biob10 Flashcards

Question

Advantages of cultured cells

Answer 1

Cells can be obtained in large quantities Most cultures constitute only one type of cell Important cell biological phenomena can be studied using cultured cells Cell movement, cell division Cells can be induced to differentiate in culture Cultured cells can be used to test the activity of drugs Also hormones or growth factors

Answer 2

Not naturally colored cuz they are too small to see Angstrom (1 hydrogen atom) Nanometer (microscope) micrometers/micron (eye)

Answer 3

A sample of cell are placed in a plastic or glass container Cell sample is usually directly taken from an organism (embryonic tissue) Instead of a singular cell sample, a population of cells (Cell Lines such as HeLa (tumour tissue) cell line) are used Layer of agar medium or any other cell culture medium Placed in a temperature controlled (37 degrees to mimic the human body) oxygen rich environment Constant contact to cell medium and container

Answer 4

Unrealistic cell environment as cells in the human body are surrounded by ECM (Extracellular Matrix) Can often result in insufficient cell division and incorrect image reading Constant and limitless contact to the Matrix (agar) Leads to the development of 2 ends of polarity in the cell sample

Answer 5

Instead of the cell sample or cell line being placed on directly the plate, it is embedded in ECM (Extracellular Matrix), mimicking its natural environment within the human body Limited contact with the Matrix

Answer 6

Provides accurate imaging of the sample No real polarity is developed

Answer 7

Problem with using light microscopes is that it cannot go past the wavelength its using Its limitations are around 2 μm (micrometer), big enough to see cells and bacteria but not the organelle in depth The higher the wavelength or lambda, the worse the resolution or quality becomes

Answer 8

Microscopes produce enlarged images of an object Cells are placed on a stage between the light source and our eyes View light that is diffracted by the cells Resolution: the extent to which details of a specimen are retained in the image (if there's 2 points on your specimen, how close can they be and you can still tell them apart when you look down the microscope) The resolution of a microscope depends both on the wavelength of light as well as numerical aperture of the lens system (wavelength of light is directly proportional to resolution) (big wave length, big resolution = low resolution) The numerical aperture impacts the light-gathering capacity of a lens: Related to the angle of the cone of light entering the lens Related to the refractive index of the medium that the lens is operating in

Answer 9

Microscopes produce enlarged images of an object Cells are placed on a stage between the light source and our eyes View light that is diffracted by the cells Resolution: the extent to which details of a specimen are retained in the image (if there's 2 points on your specimen, how close can they be and you can still tell them apart when you look down the microscope) The resolution of a microscope depends both on the wavelength of light as well as numerical aperture of the lens system (wavelength of light is directly proportional to resolution) (big wave length, big resolution = low resolution) The numerical aperture impacts the light-gathering capacity of a lens: Related to the angle of the cone of light entering the lens Related to the refractive index of the medium that the lens is operating in Stained molecules, dye combined to something like DNA, plasma membrane, er What you see is not absorbed by the stained Stained sample Incident light is used Usually not great for high-resolution

Answer 10

The background is darkened, the sample is white Oblique light is used so that the scattered rays that hit the sample and are bent toward the viewer are the only thing that shows Depends on the bending of light

Answer 11

Waves in phase are used Waves out of phase show contrast Dic = fancy filter= looking at the refraction index of the cell and converting to an intensity If nucleus is dense, it'll give the intensity of the nucleus something different from the rest of the cell Why some part of the cell looks darker than other parts Looks at rate of change

Answer 12

Tissues: embed and section first A tissue was dissected out of an organism and placed in this wax so its fixed in place and stained Can cut little slices of the wax and take a paintbrush and place it onto a slide and then put that slide to dry and then can immerse it in all kinds of different dyes Can see the layers

Answer 13

Haemotoxylin stains nucleic acids (blueish) and eosin stains proteins (pinkish) This type of staining is good to see what might be happening

Answer 14

Uses electrons as “light” source Short wavelength Image formed when electrons pass through a specimen Provides much greater resolution The resolution of a microscope is conversely proportional to the wavelength of its light source: The longer the wavelength; the poorer the resolution Light-constant wavelength Electrons-wavelength varies with speed Speed controlled by accelerating voltage applied in scope Very short wavelength possible = very high resolution

