CHAPTER 1 Flashcards
(116 cards)
1
Q
chemistry of life
A
Biochemistry
2
Q
the study of compounds of carbon, especially of carbon and hydrogen and their derivatives
A
organic chemistry
3
Q
Distinctive Properties of Living Systems
A
- Organisms are complicated and highly organized
- Biological structures serve functional purposes
- Living systems are actively engaged in energy transformations
- Living systems have a remarkable capacity for self replication
4
Q
example ofLiving systems are actively engaged in energy transformations
A
photosynthesis
5
Q
Types of molecules that Organisms capture energy in the form of special energized molecules such as ATP and NADPH
A
Energy-rich molecules
6
Q
what gets cleaved in NADPH to get energy
A
chemical bond that holds a hydrogen atom to the molecule
7
Q
what gets cleaved in ATP to get energy
A
phosphate groups
8
Q
The DNA double helix. Two complementary polynucleotide chains running in opposite directions can pair through __________ bonding between their nitrogenous bases. Their complementary nucleotide sequences give rise to structural complementarity.
A
hydrogen
9
Q
All living things make use of the same types of biomolecules, and all use energy. As a result, all living things can be studied using the methods of___________
A
chemistry and physics
10
Q
both cells and the biomolecules of which they are made must have arisen ultimately from very simple molecules, such as
components of primordial earth
A
H2O, CH4, CO2, NH3, N2, and H2
11
Q
Levels of Structural Organization in the Human Body
A
atoms, molecules, macromolecules, organelles, cell, tissue, organs
12
Q
the study of the compounds of carbon
biomolecules are part of the subject matter
the reactions of biomolecules can be described by the methods of
A
Organic chemistry:
13
Q
the cellular apparatus of living organisms is made up of
A
carbon compounds
14
Q
The experiment of Friedrich Wöhler in 1828
A
synthesized urea from inorganic starting materials (Ammonium cyanate). This experiment was the first to create an organic compound from inorganic molecules.
15
Q
The experiment of Friedrich Wöhler in 1828 proved what?
A
It has subsequently been shown that any compound that occurs in a living organism can be synthesized in the laboratory, although in many cases the synthesis represents a considerable challenge to even the most skilled organic chemist.
16
Q
an atom or group of atoms that show characteristic physical and chemical properties
The reactions of molecules are based on the reactions of their
A
Functional group
17
Q
are compounds made up of carbon, hydrogen, and oxy gen, with a general formula of (CH2O)n, where n is at least 3
A
Carbohydrates
18
Q
are the basic unit of the hereditary materials DNA and RNA. They also form the molecular currency of the cell, adenosine triphosphate (ATP).It is composed of the nitrogenous base adenine, the sugar ribose, and three phosphates.
A
Nucleotides
19
Q
The fourth major group of biochemicals
most diverse and cannot be shown with a simple structure common to all
common trait that they are poorly soluble in water
A
Lipids
20
Q
ATP and the Reactions for its Formation
A
Reaction of phosphoric acid with a hydroxyl group to form an ester
Reaction of two molecules of phosphoric acid to form an phosphoric anhydride
The structure of ATP (adenosine triphosphate), showing two anhydride linkages and one ester.
21
Q
the most widely accepted cosmological theory for the origin of the Universe
all matter was originally confined in a very small space
all the matter in the Universe was originally confined to a com paratively small volume of space. As a result of a tremendous explosion, this “primordial fireball” started to expand with great force
A
“big bang” theory
22
Q
the average temperature of the universe has been _____________ ever since the “big bang” theory
A
decreasing
23
Q
in the earliest stages of the universe, the only elements present were
A
H, He, and Li
24
Q
other elements, other than H, He, and Li, formed by
A
- thermonuclear reactions in stars
- explosions of stars
- the action of cosmic rays outside the stars
25
For our purposes, note that the most abundant isotopes of biologically important elements such as ____________ have particularly stable nuclei. These elements were produced by nuclear reactions in first-generation stars,
carbon, oxygen, nitrogen, phosphorus, and sulfur
26
Many first-generation stars were destroyed by explosions called _________, their stellar material was recycled to produce second-generation stars
supernovas
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The most important difference is that, according to most theories of the origins of the Earth, very little or no _________ existed in the early
stages
free oxygen (O2)
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Gases present in the atmosphere of the early earth included
NH3, H2S, CO, CO2, CH4, N2, H2, and H2O
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Experiments have demonstrated that important biomolecules, such as proteins and nucleic acids, could have arisen under abiotic (nonliving) conditions from reactions of these simple compounds. These places are such either
* in the earth’s oceans
* on the surface of clay particles
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The results of such experi ments indicate that these simple compounds react abiotically or, as the word indicates (a, “not,” and bios, “life”), in the absence of life, to give rise to biologically important compounds such as the components of proteins and nucleic acids.
