FINAL Unit 1 Flashcards
1
Q
What is the cell theory?
A
- all living organisms are made up of cells
- cell is fundamental unit of life
- cells come from pre-existing cells
2
Q
What are the 3 characteristics that define cells as the smallest unit of life?
A
- contain DNA that encode genes for all RNA and protein in the cell
- bounded by plasma membrane that encloses cell and is important for nutrient uptake and signalling
- use metabolism to convert energy from environment to do the work of the cell in cytoplasm and mitochondria (and chloroplasts)
3
Q
What is the difference between eukaryotic and prokaryotic cells?
A
prokaryotic: no nucleus (have a nucleoid)
eukaryotic: have a nucleus and internal organelles
4
Q
What is the endosymbiont theory? What is the evidence?
A
mitochondria and chloroplasts were free-living cells that were taken up and lived inside early eukaryotes
evidence:
- mitochondria are same size and shape as bacteria
- have prokaryotic-type circular chromosome
- DNA sequences more like bacteria than eukaryotic cells
5
Q
What is the phylogenetic tree?
A
describes relationships among organisms over evolutionary history
- all cells evolved from universal common ancestor
- 3 domains: Bacteria, Archaea, Eukarya
- hypothesized that eukarya descended from archaea
- all plants and animal on branches within eukarya
- time runs from roots to branches
6
Q
What is diffusion?
A
- movement of molecules due to random motion
- net movement of molecules across membrane will passively diffuse across membrane from high to low concentration until equilibrium is reached
- diffusion still continues but there is no net movement
7
Q
What is osmosis?
A
- diffusion of water across membrane
- semipermeable membrane allows passage fo water but not solute
8
Q
Passive diffusion vs. Facilitated diffusion
A
water moves in and out of cells by passive diffusion and can move into a cell more readily by facilitated diffusion using protein channels called aquaporins
9
Q
What is osmotic pressure?
A
continuous diffusion of water across cell membrane builds up pressure
10
Q
Describe an isotonic solution.
A
same concentration of solute inside and outside the cell
11
Q
Describe a hypotonic solution.
A
concentration of solute inside > outside the cell
12
Q
Describe a hypertonic solution.
A
concentration of solute inside < outside the cell
13
Q
What occurs in a hypotonic solution?
A
osmotic pressure builds, cell membrane might expand a little, but then will burst
14
Q
What occurs in a hypertonic solution?
A
cell shrivels due to water leaving the cell
15
Q
What are mechanisms to prevent cell lysis (bursting)?
- animal cell
- plant cell
- protozoan
- bacterial cell
A
animal cell: active shunting of ions from the cell
plant cell:
- cell wall: surrounds plasma membrane and resists cell expansion when cell takes in water, and can maintain cell shape in some organisms
- vacuoles: exert hydrostatic pressure on cell walls and provide rigidity —> dehydrated plant cell collapses vacuoles, relieves hydrostatic pressure, results in wilting
protozoan: discharging contractile vacuole
bacterial cell: have cell wall called peptidoglycan that helps counteract osmotic pressure build-ip during osmosis
16
Q
List the bond/interaction types from strongest to weakest.
A
covalent ionic ion-permanent dipole hydrogen bonding permanent dipole-permanent dipole permanent dipole-induced dipole ion-induced dipole induced dipole-induced dipole
17
Q
What is a covalent bond?
A
formed by shared pair of electrons
18
Q
What is a polar covalent bond?
A
electrons are shared unevenly between atoms
also called a permanent dipole: one atom is partially negatively charged, one partial positive
19
Q
What is a nonpolar covalent bond?
A
electrons are shared equally
20
Q
How is polar/nonpolar determined?
A
by electronegativity of atoms in a bond
21
Q
What is an ionic bond?
A
- positive and negative ions held together by electrostatic attraction
- electronegativity difference between two atoms is so extreme that electrons are completely pulled from one atom to the other
22
Q
What is an ion-permanent dipole bond?
A
electrostatic attraction between ionic group on a molecule (ie. NH^3+ or CO2-) and the dipole of a polar covalent bond
23
Q
What is hydrogen bonding?
