Exam 1 Flashcards
(188 cards)
1
Q
independent variable goes on the
A
x axis
2
Q
dependent variable goes on the
A
y axis
3
Q
the science of life
A
- Bio unifies natural science
- Living systems are most complex chem systems on Earth
- Life is constrained by properties of chem and physics
- Science is becoming more interdisciplinary
4
Q
7 characteristics of living organisms
A
- Made up of cells
- Complex and ordered
- Responds to environment
- homeostasis: Temp, pH, O2 content - Able to grow, develop, and reproduce
- Obtain and use e
- Maintain internal balance
- pH levels in body - Allows evolutionary adaptation
* Must have ALL 7 characteristics to be considered a living organism
5
Q
cellular level
A
- Simplest form of matter: atom
- Atom, molecule, macromolecule, organelle, cell
6
Q
Organismal level
A
- Tissues, organs, organ systems, organisms
- Organ systems: cardiovascular, nervous, pulmonary, digestive, etc.
- Combine organ systems to make an organ
7
Q
Populational level
A
- Population, species, community, ecosystem, biosphere (Earth is an ecosystem we call the biosphere)
- We have 23 chromosomes
- All cells have 46 chromosomes except germ cells
8
Q
Each level has __
A
emergent properties
9
Q
emergent properties
A
- Result from interaction of components
- Cannot be deduced by looking at parts alone
- “Life” is an emergent property
10
Q
science starts with __
A
observations
11
Q
much of science is __ ___
A
purely descriptive
- Classification system of all life on Earth
- Domain, Kingdom, etc.
- Human genome sequencing
12
Q
deductive reasoning
A
Using general principles to make particular predictions
13
Q
inductive reasoning
A
Uses particular observations to form general conclusions
14
Q
systemic approach of understanding
A
Observation Hypothesis formation Prediction Experimentation Conclusion
15
Q
the scientific method
A
Observation
Make a hypothesis
Test hypothesis thru experiment
Prove or disprove hypothesis
16
Q
hypothesis
A
a possible explanation for an observation
- Must be tested to determine valid or not
- Often tested in several diff ways
- Allows predictions
- Iterative; can be changed and revised w new data
17
Q
experiment
A
- Test hypothesis
- Must be carefully designed
- Test only 1 variable at a time
- Consists of a test experiment & control experiment
18
Q
predictions
A
- Hypotheses make predictions
- Predictions provide a way to test the validity of hypotheses
- More supported predictions from experiment, more valid the hypothesis
19
Q
philosophical approach to science
A
- Reductionism
- Systems biology
20
Q
reductionism
A
breaking a complicated process down into more simple parts
21
Q
systems biology
A
focus on emergent properties that can’t be understood by looking at simpler parts
22
Q
models in science
A
- Way to organize thought
- Parts provided by reductionist approach
- Shows how they fit together
- Suggests experiments to test model
23
Q
scientific theory
A
- Body of interconnected concepts
- Supported by a lot of experimental evidence and scientific reasoning
- Expresses ideas that we are certain of the most
- compared to general meaning of theory: Implies lack of knowledge or a guess
24
Q
evolution is a __
A
theory
25
prehistoric
before man
26
Darwin and evolution
- Example of how a scientist develops a hypothesis and theory gains acceptance
- Charles Darwin was a naturalist on mapping expedition around coastal South America
- 30 yrs of observing and studying b4 publishing On the Origin of Species by Means of Natural Selection
- Galapagos Islands trip was most famous
- Darwin wasn’t first to propose evolution
- Living things have changed over time
- His contribution was a mechanism
- Darwin studied Thomas Malthus’s An Essay On the Principle of Population
- Darwin saw that although every organism has the potential to produce more offspring, only a limited number do survive and reproduce themselves
- evidence supporting his theory has grown
27
Darwin's Galapagos Islands trip
- Darwin’s finches
- Darwin saw characteristics of similar species varied in each place
- 14 related species differ slightly
- Defined evolution as “Descent with modification”
28
natural selection
nature imposes its will on an organism so only organisms that adapted will be able to survive in that environment
29
what was Darwin's mechanism called?
