Unit 1: Chemistry and Cells Flashcards
Alanine - Abbreviations and properties
Ala, A
Aliphatic, Nonpolar (hydrophobic)
Glycine - Abbreviations and properties
Gly, G
Aliphatic, Nonpolar (hydrophobic)
Valine - Abbreviations and properties
Val, V
Aliphatic, Nonpolar (hydrophobic), Essential
Leucine - Abbreviations and properties
Leu, L
Aliphatic, Nonpolar (hydrophobic), Essential
Isoleucine - Abbreviations and properties
Ile, I
Aliphatic, Nonpolar (hydrophobic), Essential
Methionine - Abbreviations and properties
Met, M
Nonpolar (hydrophobic), Sulfur-containing, Essential, Start codon (AUG)
Proline - Abbreviations and properties
Pro, P
Aliphatic, Nonpolar (hydrophobic)
Phenylalanine - Abbreviations and properties
Phe, F
Aromatic, Nonpolar (hydrophobic), Essential
Tryptophan - Abbreviations and properties
Trp, W
Aromatic, Nonpolar (hydrophobic), Essential
Tyrosine - Abbreviations and properties
Tyr, Y
Aromatic, Polar (hydrophilic)
Serine - Abbreviations and properties
Ser, S
Hydroxylic, Polar (hydrophilic)
Threonine - Abbreviations and properties
Thr, T
Hydroxylic, Polar (hydrophilic), Essential
Asparagine - Abbreviations and properties
Asn, N
Amidic (derived from ammonia), Polar (hydrophilic)
Glutamine - Abbreviations and properties
Gln, Q
Amidic (derived from ammonia), Polar (hydrophilic)
Cysteine - Abbreviations and properties
Cys, C
Sulfur-containing, Polar (hydrophilic) - though only weakly
Histidine - Abbreviations and properties
His, H
Basic (positively charged), Essential
Lysine - Abbreviations and properties
Lys, K
Basic (positively charged), Essential
Arginine - Abbreviations and properties
Arg, R
Basic (positively charged)
Aspartic Acid - Abbreviations and properties
Asp, D
Acid (negatively charged)
Glutamic Acid - Abbreviations and properties
Glu, E
Acid (negatively charged)
How does a light microscope work?.
Visible light is passed though the specimen and then through glass lenses. The lenses refract (bend) the light in such a way that the imagine of the specimen is magnified.
What is magnification? (In the context of microscopes)
Magnification is the ratio of an object’s imagine size to its real size.
What is resolution? (In the context of microscopes)
Resolution is a measure of the clarity of the image. It is the minimum distance two points can be separated and still identified as two separate points.
What is staining?
The specimen is enhanced with dyes. Most staining procedures require that the cells be fixed, thereby killing them.
What is phase-contrast? (microscopes)
Variations in density within the specimen are amplified to enhance contrast in unstained cells; useful for examining living, unpigmented cells.
What is differential interference (Nomarski)? (microscopes)
Optical modifications are used to exaggerate differences in density; image appears almost 3D.
How does a confocal image work? (microscopes)
Using a laser, this “optical sectioning” technique eliminates out-of-focus light from a thick sample. By capturing sharp images at many different planes, a 3D reconstruction can be recreated.
What does a scanning electron microscope (SEM) do?
The SEM is especially useful for detailed study of the topography of a specimen. The electron beam scans the surface of the sample (usually coated with a thin film of gold). The beam excites electrons on the surface, and these secondary electrons are detected by a device that translates the pattern of electrons into an electronic signal sent to a video screen.
What does the transmission electron microscope (TEM) do?
The TEM is used to study the internal structure of cells. The TEM aims an electron beam through a very thing section of the specimen. The specimen must be stained with atoms of heavy metals. This enhances the density of some parts of the specimen.
What is cell fractionation?
In cell fractionation, broken-up cells are placed in a tube that is spun in a centrifuge. The largest components settle on the bottom of the tube, forming a pellet. The liquid above the pellet is poured into a new tube and centrifuged again. This is repeated several times, creating a series of pellets that consist of different pieces of the specimen.
