic Cells

Have a nucleus and membrane-bound organelles (e.g., mitochondria). Larger, more complex. Found in animals, plants, fungi, and protists.

Prokaryotic Cells

Lack a nucleus and membrane-bound organelles. Smaller, simpler. Found in bacteria and archaea.

Similarities between Eukaryotic and Prokaryotic Cells

Plasma membrane, cytoplasm, and ribosomes.

Central Dogma of Molecular Biology

DNA → RNA → Protein

DNA

Stores genetic information

mRNA

Transcribes genetic information

Ribosomes

Protein synthesis

RNA Polymerase

Transcribes DNA into RNA

tRNA

Brings amino acids for protein synthesis

Fluorescence Microscopy

Allows for visualization of specific molecules in cells by tagging them with fluorescent dyes, enabling detailed imaging

Excitation light

Energizes electrons in fluorophores, causing them to jump to a higher energy state

Fluorescence

Electrons return to their ground state, emitting light at a longer wavelength (lower energy) than the excitation light.

Fluorophore Properties

Organic Dyes, e.g., FITC, DAPI, rhodamine. Fluorescent Proteins, e.g., GFP. Quantum Dots Nanoscale materials that fluoresce.

DNA Dyes (e.g., DAPI)

Bind specifically to the DNA minor groove.

FITC

Conjugated to antibodies or proteins to target specific cellular structures (e.g., microtubules, proteins).

Primary antibody

Binds to the target antigen.

Secondary antibody

Conjugated with a fluorophore, binds to the primary antibody.

Visualization

Fluorescence microscopy reveals the labeled target.

Primary antibody (Zika virus)

Specific to Zika proteins.

Secondary antibody (Zika virus)

Conjugated to a red fluorophore (e.g., Alexa Fluor 594).

Observation (Zika virus)

Use fluorescence microscopy to visualize the red signal.

Immunofluorescence in Disease Research

Helps in locating and identifying disease markers, pathogens, or protein interactions in cells and tissues.

Example of Immunofluorescence

Investigates how Zika virus interacts with adult brain cells.

Negative control

Cells without primary antibody to check for non-specific binding.

Positive control

A sample known to express the antigen to verify the antibody works.

Fluorophore

Molecule that absorbs light at one wavelength and emits it at a longer wavelength.

GFP (Green Fluorescent Protein)

A naturally occurring protein that fluoresces green, used as a live-cell marker.

DAPI

Fluorescent dye that binds to DNA and is used for nuclear staining.

Immunofluorescence

Technique using antibodies conjugated to fluorophores to detect specific antigens in cells or tissues.

Antibody

Protein produced by the immune system to specifically bind to an antigen.

Antigen

Any substance that triggers an immune response, often recognized by antibodies.

Atom

the smallest unit of matter, consisting of protons, neutrons, and electrons

Element

a pure substance made up of only one type of atom (e.g., hydrogen, oxygen)

Molecule

a group of two or more atoms bonded together (e.g., H₂O)

Atomic Number

the number of protons in an atom’s nucleus, which defines the element

Electron Configuration

electrons in the outer shell (valence electrons) determine an atom's chemical reactivity and bonding behavior

Polar Covalent Bond

electrons are shared unevenly, leading to partial charges (e.g., H₂O)

Non-Polar Covalent Bond

electrons are shared equally (e.g., O₂)

Ionic Bond

one atom donates an electron to another, resulting in oppositely charged ions that attract each other (e.g., NaCl)

Hydrogen Bond

a weak bond between a hydrogen atom attached to an electronegative atom and another electronegative atom (e.g., between water molecules)

Ionic Bonds

stronger than Covalent Bonds, and Hydrogen Bonds are the weakest

Lewis Structures

diagrams showing the bonding between atoms and the lone pairs of electrons

Structural Formula

the arrangement of atoms and bonds in a molecule (e.g., H₂O)

Molecular Formula

the number of atoms of each element in a molecule (e.g., C₂H₆)

Dehydration Synthesis

water is removed to form a bond between monomers (e.g., forming a peptide bond)

Hydrolysis

water is added to break bonds between monomers (e.g., breaking a peptide bond)

Solute

the substance being dissolved (e.g., salt)

Solvent

the substance that dissolves the solute (e.g., water)

Solution

the mixture of solute and solvent

Cation

a positively charged ion (e.g., Na⁺)

Anion

a negatively charged ion (e.g., Cl⁻)

Lemon Juice

acidic (~pH 2)

Bleach

basic (~pH 12)

Proteins

made of amino acids. Examples: enzymes, structural proteins

Carbohydrates

made of monosaccharides. Examples: glucose, starch

Lipids

made of fatty acids and glycerol. Examples: phospholipids, cholesterol

Nucleic Acids

made of nucleotides. Examples: DNA, RNA

Polymerization

monomers are joined via condensation (dehydration) reactions to form polymers

Hydrolysis

polymers are broken down into monomers by adding water

R-Group

the side chain of an amino acid that determines its properties (hydrophobic, hydrophilic, charged)

Primary Protein Structure

sequence of amino acids

Secondary Protein Structure

alpha-helices and beta-sheets

Tertiary Protein Structure

3D folding of the protein

Quaternary Protein Structure

interaction of multiple protein subunits

Mutation

a change in the amino acid sequence that can affect protein structure and function

RNA

Single-stranded, ribose sugar, uracil (U) replaces thymine (T)

DNA

Double-stranded, deoxyribose sugar, thymine (T)

Nucleotide Components

Sugar, phosphate group, nitrogenous base (A, T, C, G for DNA; A, U, C, G for RNA)

Phospholipids

main component of cell membranes, forming bilayers with hydrophilic heads and hydrophobic tails

ATP (Adenosine Triphosphate)

primary energy carrier in cells

Membrane Fluidity

due to lipid molecule flexibility and cholesterol presence

Saturated Fatty Acids

no double bonds; rigid, straight chain

Unsaturated Fatty Acids

one or more double bonds; bent chain, more fluid

Trans-Fats

a type of unsaturated fat that has been hydrogenated to make it solid at room temperature

Bilayer

forms with phospholipids, where hydrophobic tails face inward

Micelle

single layer, with hydrophobic tails facing inward and heads outward

Membrane Fluidity Factors

temperature, ratio of saturated to unsaturated fatty acids

Homeoviscous Adaptation

Adjust fatty acid composition to maintain membrane fluidity in varying temperatures

Atom, Proton, Neutron, Electron

subatomic particles that make up atoms

Covalent Bond, Ionic Bond, Hydrogen Bond

types of chemical bonds

Monomer, Polymer

building blocks and their larger forms

Peptide, Polypeptide

short and long chains of amino acids

Alpha-Helix, Beta-Sheet

types of secondary protein structures

Hydrophobic, Hydrophilic

water-repelling and water-attracting properties

Amphipathic

molecules that have both hydrophilic and hydrophobic parts

Integral Membrane Proteins

span the lipid bilayer completely or partially. Function: Channels, receptors, transporters, enzymes.

Peripheral Membrane Proteins

associate with the membrane surface but do not penetrate the bilayer. Function: Structural support, signaling, or interactions with the cytoskeleton.

Lipid-Anchored Membrane Proteins

attached to the membrane via a covalent bond with a lipid molecule. Function: Cell signaling, enzyme activity.

Why Can’t a Linear/Unfolded Protein Reach Through the Lipid Bilayer?

The hydrophilic backbone of the protein cannot interact with the hydrophobic core of the membrane. The protein must adopt a specific structure (such as an alpha helix or beta barrel) to shield its hydrophilic regions from the hydrophobic interior.