Ch1 Flashcards
(122 cards)
1
Q
What are the six distinguishing features of living organisms?
A
A high degree of chemical complexity and microscopic organization.
Systems for extracting, transforming, and using energy from the environment.
Defined functions for each of an organism’s components and regulated interactions among them.
Mechanisms for sensing and responding to alterations in their surroundings.
A capacity for precise self-replication and self-assembly.
A capacity to change over time by gradual evolution.
2
Q
What boundry does the plasma membrane define?
A
The perhiphery of the cell, separating the contents from the surroundings.
3
Q
What are the universal features of living cells?
A
A nucleous or nucleoid, a plasma membrane, cytoplasm.
4
Q
The cytosol is defined as what portion of the cytoplasm?
A
The cytosol is defined as that portion of the cytoplasm that remains in the supernatant after gentle breakage of the plasma membrane and centrifugation of the resulting extract at 150,000 g for 1 hour.
5
Q
What remains in the supernatant of cytoplasm centrifuged at 150,000 g for one hour?
A
The cytosol, the supernatant of cytoplasm, a concentrated solution of enzymes, RNA, monomeric subunits, metabolites, and inorganic ions.
6
Q
What forms the pellet of cytosol when centrifuged at 150,000 g for one hour?
A
After the cytosol (the supernatant) is removed, particles and organelles are what remains:
Ribosomes, storage granules, mitochondria, chloroplasts, lysosomes, endoplasmic reticulum.
10
Q
Define the two types of phototrophs by carbon source and give examples of each:
A
Autotrophs: carbon from CO2 (inorganic).
ex: cyanobacteria, vascular plants
Heterotrophs: carbon from organic compounds.
ex: purple bacteria, green bacteria
11
Q
Define the two types of chemotrophs by energy source and give examples of each:
A
Lithotrophs: oxidise inorganic fuels.
ex: sulfur bacteria, hydrogen bacteria
Organotrophs: oxidise organic fuels.
ex: most bacteria, all nonphototrophic eukaryotes
Both types may be either autotropic or hetertrophic with regard to carbon source used for catabolism.
12
Q
List common features of bacterial cells:
A
Nucleoid, ribosomes, pili, flagella, cell envelope (Gram - or Gram +)
14
Q
ribosome
A
ribosomes synthesise protein from an RNA message, 70S in bacteria, 80S in eukaryotes.
15
Q
nucleoid
A
the nucleoid contains a single, simple, long circular DNA molecule, not membrane bound
16
Q
pili
A
pili provide points of adhesion to surface of other cells.
17
Q
flagella
A
flagellum are used propel cell through its surroundings.
18
Q
Gram + vs Gram -
A
Gram - : Inner membrane, thinner (relative to Gram +) peptidoglycan layer, LPS (lippopolysaccharide) outer membrane.
Gram + : Inner membrane, thinner (relative to Gram -) peptidoglycan layer, no outer membrane.
19
Q
peroxisome
A
peroxisome is a vesicle present in cytoplasm that oxidises fatty acids
20
Q
cytoskeleton
A
cytoskeleton supports the cell, aids in movement of organelles
21
Q
nucelar envelope
A
nucelar envelope segregates chromatin (DNA protein) from cytoplasm
22
Q
lysosome
A
lysosome is a vesicle present in cytoplasm that degrades intracellular debris (animal cells only)
23
Q
Golgi complex
A
Golgi complex processes, packages, and targets proteins to other organelles or for export
24
Q
smooth endoplasmic reticulum
A
smooth endoplasmic reticulum is the site of lipid synthesis and drug metabolism
25
Q
rough endoplasmic reticulum
A
rough endoplasmic reticulum is the site of much protein synthesis
26
Q
mitochondrion
A
mitochondrion oxidises fuels to produce ATP
27
Q
transport vesicle
A
transport vesicle shuttles lipids and proteins between the endoplasmic recticulum, Golgi complex, and plasma membrane
28
Q
nucleolus
A
nucleolus is the site of ribosomal RNA (rRNA) synthesis
29
proteasome
Proteasomes are protein complexes inside all eukaryotes and archaea, and in some bacteria. In eukaryotes, they are located in the nucleus and the cytoplasm. The main function of the proteasome is to degrade unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide bonds.
