Exam 1 Flashcards
(154 cards)
1
Q
What is the Cell Theory
A
cells consist of a membrane and the contents contained in them, organisms have 1 or more cells, cells are the basic unit of function and organization, all cells come from other cells
2
Q
What are protocells?
A
formed prior to the earliest true cells and they have an inner aqueous volume with a lipid membrane
3
Q
What are natural membranes made out of and which of these is the most common
A
made out of amphiphilic molecules and phospholipids are the most common
4
Q
What happens when phospholipids are exposed to water?
A
phospholipids spontaneously form a two layered sheet known as a lipid bilayer
5
Q
What does it mean when it says lipid bilayers are selectively permeable membranes?
A
water and dissolved solutes cannot easily diffuse through the membrane
6
Q
What does a fully enclosed membrane allow?
A
allows some materials to be concentrated within the inner volume or excluded from it
7
Q
What does the unique environment within the protocell allow?
A
chemical reactions to take place that would otherwise not outside the protocell
8
Q
What do viruses use as genetic material
A
RNA
9
Q
What is proof that RNA pre-dates DNA
A
DNA replication cannot being without first synthesizing a short segment of RNA (primer)
10
Q
Before life emerged on Earth what was thought of RNA
A
RNA preformed the functions of both proteins (catalysis) and DNA ( information storage)
11
Q
RNA replicases were found to do what?
A
catalyze their own synthesis
12
Q
What is the RNA world hypothesis?
A
More stable and efficient molecules like DNA and proteins, evolved and replaced much of RNA’s functions, but RNA was still left with major roles in gene expression, linking together information stored in DNA with the machinery needed to make proteins
13
Q
What will occur in protocells that have higher amounts of RNA and how will they grow?
A
they will outcompete protocells with little or no RNA and they grow by stealing membrane from other protocells
14
Q
In relation to protocells when RNA molecules are replicated what will occur
A
mutations will generate different RNAs some of which will be better versions that enhance competition with other protocells
15
Q
What will happen when protocells merge and what did this lead to
A
can bring RNA with other capabilities into the protocell. this led to the simplest true cells that use DNA to store genetic information and catalyze chemical reactions through enzymes
16
Q
In the domain of life describe bacteria and archaea
A
they are prokaryotes and lack a nucleus
17
Q
in the domain of life describe Eukarya
A
encompasses all eukaryotic life
18
Q
What is the nuceloid in prokaryotic cells
A
location of the chromosome
19
Q
What do ribosomes do in prokaryotic cells
A
translate mRNA and make proteins
20
Q
What does the plasma membrane do in prokaryotic cells
A
selectively permeable barrier in contact with the environment found below the cell wall
21
Q
What does the cell wall do in prokaryotic cells
A
tough structural reinforcement
22
Q
What prokaryotic cells have an outer membrane
A
Gram negative
23
Q
What does the capsule/slime layer on prokaryotic cells do?
A
adds protection, adhesion
24
Q
What does the fimbriae do in prokaryotic cells
A
allows attachment to surfaces and they have longer fimbriae called pilli
25
What does flagella do in prokaryotic cells
provide rudimentary motility
26
What are common traits in eukaryotes
intracellular membranes, at least one nucleus, mitochondria, chloroplasts
27
In eukaryotic cells what is the function of the nucleus
where chromosomes and the nucleolus is (where rRNA is made)
28
In eukaryotic cells what is the function of the Rough ER
processes proteins
29
In eukaryotic cells what is the function of the smooth ER
important for metabolism
30
In eukaryotic cells what is the function of the vesicles
bud off organelles and
merge with others, delivering
contents
31
In eukaryotic cells what is the function of the Golgi apparatus
sorts vesicle contents
32
In eukaryotic cells what is the function of the lysosomes
break down old
organelles and phagocytized
material
33
In eukaryotic cells what is the function of the plasma membrane
is the selectively
permeable barrier in contact with
the environment
34
in eukaryotic cells what is the function of the mitochondria
makes most ATP
35
in eukaryotic cells what is the function of the cytoskeleton
anchors organelles, maintains cell structure, dynamically changes shape of the cell, act as
transport lines for vesicles
36
in eukaryotic cells what is the function of the centrosomes
are the organizing centers of microtubules, important for mitosis
37
in eukaryotic cells what is the function of the ribosomes
translate mRNA, make proteins
38