Miller–Urey experiment
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explain the Miller–Urey experiment
In each trial, an electric discharge, simulating lightning, is passed through a closed system that contains H2, CH4, and NH3, in addition to H2O. Simple organic molecules, such as formaldehyde (HCHO) and hydrogen cyanide (HCN), are typical products of such reactions, as are amino acids, the build ing blocks of proteins.
32
working NUCLEOTIDES in the revised Miller–Urey experiment
used the half sugar and half nucelo base 2-aminooxazole ro make arabinoxazoline
33
Recent theories of the origin of life focus on _____________, not proteins, as the first genetic molecules. Proteins are thought to have developed later in the evolution of the earliest cells.
RNA
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is highly volatile and can vaporize and condense so as to give rise to pockets of pure material in reasonably large amounts. In turn, phosphates released by volcanic action can react with it
2-aminooxazole
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The products of 2-aminooxazole include nucleotides that are not part of present-day RNA, but intense __________, which was present on the early Earth, destroyed those nucleotides, leaving those found in RNA today.
ultraviolet light
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small molecules that may bond to many others to form a polymer
monomers
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macromolecules formed by the bonding of smaller units
polymers
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tetravalent and able to form bonds with itself and with many other elements, giving rise to different kinds of monomers, such as amino acids, nucleotides, and monosaccharides
Carbon
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When amino acids form polymers, with the loss of water accompanying this spontaneous process, the _______ of amino acids deter mines the properties of the protein formed.
sequence
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genetic code lies in the sequence of _____________ that polymerize to form nucleic acids, the molecules of heredity
monomeric nucleotides
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In polysaccharides, however, the order of monomers rarely has an important effect on the properties of the polymer, nor does the order of the monomers carry any genetic information.
true
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the ability to increase the rate of a chemical reaction
catalytic activity
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the process of increasing the rate of chemical reactions
catalysis
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Biological macromolecules and their building blocks have a __________
“sense” or directionality.
45
Polysaccharides are built by linking the first carbon of one sugar with the __________ carbon of the next sugar.
fourth
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Amino acids build proteins by connecting the ___________ of one amino acid with the ___________ of the next amino acid.
carboxyl group, amino group
47
In nucleic acids the ___________ of one nucleotide forms a bond to the ____________ of a neighboring nucleotide. All these polymerization reactions are accompanied by the elimination of water.
3'-OH of the ribose ring, to 5'-OH of the ribose ring
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a class of proteins that display catalytic activity
Enzymes
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the catalytic effectiveness of a given enzyme depends on its _____________
amino acid sequence
50
the relationship between the nucleotide
sequence in nucleic acids and the amino acid sequence in proteins
theories of the origin of life consider how such a coding system might have arisen
the information for the structure and function of all living organisms
Genetic code
51
Which came first…the chicken or the egg?
it is more believed that they arose separately
52
It has been discovered recently that certain types of ___________ have catalytic activity and are capable of catalyzing their own further processing
RNA
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_________ is now considered by many scientists to have been the original coding material
it still serves this function in some viruses
RNA
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Polynucleotides use a template mechanism to produce exact copies of themselves:
G pairs with C, and A pairs with U by a relatively weak interaction. The original strand acts as a template to direct the synthesis of a complementary strand. The complementary strand then acts as a template for the production of copies of the original strand. Note that the original strand can be a template for a number of complementary strands, each of which in turn can produce a number of copies of the original strand. This process gives rise to a many-fold amplification of the original sequence.
55
The appearance of a form of __________ capable of coding for its own replication was the pivotal point in the origin of life
both encoded for and catalyzed its own replication
this system evolved to encode for the synthesis of protein catalysts
RNA
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DNA became the primary genetic material, and __________ took on only an intermediary role in the synthesis of proteins
RNA
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Stages in the evolution of a system of self-replicating RNA molecules.
A catalytic RNA directs its own replication with the original nucleotide sequence and shape.