30
chloroplast
chloroplast harvests sunlight, produces ATP and carbohydrates (plant cells only)
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starch granule
starch granules temporarily store carbohydrate products of photosynthesis (plant cells only)
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thylakoids
thylakoids are the site of light driven ATP synthesis (plant cells only)
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cell wall
cell wall provides shape and rigidity; protects cell from osmotic swelling (plant cells only)
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vacuole
vacuoles degrade and recycle macromolecules, stores metabolites (plant cells only)
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plasmodesma
opening in the cell wall that provides a path between two plant cells (plant cells only)
36
glyoxysome
glyoxysomes contain enzymes of the glyoxylate cycle (plant cells only)
37
describe the contents of the pellet that results from centrifugation of a homogenised tissue sample at 1,000 *g* for 10 minutes
38
describe the process of differental centrifugation
Differential centrifugation is a common procedure in microbiology and cytology used to separate certain organelles from whole cells for further analysis of specific parts of cells. In the process, a tissue sample is first homogenised to break the cell membranes and mix up the cell contents. The homogenate is then subjected to repeated centrifugations, each time removing the pellet and increasing the centrifugal force. Finally, purification may be done through equilibrium sedimentation, and the desired layer is extracted for further analysis.
39
What is the typical size of an animal or plant cell?
5 to 100 *𝛍*m in diameter
40
supernatant
The liquid layer remaining after centrifugation, contrast with the pellet (precipitate in diagram shown)
41
Isopycnic centrifugation is effective for separating what kinds of particles?
Those of a different density.
In isopycnic centrifugation, a centrifuge tube is filled with a solution, the density of which increases from top to bottom; a solute such as sucrose is dissolved at different concentrations to produce the density gradient. When a mixture of organelles is layered on top of the density gradient and the tube is centrifuged at high speed, individual organelles sediment until their buoyant density exactly matches that in the gradient. Each layer can be collected separately
42
isopycnic centrifugation
In isopycnic centrifugation, a centrifuge tube is filled with a solution, the density of which increases from top to bottom; a solute such as sucrose is dissolved at different concentrations to produce the density gradient. When a mixture of organelles is layered on top of the density gradient and the tube is centrifuged at high speed, individual organelles sediment until their buoyant density exactly matches that in the gradient. Each layer can be collected separately
43
What is the size of a typical unicellular microorganism?
1 to 2 *𝛍*m long
44
what are the three general types of cytoskeleton filaments?
actin filaments, microtubules, intermediate filaments
(shown: Mitosis in a newt lung cell. Microtubules (green), attached to structures called kinetochores (yellow) on the condensed chromosomes (blue), pull the chromosomes to opposite poles, or centrosomes (magenta), of the cell. Intermediate filaments, made of keratin (red), maintain the structure of the cell)
48
What is the main difference between prokaryotic and eukaryotic ribosomes?
Prokaryotic ribosomes are smaller (70S vs 80S) than their eukaryotic counterparts.
50
name nucleotide U
Uracil
51
name nucleotide T
Thymine, 2 bonds with Adenine
52
name nucleotide C
Cytosine
53
name nucleotide A
Adenine
54
name nucleotide G
Guanine
55
what nitrogenous base is this? what type of molecule is it? where is it attatched to the ribose backbone and how many hydrogen bonds does it form in standard Watson-Crick configuration? If it can be commonly methylated, where?
Thymine, a pyrimidine, is connected to the ribose backbone at position 1, and forms two hydrogen bonds with Adenine at positions 3,4.
IUPAC name for position clarity: 5-Methylpyrimidine-2,4(1*H*,3*H*)-dione
56
what nitrogenous base is this? what type of molecule is it? where is it attatched to the ribose backbone and how many hydrogen bonds does it form in standard Watson-Crick configuration? If it can be commonly methylated, where?
Guanine, a purine, is connected to the ribose backbone at position 9 and forms three hydrogen bonds with Cytosine.
IUPAC name for position clarity: 2-amino-9*H*-purin-6(1*H*)-one
57
what nitrogenous base is this? what type of molecule is it? where is it attatched to the ribose backbone and how many hydrogen bonds does it form in standard Watson-Crick configuration? If it can be commonly methylated, where?