in eukaryotic cells what is the function of the cilia
are found on many cell types, used to move mucus/secretions normally
39
in eukaryotic cells where is flagella located
are present on animal sperm cells and various protozoa
40
in eukaryotic cells what is the function of the microvilli
increase surface area
41
Talk about bright field microscopes and how they work
series of lenses for magnification, light passes through specimen into objective lens
42
Talk about Dark-field microscopes
best for observing pale objects, only light scattered by specimen enter objective lens, specimen appears light against dark background, increases contrast and enables observations of more details
43
talk about phase microscopes
examines living organisms that would be damaged if attached to slides or stained, contrast is created out of light waves
44
widefield fluorescence microscopes
UV and short wavelength visible light source, specimen radiates energy back as a longer visible wavelength, increases resolution and contrast, some cells are naturally fluorescent; others must be stained or made to express fluorescent proteins, used in immunofluorescence to make a variety of proteins visible
45
confocal fluorescent microscopes
uses fluorescent dyes and lasers to image a single plane, emitted light passes through pinhole, increasing resolution. computer constructs 3-D image from multiple images capturing different planes of the specimen
46
Super-Resolution Fluorescent Microscopes
special optics, computer software, and reconstruction of image data can enhance the resolution of images beyond LM limits
47
Talk about electron microscopes
greater resolving power and magnification, the two types are transmission electron microscopes and scanning electron microscopes
48
an atomic microscope is a type of probe microscope what is an atomic microscope
drags a nano-scale prob across the surface of a specimen, detects bumps and valleys
49
a scanning tunneling microscope
measures a voltage difference between a probe and specimen cause by electrons tunneling through the vacuum between the specimen and probe
50
What is a covalent bond?
sharing of a pair of valence electrons by two atoms
51
what must happen for valence shells to remain complete
atoms must stay close together
52
What is a single covalent bond?
sharing of one pair of valence electrons and allows the bound atoms to freely rotate along the axis
53
what is a double covalent bond?
shares two pairs of electrons respectively and locks the orientation of the interacting atoms in place (no rotation) and established a planar structure
54
What happens after the transfer of an electron
both atoms have charges and are attracted to each other
55
What is a cation
a positively charged ion
56
What is an anion
a negatively charged ion
57
How are ionic bonds held together and what does this mean
held together by charge alone so anything else with a charge or partial charge can disrupt this interaction like water
58
Hydrogen bonds and Van der Waals interactions are called what and why?
intermolecular interactions; they dictate how molecules interact with each other and reinforce the shapes of large molecules
59
What causes intermolecular interactions
result of inequal distribution of electrons within a molecule resulting in partial charges (dipoles)
60
Where are permanent dipoles found?
polar molecules where more highly electronegative atoms are bound to less electronegative ones
61
What are the electronegative partners in hydrogen bonds
oxygen and nitrogen
62
Hydrogen bonds do what
form, stretch, and break easily
63
if electrons are distributed asymmetrically what does this cause
hot spots of positive or negative charge (dipoles)
64
What are Van der Waals interactions
attractions between molecules that are close together as a result of these partial charges
65
Dipole-dipole Van der Waals interactions
interaction between polar molecules
66
induced dipole
interaction between polar and non-polar molecules, the permanent dipole of one molecule induces a momentary dipole in the second molecule
67
What is dispersion in Van der Waals interaction
interaction between only non-polar molecules , interaction that arise as a result of instantaneous charge fluctuations
68
What do hydrophobic (nonpolar) molecules tend to do?
isolate themselves from water molecules in aqueous environments. Water forms hydration shells around substances.
69
How does water interact with hydrophilic substances
making and breaking of hydrogen bonds
70
Since water cannot interact well with hydrophobic substances what happens
water is forced into specific conformations around these substances decreasing the entropy of the system - this drives hydrophobic substances together, limiting the hydrophobic surface area available to water.