natural selection
30
fossil record
Transitional forms found at predicted positions in time
31
Earth's age
- Physicists of Darwin’s time were wrong
| - Earth is very old (4.5 billion years old)
32
mechanism for heredity
Mendel’s laws of inheritance were unknown to Darwin
33
vertebrate forelimbs
all share the same basic array of bones
34
homologous structure
same evolutionary origin but now differ in structure and function
35
analogous structure
structures of different origin used for the same purpose (butterfly and bird wings)
36
molecular evidence
- Compare genomes or proteins of different organisms
| - Phylogenetic trees
37
Phylogenetic trees
based on tracing the origin of specific nucleotide changes to reconstruct an evolutionary history (ex: hemoglobin polypeptide sequence)
38
Cell theory
1. All organisms composed of cells
2. Cells are life’s basic units
3. All cells come from preexisting cells
39
molecular basis of inheritance
- Deoxyribonucleic acid (DNA)
- Sequence of 4 nucleotides encode cell’s information
- Gene– discrete unit of information
- Genome– entire set of DNA instructions
- Continuity of life depends on faithful copying of DNA into daughter cells
40
structure and function
Study structure to learn function
Ex: Receptor on human cell for insulin known
Find similar molecule in a worm
Might conclude this molecule functions the same in the worm
41
diversity of life arises by evolution
- Underlying unity of biochemistry and genetics argues for life from the same origin event
- Diversity due to evolutionary change over time
- 3 domains
42
what are the 3 domains?
Bacteria: single-celled prokaryote
Archaea: single-celled prokaryote
Eukarya: single-celled or multicellular eukaryote
43
evolutionary conservation
- All organisms today descended from a simple creature 3.5 BYA
- Some characteristics preserved – use of DNA
- Conservation reflects that they have a fundamental role
44
cells are info-processing systems
- information in DNA used to direct synthesis of cellular components
- Control of gene expression leads to different cells/ tissue types
45
cells process environ. info
Glucose levels, presence of hormones
46
Nonequilibrium state
- Living systems are open systems
- Constant supply of energy needed
- Self-organizing properties at different levels
- Emergent properties from collections of molecules, cells, and individuals
47
Cells in multicellular organisms must ___ with each other (tissues, organs, organ systems)
coordinate
48
nature of atoms
- Matter has mass and occupies space
- All matter is composed of atoms
- Simplest form of matter is an atom
- Everything is composed of atoms
- Understanding the structure of atoms is critical to understanding the nature of biological molecules
49
atomic structure
Protons
(+) charged particles
Located in nucleus
Neutrons
(0) neutral particles
Located in nucleus
Electrons
(-) charged particles
Found in orbitals SURROUNDING nucleus
50
Protons and neutrons make up the __ , the electrons are around the ___
nucleus
51
in a neutral atom,
of protons = # of electrons = # of neutrons
52
Orbital shells/rings have a max of __
2 e-
53
atomic number
of protons
- also # of e-
- atoms are electrically neutral
- Every atom of an element has the same # of protons
54
element
- Any substance that cannot be broken down to any other substance by ordinary chemical means
- Simplest form of an atom is an element
55
atomic mass
of neutrons + # of protons
- Each proton and neutron has a mass of apprx 1 Dalton
- units for mass: daltons
56
mass
refers to amnt of substance
57
weight
refers to force gravity exerts on a substance
58
ions
imbalance of e-
- Ions and charged particles are UNBALANCED
- Cation: MORE protons than electrons = net (+) charge
- Anion: LESS protons than electrons = net (-) charge
59
isotopes
excess amnt of neutrons; imbalance in atom
- Radioactive isotopes are UNSTABLE and emit radiation as the nucleus breaks up
- Half-life: time it takes for ½ of the atoms in a sample to decay
60
e- arrangement
- Key to the chemical behavior of an atom lies in the number & arrangement of its e- in their orbitals
- Bohr model: e- in discrete orbits
- Modern physics definition of an orbital: an area around a nucleus where an e- is most likely found
- No orbital can have more than 2 e-
* Neon is a noble gas
61
energy levels
- E- have potential e related to their position
- E- farther from nucleus have more e
- K (2 e- max) is the closest orbital around nucleus, then L, M, N (8 e- max)