A
- special kind of dipole-dipole attraction that forms when dipoles involved include hydrogen atom and atom with lone pairs, specifically electronegative atoms O, N, F, or S
- donor group: functional group supplying H
- acceptor group: functional group supplying lone pairs, can form as many hydrogen bonds as it has lone pairs available
- strength influenced by electronegativity of atoms involved in bond
- more electronegative atom of H bond acceptor = stronger bond
- more electronegative atom bonded to donor H (ie. S or N) = stronger bond
24
Q
What is a permanent dipole-permanent dipole bond?
A
- among molecules that contain polar bonds, an electrostatic interaction can from between the positive and negative ends of dipoles
- much weaker than ionic bonds because the charges involved are only partial +/- charges
25
What is a permanent dipole-induced dipole bond?
dipole approaches nonpolar group, permanent dipole will create an induced dipole in nonpolar group
26
What is an induced dipole?
when ion goes near nonpolar group, it'll attract or repel electrons in nonpolar group
- since electrons in bond are constantly moving, occasionally they become unevenly distributed around atoms in bond, creating a small temporary induced dipole
27
What is an ion-induced dipole?
new induced dipole is electrostatically attracted to the ion
28
What is an induced-induced dipole bond?
two induced dipoles
| - are short-lived because induced dipoles are temporary
29
What is electronegativity?
measure of atom's tendency to attract electrons to itself in covalent bonds (stronger tendency = larger electronegativity)
higher lower
O > N >> S = C = H = P
30
What is a polar molecule?
has regions of +/- charge, tend to interact with other polar molecules (ie. O-H, N-H, S-H, C-O, O-P)
31
What is a nonpolar molecule?
does not have regions of +/- charge (ie. C-H)
32
What is a neutral molecule?
no charge
33
What is a charged molecule?
anion: negative charge
cation: positive charge
34
What is a hydrophobic molecule?
water-fearing, nonpolar
molecules poorly able to undergo hydrogen bonding with water
35
What is a hydrophilic molecule?
water-loving, polar
can undergo hydrogen bonding with water, readily dissolves in water
36
What is the hydrophobic effect?
polar molecules excluded nonpolar molecules to drive biological processes such as protein folding and formation of cell membranes
37
What is an amphipathic molecule?
has both hydrophobic and hydrophilic parts
38
What are the 4 key characteristics of living organisms?
1. complexity, with precise spatial organization on several scales
2. ability to change in response to environment
3. abilities to metabolize and to reproduce
4. capacity to evolve
39
What is the first law of thermodynamics?
energy cannot be created no destroyed and can only be transferred from one form to another
- total energy of universe is constant but the form it takes changes
- living organisms acquire energy from environment and transform to chemical form cells use
- all organisms obtain energy from sun or chemical compounds: some energy for work, some energy dissipated as heat
40
What is the second law of thermodynamics?
degree of disorder in universe tends to increase
- addition of energy increases order of system (decreases disorder)
- entropy: amount of disorder
- living organisms are highly organized, energy is needed to maintain this
- cells is not an isolated system: take into account cell and environment
- release of heat as organisms harness energy means total combination of cell + environment's entropy increases
41
What are the important molecular interactions involved in macromolecule synthesis?
- intramolecular bonds: covalent, ionic, hydrophobic
- intermolecular bonds: non-covalent
- interaction with surrounding water molecules
42
What is cytosol?
aqueous environment of the cell (outside of nucleus and organelles)
43
What is critical for cell structure and function?
how macromolecules interact with polar water molecules
44
What do non-covalent interactions determine?
3D structure of macromolecules and their interactions with water (polarity is important)
45
What is a function group?
one or more atoms that have particular chemical properties on their own
- "add chemical character to carbon chains"
- polar, therefore molecules that contain these groups become polar and soluble in aqueous environment, and they are reactive (joining simple molecules often takes place between functional groups)
46
Describe carbon skeletons.