71
How are interactions between hydrophobic molecules maintained
by Van der Waals interactions and the exclusion of water molecules
72
What are covalent bonds relation to water?
strong and unaffected by the presence of water
73
What do noncovalent interactions do?
reinforce the shapes of macromolecules and dictate the selectivity of chemical interactions within cells
74
what do carbon chains do for organic molecules? what do they vary in?
they form the skeletons of organic molecules and they vary in length, shape, number, and position of bonds
75
What are isomers
compounds with the same
molecular formula but different structures and properties
76
what are structural isomers?
have different arrangements of their atoms
77
what are Cis-trans isomers?
have the same covalent bonds but differ in spatial arrangements
78
What are enantiomers?
isomers that are mirror images of each other; chiral centers
79
Why are enantiomers important?
drug development two enantiomers of a drug can have vastly different effects
80
Differing effects of enantiomers demonstrate what?
organisms are sensitive to even subtle variations in molecules
81
Talk about enantiomers and their biological activity
usually only one drug enantiomer is so called biologically active but both enantiomers will affect an organism in some way
82
The distinctive properties of organic molecules depend on what
the carbon skeleton and the molecular components attached to it
83
Talk about functional groups in relation to the carbon skeleton
functional groups can replace the hydrogen atoms attached to skeletons of organic molecules, functional groups are the components of organic molecules that are commonly involved in chemical reactions, the number and arrangement of functional groups give each molecule its unique properties. small changes to a molecule's functional groups can yield tremendous differences in their biological effects
84
Talk about the importance of carbon in macromolecules
carbon can form four strong, covalent bonds, which allows great diversity of molecular structures. these molecules can combine to form more complex molecules including large polymers. these polymers along with lipids are called macromolecules
85
What is a solution?
a liquid that is homogenous mixture of substances
86
what is a solvent?
dissolving agent of a solution
87
what is a solute
substance that is dissolved
88
what is an aqueous solution
one where water is the solvent
89
what is a hydrophilic substance
substance that has an affinity for water
90
what is a hydrophobic substance
one that does not have an affinity for water
91
what is a colloid
a stable suspension of fine particles in a liquid
92
Talk about the importance of chemical reactions in relation to concentration
chemical reactions depend on collisions of molecules; therefore the concentration of solutes in an aqueous solution is critical (higher concentration increases likelihood of collisions)
93
Number of molecules
6.02 x 10^23 learn to convert to Da
94
Acid and bases: molecule that lost a proton
OH^-
95
Acid and bases: molecule that gained the proton
H+
96
What is an acid
substance that increases the H+ concentration of a solution
97
What is a base
any substance that reduces the H+ concentration of a solution
98
What is metabolism?
all chemical reactions that occur in an organism
99
what are catabolic pathways
break down molecules to release energy and produce intermediate metabolites
100
what are anabolic pathways
consume energy to build smaller molecules into larger ones and establish order
101
What are enzymes
biological catalysts that facilitate metabolic reactions, but they add no energy to the reactions; they only increase the speed at which the reactions may take place
102
what is conservation of energy
energy can neither be created nor destroyed
103
what is entropy
disorder; tends to increase over time: energy flows down gradient from high to low
104
what is unattainable in terms of energy
absolute zero; heat energy is always present
105
what is energy
associated with motion; heat is kinetic energy
106
what is potential energy
energy that matter possesses because of its structure or location
107
What is chemical energy
the potential energy stored in a molecule's bonds and can be released in a chemical reaction
108
what does the second law of thermodynamics say?
energy is consumed to counter entropy
109
why does a cell continue to consume energy? if energy is consumed by the cell what must happen?
a cell continues to consume energy to maintain its structures. if energy is consumed it must leave the cell in another form
110
what must happen for biological order to exist?
heat must be released from cells as waste energy. as one part of the universe gets more ordered or stays ordered (inside of a cell) another part of the universe must become less ordered (outside the cell)
111
not all forms of energy are useful to a cell for all purposes, cells can convert energy from one form to another give an example of this
cells that can carry out photosynthesis can use the energy of sunlight to drive biochemical reactions that transform electromagnetic energy into chemical energy
112
What are redox reactions used for
used to ferry energy from one reaction to the next
113
when is a molecule oxidized?
when it loses an electron or its bonds become more polar
114
when is a molecule reduced
when it gains electrons or its bonds become less polar this requires energy input and therefore the energy stored in a reduced molecules can be used to do work
115
What is the role of the equilibrium constant K
includes the concentrations of all reactants and products. K will tell you the concentrations of reactants and products when equilibrium is reached
116
K and the change of free energy are in a fixed relationship so what does this mean
at equilibrium the free energy G of the system is at its lowest but not zero
117
What do noncovalent interactions allow in relation to enzymes
to bind specific molecules to catalyze reactions
118
What are exergonic reactions
reactions that occur spontaneously and require no energy input
119
what are endergonic reactions?