- Rings determine an e- ENERGY; orbitals determine an e- LOCATION
62
redox
- During some chem rxn, e- can be transferred from 1 atom to another
- Need a balance
- E- released from an atom, need to be picked up from another atom
- Reduction oxidation rxn
- Still retain the e of their position in the atom
- Oxidation & Reduction
63
oxidation
LOSS of an e-
64
reduction
GAIN of an e-
65
Periodic table displays elements according to__
valence e-
66
valence e-
of e- in outermost e level
67
Inert (non-reactive) elements have ___ present
all 8 e-
68
octet rule
atoms tend to establish completely full outer e levels
69
periodic table of elements
- Down the columns: same # of valence e-
- C,O,H,N: 96% of all living organisms have these
- Across rows: # of orbitals around nucleus
- Top 12: H, Na, Mg, K, Ca, Fe, C, N, O, P, S, CI
- 90 naturally occurring elements
- 12 are found in living organisms in substantial amnts
- 4 elements make up 96% of human body weight
COHN
- Organic molecules contain primarily COHN
- Some trace elements are v important
70
molecules
groups of atoms held together in a stable association
71
compounds
molecules containing more than 1 type of element
72
Atoms are held together in molecules or compounds by __ __ (4 classes total)
CHEMICAL BONDS
73
ionic bonds
- Formed by the attraction of opp charged ions
- Gain or loss of e- forms ions
a) Na atom loses an e- to become Na(+)
b) Cl atom gains an e- to become Cl(-)
c) Opp charges attract so that Na(+) and Cl(-) remain associated as an ionic compound
- Electrical attraction of water molecules can disrupt forces holding ions together
74
covalent bonds
- Form when atoms share 2 or more valence electrons
- Results in no net charge, satisfies octet rule, no unpaired electrons
- Strength of covalent bond depends on the number of shared electrons
- Many biological compounds are composed of more than - 2 atoms – may share electrons with 2 or more atoms
75
electronegativity
- Atom’s affinity for electrons
- Differences in electronegativity dictate how electrons are distributed in covalent bonds
a) Non-polar covalent bonds
b) Polar covalent bonds
76
Non-polar covalent bonds
have equal sharing of electrons
77
polar covalent bonds
have unequal sharing of electrons
78
chemical rxns
- Chemical reactions involve the formation or breaking of chemical bonds
- Atoms shift from one molecule to another without any change in number or identity of atoms
- reactants and products
6 H2O + 6 CO2 (reactants) ------> C6H12O6 (sugar) + 6 O2 (products)
- Extent of chemical reaction
- Many reactions are reversible
- Increase reactants = increase the amnt of product being produced
- A catalyst (a protein/enzyme) lowers e requirements needed for the rxn to take place
79
Extent of chemical reaction influenced by
1 .Temperature
2. Concentration of reactants and products
3. Catalysts
80
reactants
original molecules
81
products
molecules resulting from rxn
82
A __ lowers e requirements needed for the rxn to take place
catalyst
83
water
- Life is inextricably tied to water
- 3 forms of water: s (ice), l (water), g (steam)
- Single most outstanding chemical property of water is its ability to form hydrogen bonds
a) Weak chemical associations that form between the partially negative O atoms and the partially positive H atoms of two water molecules
84
polarity of water
- Within a water molecule, the bonds between oxygen and hydrogen are highly polar
- Polar bond
- Oxygen is much more electronegative than Hydrogen
- Partial electrical charges develop
a) Oxygen is partially negative δ– (corrected)
b) Hydrogen is partially positive δ+ (corrected)
85
polar bond
oppositely charged attracted to one another
86
hydrogen bonds
- Cohesion
- Attraction produces hydrogen bonds
- Water to water mols attracted to one another
- There are 3 forms of water: ice, water, and steam/vapor
- O has a greater electronegative property than H
- Each individual bond is weak and transitory
- Cumulative effects are enormous
- Responsible for many of water’s important physical properties
87
cohesion
water mols stick to other WATER mols by H bonding
| Water to water interactions
88
adhesion
water mols stick to other POLAR mols by H bonding
Polar: a charge associated with it
Water to some other polar surface
89
properties of water
1) Water has a high specific heat
- A large amount of energy is required to change the temperature of water
2) Water has a high heat of vaporization
