Exam 1 Flashcards
1
Q
Atoms
A
smallest identifiable unit of matter
2
Q
What elements make up 96% of all matter in organisms today?
A
H,C,O,N
3
Q
valence shell
A
outermost shell: atoms are most stable when valence shell is filled
4
Q
covalent bond
A
the e- in a covalent bond may be shared equally or unequally, depending on the relative electronegativities of the 2 atoms involved
5
Q
np covalent bonds result from
A
equal sharing
6
Q
polar covalent bonds result from
A
unequal sharing
7
Q
ionic bonds result from
A
when an e- is completely transferred from 1 atom to another
8
Q
Properties of H2O
A
- the chemical rxns required for life take place in water
- water is polar because it is bent and has 2 polar covalent bonds
- solutes dissolve in H2O - H2O interacts w/polar molecules via hydrogen bonding and ionic attractions
- H2O has an extra high ability to absorb heat and adhere to other H2O molecules because of its ability to hydrogen bond
- H2O spontaneously dissociates into hydrogen ions (or protons H+) and hydroxide ions (OH-). (The concentration of protons in a solution determines the pH which can be altered or stabilized by buffers.)
9
Q
Beginning of chemical evolution
A
the 1st step in chemical evolution was the formation of small organic compounds from molecules such as H2 and CO2
10
Q
How is life carbon based?
A
carbon is the foundation of organic molecules based on its valence (4 bonding sites), which allows for the construction of molecules w complex shapes; organic molecules are critical to life because they possess versatility of chemical behavior due to the presence of functional groups; functional groups promote further interactions between organic molecules to form macromolecules
11
Q
Strength order of bonding types
A
- covalent
- ionic
- hydrogen
- van der waals
12
Q
covalent bonds
A
sharing of e- between 2 atoms
np covalent bonds: equal sharing because of less than ~0.5 EN difference
covalent bonds: unequal sharing (partial charges) because of >~0.5, and <~2.0 EN difference
13
Q
electronegativity (measure of an atoms ability to attract an e- pair) depends on
A
size of positive charge and distance from positive charge (nucleus)
14
Q
ionic bonds
A
- not as common as covalent
- e- transfer from 1 atom to another
- results from EN difference of >~2
- opposites attract: electrostatic interactions
15
Q
Van der Waals interactions
A
- interactions between molecules due to e- in atoms constantly moving, creates instantaneous dipoles (charge distributions)
16
Q
Hydrogen bonds
A
weak electrostatic interaction between partially (+) hydrogen and partially (-) atoms
17
Q
Proteins are
A
macromolecules
18
Q
Most of the functional molecules in the cell are
A
proteins
19
Q
polymers
A
“many units”, made up of monomers (in proteins, these are aa connected by peptide bonds (covalent connection))
20
Q
Amino Acid structure
A
- Amino group: ionized (+ charge) at physiological pH
- Side chain: R-group
- each aa has a diff R-group (20 common aa are used by cells to synthesize proteins)
- side chain gives each aa unique chemical properties
3. Carboxyl group: ionized (- charge) at physiological pH
4. Alpha carbon: central atom within aa
21
Q
Beta pleated sheet
A
parallel chains connected by H-bonds between amino and carboxyl groups (but generally not bonds involving R groups)
22
Q
Alpha Helix
A
amino acid chain spirals around a central axis: every 4th residue is linked by H-bonds between amino and carboxyl group, but generally not bonds involving R groups
23
Q
R groups tend not to contribute to alpha helix or beta pleated sheet, BUT
A
they often do inhibit the generation of these secondary structures
24
Q
How might R-groups prevent beta pleated sheet formation?
A
- charged R groups w/same charge repel
- hydrophobic R group adjacent to polar or charged aa (or to H2O)
- large size interferes with association
25
Tertiary structure
the 3D conformation of the whole polypeptide chain
26
Quaternary structure
protein structure resulting from the association of multiple polypeptide subunits
(generally proteins require assembly of 2+ polypeptides to carry out their function)
(generally they are non covalently associated with each other (van der waals + some H-bonds/ionic bonds)
27
Domain definition
Region of a polypeptide that folds or functions independently
28
sometimes even a single aa can change significantly how a protein functions
e. g. sickle cell (single aa change in hemoglobin protein)
- the change makes the proteins stick more to each other (become more attracted to each other), makes blood sickle
29
Allosteric regulation
regulation of proteins function by binding of a specific molecules that causes a change in the proteins shape
\*non-covalent
\*reversible
30
allosteric regulation examples
receptor proteins, gated channel proteins, enzymes
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receptor proteins: allosteric regulation
the receptor proteins sense specific molecules in the environment + get activated by their presence
32
gated channel proteins: allosteric regulation
allow specific molecules across membranes (visual: the molecules open the hatch)
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enzymes: allosteric regulation
catalyze specific chemical rxns when active
34
a eukaryotic cell typically expresses 5,000-10,000 diff types of proteins
with an average of 10,000 to 50,000 molecules of each type of protein per cell
35
Why do cells need energy?