What are fimbriae (prokaryotes)?
The attachment structures on the surface of some prokaryotes (not visible on TEM).
What is the nucleoid (prokaryotes)?
The region where the cell’s DNA is located (no membrane).
What is the glycocalyx (prokaryotes)?
The outer coating of many prokaryotes consisting of a capsule or a slime layer.
What do microvilli do?
Microvilli increase the cell’s surface area without increasing its volume much.
Describe the nuclear membrane
The nuclear envelope is a double membrane which is each a lipid bilayer separated by a space of 20-40 mm. The envelope is perforated by pore structures (around 100 mm in diameter). At the lip of each pore, the inner and outer membranes of the envelope are joined. An intricate protein called a pore complex lines each pore and regulates the entry/exit.
What is the nuclear laminae?
A netlike array of protein filaments (intermediate filaments in animal cells) that maintains the shape of the nucleus by mechanically supporting the nuclear envelope.
What does the nucleolus do?
The nucleolus is where rRNA is synthesized. Proteins are assembled with the rRNA are assembled into ribosomes. The ribosomes exit the nucleus via the nuclear pores.
What are the functions of the smooth ER?
- The synthesis of lipids - including steroids (sex hormones)
- The metabolism of carbohydrates
- The detoxification of drugs/poisons (adding hydroxyl groups to drug molecules; more drugs = proliferation of smooth ER = higher tolerance to the drugs)
- The storage of calcium ions (in muscle cells, calcium ions are pumped from the cytosol into the lumen)
What are the functions of the rough ER?
- Creates secretory proteins (most of which are glycoproteins - proteins with carbohydrates covalently bonded to them)
- Membrane factory (grows in place by adding membrane proteins and phospholipids to its own membrane)
What are the flattened membranous sacks of the Golgi Apparatus called?
Cisternae
Cis-side vs trans-side of the Golgi Apparatus
The cis-side usually faces the ER and receives vesicles. The trans-side gives rise to vesicles that pinch off and travel to other sites.
What does the lysosome do?
The lysosome is a membranous sac of hydrolytic enzymes that many eukaryotic cells use to digest macromolecules (the enzymes of the lysosome work best in the acidic environments found in lysosomes). Lysosomes also play a role in phagocytosis. The food vacuole fuses with the lysosome and hydrolytic enzymes digest the food particles.
What are cristae?
Cristae are the infoldings found in the inner membrane of mitochondria. They give the inner membrane a higher surface area, enhancing the productivity of cellular respiration.
What is the intermembrane space and the mitochondrial matrix?
The intermembrane space is the space between the two membranes of mitochondria. The mitochondrial matrix is the area enclosed by the inner membrane.
What are thylakoids? Granum? Stroma?
Thylakoids are the flattened interconnected sacs found in chloroplasts. Granum are stacks of thylakoids. Stroma is the fluid outside the thylakoids.
What are plastids?
A family of closely related plant organelles.
What do amyloplasts store?
Amylose - starch
What do chromoplasts store?
Pigments
What does the peroxisome do?
It removes hydrogen atoms from certain molecules and transfer them to oxygen producing hydrogen peroxide. They have a granular or crystalline core that to be a dense collection of enzyme molecules.
What are microtubules made of?
Tubulin a dimer made of alpha-tubulin and beta-tubulin. They form a hollow tube.
What are the functions of microtubules?
Maintenance of cell shape; cell motility; chromosome movements in cell division; organelle movements
What are microfilaments made of?
Filaments of actin
What are the functions of microfilaments?
Maintenance of cell shape; changes in cell shape; muscle contraction; cytoplasmic streaming (movement of cytoplasm around in plant cells); cell motility; cell division (animal cells)
What are intermediate filaments made of?
One of several different proteins (such as keratin) coiled into cables
What are the functions of intermediate filaments?
Maintenance of cell shape; anchorage of nucleus and certain other organelles; formation of nuclear lamina.
What is a centrosome?
A region that is often located near the nucleus and organizes microtubules.
- Composed of a pair of centrioles which is each composed of 9 sets of triplet microtubules arranged in a ring
What are flagella and cilia made of?