Answer 15

Specimens have to be fixed, embedded & sectioned Stained with heavy metal solutions These bind to cellular macromolecules Metals scatter electron path Image of scattered electrons is caught on photographic emulsion or recorded using a high-resolution digital camera Parts of the image that appears dark are regions where electrons have been scattered away by metal atoms (high density)

Answer 16

Best used for viewing detailed structures within cells and tissues

Answer 17

Not fixed in chemicals but using rapid freeing = cryofixation Water in the sample is supercooled into a noncrystalline state called boisterous ice

Answer 18

It gets it from all different angles Tilts the stage in order to do that Algorithm organizes the images and produces a model

Answer 19

Cells are rapidly frozen in low-temperature liquids Knife edge used to strike frozen cells Fracture plane spreads from point of initial contact, splitting cells into 2 Cellular structures deviate the place of fracture either upward or downward - irregular surface - etching removes thin layers of ice Deposit heavy metals on top of this fractured surface to get a “replica” of the plane Carbon is then deposited over the metals to cement them in place This metal-carbon replica is viewed by EM Freeze fracture: describes the technique of breaking a frozen specimen to reveal internal structure Freeze etching: sublimation of surface ice under vacuum to reveal details of the fractured face that were originally hidden

Answer 20

Specimens prepared by careful drying procedures After drying, coated with carbon and metals Image is formed by electrons reflected back by the specimen Referred to as “backscattered” electrons Gives surface view of cells, tissues, and whole animals A 3-D quality to the image

Answer 21

Best used for viewing extensions or processes that cells use to interact with the environment

Answer 22

Self-renewing Present in large quantities/ can give rise to every blood cell

Answer 23

Stem cells: Undifferentiated cells Can self-renew Can differentiate into 2 or more cell types Most organs in humans contain stem cells Adult cells Transplantation of such cells to specific areas could be future therapy

Answer 24

Are derived from human embryos (IVF clinics) Are pluripotent = capable of differentiating into every cell type in the body Can be cultured for extended periods Phenomenal resource for cell replacement therapy ES-derived oligodendrocytes - spinal cord injury patients Problems: Immunological rejection (not a problem with adult stem cells) ethical/political debates

Answer 25

Changing the genetic makeup of the cells to match that of the patient who needs the cell transplant Problems: Creating an embryo just as a source of ES cells Major ethical questions

Answer 26

reprogramed somatic cells by introducing of specific genes into them Do away with the need for human oocytes/embryos A core set of transcription regulators defines and maintains the ES cell state

Answer 27

Reactions take place in an aqueous environment (cells are 700% water) Based overwhelmingly on carbon compounds Most are enormous polymeric molecules (macromolecules) Composed of complex reactions that allow cells to obtain and use energy Built with macromolecules in mind

Answer 28

Two atoms connected by a covalent bond may exert different attractions for the electrons of the bond. In such cases, the bond is polar, with one end slightly negatively charged and the other slightly positively charged Overall neutral charge (having the same number of electrons and protons), the electrons are asymmetrically distributed making the molecule polar The oxygen nucleus draws electrons away from the hydrogen nuclei, leaving the hydrogen nuclei with a small net positive charge The excess of electron density on the oxygen atom creates weakly negative regions at the other 2 corners of an imaginary tetrahedron

Answer 29

Because they are polarized, 2 adjacent H20 molecules can form a noncovalent linkage known as a hydrogen bond. Hydrogen bonds have only about 1/20 the strength of a covalent bond Hydrogen bonds are strongest when the three atoms lie in a straight line

Answer 30

Molecules of water join together transiently in a hydrogen-bonded lattice. Even at 37 degrees, 15% of the water molecules are joined to four others in a short-lived assembly known as a flickering cluster The cohesive nature of water is responsible for many of its unusual properties, such as high surface tension, high specific heat capacity, and high heat vaporization

Answer 31

Substances that dissolve readily in water are termed hydrophilic. They include ions and polar molecules that attract water molecules through electrical charge effects. Water molecules surround each ion or polar molecule and carry it into solution Ionic substances such as sodium chloride dissolve because water molecules are attracted to the positive (Na+) or negative (Cl-) charge of each ion Polar substances such as urea dissolve because their molecules form hydrogen bonds with the surrounding water molecule