They are highly organized, thus need energy to maintain organization
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bioenergetics
the study of how living things use and convert energy
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energy
the capacity to do work
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Potential energy
stored energy, often stored in chemical bonds in living system
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kinetic energy
energy released
40
thermodynamics
study of changes in energy states: by knowing how much energy is required for an event to occur and how much energy is available, we can predict whether the event will occur
41
How do we know if a chemical rxn will take place or not?
Gibbs free energy
42
Gibbs free energy
(G) - the amount of energy in a chemical rxn available to do work = free energy in a system
a spontaneous rxn will occur without further energy input = an increase in disorder as a result of rxn
e.g. sucrose --\> glucose + fructose
43
Change in G =
Gaft - Gbef
44
Endergonic rxns
non spontaneous, results in greater order and higher PE (positive change in G)
45
Exergonic rxns
spontaneous, results in greater disorder, and lower PE (negative change in G)
46
Cells need inputs of energy to make endergonic rxns happen
true
47
How do endergonic rxs happen in cells
1. coupled rxns: use energy released from an exergonic rxn to drive an endergonic rxn
2. variation in the relative concentration of molecules involved in rxn (relative conc. of reactants and products influences direction of rxn)
48
Coupled rxns: example 1 - redox rxns
redox rxns involved exchange of e- (and protons) between redox pairs
require:
1. reductant = e- donor = reducing agent (ex: CH4)
- in many redox rxns, the e- come from H
2. Oxidant = e- acceptor = oxidizing agent (ex: O2)
\*e- donors and acceptors are always paired in redox rxns (no free e-)
\*e- often move w/protons in biological systems: depicted as "H" \<--(H+ + e-)
The shift in location of electrons causes a change in G, can be exergonic (releases energy)!
49
Coupled rxns: example 1 - ATP as cellular energy source (adenine triphosphate)
Energy released from hydrolysis of phosphate from ATP (turns into ADP) can be used to allow an endergonic rxns to happen
[A][P][P][P] + H2O --\> [A][P][P] + P
Change in G = -7.3kcal/mol in STP (exergonic)
50
The "But" abt exergonic rxns
Even they often dont proceed rapidly...
(-Change in G does not necessarily indicate rapid rxn)
Because of activation energy!!!
51
How do cells get chemical rxns to overcome activation energy
Enzymes (only for exergonic rxns)
52
Enzyme
a protein that catalyzes specific chemical rxns
- lowers Ea for conversion of substrate (S) to product (P)
\*note enzyme names end with suffix -ase
\*enzyme catalyzed rxns = S + E --\> ES -------\> P + E
53
How do enzymes lower activation energy?
Enzyme and substrate physically interact to form ES complex
\*formation of ES complex lowers EA for conversion of S--\> P.... how?
1. May orient substrate (s) for more efficient chemical rxn
2. may change shape of substrate, causing bonds to break or form (ex: sucrose --\> glucose + fructose)
3. may change chemical reactivity of substrate
any of these changes can lower Ea required to catalyze chemical rxns
54
Characteristics of enzymes
1. increase rate of rxns that would occur spontaneously
2. perform an activity repeatedly without getting "used-up"
3. same enzyme can be used for both forward and reverse rxns
4. a particular enzyme has high specificity for a particular substrate
5. enzymes are often "assisted" by cofacters or coenzymes: add some chemical behavior to enzyme to allow it to catalyze rxn
55
active site
that part of the enzyme that associates with the substrate
56
cofactors
= inorganic molecules (often metal ions: iron, magnesium, etc)
57
coenzymes
organic molecules (often vitamins: riboflavin, niacin)
58
enzyme kinetics
the study of the rate of enzyme-catalyzed reactions = study of how fast substrate (S) is converted to product (P)
59
Some observations made by researchers studying kinetics of chemical rxns:
1. the rate (velocity) of formation of product in an uncatalyzed rxn (no enzyme added) is linear with increasing [S]
2. the rate of the same rxn when catalyzed by an enzyme is an asymptotic curve with increasing [S]
60
Why is the curve when enzyme is present initially so much steeper than when enzyme is not present?
Enzymes speed up exergonic rxns... velocity = rate of substrate --\> product
61
Why does the curve flatten when [S] increases?
more and more enzymes become "full" - enzymes present are saturated with substrate
62
Enzyme catalyzed reactions require substrate binding with
enzyme at active site
63
chemical rxns arent instantaneous (require some time to occur) = ?