- nonpolar
| - functional group permits them to interact with water and link macromolecules
47
Proteins (polypeptides)
- function
- monomer
- covalent bond
- directionality
- function: cell's work (ie. enzymes, structural components)
- monomer: amino acids (identity determined by R group)
- covalent bond: peptide bond (carboxyl releases O2, amino group releases 2 hydrogens)
- directionality: one end carboxyl and other amino, it affects function - some enzymes in our body only work on one end of the polypeptide and some digest both ways
48
Nucleic acids (DNA and RNA)
- function
- monomer
- covalent bond
- directionality
- function: carry info in sequence of nucleotides
- monomer: nucleotide
- covalent bond: phosphodiester bond (phosphate group joins sugar, loss of H2O)
- directionality: 3' (sugar) and 5" (phosphate), impacts how new DNA is put together during replication and affects function of RNA during translstion
49
Carbohydrates
- function
- monomer
- covalent bond
- directionality
- function: energy source, cell wall in bacteria/plants/algae
- monomer: monosaccharide (simple sugar)
- covalent bond: glycosidic bond (between 1' carbon of one monosaccharide, and hydroxyl group carried by carbon atom in different monosaccharide)
- directionality: location of OH group and CH2OH group, diversity stems in part from monosaccharides that make up carbohydrates
50
Lipids
- function
- monomer
- covalent bond
- directionality
- function: cell membrane, store energy, signalling molecules
- monomer: 3 fatty acids and glycerol
- covalent bond: Ester linkage
- directionality: none
51
Describe characteristics of lipids.
- hydrophobic
- not defined by chemical structure
- form oil droplets in cells
52
What are saturated fats?
no C=C
max. H atoms is attached to each carbon, chain is straight
53
What are unsaturated fats?
have C=C
fatty acid chains have kink at each double bond
54
Describe the hydrocarbon chain of fatty acids.
- fatty acids differ in length of hydrocarbon chain (# carbons)
- don't contain polar covalent bonds
- electrons are distributed uniformly, therefore uncharged
- BUT constant motion of electrons lead to slight +/- charges
- affects neighbouring molecules
- temporarily polarized molecules weakly bind to one another (van der Waals forces)
55
What are van der Waals forces?
only come into play when atoms are close enough and are weaker than H bonds
56
What are membranes made up of?
amphipathic lipid bilayers and proteins
57
Describe the Fluid Mosaic model of the biological membrane.
membranes are made up of phospholipids embedded with proteins
- lipids provide permeability barrier and fluidity
membrane lipids are important for cells because cells are dynamic and membranes must be able to form, reseal, bud, and fuse
58
What is the shape of structure of membranes determined by?
bulkiness of head group relative to hydrophobic tails
59
What is a micelle?
lipids with bulky heads and single hydrophobic tail are wedge-shaped and pack into spheres
60
What is a liposome?
purified lipids with small heads and double tails
- pH important because it ensures head groups are in their ionized form and hydrophilic
- if phospholipids are added to a test tube of water at neutral pH, they spontaneously form spherical bilayer structures (liposomes) that surround a central space
- as liposomes form, they may capture macromolecules present in solution
61
What are bilayers?
lipids with less bulky heads and 2 hydrophobic tails are roughly rectangular
- form closed structures with an inner space because free edges would expose hydrophobic chains to aqueous environment
62
What is the bilayer formed of?
two layers of lipids in which hydrophilic heads are the outer surfaces and hydrophobic tails are sandwiched between and away from aqueous environment
63
Bilayers form closed structures with an inner space because free edges would expose hydrophobic chains to aqueous environment. What does this explain?
- why bilayers are effective cell membranes
- why membranes are self-healing: small tears in membrane are rapidly sealed by spontaneous arrangement of lipids surrounding damaged region because of the tendency of water to exclude nonpolar molecules
64
Why do lipids freely associate with one another?
because of the extensive van der Waals forces between tails
- weak bonds, therefore easily broken and reformed
- lipids can move within plane of membrane
65
Describe how the degree of membrane fluidity depends on type of lipid that makes up the membrane.
- in single layer of bilayer, van der Waals interactions between tails depends on length of fatty acid tails and presence of double bonds between neighbouring carbon atoms
- saturated tails: no C=C, straight and tightly packed which reduced mobility
- unsaturated tails: have C=C, kinks in tail which increases mobility
- cholesterol helps maintain consistent fluidity by preventing big transitions from fluid to solid
66
What is an energetically favourable reaction?
- spontaneous
- likely to happen in this direction
- reaction moves from less stable to more stable
67
What is an energetically unfavourable reaction?