Answer 32

Molecules that contain a preponderance of nonpolar bonds are usually insoluble in water and are termed hydrophobic. This is true, especially for hydrocarbons which contain many C-H bonds. Water molecules are not attracted to such molecules and so have little tendency to surround them and carry them into solution

Answer 33

certain combination of atoms, functional groups (carbon + friends), occur repeatedly in cells Confer distinct physical and chemical properties

Answer 34

Macromolecules are polymers of building blocks known as monomers Polymers form by joining monomers-condensation reaction = water is removed Polymers are broken into monomers-hydrolysis reaction = water is added

Answer 35

Have 2 or more hydroxyl groups Contains either an aldehyde group and is called aldoses or a ketone group and are called ketosis

Answer 36

Ring formation: in aqueous solution, the aldehyde or ketone group of a sugar molecule tends to react with a hydroxyl group of the same molecule, thereby closing the molecule into a ring Isomers: many monosaccharides differ only in the spatial arrangement of atoms-that is, they are isomers These small differences make only minor changes in the chemical properties of the sugar. But they are recognized by enzymes and other proteins and therefore can have major biological effects

Answer 37

The hydroxyl group on the carbon that carries the aldehyde or ketone can rapidly change from one portion to the other. These 2 positions are called α and β As soon as one sugar is linked to another, the α or β form is frozen

Answer 38

Linked by covalent bonds: between C1 of one sugar and hydroxyl (OH) of another sugar Generates C-O-C linkage between sugars

Answer 39

Disaccharides: 2 monosaccharides covalently bonded together Energy storage Ex. sucrose, maltose, lactose Oligosaccharides: a small chain of sugars (oligo = a few) Attached to lipids or proteins converting them to glycolipids and glycoproteins Polysaccharides: a long chain of sugars bonded together Very large molecules with a structural or storage function Ex. chitin, cellulose, scratch, glycogen

Answer 40

Glycogen: stores of chemical energy in most animals (linkage in 1 configuration) Scratch: stores of chemical energy in most plants Cellulose: durable structural polymer (ex: plant cell walls) Chitin: polymer of N-acetylglucosamine Durable structable polymer (ex: exoskeletons of invertebrates)

Answer 41

The hydroxyl groups of a simple monosaccharide such as glucose can be replaced by other groups

Answer 42

A large group of non-polar biological molecules Composed mainly of C, H, and O Dissolve in organic solvents but not in water Lipids with important cell functions: Fats, steroids, phospholipids, glycolipids Dont like water; organize itself away from water

Answer 43

Fats = triacylglycerol = glycerol + 3 fatty acids Fatty acids linked by ester bonds Fatty acids: long hydrocarbon chains with a single carboxy at one end Fatty acids vary in length No double bonds = saturated Double bonds = unsaturated

Answer 44

Complex ring structures - 4 hydrocarbon rings Ex. cholesterol - important animal plasma membrane component Building blocks of many steroid hormones

Answer 45

Composed of glycerol = 2 fatty acids + phosphate + head group Major components of plasma and organelle membranes Hydrophobic on one end and hydrophobic on the other = amphipathic

Answer 46

Glycolipids: like phospholipids, these compounds are composed of a hydrophobic region, containing two hydrocarbon tails, and a polar region, which contains one or more sugars. Unlike phospholipids, there is no phosphate

Answer 47

Arrange into a bilayer Hydrophobic regions point inwards (interior); hydrophilic regions on the outside

Answer 48

Fatty acids have a hydrophilic head and a hydrophobic tail In water, they can form either a surface film or small, spherical micelles Their deviates can form larger aggregates held together by hydrophobic forces Triacylglycerols form large, spherical fat droplets in the cell cytoplasm Phospholipids and glycolipids form self-sealing lipid bilayers, which are the basis for all cell membranes

Answer 49

DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) DNA: genetic material; governs all cellular activities; codes for proteins required for the cell’s functions RNA: many roles; central to the synthesis of proteins; regulates expression of genes; genetic material of some virus Types: transfer RNA (tRNA); messenger RNA (mRNA); ribosomal RNA (rRNA) Polymers of nucleotides

Answer 50

A nucleotide consists of a nitrogen-containing base, a five-carbon sugar, and one or more phosphate groups Nucleotides are the subunits of the nucleic acids What is the difference between a nucleotide and a nucleoside? Nucleoside: Consists of a nitrogenous base (adenine, guanine, cytosine, thymine, or uracil) attached to a sugar molecule (ribose in RNA, deoxyribose in DNA). Nucleotide: Contains a nucleoside (nitrogenous base + sugar) and one or more phosphate groups attached to the sugar.

