Cliff's - Chapter 1- Chemistry Flashcards
(108 cards)
1
Q
Atom
A
- postively charged protons
- neutrall charged nuetrons
- negatively charged electrons oriented around nucleus
2
Q
molecules
A
two or more atoms conneced by bonds
3
Q
chemical bonds formed via
A
interaction between their electrons of atoms
4
Q
electronegativity
A
ability of an atom to attract electrons
5
Q
chemical bonds
(types)
A
- ionic
- covalent
- polar covalent
- nonpolar covalent
- hydrogen
6
Q
ionic bonds
A
electrons are transferred from one atom to another
electronegativities of atoms are very different
more en atom pulls electron
atom that gains electron: negatively charged
atom that loses electron: positively charged
charges –> ions
ionic bond = attraction bw positve and negative charge ions
e.g. NaCl
7
Q
Covalent Bond
A
electrons between atoms are shared
electronegativities of atoms are similar
polar covalent
nonpolar covalent
8
Q
nonpolar covalent bond
A
electrons shared equally
two atoms sharing electrons are identical - en are identical
e.g. O2
9
Q
polar covalent bonds
A
electrons shared unequally
atoms have different electronegativities
electrons forming bond closer to atom with greater en
negative charge (pole) on more en atom
postiive pole on less en atom
e.g. h2o
10
Q
single, double, triple covalent bonds
A
2, 4, 6 electrons are shared, respectively
11
Q
hydrogen bonds
A
weak bonds bw molecules
positively charged hydrogen atom in one covalently bonded molecule attracted to a negatively charged atom (O, N or S) in another covalently bonded molecule
12
Q
Properties of Water
(due to H bonding b/w water molecules)
A
- water is excellent solvent
- water has high heat capacity
- ice floats
- water has strong cohesion and high surface tension
- water has strong adhesion
13
Q
Water is an excellent solvent
A
ionic substances soluble in water - poles of polar water mlc interact with and separate ionic substances into ions
polar covalent substances also soluble - interactions of poles with water
nonpolar covalent substances do not dissolve in water - no charged poles
14
Q
hydrophilic
A
substances that dissolve in water
“water-loving”
15
Q
hydrophobic
A
substances that do not dissolve in water
“water fearing”
16
Q
heat capacity
A
degree to which substances change temperature in response to gain or loss of heat
17
Q
water has high heat capacity
A
water changes temp very slowly with changes in heat content
temp of large bodies of water very stable in response to air
a lot of energy need be added/removed to heat/cool water
18
Q
ice floats
A
most substances contract and become more dense when frozen
water expands and becomes less dense when frozen
thus - floats in liquid water
solid state of water - h bonds rigid and form crystal, keeping mlc separated
19
Q
water has strong cohesion and high surface tension
A
cohesion - attraction bw like substances - because of h bonding
cohesion produces high surface tension
20
Q
water has strong adhesion
A
adhesion - attraction of unlike substances
when water adheres, demonstrates capillary action:
rises up tubing or creeps through papers
21
Q
Organic Molecules
A
have carbon atoms
22
Q
macromolecules
A
large organic molecules
23
Q
polymers
A
molecules consisting of a single monomer repeated many times
24
Q
functional groups
A
in organic molecules
each gives molecule particular property
25
hydroxyl
(functional group)
-OH
alcohols
polar
hydrophilic
26
carboxyl
| (functional group)
carboxylic acids
polar
hydrophilic
weak acid
27
amino
amines
polar hydrophilic
weak base
28
phosphate
organic phosphates
polar
hydrophilic
acid
e.g. DNA, ATP, phospholipids
29
carbonyl
| (functional group)
ketones, aldehydes
polar
hydrophilic
30
methyl
| (functional group)
nonpolar
hydrophobic
31
Four classes of organic molecules
carbohydrates
lipids
proteins
nucleic acids
32
Carbohydrates
classified into 3 groups based on number of sugar (saccharide) molecules present
* monosaccharide
* disaccharide
* polysaccharide
33
monosaccharide
simplest carbohydrate
single sugar molecule
e.g. fructose, glucose
34
sugar molecule formula
(CH2O)*n*
n = 3,4,5,6,7,8