- not spontaneous
- requires energy input to happen in this direction
- reaction moves from more stable to less stable
68
What is enthalpy?
measures how strongly bonded a system is
69
What is entropy?
measures freedom to move of components of a system
70
How does the structure of lipid molecules dictate the properties of membrane bilayers?
important factors: chain length and degree of unsaturation
- shorter tails are more fluid than longer tails
- double bonds form kinks, therefore are more fluid than saturated lipids
71
Which molecules can diffuse through a bilayer without protein transporter?
small nonpolar molecules
small uncharged polar molecules
gases
72
Which molecules cannot diffuse through a bilayer without protein transporter?
large uncharged polar molecules
ions (in aqueous solution, are surrounded by hydration shells)
- prevented by hydrophobic interior of lipid bilayer
73
What is the importance of selective permeability?
biological membranes control environment inside cells
- plasma membrane encloses cell
- internal membrane encloses an intracellular component
74
What is a transporter?
moves ions or other molecules across membrane
75
What is a receptor?
allows cell to receive signals from environment
76
What is an enzyme?
catalyzes chemical reactions
77
What is an anchor?
attaches to other proteins and helps maintain the cell structure and shape
78
What is an integral membrane protein?
permanently associated with cell membrane and cannot be separated from membrane experimentally without destroying the membrane
79
What is a peripheral protein?
temporarily associated with lipid bilayer or with integral membrane proteins through weak non-covalent interactions (easily separated from membrane)
- interact with either polar heads or with integral membrane proteins
- limit ability of transmembrane proteins to move within membrane
80
What is a transmembrane protein?
(type of integral membrane protein)
- spans entire lipid bilayer
- composed of 3 regions: 2 hydrophilic and 1 connecting hydrophobic
- allows for separate functions and capabilities of each end of protein
81
What are channel proteins?
provide an opening between inside and outside of cell through which certain molecules can pass, depending on their shape and charge
- some are gated (open in response to a chemical or electrical signal)
82
What are carrier proteins?
binds to, then transports specific molecules
- exist in two conformations: one open to one side of the cell, other open on other side
- binding of transported molecules induces conformational change in membrane protein, allowing molecule to be transported across lipid bilayer
83
What are aquaporins?
channel proteins that water molecules move through plasma membrane by
- allows water to move much more readily across plasma membrane by facilitated diffusion than is possible for simple diffusion
- water molecules are small enough to move polarity through bilayer by limited simple diffusion
84
What is passive transport?
goes down concentration gradient
- simple diffusion: diffuses through lipid bilayer
- facilitated diffusion: uses a protein channel in bilayer to diffuse across bilayer
85
What is active transport?
goes against concentration gradient
- requires energy
- uses a protein transporter
86
What is the sodium-potassium pump?
- ATP is used as energy source to pump ions
- sodium moving out of cell, potassium moving in
- pumps are examples of membrane proteins that help with some type of active transport of molecules across the membrane
87
What do cells use active transport for?
to establish an electrochemical gradient which is an energy source for secondary active transport
88
What is primary active transport?
active transport that uses energy directly (ie. movement of ions take energy, which comes from energy stored in ATP)
89
What is secondary active transport?
driven by electrochemical gradient
- because small ions cannot cross lipid bilayer, many cells use a transport protein to build up the concentration of a small ion on one side of the membrane
- resulting [ ] gradient stores potential energy that can be harnessed to drive movement of other substances across membrane against their [ ] gradient
- electrochemical gradient and co-transports one solute down its [ ] gradient as another solute is transported up its [ ] gradient
MOVEMENT IS DRIVEN BY MOVEMENT OF PROTONS, NOT ATP DIRECTLY
90
Describe the mechanism of active transport.
1. protons are pumped across membrane by primary active transport
2. proton pump generated electrochemical gradient with higher [ ] of protons outside cell and lower [ ] of protons inside cell
3. antiporter uses gradient to move different molecule out of a cell against its [ ] gradient
91
What are some roles of proteins in cellular activities?
```
regulation
transport
signalling
structure
force generation
catalysis
transcription and translation
```
92
Describe the primary structure of polypeptides.
sequence of amino acids in a protein joined by peptide bonds
- determines how a protein folds (structure)
- determines non-covalent interactions of a protein with itself and its environment
93
Describe the secondary structure of polypeptides.
interactions between stretches of amino acids in a protein
- result from hydrogen bonding in polypeptide between carbonyl and amide groups
- forms alpha helix or beta pleated sheet
94
What is an alpha helix?
- H bonds along peptide backbone
- backbone is twisted tightly, R groups projected outward (chemical properties of R groups determines where helix is positioned in folded protein and how it'll interact with other molecules)
- spanning lipid bilayer: peptide backbone in helix is shielded from tails by hydrophobic R groups and secondary structure is stabilized by H bonds between amide and carbonyl groups
95
What is a beta sheet?
