Term
| Cells contain four major families of small organic molecules |
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Definition
| sugars (polysaccharides), fatty acids (fats, lipids, membranes), amino acids (proteins, polypeptides), and nucleotides (nucleic acids) |
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Definition
| a bond in which a molecule of water is expelled as the bond is formed |
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Term
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Definition
| breaking a bond in which a molecule of water is consumed |
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Term
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Definition
| Molecules such as phospholipids, with both hydrophobic and hydrophilic regions |
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Term
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Definition
| all possess a carboxylic acid group and an amino group, both linked to a single carbon atom called the alpha-carbon. Their chemical variety comes from the side chain that is also attached to the alpha-carbon. Amino Acids are linked together to form proteins. Exist as optical isomers in D- and L-forms. Only L-forms are found in proteins. |
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Term
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Definition
| Cytosine, Thymine, Uracil - all derive from a six-membered pyrimidine ring |
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Term
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Definition
| Adenine, Guanine - have a second, five-membered ring fused to the six-membered ring. |
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Term
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Definition
| a ribonucleotide transfers energy in hundreds of different cell reactions |
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Term
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Definition
| A, G, C, U - based on ribose sugar |
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Term
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Definition
| A, G, C, T - hydroxyl at the 2' position of the ribose carbon ring is replaced by a hydrogen |
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Term
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Definition
| condensation reactions that bond monomers of sugars to form polysaccharides |
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Term
| Examples of polysaccharides |
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Definition
starch and glycogen
cellulose and chitin
glycoproteins (oligosaccharide bound to proteins) and glycolipids (oligosaccharides bound to lipids) |
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Term
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Definition
| the pH at which exactly half of the carboxylic acid or amine residues are charged. |
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Term
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Definition
| Are composed of a nitrogen-containing base (A, C, G, T and U), a five-carbon sugar (ribose or deoxyribose) and one or more phosphate groups |
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Term
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Definition
Polymers of nucleotides form through the formation of phosphodiester bonds. They form between the phosphate group of one nucleotide and the hydroxyl group on the sugar of another.
The bond is between the phosphate of one nucleotide and a hydroxyl (OH) group on the sugar of another nucleotide |
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Term
| phospholipid structure of bacteria and eukaryotes |
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Definition
| Bacterial and eukaryotic lipids have fatty acids attached to glycerol via ester bonds |
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Term
| phospholipid structure for archaeabacteria |
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Definition
| Archaeal lipids have fatty acids attached to glycerol via ether bonds |
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Term
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Definition
| involves the breakdown of organic molecules (food stuff) and the release of energy. |
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Term
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Definition
| involves the formation of organic molecules and the use of energy. |
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Term
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Definition
Oxidation refers to the removal of electrons and reduction means addition of electrons. Reduced molecules contain more energy than oxidized molecules
Reduction requires energy/oxidation releases energy |
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Term
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Definition
| observations of "little boxes" led to Cell Theory |
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Term
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Definition
| states that all living things are composed of cells |
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Term
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Definition
| Used microscopes to identify "animalcules" in rainwater and other specimens. First documented observation of microorganisms. |
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Term
| Universal Features of Cells (4) |
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Definition
The structure and function of nucleic acids (DNA and RNA)
The production and composition of proteins
A requirement for free energy
Being enclosed by a selectively-permeable membrane |
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Term
| Structure and Function of Proteins |
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Definition
Proteins have a 3D structure based on their amino acid sequence.
Proteins are enzymes that act as catalysts for specific chemical reactions
Some proteins act as regulatory proteins and can promote production of other proteins |
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Term
Phototrophs
Chemoorganotrophs
Chemolithotrophs |
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Definition
Phototrophs get free energy from sunlight
Chemoorganotrophs get free energy from oxidation of organic molecules
Chemolithotrophs get free energy from oxidation of inorganic molecules |
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Term
| Semipermeable membranes do what? |
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Definition
| allow for the uptake of nutrients and the export of waste |
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Term
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Definition
Prokaryotes, Archaea, Eukaryotes
Pro- and Archaea are pre-nucleus
Eukaryotes have a true nucleus and include all multicellular organisms, but are also single cell organisms
Eukaryotes do not have a cell wall. |
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Term
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Definition
All cells are descended from a common ancestor
Use simple systems to study a biological question and extrapolate the results to higher organisms. |
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Term
| What makes a good model organism? |
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Definition
represent the simplest possible system to study a biological question.