Answer 51

- pentose: a five carbon sugar - each numbered carbon on the sugar of a nucleotide is followed by a prime mark - two kids of pentoses are used

Answer 52

- the bases are nitrogen containing ring compounds, either pyrimidines or purines - pyrimidine (one ring): u,c,t purine (two ring): a, g

Answer 53

- nucleotides are joined by sugar-phosphate linkages - 3' hydroxyl attaches to 5' phosphate of the adjoining nucleotide (phosphodiester bond)

Answer 54

To form nucleic acid polymers, nucleotides are joined together by phosphodiester bonds between the 5’ and 3’ carbon atoms of adjacent sugar rings. The linear sequence if nucleotides in a nucleic acid chain is abbreviated using a one-letter code such as AGCTT, starting with the 5’ end of the chain

Answer 55

As nucleotide di- and triphosphates, they carry chemical energy in their easily hydrolyzed phosphoanhydride bonds (example ATP) They combine with other groups to form coenzymes (example: coenzyme A; CoA) They are used as small intracellular signaling molecules in the cell (example: cyclic AMP; cAMP)

Answer 56

The second law of thermodynamics states the degree of disorder, or entropy, increases in any isolated system in the universe How then do cells appear to defy this law by generating order? Cells take in energy from the environment and use it to generate order within it. The many chemical reactions that create this order in cells, convert some of this energy to heat. The heat released then creates disorder in the cell’s environment, increasing entropy and hence abiding by the second law of thermodynamics Hate generating reactions within the cell are coupled to those that generate molecular order Each cell is a tiny factor and carries out millions of chemical reactions every second Catalyze the oxidation of organic molecules in small steps -> allows useful energy to be harvested The vast majority of these chemical reactions only occur in cells under normal temperatures because of proteins known as enzymes. These catalalysts increase the rate of reactions by lowering the activation energy required Enzymes can speed up reactions, but they cannot force energetically unfavorable ones to occur ΔG is a measure of the change in the amount of energy available to do work Favorable reactions decrease the ΔG (negative ΔG) and increase the disorder of the universe The cell uses reaction coupling to drive energetically unfavorable reactions We use the standard free energy change, ΔG° (standard conditions, same concentrations, same concentrations of reactants), of reactions to predict the course of biological reactions

Answer 57

energetically favourable: the free energy of Y is greater than the free energy of X. there G < 0, and the disorder of the universe increases during the reaction energetically unfavourable: G > 0 and the universe would become more ordered

Answer 58

Cells catalyze the oxidation of organic molecules in small steps -> allows useful energy to be harvested This energy is stored in a small set of the activated “carrier molecules” which diffuse through the cell through sites in which they are generated to sites in which biosynthesis will occur Cells use these carrier molecules like money to pay for reactions that would not otherwise occur The activated carrier molecules are formed by coupling to favorable reactions The carrier molecule (bucket) picks up sufficient energy to power an unfavorable reaction elsewhere The activated carrier molecules are formed by coupling to favorable reactions The carrier molecule (bucket) picks up sufficient energy to power an unfavorable reaction elsewhere glucose and other food we eat are broken down by stepwise oxidation reactions to produce chemical energy in the form of ATP and NADH These reactions also help produce many of the small molecules that are the substrates for biosynthesis of macromolecues Macromolecules like glycogen and fats can be stored in cexlls as a major source of energy

Answer 59

About 1x10^4 proteins made in every mammalian cell Carry out almost all cellular functions. Examples: Enzymes: accelerate chemical reactions in the cell Signaling: kinases, phosphatases are involved Hormones: long range messenger molecules Growth factors Membrane receptors: communication between cells Cell movement: cytoskeleton

Answer 60

Polymers of amino acids; 20 different types Amino acids: Amino (NH2) and carboxyl (COOH) groups These groups are separated by a single carbon (α-carbon) R groups (side chains) give amino acids their variability

Answer 61

1. Polar charged - can form ionic interactions 2. Polar unchanged - can form H bonds 3. Nonpolar - mostly hydrocarbons (Hydrophobic Usually in the core of protein structure (away from water) 4. Other (glycine, cysteine, and proline)