- H bonds between areas of the peptide backbone
- polypeptide folds back and forth on itself, forming a pleated sheet
- R groups project alternately above and below plane of sheet
96
Describe the tertiary structure of polypeptides.
longer-range interactions between secondary structures support 3D shape of a protein
- determined by sum of all non-covalent interactions of R groups
- final folded protein structure: stabilized by side-chain interactions (non-covalent interactions and disulfide bonds) as well as interactions between side chains and backbone atoms
- determined by spatial distribution of hydrophilic and hydrophobic R groups
- includes loops/turns in backbone that allow R groups to sit near each other and for bonds to form
- determines function because its the 3D shape of the molecule that enables protein to serve as structural support, membrane channel enzyme, signalling molecule
97
Describe the quaternary structure of polypeptides.
polypeptide subunits can come together to form one functional unit
- subunits can influence each other in subtle ways and influence their function
- subunits can be identical or different
98
Describe protein denaturation.
- proteins can lose their tertiary structure and unfold or denature due to disruption of non-covalent interactions
- can happen by chemical treatment, high temperature that disrupts hydrogen and ionic bonds
- proteins lose their functional activity ---> not all proteins can re-nature
- mutant protein with amino acid that prevents proper folding are inactive/don't function
- strong interactions between side chains = more difficult to denature
- weak interactions between side chains = earlier to denature
- stronger interactions = more stable protein
99
What does protein stability depend on?
R group interactions
the make-up of R groups in polypeptide chain determines structure and function
100
What are enzymes?
proteins with active sites in their tertiary structures
- proteins fold to form active sites as enzymes, to bind substrates
- form a complex with reactant and products
- folds in a way such that amino acids important for binding substrate are in right position
101
How do enzymes catalyze reactions?
1. binding of substrates in active site of enzymes trigger a shape change in enzyme
2. this helps the enzyme to make the transition state more stable
3. reaction is catalyzed, producing products
4. products are released
102
Why is tertiary structure important for enzyme activity?
- protein folding brings specific amino acids close to each other to form the active site
- amino acids that form active site are often far apart in linear sequence of unfolded enzyme
103
Why does heating an enzyme lead to loss of enzyme activity?
- proteins are denatured by heat
- enzyme activity requires 3D tertiary structure of protein to bind substrate and catalyze enzymatic reaction
- heating breaks up non-covalent interactions among R groups on side chains of amino acids which leads to loss of structure and function
104
How do enzymes increase reaction rates?
by reducing activation energy of a chemical reaction
- does not determine spontaneity
- reducing activation energy stabilizes transition state
- enzymes change path of reaction between reactants and products but not start or end points
- less activation energy = faster reaction
- enzymes not consumed in reaction
- ΔG is the same with or without enzyme
105
What is activation energy?
required input of energy for the reaction to proceed
106
What is the transition state?
compound is formed when old bonds are breaking and new ones are forming
- highly unstable
- large amount of free energy
107
What are the steps in enzyme catalysis?
1. initiation: enzymes bind substrates in specific orientation in active sites, bringing the substrates close together
2. transition state stabilization: enzymes shape the "fit" at transition of products better than the substrate
3. termination: products released from active site
108
What is an inhibitor?
decrease activity of enzyme
109
What is an activator?
increase activity of enzyme
110
What is an irreversible inhibitor?
usually form covalent bonds with enzymes and irreversibly inactivate them
111
What is a reversible inhibitor?
form weak bonds with enzymes therefore dissociate easily from them
112
What is a competitive reversible inhibitor?
bind at active site and prevent substrate from binding (competes with substrate and reduce rate of reaction)
113
What is a non-competitive reversible inhibitor?
bind to a different site than the active site and affect substrate binding by changing shape of enzyme and reducing the rate of reaction at which enzyme converts substrate to product
- often, but not always, happens at allosteric site
114
What is an allosteric enzyme?
enzyme that is regulated by molecules that bind at sites other than active site
- activity of enzymes can be influenced by both inhibitors and activators
- play a key role in metabolic pathways
- negative feedback: enzyme changes shape and alter activity of enzyme, final product inhibits first step of reaction
115
What is the allosteric affect?
change in activity or affinity of a protein as the result of binding of a molecule to a site other than the active site