Amenable to genetic manipulation
Reproduce rapidly
Easy to grow in a laboratory |
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Term
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Definition
E. coli - a model prokaryote
Yeast - lowest eukaryote, few genes, haploid, cheap, and fast growing
Drosophila (Fruit fly) - Diploid, easy and cheap to grow, oldest organism for genetics, multicellular organism
Nematode - unusual life cycle make it suitable for genetics, easy and cheap to grow, precise timing of development from single cell to adult with 959 cells
Mouse - foremost model for vertebrate studies, development, immunology, mammalian genetics
Arabidopsis thaliana - plant model, easy to grow indoors, produces thousands of offspring in 8-10 weeks, genome is completely sequenced |
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Term
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Definition
Use microscopy to reveal size, shape, and location of cell components
- Immunofluorescence = using antibodies to visualize specific protein
- Green fluorescent protein (GFP) = adding GFP tag to a protein allows visualization of the hybrid protein in living cells |
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Term
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Definition
| Use fractionation and x-ray crystallography to reveal molecular structure and chemistry of purified cell constituents |
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Term
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Definition
| Identify mutant phenotypes and determine genotypes to reveal roles of healthy genes and consequences of damaged genes |
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Term
Techniques
Developmental Biology |
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Definition
| reveals changes in cells as they specialize |
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Term
Techniques
Molecular Biology |
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Definition
| Use DNA cloning, Polymerase chain reactions, and Western blotting to reveal the molecular basis of biological activity |
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Term
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Definition
Use DNA microarrays to reveal differences in structure and expression of entire genomes
- monitor global patterns of gene expression
- detect all the mRNAs present in a cell (identify which genes are active)
A microarray tells us changes gene expression during disease progression, in response to drugs, and during development |
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Term
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Definition
| Monitors the presence and interactions of numerous proteins simultaneously |
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Term
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Definition
| smallest living unit in an organism |
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Term
Definition:
Eukaryotic cells |
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Definition
| compartmentalized, resulting in membrane-bound, functionally distinct organelles |
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Term
| Structural Commonalities of prokaryotic and eukaryotic cells |
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Definition
All cells:
Are composed primarily of water and carbon compounds
Are enclosed in a lipid membrane (separates life from the environment)
Contain ribosomes (translate mRNAs into proteins)
Contain DNA as the genetic material (instruction for making the cell) |
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Term
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Definition
cell walls are external to the cell membrance and are usually composed of carbohydrates.
Prokaryotes have a cell wall composed of peptidoglycan.
Arcahea cell walls are composed of pseudomrein (or S-Layers, surface layers of protein)
Algae and Plants have cell walls of cellulose
Animal cells don't have cell walls, but have a glycocalyx - a think outer layer of carbohydrates. |
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Term
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Definition
| made up of oligosaccharide side chains of glycolipid, integral membrance glycoproteins and proteoglycans. |
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Term
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Definition
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Term
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Definition
-Lack membrane enclosed organelles
-DNA in the form of a closed circle
-DNA not enclosed in a membrane but may be attached to the inner membrane of the cell.
-May have extra-chrosomal plasmids that can endow the cell with useful traits.
-Inclusion bodies are often found in the cytoplasm that are used to store energy or carbon reserves.
-Possess a cytoskeleton that helps to localize structures within the cell and plays an essential role in cell division and polarity determination.
-Posses extracellular appendages - flagella are used for propulsion
-Pili are used for attachment.
-Structurally, little divergence (sperical, rod-shaped, spiral)
-Metabolically diverse (phototrophs, chemoorganotrophs, chemolithotrophs)
-Though both eukaryotes and prokaryotes can fix CO2 and generate oxygen, only prokaryotes can fix nitrogen and make it available for other organisms. |
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Term
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Definition
-May have evolved from a collection of prokaryotes living symbiotically (the endosymbiotic theory)
-Ribosomes are larger than prokaryotic ribosomes (80s vs. 70s)
-Possess an extensive network of membrane enclosed compartments
-Cytosol is the site for protein synthesis and degradation as well as metabolism
-Posses a true nucleus enclosed by a double membrane perforated with nuclear pores to connect with the cytosol.
