BIL150 Mallery exam 2

Bacteria

Bacteria

any of a group of microscopic organisms that are prokaryotic, i.e., that lack a membrane-bound nucleus and organelles. Bacteria are unicellular (one-celled) and may have spherical (coccus), rod-like (bacillus), or curved (vibrio, spirillum, or spirochete) bodies. Different bacteria inhabit virtually all environments, including soil, water, organic matter, and the bodies of eukaryotes (multicellular animals). Some bacteria are known to be beneficial to humans and the higher animals, while many others are harmful; bacteria are the chief cause of infectious diseases in humans.

Prokaryote

any self-contained cell or organism that lacks internal unit membranes. Bacteria are among the best-known procaryotic organisms. Procaryotes lack a nuclear membrane and most of the components of eucaryotic cells. The cell membrane consists of a phospholipid unit membrane and constitutes the cell's primary osmotic barrier. The cytoplasm includes ribosomes that carry out translation and protein synthesis. The nuclear region usually consists of circular, double-stranded deoxyribonucleic acid (DNA). Many procaryotes also contain accessory, self-replicating genetic structures, called plasmids, with additional dispensable cell functions, such as encoding proteins to inactivate antibiotics. The flagella are distinct from those of eucaryotes in design and movement. The organelles that are present, such as storage vesicles, are surrounded by a non-unit membrane consisting principally of proteins.

Archaebacteria

aquatic or terrestrial microorganisms that exhibit a diversity of shapes, including spherical, rod-shaped, and spiral forms. Archaebacteria lack murein (ester lipids) in the cell walls, which is characteristic of eubacteria; instead, they have ether lipids, as well as a number of different cell-wall constituents. Archaebacteria also differ from eubacteria in the structure of their ribosomal RNA's, which are used in genetic testing to assess the degree of genetic relatedness among different species. The archaebacteria reproduce using a wide variety of mechanisms, including binary and multiple fission, budding, and fragmentation. Archaebacteria survive in a number of extreme environments, including very hot or saline ones. Archaebacteria may be aerobic, anaerobic, or facultatively anaerobic in their metabolic requirements. Some archaebacteria, such as Halobacterium, require a highly saline environment. Others, such as Methanobacterium, produce methane (CH4) as an end product, while still others are dependent on sulfur for their metabolism. The latter group are among the most thermophilic of the archaebacteria, surviving in temperatures higher than 45 to 50 C (113 to 122 F).

Eubacteria

any of a group of true bacteria species and one of two major groups of prokaryotic organisms. The other major group, the archaebacteria, are as different from eubacteria as either is from the eukaryotes. The division of the bacteria into two groups has been suggested by ribosomal RNA studies of the genetic information of the organisms. Eubacteria and archaebacteria are thought to have evolved separately from a common ancestor early in Earth's history. Eubacteria and archaebacteria differ in important characteristics, such as the number of ribosomal proteins and the size and shape of the ribosomal S unit.

Eucaryote

any cell or organism that possesses a clearly defined nucleus, a description that excludes bacteria and blue-green algae. The eucaryotic cell has a nuclear membrane, well-defined chromosomes (bodies containing the hereditary material), mitochondria (cellular energy exchangers), a Golgi apparatus (secretory device), an endoplasmic reticulum (a canal-like communication system within the cell), &lysosomes (digestive apparatus within many cell types).

Virus

an infectious agent of small size and simple composition that can reproduce only in living cells of animals, plants, or bacteria. A virus consists of a single-or double-stranded nucleic acid and at least one protein surrounded by a protein shell, called a capsid. The nucleic acid carries the virus's genome--its collection of genes--and may consist of either DNA or RNA. The protein capsid provides protection for the nucleic acid and may contain enzymes that enable the virus to enter its appropriate host cell. Some viruses are rod-shaped, others are icosahedral (a roughly spherical shape that is actually a 20-sided polygon), and still others have complex shapes consisting of a multisided "head" and a cylindrical "tail."

Cell division

nucleus, chromosomes, centrioles, microtubules (spindle fibers) microfilaments (cell furrow pinching it apart

Information storage & transfer

nucleus, chromosome, DNA--> mRNA --> ribosomes --> enzymes & proteins

Energy conversion

mitochondria

Manufactures membranes & products

ribosomes, rough E.R., smooth E.R., Golgi apparatus and its vesicles

Lipid synthesis & drug detoxification

smooth E.R.