3) Solid water is less dense than liquid water
4) Water is a good solvent
- Water dissolves polar molecules and ions
- Water is a POLAR MOLECULE
5) Water organizes non-polar molecules
- Non-polar molecule ex: oils
- Hydrophilic & Hydrophobic
- Water causes hydrophobic molecules to aggregate or assume specific shapes
6) Water can form ions
H2O ---> OH(-) hydroxide ion + H(+) hydrogen ion
90
pure water
- [H+] of 10–7mol/L
- Considered to be neutral pH
- Neither acidic nor basic
- Pure water has a pH of 7
- pH ranges from 0-14
- ½ of H ions of water is H, ½ of H ions are hydroxyls
91
pH
the negative logarithm of hydrogen ion concentration of solution; ranges 0-14
92
acid
- Any substance that dissociates in water to increase the [H+] (and lower the pH)
- Stronger an acid is, the more H+ ions it produces and the lower its pH
- 0-6 is ACIDIC
93
base
- Substance that combines w/ H+ dissolved in water, and lowers the [H+]
- 8-14 is BASIC
94
buffers
- Substance that resists changes in pH
- Act by
1) Releasing hydrogen ions when a base is added
2) Absorbing hydrogen ions when acid is added
- Overall effect of keeping [H+] relatively constant
1) Drink too much soda, bicarbonate that is produced in blood that’s gonna neutralize the acid so there isn’t too much acid
2) Add base to a solution, it INCREASES the pH value
3) Buffers maintain a moderate pH range
4) Buffers maintain homeostasis
95
biological buffers
- Most biological buffers consist of a pair of molecules, one an acid and one a base
- Carbonic acid can be converted to bicarbonate
96
carbon
- Framework of biological mols consists primarily of C bonded to
a) Carbon
b) O, N, S, P, or H
- Can form up to 4 covalent bonds
- C has 4 valence e- in its outermost layer
- Hydrocarbons
97
hydrocarbons
molecule consisting ONLY of C and H
- Non-polar
- Functional groups add chemical properties
Ex: controlling ur car is a hydrocarbon; high E mol used to drive the engine
98
amino group
ex: alanine
| found in: proteins, nucleic acids
99
sulfhydryl group
ex: cysteine
| found in: proteins
100
phosphate group
ex: glycerol phosphate
| found in: nucleic acids
101
methyl group
ex: alanine
| found in: proteins
102
hydroxyl group
ex: ethanol
| found in: carbs, proteins, nucleic acids, lipids
103
carbonyl group
ex: acetaldehyde
| found in: carbs, nucleic acids
104
carboxyl group
ex: acetic acid
| found in: proteins, lipids
105
isomers
- Mols with the same molecular or empirical formula
a) Structural isomers
b) Stereoisomers
- Enantiomers
106
Stereoisomers
differ in how groups attached
| -Enantiomers
107
Enantiomers
- Mirror image molecules
- Chiral
- D-sugars and L-amino acids
108
polymer
built by linking monomers
109
monomer
small, similar chemical subunits
110
major macromolecules
- carbohydrates
- proteins
- nucleic acids
111
carbohydrates
- starch, glycogen
subunit: glucose
function: e storage
ex: potatoes
- cellulose
subunit: glucose
function: structural support for plant cell walls
ex: paper, strings of celery
- chitin
subunit: modified glucose
function: structural support
ex: crab shells
112
proteins
- functional
subunit: amino acids
function: catalysis, transport
ex: hemoglobins
- structural
subunit: amino acids
function: support
ex: hair, silk
113
nucleic acids
- DNA
subunit: nucleotides
function: encodes genes
ex: chromosomes
- RNA
subunit: nucleotides
function: needed for gene expression
ex: mRNA
114
dehydration synthesis
- Formation of large mols by the REMOVAL OF WATER
| - monomers are joined to MAKE POLYMERS
115
hydrolysis
- Breakdown of large mols by the ADDITION OF WATER
| - Polymers are BROKEN DOWN TO MONOMERS
116
carbohydrates
- Mols with a 1:2:1 ratio of C, H, O
- Empirical formula (CH2O)n
- C-H covalent bonds hold much E
- Carbs are good e storage molecules
Ex: sugars, starch, glucose
117
monosaccharides
- Simplest form of carbohydrate
- 6 C sugars play important roles
- Glucose (C6H12O6)
- Fructose is a structural isomer of glucose
- Galactose is a stereoisomer of glucose
- Enzymes that act on diff sugars can distinguish structural and stereoisomers of this basic 6 C skeleton
118
disaccharides
- 2 monosaccharides linked together by dehydration synthesis
- Used for:
1) Sugar transport
2) E storage
119
polysaccharides
- Long chains of monosaccharides
1) Linked thru dehydration synthesis
- E storage
1) Plants use starch
2) Animals use glycogen
- Structural support
1) Plants use cellulose
2) Arthropods and fungi use chitin
120
Which of the following is NOT a property of life?