Vmax
64
Velocity (Vo) of an enzyme-catalyzed rxn is dependent upon 4 factors
1. [E]
2. [S]
3. Vmax
4. Km (michaelis constant)
65
Vmax
= rate of ES --\> E+P = constant for any enzyme-substrte pair
\*the higher the Vmax, the faster the rxn happens after ES forms
66
Km (michaelis constant)
measurement of enzyme-substrate affinity = how tightly the enzyme and substrate bind to each other
= [S] at which V0 = 1/2 Vmax = constant for any enzyme-substrate pair
67
The more tightly enzyme and substrate can bind,
the faster the velocity at low [S]
68
Michaelis-Menten plot
- plot of rxn rate (Vo) vs [S]
- [E] remains constant and is \<\<\<\<[S]
- helps us to calculate Vmax and Km for a particular enzyme-substrate pair
69
Cells sometimes need enzymes to be inactive or have decreased activity. How can this be done?
Regulating enzyme activity:
1. allosteric regulation
2. competitive inhibition
70
Allosteric regulation
inhibitor molecule binds with enzyme at a site other than its active site and changes the shape of the enzyme = non-competitive inhibitor (not competing with substrate for binding to active site on enzyme)
\*change in shape alters enzyme's activity, often by slowing ES-\> E+P
--\> decreases Vmax, can also affect Km
71
Competitive Inhibition
inhibitor molecule competes with substrate for binding to active site on enzyme = competitive inhibitor
\*can be overcome by increased [S]
--\> does not affect Vmax, increases apparent Km
72
Inhibitors
regulate the activity of specific enzymes to regulate what products are made when in cells
73
Organelles
membrane-bound compartments within cells
74
why are organelles important?
allow for different regions within cells to have different proteins and other molecules present
- provide for specialized functions in regions within cell
75
Eukaryotic organelles
nucleus, mitochondria, chloroplasts, endomembrane system (ER, golgo apparatus, lysosomes, exocytic, endocytic, and other vesicles), peroxisomes
76
There are other complex structures that are important for cell function, but are not organelles
e.g. ribosomes, cytoskeleton, etc
these are not membrane-bound
77
Nucleus
1. contains most of the cell's DNA
2. location of RNA transcription and other activities
3. movement of molecules in and out of nucleus is regulated by nuclear pore complexes
78
Cystoplasm
entire area of cell outside nucleus, but within plasma membrane
79
Cystosol
area of cystoplasm not found within any organelle
80
Mitochondria
site of ATP synthesis by aerobic respiration
2 membranes
mitochondrial DNA - descended from aerobic bacterium
81
Chloroplast
Site of photosynthesis
descended from photosynthetic bacteria
82
Endomembrane system
Er (rough + smooth), Golgi apparatus, lysosomes, exocytic (secretory, endocytic, and other) vesicles
- moves and modifies proteins and lipids being sent to cell surface, and brings in and modifies molecules from outside cell
83
Endoplasmic reticulum
starts macromolecules on path to cell surface
84
rough ER
site of protein entry into endomembrane system (covered w ribosomes)
85
smooth ER
lipids synthesized and inserted into membrane
86
Vesicles
vesicles "bud" off of organelle + transport material to another organelle (ex: ER--\> Golgi)
87
Golgi apparatus
modifies and sorts proteins and lipids
88
Lysosome
degrades macromolecules using acid hydrolase enzymes
89
Path of proteins and lipids to outside of cell
Er---\> Golgi---\> lysosomes
- exocytic (secretory) vesicles: carry proteins and lipids from Golgi to cell surface
- molecules inside vesicle are released outside cell (ex: proteins involved in cell interactions; secreted peptide proteins)
- molecules in vesicle membrane become part of plasma membrane (ex: membrane phospholipids, transmembrane proteins)
- endocytic vesicles carry proteins and lipids from cell surface into cell
90
Biological membranes functions
1. regulate what goes in/out of cell/organelle
2. compartamentalize cell regions/form cell boundary
3. sensing environment
4. cell protection
91
Lipids
organic macromolecules that are insoluble in H2O --\> largely nonpolar
92
Lipid structure
Lipid monomer = fatty acid
- typically 12-20 carbons
- COOH group at 1 end (COO- at neutral pH)
- is amphipathic - has both hydrophobic and hydrophilic regions
93
Some biologically important lipids
Triaglycerols, Phospholipids, Sterols
94
Triaglycerols
= glycerol + 3 fatty acids
- non polar
- great energy storage molecule: all the C-H bonds can be involved in redox rxns that release energy
95
Phospholipids
= glycerol + 2 fatty acids + (PO4 + hydrophilic functional groups)