Digestion & recycling

lysosomes and food vacuoles

Conversion of H2O2 to water

peroxisomes

Structural integrity

cytoskeleton: microtubules, microfilaments, intermediate filaments

Movement

cilia and flagella, microtubules, microfilaments (actin in muscles) and pseudopodia

Exchanges with the environment

plasma membrane and vesicles

Cell to cell connections

tight junctions, desmosomes, gap junctions, plasmodesma

Plant cell inter-cell communication

plasmodesma

photosynthesis

chloroplast

membrane cavity of metabolic waste

vacuole

Microtubules

Monomers and Structure:
hollow tube, helix of a and b tubulin dimers, forming a hollow tube 25-nm diameter

Functions:
cell shape and support, tracks for moving organelles around, chromosome movements, beating of cilia and flagella.

Microfilaments(actin filaments)

two twisted chains of actin monomers about 7 nm in diameter

muscle contraction, maintain cell shape, pseudopod movement,cytoplasmic streaming

Intermediate filaments

supercoiled fibrous protein in the keratin family about 1-12 nm in diameter

reinforce cell shape, anchor nucleus in place

Golgi:

processes products of E.R.; makes polysaccharides, packages products in vesicles targeted to specific locations

Transport vesicle

carries products of E.R. to various intracellular locations

Nuclear envelope

double membrane that encloses nucleus;pores regulate passage of materials

rough E.R.

attached ribosomes produce proteins that enter cisternae, and makes secretory protein and membranes

smooth E.R.

houses enzymes that synthesize lipids, metabolize carbohydrates, detoxify drugs and alcohol; stores/releases Ca for muscle cells

transport vesicle

fuses with plasma membrane secreting contents and adding to membrane

plasma membrane

selective barrier that regulates passage of material into & out of cell

lysosome

houses hydrolytic enzymes to digest macromolecules.

transport vesicles

ransport membranes and products to various cellular locations

cristae

infoldings of mitochondrial membrane with attached enzymes

extracellular matrix

consists of collagen, proteoglycans, and fibronectins

peroxisomes

small sacs with specific enzymes for particular metabolic pathways

grana

stacks of flattened sacs inside chloroplasts

basal body

anchoring structure for cilia or flagella

cytosol - cytoplasm

semi-fluid medium between nucleus and plasma membrane

cytoskeleton

system of fibers that maintain cell shape and anchors organelles

tight junctions

connections between animal cells that creates an impermeable layer

vacuolar membrane (tonoplast)

membrane surrounding central vacuole of plant cells

Seven (7) different forms of energy include :

Mechanical,Heat, Sound, Electrical, light, radioactive radiation, and magnetic.

nature of chemical bond

pairs of electrons being shared between atoms, which represent stored energy, potential energy. When a covalent bond is broken in a chemical reaction, energy is released. If the bond being broken is within an organism, the organism may be able to use the released energy to do work and carry out its life processes.

proton pump

a proton pump establishes a hydrogen ion gradient across a cell membrane and uses that gradient to produce ATP. Protons are actively pumped across the membrane, and their diffusion back through special protein channels in the enzyme ATP synthase is coupled to the phosphorylation of ADP with P producing ATP.

entropy

is defined as a measure of the randomness or disorder of a system. Entropy is the tendency ofenergy to spontaneously convert to a less organized pattern and therefore provides a directionality to all energetic processes, i.e., disorder is constantly increasing in the universe

potential vs. kinetic energy

Potential energy is "Stored Energy", while kinetic energy is the "energy of motion

free energy

A thermodynamic quantity that is the difference between the enthalpy (heat content) & theproduct of the absolute temperature and entropy of a system; also called Gibb's free energy. Best defined as the energy content in a system available to do work

anaerobic

does not require oxygen directly; referring to organisms or cellular process that may occurin oxygenated environments but do not use oxygen as the terminal electron acceptor of metabolism.

