BMSC 220 (Up to Midterm)

Chapters 1 - 9

Cell biology

The study of cells and their structure, function, and behavior.

Microscopy

The use of microscopes to visualize and study cells and other small structures.

Confocal microscope

A type of microscope that uses fluorescence imaging and a pinhole to increase optical resolution and create 3D images of structures within cells.

Light-sheet microscopy

A fluorescence imaging technique that uses a sheet of laser light to illuminate a thin slice of a sample, allowing for faster acquisition and visualization of intact embryos or cleared organs.

Electron microscopy

A type of microscopy that uses electrons instead of light to visualize samples, often used for samples too small to be seen with light microscopes, such as viruses.

Cell theory

The theory that all organisms are composed of one or more cells, the cell is the structural unit of life, and cells arise only by division from pre-existing cells.

added: cells contain genetic information (DNA) passes to next cell generations

HeLa cells

Cultured tumor cells isolated from a cancer patient named Henrietta Lacks, commonly used in cell biology research.

named after Henrietta Lacks

Genetic program

The information encoded in genes (constructed from DNA) that provides instructions for building an organism, constructing cellular structures, running cellular activities, and making more of themselves.

Cell reproduction

The process by which a cell divides into two daughter cells, distributing the contents of the mother cell.

ATP (Adenosine TriPhosphate)

A molecule that stores and provides readily available energy for cellular processes.

Metabolism

The sum total of chemical reactions that occur in a cell.

Motor proteins

Proteins that undergo dynamic, mechanical changes within cells, allowing for activities such as transport, assembly, disassembly, and cell movement.

Receptors

Proteins on the surface of cells that interact with substances in the environment, allowing cells to respond to stimuli.

Self-regulation

The ability of cells to maintain a complex, ordered state through constant regulation and feedback circuits.

LUCA (Last Universal Common Ancestor)

The hypothetical single, common ancestral cell from which all living organisms evolved more than three billion years ago.

Prokaryotic cells

Cells that lack a nucleus and membrane-bound organelles, including bacteria.

Eukaryotic cells

Cells that have a nucleus and membrane-bound organelles, including plants, animals, protists, and fungi.

besides simple yeasts (12Mb) most cells contain large amounts of DNA

divide my mitosis and meiosis

Prokaryotic cells

Cells that do not have a nucleus and have simple structures.

relatively small amounts of DNA; 600-800 Mb

divide fission

Cytoplasm

The gel-like substance inside a cell that contains organelles.

Ribosomes

Structures in a cell that synthesize proteins.

Mitosis

The process of cell division in eukaryotic cells.

Flagella

Whip-like structures that help with cell movement.

Conjugation

The transfer of DNA between prokaryotic cells.

mitotic spindle

Eukaryotic mitosis structure that segregates condensed chromosomes allowing each daughter cell to receive an equivalent area of genetic material.

Archaea (Extremophiles)

Organisms that live in extreme environments.

Cyanobacteria

Bacteria that can perform photosynthesis.

some are capable of nitrogen fixation.

Methanogens

convert CO2 and H2 gasses into methane

Protists

Single-celled eukaryotic organisms.

Hyperthermophiles

live in hydrothermal vents of the ocean floor up to a temperature of 121 Celsius

thermophiles

live at very high temperatures

acidophiles

acid-loving, thrive at pH as low as 0

Halophiles

live in extremely salty environments, like the dead sea or deep sea brine pools with salinity equivalent to 5M MgCl2

Cell differentiation

The process of cells becoming specialized for specific functions.

Model organisms

Organisms that are commonly used in scientific research.

Differentiating Prokaryotes

• no nucleus

• small and simple

• no organelles

• unicellular

• DNA id organized as long a long strand

• all are bacteria/archaea

Differentiating Eukaryotes

• have nucleus

• have organelles

• can be multi or unicellular

• DNA is organized in chromosomes

• plants/animals/fungi/protists

similarities between Prokaryotes and Eukaryotes

• have ribosomes

• have DNA

• Have cytoplasm

• have cell membrane

• some have flagella

Nucleus

The organelle in eukaryotic cells that contains genetic material.

what is cell size limited by

1. The volume of cytoplasm that can be supported by the genes in the nucleus.

2. The volume of cytoplasm that can be supported by the exchange of nutrients.

3. The distance over which substances can efficiently travel through the cytoplasm via diffusion.

Viruses

Pathogens that are obligate intracellular parasites.