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disaccharide
two sugar molecules joined by glycosidic linkage
in joining, water molecule lost
(formula = -H2O)
36
condensation reaction
chem rxn where simple molecule is lost
37
dehydration reaction
chem rxn where water molecule is lost
38
common disaccharides
sucrose = glucose + fructose (table sugar)
lactose = glucose + galactose (sugar in milk)
maltose = glucose + glucose
39
glycosidic linkage
covalent bond
joins hemiacetal group of saccharide to hydroxyl group of another organic compound
40
polysaccharide
series of connected monosaccharides
polymer (repeating units of a monosaccharide)
e.g.: starch, glycogen, cellulose, chitin
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starch
polymer of alpha-glucose molecules
principle energy storage molecule in plants
42
glycogen
polymer of alpha-glucose molecules
differs from starch by pattern of polymer branching
major energy storage molecule in animals
43
cellulose
polymer of beta-glucose molecules
structural molecule in walls of plant cells
major component of wood
44
chitin
similiar to cellulose
each beta-glucose mlc has nitrogen-containing group attached to ring
structural molecule in walls of fungus cells and exoskeletons of insects, arthropods, mollusks
45
alpha-glycosidic linkages vs. beta in digestion
easily broken down by humans and other animals
only specialized organisms - bacteria in guts of termites - can break down beta glycosidic
46
Lipids
major groups
soluble in nonpolar substances (e.g. ether, chloroform)
1. triglycerides
2. phospholipid
3. steroids
47
triglycerides
fats and oils
three fatty acids attached to glycerol molecule
glycerol + 3 fatty acids = triglyceride
48
fatty acids
hydrocarbons with carboxyl group at one end
very in structure by number of C and placemtn of single/double bonds
49
types of fatty acids
saturated - all single covalent bonds
monounsaturated - one double covalent bond
polyunsaturated - two+ covalent bonds
50
phospholipids
just like triglyceride, but one fatty acid chain replaced with phosphate group (-PO32-) with R group attached
two fatty acid tails hydrophobic, nonpolar
phosphate head hydrophilic, polar
an amphipathic molecule
often grouped in sandwich manner - hydrophobic tails on inside, hydrophilic heads oriented outside, facing aqeuous env. (structural formation of cell membranes)
51
amphipathic molecule
both polar and nonpolar regions
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steroids
backbone of four linked carbon rings
e.g. cholesterol, testosterone, estrogen
(cholesterol is component of cell membrane)
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Proteins
polymers of amino acids
functions are diverse, structures are similar
proteins differ by number and arrangement of amino acids
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major groups of proteins
1. structural proteins
2. storage proteins
3. transport proteins
4. defensive proteins
5. enzymes
55
eg of:
structural proteins
storage proteins
transport proteins
defensive proteins
enzymes
keratin in hair and horns of animals, collagen in connective tissues, silk in spider webs
casein in milk, ovalbumin in egg whites, zein in corn seeds
oxygen carrying hemoglobin in red blood cells, in membranes of cells that transport materials into and out of cells
antibodies
enzymes
56
peptide bonds
bonds between amino acids
57
polypeptide (peptide)
chain of amino aicds, connected by peptide bonds
58
amino acid makeup
consists of central carbon atom bonded to amino group, carboxyl group, H, and R group
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structure of a protein
primary structure
secondary structure
tertiary structure
quaternary structure
60
primary structure
| (protein)
order of amino acids
e.g. ADH (antidiuretic hormone)
Cys-Tyr-Phe-Gln-Asn-Cys-Pro-Arg-Gly
61
secondary structure
| (protein)
3D shape resulting from h-bonding bw amino and carboxyl groups of adjacent amino acids
bonding produes spiral (alpha helix) or folded plane (beta pleated sheet)
protein dominated by two patters - fibrous proteins