Redox reaction

Oxidation is the loss of an electron by an atom or molecule, while reduction is thegaining of an electron by an atom or molecule. The e- is frequently accompanied by a hydrogen proton. Oxidation involves the release of energy from the molecule, while reduction signifies the addition of energy to a molecule. By definition, whenever one substance is oxidized, another substance must be reduced; therefore oxidation-reduction reactions (redox Rx) transfer energy between molecule within cells.

chemiosmosis

the major pathway by which aerobic cells produce ATP. A proton pump in the innermitochondrial membrane forces protons out of the mitoplasm producing a concentration gradient between the mitoplasm and peri-mitochondrial space. Following their diffusive concentration gradient, the protons diffuse back into the mitoplasm through an integral membrane protein, ATP synthase, which facilitates the phosphorylation of ADP with P.

catabolic/anabolic

Anabolic metabolism is the phase of metabolism in which simple substances aresynthesized into the complex materials of living tissue; smaller inorganic [CO2and H2O] are made into carbohydrates; the biosynthetic pathways of cellular metabolism are anabolic. Catabolic metabolism is the metabolic breakdown of complex molecules into simpler ones, often resulting in a release of energy; larger organic are degraded into smaller inorganics [glucose to CO2and H2O]. The oxidative pathways of cellular respiration are catabolic.

phosphorylation

o add a phosphate group to (an organic molecule); commonly involves addingto ADP to make ATP; reaction is often catalyzed byenzymes called kinases; is the primary mechanism by which cells make and transform energy poor compounds into energy rich molecules

dehydrogenase

one of the six main classes or types of enzymes that catalyzes the removal and transfer of hydride ion from a donor substrate in an oxidation-reduction reaction

cytochrome

any of a class of iron-containing proteins that are important in cell respiration as catalysts of oxidation-reduction reactions; found in the inner cristae membranes of mitochondria.

endergonic reaction

products contain more energy than reactants

exergonic reaction

products contain less energy than reactants

all forms of cellular energy are derived from

the electromagnetic radiation of sunlightand are converted into more useful intracellular form (ATP, ADP, P) allowing work to be done as the energy is eventually transformed and lost within cells

Glycolysis produces

ATP, NADH, & Pyruvate

Fermentation produces

NAD+& Alcohol + CO2 or Lactate

Oxidation of Pyruvate produces

NADH, Acetyl-CoA, CO2

Citric Acid Cycle produces

GTP, FADH2, NADH, OAA,

Electron Transfer Chain produces

ATP,FAD, NAD+, & H2O

GLYCOLYSIS-Two phases

energy investment phase

the cell uses ATP to phosphorylate glucose and then fructose, raising those glycolytic intermediate to higher free energy states [more chemically reactive], thereby allowing them to be acted upon and converted into other intermediates, providing a favorable directionality for the oxidation of glucose to pyruvate to proceed. Glucose is phosphorylated to Glu-6-P as ATP is hydrolyzed by the enzyme hexokinase and fructose-6-P is phosphorylated to Fruc-1,6-diP by Mallery - BIL 150 Energy & Metabolism : Answers - Page 3ATP hydrolysis.


energy-yielding phase

the favorable intermediates produced above now can undergo oxidation producing 2 molecules of NADH, where some energy is conserved and can be used to make ATP by Chemiosmosis later in the mitochondria. 2 molecules of glyceraldehyde-P are oxidized and the electrons used to reduce 2 molecules of NAD+. Additionally, 4 molecules of ADP are phosphorylated to make 4 ATP's by substrate level phosphorylation, producing a net yield of 2 ATP, thus energy yielding.

Cytochromes

four organic rings binding an iron atom

iron-sulfur proteins

iron and sulfur complexes

Flavoproteins

FMN and FAD; Flavin mononucleotide & Flavin adenine dinucleotid

Ubiquinone

an organic phenolic ring capable of being reduced to a semiquinone or hydroquinone

peri-mitochondrial (inner membrane) space

is the site of the higher [H+].

why is wine alcoholic

Wine (from Latin vinum) is an alcoholic beverage made from grapes, generally Vitis vinifera, fermented withoutthe addition of sugars, acids, enzymes, water, or other nutrients. Yeast consumes the sugar in the grapes andconverts it to ethanol and carbon dioxide

what are the four chemical products made by the process of fermentation of grapes into wine?

he four chemical products made in the process of the fermentation of wines are: a. NAD+, b. CO2 , c. ethanol,and d. lactic acid (but also, acetic acid = vinegar, butyric acid- of butter, and propionic acid, a mold inhibitor in breads). The alcoholic content of natural wine comes from fermentation. Wine contains alcohol because of the yeast that live in the grape juices. The yeast carry out fermentation because conditions are anaerobic in a wine vator bottle where the wine is fermenting. Fermentation starts when yeast on the skins of ripe grapes comes into contact with the grape juice (called must). Run off into casks, the new wine then undergoes a series of chemical processes, including oxidation, precipitation of proteins, and fermentation of chemical compounds, that create characteristic bouquet. After periodic clarification and aging in casks, the wine is ready to be bottled.

fortified wine is defined as one in which alcohol has been added to the naturally fermented wine. Naturally fermented wines do not contain an alcohol content greater than about 12% ethanol. Why?

natural wines do not have alcohol levels higher than about 12%, because at higher levels the alcohol becomes toxic to the yeast cells and kills them, thus preventing further fermentation or further production of alcohol.