Cytosine, a pyrimidine, is connected to the ribose backbone at position 1, and forms three hydrogen bonds to Guanine. Can be methylated at position 5.
IUPAC name for position clarity: 4-aminopyrimidin-2(1*H*)-one
58
what nitrogenous base is this? what type of molecule is it? where is it attatched to the ribose backbone and how many hydrogen bonds does it form in standard Watson-Crick configuration? If it can be commonly methylated, where?
Adenine, a purine, is connected to the ribose backbsone at position 3 and forms two hydrogen bonds with Guanine.
IUPAC name for position clarity: 9*H*-purin-6-amine
59
What four elements are the most abundant in living organisms and why?
The four most abundant elements in living organisms, in terms of percentage of total number of atoms, are hydrogen, oxygen, nitrogen, and carbon, which together make up more than 99% of the mass of most cells. They are the lightest elements capable of forming one, two, three, and four bonds, respectively; in general, the lightest elements form the strongest bonds.
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methyl
64
methyl
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amino
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amino
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ethyl
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ethyl
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amido
70
amido
71
phenyl
72
phenyl
73
guanidino
74
guanidino
75
carbonyl
76
aldehyde
carbonyl
77
carbonyl
| (aldehyde)
78
imidazole
79
imidazole
80
ketone
carbonyl
81
carbonyl
| (ketone)
82
sulfhydryl
83
sulfhydryl
84
disulfide
85
disulfide
86
carboxyl
87
hydroxyl
88
ether
89
ester
90
thioester
91
phosphoryl
92
phosphoanhydride
93
mixed anhydride
(shown: dehydration of carboxylic acid and phosphoric acid, also called **acyl phosphate**)
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anhydride
(dehydration of two carboxcylic acids)
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carboxyl
96
hydroxyl
97
ether
98
ester
99
thioester
100
phosphoryl
101
phosphoanhydride
102
mixed anhydride
103
anhydride
105
acetyl
106
acetyl
107
Vitamin B5
**Pantothenic acid**, also called **pantothenate** or **vitamin B5**, is a water-soluble vitamin. For many animals, pantothenic acid is an essential nutrient. Animals require pantothenic acid to synthesize coenzyme-A (CoA), as well as to synthesize and metabolize proteins, carbohydrates, and fats.
108
pantothenic acid
**Pantothenic acid**, also called **pantothenate** or **vitamin B5**, is a water-soluble vitamin. For many animals, pantothenic acid is an essential nutrient. Animals require pantothenic acid to synthesize coenzyme-A (CoA), as well as to synthesize and metabolize proteins, carbohydrates, and fats.
117
describe ATP
**Adenosine triphosphate (ATP)**
The removal of the terminal phosphoryl group (shaded pink) of ATP, by breakage of a phosphoanhydride bond, is highly exergonic, and this reaction is coupled to many endergonic reactions in the cell
120
nucleus
nucleus contains the genes (chromatin)
130
134
what organises the cytoplasm?
cytoskeleton
136
137
describe cytoskeletal filaments and their structure:
Each type of cytoskeletal component is composed of simple protein subunits that associate noncovalently to form filaments of uniform thickness. These filaments are not permanent structures; they undergo constant disassembly into their protein subunits and reassembly into filaments. Their locations in cells are not rigidly fixed but may change dramatically with mitosis, cytoki- nesis, amoeboid motion, or changes in cell shape. The assembly, disassembly, and location of all types of fila- ments are regulated by other proteins, which serve to link or bundle the filaments or to move cytoplasmic organelles along the filaments.
138
what is the purpose of the endomembrane system?
segregates specific metabolic processes and provides surfaces on which certain enzyme-catalysed reactions occur
139
exocytosis
140
endocytosis
transport into a cell
151
Generally, why are trace elements essential for life even though they are present in such small relative quantaties?
Usually because they are essential for the function of specific proteins, including those that act as enzymes.
152
Describe the bond angles and length of a typical carbon atom bound to four ligands.
109.5° with an average length of .154 nm
153
What is a polyfunctional molecule?
A biomolecule with two or more different kinds of functional groups
195
what is dissolved in the cytosol of all cells?
100 to 200 central metabolites of the major pathways that occur in nearly every cell (*M*r ~100 to ~500), including the common amino acids, nucleotides, sugars and their phosphorylated derivatives, and a number of mono-, di-, and tricarboxylic acids.