movement
121
The process of inductive reasoning involves
the use of specific observations to develop general principles
122
a hypothesis in bio is best described as
a possible explanation of an observation
123
a scientific theory is
a statement of how the world works that is supported by experimental data
124
the cell theory states that
all living things are made up of cells
125
the molecule of DNA is important to biological systems bc
it encodes the info for making a new individual
126
The organization of living systems is
hierarchical with cells at the base, and the biosphere at the top
127
the idea of evolution
predated Darwin and Wallace
128
the property that distinguishes an atom of one element (C, for example) from an atom of another element (O, for example) is
the number of protons
129
if an atom has one valence e- - that is, a single e- in its outer e level- it will most likely form
an ionic bond
130
an atom w a net (+) charge must have more
protons than e-
131
the isotopes carbon-12 and carbon-14 differ in
the number of neutrons
132
which of the following is NOT a property of the elements most commonly found in living organisms?
elements possess 8 e- in their outer e- level
133
ionic bonds arise from
attractions between ions of app charge
134
a solution with a high conc of hydrogen ions
is called an acid
135
1. how is a polymer formed from multiple monomers
| 57
by the removal of an -OH group and a hydrogen atom
136
why are carbohydrates important molecules for e storage?
the C-H bonds found in carbs store e
137
plant cells store e in the form of __, and animals cells store e in the form of __
starch, glycogen
138
which carb would u find as part of a molecule of RNA?
ribose
139
a molecule of DNA or RNA is a polymer of
nucleotides
140
what makes cellulose diff from starch?
cellulose forms long filaments, and starch is highly branched
141
what monomers make up a protein?
amino acids
142
a triglyceride is a form of __ composed of __
lipid; fatty acids and glycerol
143
u can use starch or glycogen as an e source, but not cellulose bc
starch and glycogen have similar structures
144
which of the following is NOT a difference between DNA and RNA?
phosphodiester versus hydrogen bonds
145
which part of an amino acid has the greatest influence on the overall structure of a protein?
the R group
146
a mutation that alters a single amino acid within a protein can alter
the primary, secondary and tertiary levels of protein structure
147
2 diff proteins have the same domain in their structure. from this way we can infer that they have
similar function
148
what aspect of triglyceride structure accounts for their insolubility in water?
the non-polar C-H bonds in fatty acids
149
the spontaneous formation of a lipid bilayer in an aqueous environment occurs bc
- the polar head groups of the phospholipids can interact with water
- the fatty acid tails of the phospholipids are hydrophobic
150
which of the following atoms would u predict should form a positively charged ion (cation)?
Potassium (K)
151
a molecule w/ polar covalent bonds would
be soluble in water
152
hydrogen bonds are formed
when H is part of a polar bond
153
if u shake a bottle of oil and vinegar then let it sit, it will separate into 2 phases bc
non polar oil is not soluble in water
154
what is the significance of Pasteur's experiment to test the germ hypothesis?
it demonstrated that cells can only arise from other cells
155
which of the following is NOT an example of reductionism?
an evaluation of the overall behavior of the cell
156
how is the process of natural selection diff from artificial selection?
artificial selection is a result of human intervention
157
if u found a fossil for a modern organism next to the fossil of a dinosaur, this would
- have no bearing on evolution by natural selection
| - indicate that dinosaurs may still exist
158
the theory of evolution by natural selection is a good example of how science proceeds bc
- it makes predictions that have been tested by a variety of approaches
- it represents Darwin's belief of how life has changed over time
159
in which domain of life would u find only single-celled organisms?