In Photosynthesis

ants convert _light_ energy of the sun into __chemical bond__ energy stored in _organic_ molecules. Plant are _autotrophic_ organisms that "feed themselves", in the sense that theymake their own organic molecules from _inorganic_ raw materials. Some bacteria are _chemoautotrophs_,which means they use energy from oxidizing inorganic substances to produce organic compounds

Thylakoid

a flattened membrane sac inside the chloroplast, used to convert light energy into chemical bond energy. Stacks of thylakoid membranes are called grana

Chloroplasm

the fluid (aqueous) portion of the chloroplast surrounding the thylakoid membranes,contains bacterial size ribosomes, DNA, enzymes of CO2 fixation, and solutes. Also calledthe stroma

Calvin Cycle

a major biochemical pathway of photosynthesis involving the reduction of atmospheric carbon dioxide into carbohydrate, as glucose

Electromagnetic energy

the entire spectrum of radiation, produced by the fusion reactions of thesun; expressed in wavelengths, which run from less than a nanometer to more than a kilometer.A portion of the spectrum is referred to as the visible spectrum, which includes the light seenby the human eye, and runs from 340 nm to 720 nm.

Absorption spectra

a graphical plot of the amount of light absorbed by a purified form of a molecule vs. the wavelengths of the electromagnetic (visible light)

PEP Carboxylase -

- an enzyme found in C4 plants, which reduces carbon dioxide by combination ofCO2 with PEP to make malate. The efficiency of PEP carboxylase for CO2 is much greater than that of RuBP carboxylase, the enzyme of CO2 reduction in C3 plants

CAM Plant

a plant that uses Crassulacean acid metabolism (CAM), an adaptation for photosynthesis In arid conditions, first discovered in the plant family Crassulaceae. CO2 entering openstomata during the night is first converted into organic acids (malate) which releases CO2 for use in the Calvin cycle during the day, when the stomata are closed, thus these processes are temporally separated

Photosystem

light harvesting complex located within the thylakoid membranes & consisting of anantennae complex of chlorophyll molecules & a reaction center pigment molecule

Cyclic electron flow

a route of electron flow, during the light reactions of photosynthesis, which Involves only photosystem I (PSI), produces ATP, but not NADPH, and has the electron returning to its original source pigment - P700

Photorespiration

metabolic pathway that consumes oxygen (like cell respiration) and releases carbon dioxide, generates no ATP, and decreases photosynthetic output of carbohydrate. It occurs most commonly on hot, dry, bright days, when plant stomata are closed and the oxygen concentration in the leaf exceeds that of carbon dioxide in Calvin plants

Plastoquinone

a cytochrome-like component of the photsynthetic electron transfer chain which undergoes a redox reaction by gaining/losing electrons and/or protons.

1. Why is no oxygen generated by cyclic electron flow?

No electrons are released from PSII (P680) and therefore without an oxidized P680 there is no need to split water to re-reduce the P680.

During chemiosmosis in chloroplasts the proton gradient across the membranes is as great as 1.0 to 2.0pH units. Name the side of the membrane with the lowest pH?

Inside the thylakoid compartment (locule) is the site of the lowest pH, greatest H+ concentrations.

What possible explanation is there for photorespiration, a process that can result in the loss of as muchas 50% of the carbon dioxide reduced in the Calvin Cycle?

photorespiration may be an evolutionary relic from the time when there was little oxygen in the atmosphereand the ability of the enzyme Rubisco to distinguish between O2 and CO2 was not that critical.Now in our oxygen rich atmosphere, Photorespiration seems to be a great agricultural liability.

Exactly where does the Calvin Cycle take place in C4 plants?