-The space between the nuclear double membranes is continuous with the endoplasmic reticulum, which is a network of branching tubules and sacs that run throughout the cell. The Rough ER is studded with ribosomes and is involved with protein synthesis. The smooth ER is involved with lipid synthesis, detoxication of harmful molecules, and Ca2+ sequestration.
-The Golgi apparatus was first identified by Camillo Golgi and serves as a site for the synthesis and/or modification of molecules destined for transport out of the cell as well as the modification of imported molecules. It consists of a cis face (closest to the nucleus) and a trans face (closest to the cell membrane).
-Mitochondria serve as the site of oxidative phosphorylation in the cell and contain an outer membrane and an inner membrane that are separated by an intermembrane space.
-Chloroplasts belong to the plastid family and are only found in plant cells. They can function in either photosynthesis or the storage of various molecules (starch or pigments). Chloroplasts have 2 membranes and form thylakoids, which are the sites of photosynthesis (in the inner membrane).
-Peroxisomes have a single membrane and carry out oxidative reactions and are involved in the breakdown of toxins (ethanol) and fatty acids.
-Lysosomes are membrane bound compartments containing hydrolytic enzymes (acid hydrolases) and are responsible for digesting macromolecules into monomers
-Cytoskeletons are made up of 3 major types of proteins - actin filaments (stain red and form a contractile ring that pinches the cell into two), microtubules (stain green and rearrange to form the bipolar mitotic spindle), and intermediate fibers. They serve to organize the internal and external structure of the cell. |
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Term
| hydrogen is the exception to the equal neutrons and protons why? |
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Definition
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Term
| Largest amount of chemical elements in the body by percentage |
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Definition
| Hydrogen (65%), Oxygen(25%), Carbon(10%), Nitrogen (2%) |
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Term
| All elements found in living organisms have a common chemical property |
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Definition
| they have unfilled outermost electron shells which can participate in reactions |
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Term
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Definition
| are formed by atoms sharing electrons - strongest and unaffected by presence of water |
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Term
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Definition
| formed by the transfer of electrons from one atom to another - lose most of its strength in presence of water |
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Term
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Definition
| formed when two electronegative atoms share and electropositive hydrogen atom (water molecules) - loses some strength in presence of water |
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Term
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Definition
| are weak, but not affected by water. created at minimum energy states at which attractive and repulsive forces precisely balance. Zero energy is the energy when the two nuclei are at infinite separation. |
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Term
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Definition
| caused by hydrophobic molecules avoiding water by interacting with other hydrophobic molecules. Important for the proper folding of protein molecules. |
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Term
| What is the most abundant molecule in cells |
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Definition
| water, then proteins, RNA, miscellaneous small metabolites |
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Term
What are the names of larger units of these building blocks:
Sugars
Fatty Acids
Amino Acids
Nucleotides |
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Definition
Polysaccharides
Fats, lipids, membranes
proteins
nucleic acids |
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Term
Sugar chemical formula
energy source - glucose |
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Definition
(CH2O)n using a condensation reaction forming a glycosidic bond
disaccharide has 11 different linkages |
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Term
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Definition
Starch and glycogen (used to store energy)
Cellulose and Chitin (used for structure)
Glycoproteins (oligosaccharide bound to proteins) and glycolipids (oligosaccharide bound to lipids) |
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Term
| monomers assemble via what bonds? |
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Definition
| covalent bonds to form macromolecules. Energy is required for the formation of the bonds. |
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Term
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Definition
| energy carriers drive a carbon fixation process in which sugars are manufactured from CO2 and water. |
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Term
| glycogen and triglycerides - food reserves |
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Definition
animals store glucose reserves in this form. They have many branch points. plants store it as starch, which has fewer branch points.