One RNA molecule in a group catalyzes the synthesis
The RNA sequence becomes a template for the sequence of amino acids in the protein by using the adaptor mechanism.
More catalytic RNAs evolve. Some (adaptor RNAs) bind to amino acids. The adaptor RNAs also engage in complementary pairing with coding RNA.
With compartmentalization by cell membrane
The protein made by the cell’s RNA is retained for use in the cell. The RNA can be selected on the basis of its use of a more effective catalyst.
Without compartments
Self-replicating RNA molecules, one of which can direct protein synthesis
58
A key point in the development of living cells is the formation of ___________ that separate cells from their environment
membranes
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the development of a coding system and the development of catalysis came about separately
a combination of the two later in time produced life as we know it.
life began on clay particles
Double-Origin theory
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vital importance of a cell membrane in the origin of life
Without compartments, groups of RNA molecules must compete with others in their environment for the proteins they synthesize. With compartments, the RNAs have exclusive access to the more effective catalysts and are closer to each other, making it easier for reactions to take place.
61
Hypothetical beginning of replication
(1 ) On the cold side of the pond, RNA strands become surrounded by simple membranes. Nucleotides enter and form complementary strands by base pairing.
(2) Over time, these protocells gain more molecules and complexity.
(3) Cells find their way to the warm side of the pond, where the heat allows the RNA molecules to separate.
(4) The protocell grows and gains more components.
(5) Finally, the cell divides, produces daughter cells, and the process repeats.
62
Hypothetical evolution of simple protocells to more complex cells.
( ) Protocells were just a simple sac containing simple RNA molecules. They could not even replicate without cycling between cold and warm temperatures.
( ) In time the cells started replicating on their own using ribozymes.
( ) With increasing complexity of RNA molecules, ribozymes begin to catalyze metabolic pathways.
( ) As metabolism grows in complexity, RNA begins to be translated into proteins. Proteins prove to be more efficient catalysts.
( ) Proteins gradually take over metabolism, replacing most of the functions of ribozymes.
( ) New enzymes start producing DNA, which due to its superior stability, replaces RNA as the primary heredity material.
( ) Organisms resembling bacteria evolve all over the Earth and rule for a billion years before evolution works to create more complex organisms.
63
Greek derivation meaning “before the nucleus”
single-celled organisms
include bacteria and cyanobacteria
Prokaryote
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Greek derivation meaning “true nucleus”
contain a well-defined nucleus surrounded by a nuclear membrane
can be single celled, such as yeasts and Paramecium, or multicellular, such as animals and plants
Eukaryotes
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A Comparison of Prokaryotes and Eukaryotes
Nucleus
Prokaryotes
No definite nucleus; DNA present but not separate from rest of cell
Eukaryotes
Present
66
A Comparison of Prokaryotes and Eukaryotes
Cell membrane
Prokaryotes
Present
Eukaryotes
Present
67
A Comparison of Prokaryotes and Eukaryotes
Cell membrane
Prokaryotes
None; enzymes for oxidation reactions located on plasma membrane
Eukaryotes
Present
68
A Comparison of Prokaryotes and Eukaryotes
Endoplasmic reticulum
Prokaryotes
None
Eukaryotes
Present
69
A Comparison of Prokaryotes and Eukaryotes
Ribosomes
Prokaryotes
Present
Eukaryotes
Present
70
A Comparison of Prokaryotes and Eukaryotes
Chloroplasts
Prokaryotes
None; photosynthesis (if present) is localized in chromatophores
Eukaryotes
Present in green plants
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refers to the portion of the cell outside the nucleus
Cytoplasm
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is the aqueous portion of the cell that lies outside the membrane-bounded organelles
cytosol
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organelles in which photosynthesis takes place, are found in plant cells and green algae
Chloroplasts
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prokaryotes that are capable of photosynthesis, the reactions take place in layers called
which are extensions of the plasma membrane, rather than in chloroplasts.
chromatophores
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Prokaryotic Cells, Although no well-defined nucleus is present in prokaryotes, the DNA of the cell is concentrated in one region called the
nuclear region
76
perhaps the most important eukaryotic organelle. A typical nucleus exhibits several important structural features. It is surrounded by a nuclear double membrane.
nucleus
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prominent feature of a nucleolus, rich in RNA
the RNA is synthesized on a DNA template in the _______ for export to the
cytoplasm through pores in the nuclear membrane.