In the Bundle Sheath cells

In the figure to the right the isolated chloroplasts were first allowed to equilibrate in an acidic solution atpH 4.0. After the chloroplast's thylakoid compartments reached a pH of 4.0, the chloroplasts were collected and transferred to a basic solution at pH 8.0. This caused the chloroplasts to make ATP, even if placed in the dark. Explain?

the higher concentration of H+ ions inside the locules after being equilibrated at pH4.0 means that these H+ ions will move from the locules, with the existing H+ ion gradient, back out into the high pH media (low H+ concentrations) of the stroma ,probably through the ATP synthase in these membranes, thereby making ATP.

if there are 12 chromosomes in a plant cell at the G1 stage of the cell cycle, then ?

a) what is the diploid chromosome number of this plant? and explain your answer?

b) how many chromatids would be present at anaphase?

c) the progeny cells, after cytokinesis, would contain how many chromosomes?

a) The diploid chromosome number of this plant is most likely 12. G1 is the stage prior to DNA duplication and normally contains the diploid amount of DNA for a species.

b)Since each chromosome duplicates itself and becomes visible during mitosis, there should be 24 chromatids presentat anaphase. When the centromere duplicates during mitosis at that point we would refer to the chromatid as another chromosome.

c)The daughter cells, after cytokinesis, would contain the diploid number of chromosomes for this species which is 12

Measurements of the amount of DNA per nucleus were taken on a large number of cells from a growing cell culture of mouse fibroblasts. The measured DNA levels ranged from 3 to 6 picograms per nucleus. One nucleus had 5 picograms of DNA. What stage of the cell cycle was this nucleus in? and how did you know?

The nucleus, which had 5 picograms of DNA, is probably in late S, just before G2. The measurements of the amount of DNA ranged from 3 to 6 picogram. Assuming that these cells are dividing mitotically and allowing for statistical error this suggests that the diploid amount of DNA for these cells is near 3 picograms and the tetraploid (doubled)amount of DNA would be 6 picograms. Thus 5 picograms places the cell in late S, just before G2

A common chemo-therapeutic drug used to treat cancerous cell growth is Taxol, a compound extracted from the Pacific Yew tree. In animal cells this anticancer drug disrupts microtubule formation by binding to MT's and accelerating their assembly from the precursor, tubulin. How might showing such a drug affect cancer cells?

Taxol is one of several cytoskeletal drugs (another is Colchicine) which function by interfering with the dividing cell's ability to process microtubules and the mitotic spindle. Taxol stabilizes microtubule polymers preventing disassembly thus chromosome are unable to form a metaphase spindle configuration blocking the progression of mitosis. Unable to complete the division cycle the cell dies

if a liver cell of an animal contains 24 chromosomes, then the sperm cells of this animal would have how many chromosomes? Why?

The sperm cells would have half the chromosome number of the diploid content of this animal species. If the diploid number of chromosomes is 24 then the haploid number ought to be 12.

How does the process of sex and sexual cell division increase the genetic variability in a species

allowing the recombination of chromosomes from two different individuals, 2) by allowing recombination of alleles on a chromosome and 3) by producing gametes with different combinations of parental chromosomes ?

the major significant differences between asexual cell division and sexual cell division include:

a)the number of cells divisions that occur - one for mitosis and two for meiosis.

b)the fact that reduction division takes place in meiosis but not mitosis, where the chromosome number if halved

c)the process of crossing over, which allows for the creation of new chromosome variations that did not exist in the parental cell, and which forms the basis of genetic variability in a population of organisms.

d)the process of random assortment, which allows the homologs of a homologous pair to align at the equatorial plate prior to separation in a random pattern, meaning that an infinite number of combinations of homologous pairings is possible. Therefore, the progeny cells have a multitude of various combination of genes and that contributes greatly to genetic variation in a species

Which of these microscopes do you think achieves the highest resolution?


Transmission electron microscopes
Answers:
Light microscopes
Scanning electron microscopes
Confocal laser scanning microscopes
Transmission electron microscopes
Dissecting microscopes

Transmission electron microscopes

The type of microscopy that requires the use of two sets of filters. The 1st filter narrows the wavelength range that reaches the specimen and the 2nd filter blocks out all wave lengths that pass back up to the eyepiece except for those emitted by the dye in the sample is?

Fluorescence microscopy

Gram staining of bacteria can distiguish between species of bacteria based upon the bacteria's?

Cell wall structure

Which of the following is (are) characteristics of prokaryotic cells?

all the the above:

Absence of cell organelles

Absence of a nucleus

Presence of ribosomes

Circular DNA

Why do you think that biologists are interested in organisms that can live in extreme environments on Earth?

because they may help one understand how life might exist on other planets

What is the most likely pathway taken by a newly synthesized protein that will be secreted by a cell?

ER → Golgi → vesicles that fuse with plasma membrane