BIO130: Section 1

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Cell Theory

The theory that the cell is the basic unit of life, all organisms are composed of one or more cells, all cells come from pre-existing cells

Prokaryotic Cells

These cells are smaller in size, contain no nucleus but instead a nucleoid, 70s ribosomes, and no membrane-bound organelles

Eukaryotic Cells

These cells are larger in size, contain a nucleus with a nuclear envelope, 80s ribosomes, and membrane-bound organelles

Mitochondria

These were originally free-living aerobic prokaryotes able to use oxygen to help generate ATP, but eventually evolved to be an organelle in the cell which helps to generate ATP

Ectosymbiosis

A form of symbiotic behaviour in which an organism lives on the surface of another organism

Endosymbiosis

A form of symbiotic behaviour in which an organism inside another organism

Model Organism

A living thing that’s selected for intensive study as a representative of a large group of species; they have relatively short life spans, are readily available, reproduce quickly, and are tractable

Genome

All of the DNA or DNA sequences within a cell or an organism

Transcriptome

All the RNA or RNA sequences within a cell or genome

Proteome

All the proteins or protein sequences within a cell or genome

Interactome

All the protein-protein interactions within the cell or organism

Metabolome

All the small molecule metabolites (such as glucose or waste) in the cell or organism

Phenome

All the phenotypes of the cell or organism

Nucleic Acids

These are the genetic material in a cell, organisms’ blueprints

Nucleotides

Consists of a nitrogen-containing base, a five-carbon sugar, and one or more phosphate groups; they are the subunits of the nucleic acids

Nucleosides

These consist of a nitrogenous base and a five-carbon sugar but not a phosphate group

Phosphodiester Bonds

These bonds link nucleotides together

Hydrogen Bonds

An intermolecular bond that occurs when hydrogen bonds with O, N, or F

Dipole-Dipole Bonds

An intermolecular bond that occurs due to uneven distribution of electrons in a molecule, causing partial positive and negative charges

Electrostatic Bonds

A chemical bond in which one atom loses an electron to form a positive ion and the other atom gains an electron to form a negative ion

Van Der Waals (London Dispersion) Forces

Weak electrostatic forces that occur when two molecules come in proximity of one another

DNA Bases

Adenine, thymine, guanine, cytosine

RNA Bases

Adenine, uracil, guanine, cytosine

Major Groove

Occurs where the backbones are far apart

Minor Groove

Occurs where the backbones are closer together

Pyrimidines

One-ringed nitrogenous bases (C, T, and U)

Purines

Two-ringed nitrogenous bases (A and G)

Denaturation

The destruction of hydrogen bonds between nucleotide pairs at high temperatures which changes the shape of the DNA

70s Ribosomes

Ribosomes that are smaller in size and freer in cytoplasm, made of 30s and 50s subunits, used for protein synthesis

80s Ribosomes

Larger ribosomes in eukaryotic cells that are made up of a smaller 40s subunit and a larger 60s subunit and are often associated with different cell organelles

Homeostasis

The maintenance of relatively stable internal conditions within an organism; can be achieved through physical features, metabolism, and actions and interactions, therefore the body must recognize stresses and respond appropriately to them

Characteristics of Living Things

Made of cells, respond to changes in the environment, can reproduce, exchanges energy and matter with the environment, has metabolism, maintains homeostasis, can grow

Archaea

Extremophile bacteria with DNA in a circular genome, histones present, usually no introns in genes, cell walls not made of peptidoglycan, and membranes that differ from those of eubacteria and eukaryotes

Eubacteria

True bacteria with DNA in a circular genome, histones absent, usually no introns in genes, and cell walls made of peptidoglycan

Eukaryota

True eukaryotes with DNA in chromosomes, histones present, frequent introns in genes, and sometimes have cell walls that are never made of peptidoglycan

Chloroplast

Contains chlorophyll used for photosynthesis Only in plants

Thylakoids

Sacs inside the chloroplast that collects light energy from sun

Rough Endoplasmic Reticulum

Makes proteins for the cell, and has ribosomes

Smooth Endoplasmic Reticulum

Produces fats and oils for the cell, and has no ribosomes

Ribosomes

Assembles the proteins

Golgi Apparatus

Modifies, sorts, and packages proteins from the endoplasmic reticulum for delivery

Endocytosis

A process in which a vesicle is formed on the inside of the plasma membrane and allows water, solutes, and larger molecules that cannot pass through the cell membrane to enter the cell

Exocytosis

A process in which a vesicle fuses with the plasma membrane and releases contents such as waste products and unwanted material out of the cell

Cytosol

The part of the cytoplasm not concentrated within intracellular membranes; is aqueous

Cytoskeleton

An internal network of fibres that helps to maintain the cell's shape and is responsible for directing cell movements; composed of actin filaments, microtubules, and intermediate filaments

Actin Filaments

These are the thinnest filaments and provide structure support

Microtubules

These move chromosomes during cell division and are the largest filaments

Intermediate Filaments

These filaments serve to strengthen cells

Protozoans

Free-living, solitary, motile, unicellular eukaryotes

Hydrophobic Forces

Nonpolar surfaces pushed away from water and vice versa

Primary Protein Structure

Amino acid sequence

Secondary Protein Structure

Local folding, alpha helix, beta pleated sheet

Tertiary Protein Structure

Long-range folding, 3D structure of the protein

Quaternary Protein Structure

Multimeric organization, more than one polypeptide chain, multiprotein complexes and molecular machines