Triglycerides/fats only differ in plants and animals by the types of fatty acids they are composed of |
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Term
granules in animal cytoplasm
adipocytes
where stored in plants? |
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Definition
cytoplasm storage of glycogen
adipocytes are the animal storage place for triglycerides
both starch and triglycerides are stored in the chloroplasts where they are manufactured |
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Term
| obtaining energy from sugars |
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Definition
| series of 10 oxidation reactions which breaks down sugar into energy, CO2 and H2O. The energy is stored in carrier molecules such as ATP, GTP, NADH, and NADPH. |
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Term
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Definition
| ATP - Energy carrier, nucleotide. Adenine + ribose + tri phosphoanhydride bonds |
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Term
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Definition
| Nicotinamide adenine dinucleotide phosphate carries high energy electrons and hydrogen atoms |
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Term
| Activated carrier molecules widely used in metabolism |
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Definition
ATP - phosphate group
NADH, NADPH, FADH3 - carries electrons and hydrogens
Acetyl CoA - acetyl group
Carboxylated biotin - carboxyl
S-Adenosylmethionine - methyl group
Uridine diphosphate glucose - glucose |
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Term
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Definition
A series of enzymatic reactions that results in the oxidation of glucose (C6) to 2 molecules of pyruvate (C3).
Results in the net syntheis of 2 molecules of ATP and 2 NADH.
It occurs in the cell cytosol and does not require O2. |
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Term
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Definition
Glycolysis inthe absence of O2, NADH reduces pyruvate to regenerate oxidized NAD+.
Different cells produce different end products - lactic acid in muscles, ethanol and CO2 in anaerobic organisms. |
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Term
| Pyruvate can be oxidized to what by pyruvate dehydrogenase |
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Definition
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Term
| Where are pyruvate and fatty acids oxidized? |
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Definition
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Term
| Krebs Cycle, TCA, Citric Acid Cycle |
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Definition
| an 8-step process for the oxidation of acetyl CoA by combining with citrate and is eventually oxidized to two molecules of CO2. Generates 1 GTP, 3 NADH, and 1 FADH2. Also creates lots of important intermediates along the way. |
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Term
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Definition
| In the presence of O2, NADH donates 2 electrons to an electron carrier chain. The electrons are eventually combined with O2 to generate H2O and lots of ATP. |
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Term
| Pyruvate kinase deficiency |
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Definition
| creates hemolytic anemia. lack of enzyme production |
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Term
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Definition
| Otto Warburg found that the rate of glycolysis in tumor cells goes up 200x |
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Term
| Why do we need to study proteins |
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Definition
| Proteins constitute most of the cell's dry mass and execute nearly all of the cell's functions. |
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Term
| Amino Acid side chains determine what? |
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Definition
| If the amino acid will be charged or uncharged, polar or non-polar |
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Term
| Proteins are folded using what noncovalent forces |
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Definition
| electrostatic attractions, hydrogen bonds, ven der Waals attractions, hydrophobic interacions (nonpolar side chains move to inside and folds it into compact conformation) |
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Term
| What are the 3 protein folding conformations |
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Definition
alpha helix - result from hydrogen bonding between N-H and C=O groups. Twists around itself to form a rigid cylider, turns after every 3.6 amino acids. found in cell membrane proteins like transport proteins and receptors.
Coiled coil structures where two alpha helices wrap around each other. Hydrophobic side chains face inward. Form framework for many elogated proteins like alpha keratin.