reactions that do not occur spontaneously and require an input of energy. they will not go forward on their own but with an addition of energy the total reaction becomes exergonic and will occur spontaneously
120
What does change of Gibb's free energy tell us (delta G)
tells us how much energy must be put into the system for the reaction to go forward and whether or not the reaction occurs spontaneously
121
How is delta G related to enthalpy, entropy, and temperature
The change in free energy during a process is related to changes in enthalpy and entropy and temperature in degrees Kelvin
122
what are processes with a negative delta G
spontaneous (exergonic) which means that in chemical reactions the products of the reactions are in a lower energy state than the reactants
123
Spontaneous processes can be harnessed to do what?
perform work and drive other processes forward
124
Just because a reaction is spontaneous what does this not mean
it does not mean the reaction will be rapid
125
What is equilibrium
maximum stability
126
Reactions in a closed system work towards what and then what happens
they eventually reach equilibrium and then no longer do work
127
what is never at equilibrium
metabolism
128
cells are an example of what type of system and why
closed system because they are experiencing a constant flow of materials into and out of the cell
129
in a catabolic pathway how do cells release energy
in a series of reactions one reaction driving the next reaction
130
What are the main kinds of work going on within cells
chemical - making and breaking bonds
transport - movement of material around a cell into/out of the cell
mechanical - exerting force
131
To do work cells manage resources by energy coupling which is what
the use of an exergonic process to drive an endergonic one
132
What is ATP composed of
ribose, adenine, and three phosphate groups
133
ATP can be used to do what
drive an endergonic reaction forward - the coupling of ATP hydrolysis and an endergonic reaction results in an overall exergonic reaction
134
What is an activation energy barrier
some amount of energy must be put in so that a much larger amount of energy is released
135
what is a catalyst
an agent that reduces the activation energy required for the reaction
136
What are enzymes
biological catalysis built out of multiple polypeptide subunits. most enzymes require additional cofactors like ions and other organic compounds to function
137
what are ribozymes
biological catalysis built out of RNA molecules
138
molecules that an enzyme acts upon is called what
the enzyme's substrate
139
when the enzyme binds to its substrate what forms
an enzyme substrate complex
140
what is the region on the enzyme where the substrate binds
active site
141
What does induced fit of a substrate do
brings chemical groups of the active site into the positions that enhance their ability to catalyze the reaction
142
how can the active site lower an Ea barrier
orienting substrates correctly, straining substrate bonds, providing a favorable microenvironment, covalently bonding to the substrate
143
Each enzyme has what
a optimal temperature, pH, and salinity
144
what are cofactors and what do they do
they are non-protein enzyme helpers; help substrates bind to the active site or bind to another part of the enzyme to alter its conformation to improve enzyme-substrate associations
145
what is an apoenzyme
an enzyme without cofactors and its inactive
146
what is a holoenzyme
an enzyme with cofactors
147
What are competitive inhibitors
molecules that bind to the active site of an enzyme competing with the substrate
148
if a substrate concentration increases...
the substrate can outcompete the inhibitor and the enzyme's maximal activity will be restored
149
What are irreversible inhibitors
covalently bind to the enzyme’s active site, permanently blocking substrate from entering
it; enzyme activity cannot be restored no matter how much substrate is present
150
what are allosteric inhibitors
inhibitors bind to a region other than the active site (an allosteric site); they do not block association
of substrate with the active site; they cause the enzyme to change shape to a less than optimal conformation
151
What are compounds that bind to allosteric sites on enzymes
allosteric inhibitors (negative
modulators) or allosteric activators (positive modulators)
152
enzyme allosterism is critical for what
metabolic regulation
153
what does cooperativity do
amplify enzyme activity – once a
substrate binds to one subunit, the other subunits can bind substrate more readily
154
what happens in feedback inhibition and why is it important?
the end product of a
metabolic pathway shuts down the pathway. Feedback inhibition prevents a cell from
synthesizing more product than needed,
preventing the waste of chemical resources