Microtubules
What is the arrangement of microtubules in flagella and motile cilium? Nonmotile cilium?
Motile cilia and flagella: 9 doublets of microtubules arranged in a ring with 2 single microtubules in the center. “9+2” pattern
Nonmotile cilia: Same as motile cilia, but lacking the 2 microtubules in the center. “9+0” pattern
What is a basal body?
A structure that anchors the microtubule assembly of a cilium or flagellum. Structurally similar to a centriole (microtubule triplets in a 9 + 0 pattern)
What are dyneins?
Large motor proteins that attach along each outer microtubule doublet. A typical dynein protein has two “feet” that “walk” along the microtubule of the adjacent doublet, using ATP for energy.
Primary vs secondary cell wall
The primary cell wall is the first cell wall a young plant secretes which is relatively thin and flexible. When the cell matures and stops growing, it strengthens its wall. Some plants cells do this by simply secreting hardening substances into the primary wall. Others add a secondary cell wall. The secondary wall is often deposited in several laminated layers and has a strong and durable matrix that affords the cell protection and support.
What is middle lamella?
Middle lamella is a thin layer rich in sticky polysaccharides called pectin. It glues adjacent cells together and is between the primary and secondary cell walls.
What are proteoglycans?
A small core protein with many carbohydrate chains covalently atached
What are integrins?
Cell-surface receptor proteins that bind on their cytoplasmic side to associated proteins attached to microfilaments and transmits signals between the ECM (extracellular matrix) and the cell.
What are tight junctions?
A junction that occurs at the plasma membranes of neighboring cells that are tightly pressed against each other, bound by specific proteins. This prevents leakage of extracellular fluid.
Describe desmosomes
Junctions that function like rivets, fastening cells together. Intermediate filaments made of keratin proteins anchor desmosomes in the cytoplasm.
Describe gap junctions
Junctions that provide cytoplasmic channels from one cell to an adjacent cell (similar to plasmodesmata in plants).
Muscle cells are attached by…
Desmosomes
What is the nuclear matrix?
The nuclear matrix is an intricate meshwork of proteins spread throughout the nucleus. The matrix plays a role in essential nuclear functions, which include gene expression, RNA splicing, RNA export, and nuclear protein import and export.
In what cells is the Golgi Apparatus wide-spread?
Secretory cells
What are glyoxysomes?
Fat-storing tissues in plant seeds. They convert fatty acids into sugar.
What bond angle to tetrahedrons have? (CH4)
109.5º
Name some examples of aldoses (carbohydrates)
Glucose, galactose
Name some examples of ketoses (carbohydrates)
Carbonyl in the middle of the chain
Fructose
What links two monosaccharides?
Glycosidic linkages
What is the most abundant organic molecule on Earth?
Cellulose
What type of structure does amylose have?
Helical
What type of structure does amylopectin have?
Branched
What type of structure does glycogen have?
Heavily branched
α-glucose vs ß-glucose
α-glucose has an H on top and an OH on the bottom of Carbon 1, while ß-glucose has an OH on top and an H on the bottom of Carbon 1.
ß glucose is more stable and harder to break down in humans’ digestive systems.
In cellulose, every ß glucose is upside down.
What type of bond is between glycerol and a fatty acid?
An ester linkage
What type of bond is between amino acids (to form a protein)?
Peptide bonds.
In a peptide bond, the O double-bonded to the C of the carboxyl group and the N from the amine group are on opposite sides.
Describe the structure of an amino acid
An alpha carbon has an amine group (NH2) and a carboxyl on the other. An H is attached above the alpha carbon, and an R group is attached below the alpha carbon.
What are the functions of a protein?
Storage, enzymes, defensive, transport, hormones, receptors, motor, structure
Between which amino acids do alpha-helices form?
The xth amino acid and the (x+4)th amino acid.
Ex. Between the 1st amino acid and 5th amino acid.
What are the characteristics of a purine?
2 rings, Guanine and Adenine
What are the characteristics of a pyrimidine?
1 ring, Cytosine, Uracil, Thymine
What direction is DNA built in?
5’ to 3’