Beta pleated sheets - core of many proteins contain these. Caused by hydrogen bonding between neighboring polypeptide strands creating very rigid structure. These can run in parallel orientation or anti-parallel orientation. |
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Term
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Definition
| result from hydrogen bonding between N-H and C=O groups. Twists around itself to form a rigid cylider, turns after every 3.6 amino acids. found in cell membrane proteins like transport proteins and receptors. |
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Term
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Definition
| where two alpha helices wrap around each other. Hydrophobic side chains face inward. Form framework for many elogated proteins like alpha keratin. |
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Term
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Definition
| core of many proteins contain these. Caused by hydrogen bonding between neighboring polypeptide strands creating very rigid structure. These can run in parallel orientation or anti-parallel orientation. |
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Term
| Levels of protein organization |
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Definition
Primary - amino acid sequence
Secondary - stretches of the polypeptide chain that form alpha helices and beta pleated sheets
Tertiary - three dimensional organization
Quaternary - a protein molecule formed of more than one polypeptide |
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Term
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Definition
| 1838 by Schleiden and Schwann and stated that all plant and animal tissues are made up of cells. This doctrine marked the birth of cell biology. |
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Term
| Stains used for microscopy |
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Definition
dyes - eosin, hematoxylin, Gram Stain
Radioisotopes
Fluorophores
Fluorescent antibodies
Fluorescent Tags (GFP, CFP, RFP)
IR dyes and tagged proteins
Photophores-photoactivation, photobleaching
Luminescent proteins-Aequorin |
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Term
Size of cells
Light Microscope resolution size and size of objects that can be viewed |
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Definition
10-20 micrometers
.2 micrometer apart, .5 micrometer wide |
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Term
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Definition
| condenser lens, objective lens, ocular lens |
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Term
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Definition
| inactive enzyme without the cofactor |
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Term
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Definition
| activated enzyme with cofactor - complete |
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Term
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Definition
| inorganic molecule required for holoenzyme |
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Term
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Definition
| organic molecule needed for holoenzyme |
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Term
| negative feedback (feedback inhibition) |
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Definition
| the product inhibits the previous step thereby inhibiting its own production. Most common step of regulation. Reversible. |
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Term
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Definition
| in feedback inhibition the inhibitor binds in such a way that it brings conformational change and that makes the active site non-functional. |
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Term
Protein phosphorylation
dephosphrylation |
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Definition
Common regulatory modification in higher eukaryotes.
Phosphorylation is addition of phosphate group as modification of amino acid side chain (covalently linked).
Phosphorylation and dephosphorylation regulate conformational properties of protein complexes. |
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Term
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Definition
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Term
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Definition
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Term
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Definition
A fluorescent molecule absorbs light at a given wavelength and then emits light at a longer wavelength
Use GFP, DAPI, rodamine B |
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Term
| Indirect immunocytochemistry |
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Definition
| Use primary and secondary antibodies and fluorescein to visualize specific antigens |
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Term
| Enzyme linked immunocytochemistry |
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Definition
| attach color producing enzyme to primary or secondary antibody. example - alkaline phosphotase. |
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Term
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Definition
| uses lasers - Z stacking, reduced background noise, use fluorophore probes |
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Term
| GFP from Aequoria victoria |
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Definition
| Green Fluorescent Protein, gene can be introduced into other species |
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Term
| Fluorescence Resonance Energy Transfer (FRET) |
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Definition
| method to establish protein-protein interaction and proteins in macromolecular complexes using combinations of fluorescent proteins |
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Term
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Definition
method to establish signal transduction and movement of cytoskeletal proteins.
-inactive photosensitive fluorophore probe (caged molecules)
-activated with laser light-photoactivation |
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Term
| Fluorescence recovery after photobleaching (FRAP) |
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Definition
method to establish diffusion experiments, active transport, binding and dissociation rates.
A strong focused pulse of laser light will extinguish, or bleach, the fluorescence of GFP.
Based on time to recover after bleaching with strong laser light. |
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Term
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Definition
Has a tip made up of silicon that can measure the mechanical force.
Can visualize single molecules
unfolds individual protein
measures the energetics of domain folding
gives mechanical properties of protein molecules |
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Term
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Definition
The light microscope can resolve structures that are 0.2 μm apart or greater.
The electron microscope can resolve structures that are 0.1 nm apart or greater. |
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Term
| Light microscopy vs. Transmission electron microscopy (TEM) |
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Definition
Differences:
•An electron beam as a source of illumination.
•Lenses in the light microscope are made of glass, but in EM are magnetic coils, which focus the electron beam.
•Specimen is placed in a vacuum.
•The specimen is stained with electron-dense material (metals such as osmium tetroxide) that absorbs electrons.
Advantage:
•Resolution 200 times better than light microscope.
Disadvantages:
•Sample preparation is very laborious.
•EM cannot be used to view living cells (a sample is chemically frozen). |
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Term
| Scanning Electron microscopy |
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Definition
Cheaper than TEM
directly gives 3D structure
has z stacking capacity
Uses electrons that are scattered to make image
provides great depth of field |
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