bacteria and archaea
160
evolutionary conservation occurs when a characteristic is
important to the life of the organism
161
nucleic acids
- Monomers: nucleotides
- Structure: sugar, phosphate, N base
- Sugar is deoxyribose for DNA or ribose for RNA
- N base include:
- Purines (A and C) and pyrimidines (C,U,T)
- Nucleotides are connected by phosphodiester bonds
1. DNA
2. RNA
3. Other nucleotides:
- ATP
- NAD+ and FAD+
162
DNA
deoxyribonucleic acid
- Encodes info for aa sequence of proteins
- Sequence of bases
- Double helix shape- 2 polynucleotide strands connected by H bonds
- Base pairing rule (A goes with T (or U for RNA); C goes with G)
163
RNA
ribonucleic acid
- RNA is similar to DNA except that it…
- Has ribose instead of deoxyribose
- Has uracil (U) instead of thymine (T)
- Single polynucleotide strand
- RNA uses info in DNA to specify sequence of aa in proteins
164
ATP
type of nucleotide
| (adenosine triphosphate): primary e currency of the cell
165
NAD+ and FAD+
nucleotides
| e- carriers for many cellular rxns
166
proteins
- functions
- Composed of 1 or more long, unbranched chains
- Each chain is a polypeptide
- made up of amino acids
- 4 levels of structure
- additional structural characteristics
1. motifs
2. domains
3. chaperones
4. denaturation
167
protein functions include..
1. Enzyme catalysis
2. Defense
3. Transport
4. Support
5. Motion
6. Regulation
7. storage
168
amino acid structure
- Central C atom
- Amino group
- Carboxyl group
- Single H
- Variable R group
* * Amino acids joined by dehydration synthesis peptide bonds
169
what are the 4 levels of protein structure?
1. primary
2. secondary
3. tertiary
4. quaternary
170
primary structure
sequence of amino acids
171
secondary structure
interaction of groups in the peptide backbone
ß-sheet
a- helix
172
tertiary structure
final folded shape of a globular protein
- Stabilized by a number of forces
- Final level of structure for proteins consisting of only a single polypeptide chain
173
quaternary structure
arrangement of individual chains (subunits) in a protein w/ 2 or more polypeptide chains
174
proteins: motifs
Common elements of secondary structure seen in many polypeptides
- Useful in determining the function of unknown proteins
175
proteins: domains
Functional units within a larger structure
| - Most proteins made of multiple domains that perform different parts of the protein’s function
176
proteins: chaperones
- Once thought newly made proteins folded spontaneously
- Chaperone proteins help protein fold correctly
- Deficiencies in chaperone proteins implicated in certain diseases
- Cystic fibrosis is a hereditary disorder
- In some individuals, protein appears to have correct amino acid sequence but fails to fold
177
proteins: denaturation
- Protein loses structure and function
- Due to environmental conditions
1. pH
2. Temp
3. Ionic conc of solution
178
lipids
- Loosely defined group of molecules with one main chemical characteristic
- They are insoluble in water
- High proportion of non-polar C—H bonds causes the molecule to be hydrophobic
- Fats, oils, waxes, and even some vitamins
179
fats
- triglycerides
| - fatty acids
180
fats: triglycerides
Composed of 1 glycerol and 3 fatty acids
181
fats: fatty acids
- Need not be identical
- Chain length varies
- Saturated
- Unsaturated
- Trans fats
182
3 types of fatty acids
- saturated
- unsaturated
- trans fat
183
saturated fatty acids
no double bonds between carbon atoms
| -Higher melting point, animal origin
184
unsaturated fatty acids
1 or more double bonds
| -Low melting point, plant origin
185
trans fat fatty acids
produced industrially
186
phospholipids
- Composed of
1. Glycerol
2. 2 fatty acids- non-polar tails
3. Phosphate group- polar heads
* Forms all biological membranes
- micelles
- phospholipid bilayer
187
phospholipids: micelles
lipid mols orient w/ polar (hydrophilic) head toward water and nonpolar (hydrophobic) tails away from water
188
phospholipid bilayer
more complicated structure where 2 layers form
- Hydrophilic heads point outward
- Hydrophobic tails point inward toward each other