- amphipathic
- primary components of cell membranes
96
Sterols
= 4 carbon-based rings, often with -OH or another functional group attached
- slightly amphipathic
- functions: membrane structure (ex; cholesterol), and cell-cell signaling (ex: steroid hormones)
97
Cell Membranes
Contents of cell membranes:
1. lipids --\> lipid bilayer - amphipathic
- phospholipids = primary component of membranes
\* diff phospholipids (diff head groups + fatty acid tails have diff properties and functions)
\* diff phospholipids are inserted into diff membrane layers
- cholesterol = helps influence the permeability and fluidity of the membrane
\*an increase in cholesterol ---\> membrane becomes more fluid + less permeable
\*a decrease in cholesterol ---\> membrane becomes less fluid and more permeable
98
There are 3 basic types of amino acids:
1. Hydrophobic aa (9/20)
2. Polar aa (6/20)
3. Charged aa (2 types, 5/20)
99
Hydrophobic amino acids
most of R group is made up of nonpolar covalent bonds
9/20 of basic amino acids are hydrophobic:
includes Glycine, alanine, valine, leucine, isoleucine, proline, phenylalaline, methionine, trytophan
100
Polar Amino Acids
R-group contains 1 or more functional groups that are polar
6/20 basic aa are polar:
tyrosine, serine, threonine, asparagine, cysteine, glutamine,
101
Charged amino acids
2 types:
1. R-group contains positive charge at cellular pH (basic)
1. arginine, lysine, histidine
2. R-group contains negative charge at cellular pH (acidic)
1. glutamate, aspartate
102
All amino acids can form ___ bonds between the ____ group and ____ group of 2 amino acids
Hydrogen, carboxyl, amino
103
R groups can form the following
Hydrophobic, polar, charged aa: van der waals
polar, charged aa: H-bonds
Charged aa: ionic bonds
104
Features of carbon that makes it important
1. can bond with itself (C-C)
2. can form 4 covalent bonds
105
Basics of Carbon
1. 4 e- in outer shell; can form 4 covalent bonds
2. can covalently bond w other carbons to form long chains + branches
3. carbon atoms can have other types of atoms or groups of atoms covalently bond
1. Or H, functional groups
106
Common R groups in Bio 182
1. Amino: NH2 or NH3+, usually in normal pH, the amino group is ionized (gains an H+)
2. Hydroxyl: -OH (polar)
3. Carboxyl: COOH or COO- (NP)
4. Methyl: CH3
5. Phosphate: PO4 2- (strong negative charge)
6. Sulfhydryl (SH)
Be able to recognize names, structures, characteristics
107
biochemicals
organic molecules synthesized and used by living cells
108
biological macromolecules
large, organic molecules synthesized in living organisms → composed or repeating units of similar smaller molecules (monomers)
109
polymer
a large molecule that contains multiple monomers
110
How are macromolecules synthesized?
by covalently linking monomer subunits - condensation rxn (hydrolysis rxn to break back down)
111
4 families of biological macromolecules
0. polymers → monomers
1. proteins → amino acids
2. Nucleic acids → nucleotides
3. Carbohydrates → sugars (monosaccharides)
4. Lipids → fatty acids (kind of)
112
functions that proteins share with cells/organisms
eat, develop, reproduce (replicate DNA), respirate, store + use energy, maintain homeostasis (regulate state of inside of cell - sensing environment)
113
Specificity of proteins
each protein has a specific function or activity (function determined by structure)
114
What determines protein structure?
amino acid sequence
each aa has different chemical properties, together, characteristics of all aa in a protein influence that proteins folding and activity
115
General characteristics to keep in mind for aa
1. charged vs uncharged → hydrophobic vs hydrophilic
2. polar vs nonpolar
3. relative size (large side chain vs smaller) and shape
116
The two “special” aa
Proline and cysteine
117
Cysteine
can form a covalent sulfide linkage with another cysteine: can stabilize parts of a peptide chain or connect to other proteins
Has a sulfhydryl R group (-S-H) with allows it to form covalent bonds with other cysteine
118
How can a bunch of amino acids generate a protein?
aa link covalently to form polypeptides
(protein = polypeptides that perform a function)
119
Peptide bond
a covalent bond that occurs in the ribosomes of cells that links amino acid residues
(COO- on 1 aa is covalently linked to NH3+ on the next → H2O is released (condensation rxn))
120
N terminus and C terminus
“front” of protein always has an amino group (N term) while “tail” always has a carboxyl group (C term)
- the next aa is only added at C-term end of an elongating polypeptide