Viroids

Small RNA molecules that can cause disease in host cells.

Viral capsids (envelope)

Protein structures that make up the outer shell of a virus.

bacteriophages

viruses that infect bacteria

Viral specificity

The ability of a virus to infect a specific host due to the interaction between the virus' surface proteins and the host cell's surface proteins.

Lytic infection

A type of viral infection where the virus redirects the host cell to produce more virus particles, leading to the lysis (bursting) of the host cell and release of the viruses.

Integration

A type of viral infection where the virus integrates its DNA, known as a provirus, into the chromosomes of the host cell.

Cell theory

The four tenets of cell theory include:all living organisms are composed of cells, cells are the basic unit of structure and function in living organisms, cells arise from pre-existing cells, and cells carry genetic information in the form of DNA.

Fundamental properties of cells

The shared characteristics of all cells, including the presence of a cell membrane, genetic material, and the ability to carry out metabolic processes.

Chemical origins of life hypothesis

The suspected origin of life is the hypothesis that earliest cells, called protocells, were very simple and made up of nucleic acids surrounded by a membrane. This hypothesis suggests that the organic compounds necessary for the formation of early cells may have been created in Earth's early atmosphere, as simulated by Urey and Miller in 1952.

Covalent Bonds

Covalent bonds are chemical bonds formed when two atoms share a pair of electrons. They are the strongest type of chemical bond and are responsible for holding atoms together in molecules.

nm and nm

Polar Molecules

Polar molecules are molecules that have an uneven distribution of charge due to the presence of electronegative atoms. They have a positive and negative end, creating a dipole moment.

(contain O,N,S)

Nonpolar Molecules

Nonpolar molecules are molecules that have an even distribution of charge and lack electronegative atoms. They do not have a dipole moment.

(contain C,H)

Ionic Bonds

Ionic bonds are chemical bonds formed between positively and negatively charged ions. They are formed through the attraction of opposite charges.

ex. NaCl

Hydrogen Bonds

Hydrogen bonds are weak chemical bonds formed between a hydrogen atom with a partial positive charge and an electronegative atom with a partial negative charge.

Hydrophobic Interaction

Hydrophobic interaction is the tendency of nonpolar molecules to aggregate together in the presence of water, minimizing their contact with water molecules.

Due to them lacking the charged regions that would attract water.

Van der Waals Forces

Van der Waals forces are weak attractive forces between molecules due to temporary fluctuations in electron distribution, resulting in temporary dipoles.

What is the importance of water in protein structure

Water is important in protein structures because it can form weak interactions with polar organic molecules like amino acids and sugars. These weak interactions help maintain the structure and function of macromolecules and the complexes that they form.

Additionally, hydrophobic interactions, which are driven by water, play a significant role in protein folding and contribute to the overall stability of the protein.

Acids

Acids are substances that release protons (H+) when dissolved in water, increasing the concentration of H+ ions.

Bases

Bases are substances that accept protons (H+) when dissolved in water, decreasing the concentration of H+ ions.

Buffers

Buffers are substances or systems that resist changes in pH by accepting or donating protons to maintain a relatively constant pH.

Biochemicals

Biochemicals are compounds produced by living organisms, including carbohydrates, lipids, proteins, and nucleic acids.

Functional Groups

Functional groups are specific groups of atoms within organic molecules that determine their chemical reactivity and physical properties.

Macromolecules

Macromolecules are large, complex molecules that are essential for the structure and function of cells. They include proteins, nucleic acids, polysaccharides, and certain lipids.

Monomers

Monomers are the individual subunits that make up macromolecules. They can be joined together through polymerization to form larger polymers.

4 major categories: proteins, nucleic acids, polysaccharides and certain lipids.