Answer 62

Peptide bonds: carboxyl group of one amino acid becomes attached to the amino group of another Forms polypeptide chains = proteins

Answer 63

Protein structures are defined by 4 different levels of organization Primary structure (1°): specific sequence of amino acids Determined by the sequence of the gene encoding the protein (DNA) 20^n variations of proteins (20 amino acids) N = the number of amino acids in the chain Typical protein is over 100 amino acids long - infinite number of sequences possible Sequence contains most of the information needed to specify 3-D shape and function of protein Changes in the primary structure can have dire consequences for protein function - ex. Sickle cell anemia Affects red blood cell shape- sickle-shaped Clogs arteries

Answer 64

While some proteins do fold by a process of simple self-assembly, most proteins need some help Help = chaperons = proteins that aid in the folding of newly made proteins by preventing inappropriate interactions Prevent inappropriate interactions with other cellular components Bind hydrophobic segments of proteins Are single proteins or a large protein complex with intricate structure

Answer 65

Conformation of portions of the polypeptide chain Arranged to maximize the number of H-bonds made between neighboring amino acids of peptide backbone only 2 common folding patterns: α-helix and β-pleated sheets

Answer 66

α-helix: Hydrogen bonding that links the C=O of one to the N-H of another (between every fourth amino acid) Cylindrical twistin spiral R groups project outwards β-pleated sheets: Hydrogen bonds extend from one part of the chain to another Polypeptide segments lie side by side

Answer 67

Conformation of the entire protein Interactions between R-groups in the protein Hydrophobic interactions Van der Waals interactions Disulfide bridges 3 types: fibrous, globular, and intrinsically disordered proteins Non-covalent bonds that hold protein tertiary structure together

Answer 68

Elongated shape Usually structural materials outside of cells Keratin, collagen (hair, skin, fingernails) Form long strands or flattened sheets that resist shearing forces

Answer 69

Compact shape Polypeptide chain folds into complex shapes Usually have functions within the cell Enzymes, hormones Most proteins

Answer 70

Loops or tails (or entire proteins) that remain disordered in structure Contain repeated sequences of amino acids Have important functions E.g. elastin (stretchy) Parts of a protein folded into the tertiary structure can have distinct functions from other regions Modules or domains of proteins Substructure produced by any continuous part of a polypeptide Can function in a semi-independent manner Can be swapped between proteins Allow for unique protein activities Ex. move independently; bind different molecules Domains can be constructed from alpha-helices, beta-sheets, or various combinations of fundamental folding elements

Answer 71

Linking of multiple proteins to from large complexes with multiple “subunits”-multiprotein complexes Intermolecular interactions of R groups Disulfide bonds Noncovalent interactions-mostly

Answer 72

Cleaved into smaller polypeptides (“pro-form” cut into smaller fragments) Sugar chains can be added (“glycoproteins”) Lipids added (anchored to cell membranes) metal/ions added (important for function) Phosphate groups added (signaling functions; alters structure or interactions) GTP or calcium binding (alters protein activity) Degradation (controls protein lifespan)

Answer 73

Regulation by degradation The life span of proteins differs a great deal Few minutes = mitotic cyclins Your whole life = crystallin in lens for the eye Controlled by regulated degradation pathways

Answer 74

Lysosomes Autophagy Proteasomes = 90% of protein degradation in mammalian cells

Answer 75

In a “cellular chamber of doom,” proteins suffer “a death by a thousand cuts”

Answer 76

How can it tell which ones needs to degrade? Mark = ubiquitination Ubiquitin (Ub) = 76 reside protein Typically multiple copies of Ub are attached to a protein tagged for proteasomal degradation = polyubiquitination (4 or more Ub) Required the activity of E1, E2, anf E3 enzymes that work in sequence to bring about polyubiquitination

Answer 77

Non-covalent binding to GTP can act as a “switch” to regulate protein activity GTP binding proteins = GTPases GTP bound = active = regulate the activity of target proteins (effectors) in this state GDP bound = inactive The rate of GTPases activity diffeers between proteins GEFs and GAPs aid in regulating the “switch” that regulates these protein

Answer 78

mutations in gene encoding Ras = a GTPase mutant Ras has defective (decreased) intrsitic GTPase activity and is resistant to GAPs

biob10 Flashcards

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