Disulfide Bonds

Behaves differently under oxidation and reduction conditions; under oxidation, forms disulfide bonds and you get a strong covalent bond, which helps to hold the protein shape, acts as a “brace”; under reduction conditions, no additional bonds are formed, in cysteine

Polypeptide Chain

When you put two or more amino acids together to form a peptide bond

Peptide Bond

A bond formed by the amino group of one amino acid and the carboxyl group of another one via a condensation reaction to form a polypeptide chain

Condensation Reaction

Covalent bond reaction which produces a water molecule

Hydrolysis Reaction

Uses one water molecule to break a covalent bond

Protein Backbone

All of the protein’s atoms EXCEPT for the side chains (R groups)

Alpha Helix

In this secondary formation, all the R-groups stick out to form a coil, and in the middle, along the coil, is the backbone of the protein and hydrogen bonds are formed between residues to stabilize the alpha helix, residue n forms a hydrogen bond with residue n+4

Beta Pleated Sheet

Basically shaped like a folded sheet with pleats, sort of like a zig-zag

Anti-Parallel (Beta Sheet)

The segments in the polypeptides alternate the direction in which they're facing

Parallel (Beta Sheet)

All the segments face the same direction

Amphipathic

A molecule which exhibits both hydrophobic and hydrophilic properties

Hydrophobic

A molecule that is nonpolar and hates water

Hydrophilic

A molecule that is polar and loves water

Protein Domain

Portion of a protein that has its own tertiary structure, often functioning in semi-independent manner

Multiprotein Complexes

More than one protein get together and work together to achieve a similar goal

Proteomics

The large-scale study of proteins

Monosaccharides

Have the generic formula (CH2O)n where n can be 3–6 and have two or more hydroxyl groups; they either contain an aldehyde (aldoses) or ketone (ketoses), a ring forms when the aldehyde/ketone reacts with the hydroxyl of the same molecule

Isomers

Same molecular formula but different connectivity

Disaccharides

Occurs when two monosaccharides link together via a condensation reaction

Polysaccharides

Occurs when multiple (more than two) monosaccharides link together via a condensation reaction

Oligosaccharides

Basically shorter polysaccharides

Fatty Acids

Composed of a carboxyl group at one end and a hydrocarbon tale at the other; they are nonpolar and can be saturated, unsaturated, cis, or trans

Triacylglycerols

Formed when fatty acids link to a glycerol via an ester linkage

Phospholipids

Two of the –OH groups in glycerol are linked to fatty acids, while the third –OH group is linked to phosphoric acid; has a hydrophilic head and hydrophobic tail

Lipids

Water-insoluble molecules that are soluble in organic solvents

Steroids

An organic compound with four fused rings in a specific manner

Protein

Macromolecule built from amino acids that provides cells with their shape and structure and performs most of their activities; they are very diverse and have many different functions

Enzymes

These proteins catalyze covalent bond breakage or formation (eg pepsin)

Transport Proteins

They provide mechanical support to cells and tissues (eg collagen)

Structural Proteins

These proteins carry small molecules or ions (eg hemoglobin)

Motor Proteins

They generate movement in cells and tissues (eg myosin)

Storage Proteins

These proteins store amino acids or ions (eg ferritin)

Signal Proteins

They carry extracellular signals from cell to cell (eg insulin)

Receptor Proteins

These proteins detect signals and transmit them to the cell's response machinery (eg rhodopsin)

Transcription Regulators

These proteins bind to bind to DNA to switch genes on and off (eg DNA binding proteins)

Special Purpose Proteins

These proteins have various highly specialized and specific functions that may differ from the other proteins (eg antifreeze protein in arctic fishes which protect them from the cold)

Functions Carried Out By Proteins

Catalysis (enzymes), muscle contraction (actin myosin), cytoskeleton, cell adhesion, membrane transport (Na/K pumps), immunity, tensile strengthening, blood clotting, transport of nutrients and gases, receptors, hormones, and packing of DNA (histone)

Chaperone Proteins

Proteins whose job is to aid other proteins to make protein folding more efficient

Amyloid Structures

A protein aggregate with a cross-β sheet structure, which is characterized by β-strands that run perpendicular to the fibril axis with fibrils that are unbranched, smooth-surfaced, and physically and chemically robust

Prions

These are proteins that can cause fatal brain diseases in humans and animals and are considered “infectious” because the amyloid form of the protein can convert properly folded molecules of the protein into the abnormal, disease-causing conformation

Dimer

Two identical, folded polypeptide chains form a symmetrical complex of two protein subunits that is held together by interactions between two identical binding sites

Feedback Inhibition

A form of metabolic control in which the end product of a chain of enzymatic reactions reduces the activity of an enzyme early in the pathway

Allosteric

Describes a protein that can exist in multiple conformations depending on the binding of a molecule (ligand) at a site other than the catalytic site; such changes from one conformation to another often alter the protein’s activity or ligand affinity

Protein Phosphorylation

The covalent addition of a phosphate group to a side chain of a protein, catalyzed by a protein kinase; serves as a form of regulation that usually alters the activity or properties of the target protein

Protein Kinase

Enzyme that catalyzes the transfer of a phosphate group from ATP to a specific amino acid side chain on a target protein

Protein Phosphatase

Enzyme that catalyzes the removal of a phosphate group from a protein, often with high specificity for the phosphorylated site