Polymerization

Polymerization is the process of joining monomers together to form a polymer through the formation of covalent bonds.

Hydrolysis

Hydrolysis is the process of breaking down a polymer into its monomer subunits by adding water molecules.

Carbohydrates (glycan)

Carbohydrates, also known as glycans, are organic molecules that include simple sugars (monosaccharides) and larger molecules composed of sugar building blocks.

They function primarily as a source of energy and as structural components in cells.

The structure of simple sugars

they tend to be highly water soluble due to their hydroxyl groups

has a backbone of carbon atoms linked together in a linear array by single bonds

Stereoisomerism (stereoisomers/enantiomers)

Stereoisomerism refers to the existence of two or more molecules that have the same chemical formula and connectivity but differ in the spatial arrangement of their atoms.

Disaccharides

Molecules composed of only two sugar units that serve primarily as readily available energy stores. Examples include sucrose and lactose.

Polysaccharides

Molecules composed of identical sugar monomers but with dramatically different properties. They are polymers of sugars joined by glycosidic bonds. Examples include glycogen and starch.

Structural Polysaccharides

Polysaccharides that have structural functions. Examples include cellulose, chitin, and glycosaminoglycans (GAGs).

Glycogen

animal product made of branched glucose polymers

Fats

Lipids that dissolve in organic solvents, not water. They have glycerol linked by ester bonds to three fatty acids, forming a triacylglycerol.

Starch

plant product made of both branched and unbranched glucose polymers

Soaps

In soaps, the hydrophobic end of each fatty acid can embed itself in grease, while the hydrophilic end can interact with water.

Saturated Fatty Acids

Fatty acids that lack double bonds.

Unsaturated Fatty Acids

Fatty acids that have double bonds.

Steroids

Lipids built around a four-ringed hydrocarbon skeleton. Cholesterol is an example of a steroid found in animal cell membranes and a precursor of steroid hormones.

Phospholipids

Lipids that resemble fats but have only two fatty acid chains and a phosphate group. They are important components of cell membranes.

Proteins

Macromolecules that carry out a cell's activities. They can be enzymes that accelerate reactions or structural proteins that provide mechanical support.

Amino Acids

The building blocks of proteins. Proteins are unique polymers made of amino acid monomers. There are twenty different amino acids with different chemical properties commonly used in protein construction.

Primary Structure

The amino acid sequence of a protein.

Side Chains

The variable groups bonded to the α-carbon of amino acids, which give proteins their diverse structures and activities.

Disulfide Bridges

Covalent bonds that form between two cysteine residues and help stabilize the shapes of proteins.

Secondary Structure

The conformation of portions of the polypeptide chain. It can be in the form of an α-helix or β-sheet.

Tertiary Structure

The conformation of the entire polypeptide chain.

used to decide decide whether two proteins may have similar structure and function as interactions and enzymatic activity of a protein are deduced from there tertiary structure.

ex. actin and MreB show similarities at tertiary stages but not at primary

Prions

they are misfolded proteins that have the ability to transmit their misfolded shape onto normal variants of the same protein

How are proteins categorized?

Proteins are categorized based on their shape as either fibrous proteins, which are elongated, or globular proteins, which are compact.

Myoglobin

The first globular protein whose tertiary structure was determined

Protein Domains

Spatially distinct modules or functional units within a protein that fold independently.

Hemoglobin

The O2-carrying protein of red blood cells consisting of two α-globin and two β-globin polypeptides.

Quaternary Structure

The arrangement of multiple protein subunits to form a larger protein complex.

Protein-Protein Interactions

The physical association of different proteins to form a multiprotein complex.

Denaturation

The unfolding of a protein caused by detergents, solvents, heat, or other compounds.

Molecular Chaperones

Helper proteins that assist unfolded proteins in achieving their proper 3D conformation.

Alzheimer's Disease

A common disorder characterized by memory loss, confusion, and the presence of amyloid aggregates in the brain.

Proteomics

The study of the entire inventory of proteins produced by an organism or present in a specific tissue, cell, or organelle.