200
secondary metabolites
Secondary metabolites are organic compounds that are not directly involved in the normal growth, development, or reproduction of an organism. Unlike primary metabolites, absence of secondary metabolites does not result in immediate death, but rather in long-term impairment of the organism's survivability, fecundity, or aesthetics, or perhaps in no significant change at all. Secondary metabolites are often restricted to a narrow set of species within a phylogenetic group. Secondary metabolites often play an important role in plant defense against herbivory and other interspecies defenses. Humans use secondary metabolites as medicines, flavorings, and recreational drugs.
201
primary metabolites
A primary metabolite is a kind of metabolite that is directly involved in normal growth, development, and reproduction. It usually performs a physiological function in the organism (i.e. an intrinsic function).
A **primary metabolite** is typically present in many organisms or cell, while a **central metabolite** has an even more restricted meaning: present in any autonomously growing cell or organism
202
primary metabolite vs. central metabolite
A **primary metabolite** is typically present in many organisms or cell, while a **central metabolite** has an even more restricted meaning: present in any autonomously growing cell or organism
203
metabolome
the entire collection of small molecules (metabolites) in a given cell, similar to a cell's genome or proteome
204
*M*r
**Molecular weight**, or **relative molecular mass**, denoted ***M*r**. The molecular weight of a substance is defined as the ratio of the mass of a molecule of that substance to one-twelfth the mass of carbon-12 (12C). Since *M*r is a ratio, it is dimensionless—it has no associated units. The second is *molecular mass*, denoted *m*. This is simply the mass of one molecule, or the molar mass divided by Avogadro’s number. The molecular mass, *m*, is expressed in daltons (abbreviated Da). One dalton is equivalent to one-twelfth the mass of carbon-12; a kilodalton (kDa) is 1,000 daltons; a megadalton (MDa) is 1 million daltons.
Consider, for example, a molecule with a mass 1,000 times that of water. We can say of this molecule either *M*r = 18,000 or *m* = 18,000 daltons. We can also describe it as an “18 kDa molecule.” However, the expression *M*r = 18,000 daltons is incorrect, because *M*r is dimensonless.
Another convenient unit for describing the mass of a single atom or molecule is the atomic mass unit (formerly amu, now commonly denoted u). One atomic mass unit (1 u) is defined as one-twelfth the mass of an atom of carbon-12. Since the experimen- tally measured mass of an atom of carbon-12 is 1.9926 x 10-23 g, 1 u = 1.6606 x 10-24 g. The atomic mass unit is convenient for describing the mass of a peak observed by mass spectrometry.
numerically, *M*r = Da = u
205
define closed and open systems in relation to the universe
For chemical reactions occurring in solution, we can define a **system** as all the reactants and products present, the solvent that contains them, and the immediate atmosphere—in short, everything within a defined region of space. The system and its surroundings together constitute the **universe**. If the system exchanges *neither* matter nor energy with its surroundings, it is said to be **isolated**. If the system exchanges energy but *not* matter with its surroundings, it is a **closed** system; if it exchanges *both* energy and matter with its surroundings, it is an **open** system.
206
living organisms are isolated, open or closed systems?
open systems, they exchange energy and matter with their surroundings
207
first law of thermodynamics
in any physical or chemical change, the total amount of energy in the universe remains constant, although the form of the energy may change.
209
how is the randomness or disorder of the components of a system expressed?
**entropy, *S***
any change in the randomness of the system is expressed as entropy change, Δ*S*, by convention a positive value when randomness increases
210
what is meant by a positive Δ*S ?*
an increase in randomness of the system
211
what is the formula for Gibbs free energy?
*G* = *H* - *TS*
## Footnote
free-energy content, *G*, of any closed system can be defined in terms of three quantities: enthalpy, *H*, reflecting the number and kinds of bonds; entropy, *S*; and the absolute temperature, *T* (in degrees Kelvin)
212
at what value of Gibbs free-energy change do reactions tend to occur spontaneously?
at negative Δ*G*
213
Δ*G°*
The standard free-energy change for a reaction, Δ*G°*, is a physical constant that is related to
the equilibrium constant by the equation:
Δ*G°* = -*RT* ln *K*eq.