This RNA is ultimately destined for the ribosomes.
nucleolus
78
an aggregate of DNA and protein
visible in the nucleus
chromatin
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When a cell is about to divide, the loosely organized strands of chromatin become tightly coiled, and the resulting in
chromosomes
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has a double membrane. The outer membrane has a fairly smooth surface, but the inner membrane exhibits many folds called cristae. The space within the inner membrane is called the matrix. Oxidation processes that occur
mitochondrion
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Continuous membrane throughout the cell; rough part studded with ribosomes (the site of protein synthesis)
endoplasmic reticulum (ER)
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Series of flattened membranes; involved in secretion of proteins from cells and in reactions that link sugars to other cellular components
Golgi apparatus
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Membrane-enclosed sacs containing hydrolytic enzymes
Lysosomes
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Sacs that contain enzymes involved in the metabolism of hydrogen peroxide
Peroxisomes
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Separates the cell contents from the outside world; contents include organelles (held in place by the cytoskeleton*) and the cytosol
Cell membrane
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Rigid exterior layer of plant cells
Cell wall
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Membrane-enclosed sac (plant cells)
Central vacuole
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are found in plant cells only. They contain the enzymes that catalyze the glyoxylate cycle, a pathway that converts some lipids to carbohydrate with glyoxylic acid as an intermediate
Glyoxysomes
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* Contains most cellular DNA
* Surrounded by a double membrane
* Site of RNA synthesis
Nucleus:
90
* Energy production through oxidation processes
* Double membrane with inner membrane folds (cristae)
* Contains its own DNA and ribosomes
Mitochondrion:
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* Network of single membranes throughout the cell
* Rough ER: studded with ribosomes for protein synthesis
* Smooth ER: lacks ribosomes, involved in various functions
Endoplasmic Reticulum (ER)
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* Photosynthesis
* Contains grana (membranous bodies) and its own DNA
and ribosomes
Chloroplast (plant cells only)
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processes and packages molecules for secretion
Golgi apparatus
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break down materials for cellular use
Lysosomes
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contain enzymes to neutralize hydrogen peroxide
Peroxisomes
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enzymes for glyoxylate cycle
Glyoxysomes
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network of protein strands providing structure and support
Cytoskeleton
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Classifcation Developed in the 20th century
Considers the difference between prokaryotes and eukaryotes
Five-Kingdom System:
99
Five-Kingdom System:
* Monera (prokaryotes - bacteria and cyanobacteria)
* Protista (single-celled eukaryotes - Euglena, Amoeba)
* Fungi (yeasts, molds, mushrooms)
* Plantae (plants)
* Animalia (animals)
100
are included in Monera but are different from Eubacteria (true bacteria). They are extremophiles living in harsh environments.
Archaebacteria
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Classifcation Based on evolutionary relationships and ribosomal RNA sequences
Three-Domain System:
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Three-Domain System:
* Bacteria (most common, found in normal environments)
* Archaea (prokaryotes in extreme environments)
* Eukarya (all eukaryotes with a true nucleus and organelles)
103
The rise of eukaryotes is believed to be linked to _________, a partnership between organisms. Mutualism is a beneficial symbiotic relationship (e.g., lichen, leguminous plants with nitrogen-fixing bacteria).
symbiosis
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All cells require energy to functions
true
105
Light from the sun is the ultimate source of energy for all life on earth
true
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photosynthetic organisms use light energy to drive the energy-requiring synthesis of
carbohydrates
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non-photosynthetic organisms consume these __________ and use them as energy sources
carbohydrates
108
The energetics of a chemical reaction
if the change in free energy is negative (free energy decreases), the reaction is _______
spontaneous
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The energetics of a chemical reaction
if the change in positive (free energy increases), the reaction will __________ unless energy is supplied from an external source
not occur as written
110
branch of science that answers questions about processes that are energetically favorable
Thermodynamics
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Free Energy of a System
△G < 0 spontaneous exergonic- energy released
△G = 0 Equilibrium
△G > 0 Nonspontaneous endergonic- energy required
112
△G =
△H - T△S
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heat of a reaction at constant pressure
△H
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change in entropy
△S
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change in free energy
△G
116
are genetic elements enclosed in a protein coat.
are not free-living organisms and can reproduce only within cells.
show an almost absolute specificity for their particular host cells, infecting and multiplying only within those cells.
are known for virtually every kind of cell.
Viruses