62
tertiary structure
3D shaping
dominates structure of globular proteins
factors contributing to tertiary structure:
* hydrogen bonding between R groups of aa
* ionic bonding between R groups of aa
* hydrophobic effect caused by R groups moving toward center of protein (protein usually immersed in water)
* disulfide bonds
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disulfide bonds
sulfur atom in aa cysteine bonds to sulfur atom in another cysteine
forms cystine (double amino acid)
disulfide bridge helps maintain turns of amino acid chain
64
globular proteins
globe-like
soluble in water
65
quaternary structure
| (protein)
protein assembed from two+ separate peptide chains
e.g. hemoglobin: 4 peptide chains; held together by hydrogen bonding, interactions among R groups, disulfide bonds
66
Nucleic Acids
genetic information of cell stored in molecules of DNA (deoxyribonucleic acid)
DNA ---\> RNA ---\> directs metabolic activities of cell
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DNA
polymer of nucleotides
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nucleotides
| (composition)
three parts: nitrogen base, deoxyribose (5-carbon sugar), phosphate group
69
4 nitrogen bases of nucleotides
adenine - double ring base (purine)
guanine - double ring base (purine)
thymine - single ring base (pyrmidine)
cytosine - single ring base (pyrimidine)
70
purine
adenine and guanine
end with nine
two rings of purine have nine unshared carbon bonds
71
DNA
| (composition)
two strands of nucleotides, paired by weak h bonds between bases, form double stranded dna
two stranded spiral --\> double helix
two strands are antiparallel (oriented in opposite directions)
one strand 5'--\>3'; other strand 3'---\>5'
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5' ---\> 3'
phosphate group attached to fifth carbon of deoxyribose (5' end)
ends where phosphate of next nucleotide would attach - third deoxyribose carbon (3')
73
RNA
sugar in nucleotides is ribose, not deoxyribose
thymine replaced by uracil
A-U instead of A-T
single-stranded
does not form double helix
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75
Activation Energy
energy that must be overcome for a chem rxn to take place
76
for a chem rxn to take place
molecules or atoms must collide and have sufficient energy to overcome Ea and to form new bonds
77
catalyst
many rxns occur spontaneously
catalyst accelerates rate of rxn by lowering Ea
any substance that accelerates rxn but does not change during rxn
can be used over and over again (remains unchanged by rxn)
78
metabolism
chemical rxns that occur in biological systems
* catabolism
* anabolism (synthesis)
* transferring energy from one substance to another
79
catabolism
| (metabolism)
breakdown of substances
80
anabolism
formation of new products
81
Characteristics of metabolic processes
1. net direction determined by concentration of reactants and products
2. enzymes (globular proteins) act as catalysts
3. Cofactors assist enzymes
4. ATP common source of activation energy
82
Equilibrium
* rate of rxn in forward = rate of rxn in reverse
* no net production of reactants or products
83
Characteristics of Enzymes
1. acts on substrate
2. substrate specific
3. unchanged as a result of rxn
4. catalyzes in forward and reverse directions
5. efficiency affected by temp and pH
6. suffix "-ase"
7. operate according to induced-fit model
84
e.g. enzyme and substrate
enzyme amylase catalyzes breakdwon of substrate amylose (starch)
85
e.g. of substrate specific
amylase catalyzes rxn that breaks alpha-glyco linkage in starch but cannot break beta-glyco linkage in cellulose
86
e.g. unchanged as result of rxn
can perform repeatedly
87
e.g. catalyzes in forward and backward
direction determined by substrate concentration
88
e.g. efficiency of enzyme affected by temperature
human body maintained at 98.6 - optimal temp for human enzymes
about 104 - enzymes lose ability to catalyze rxns - become denatured
89
denatured enzymes
lose 3D shape
hydrogen bonds and peptide bonds begin to break down
90
e.g. efficiency of enzyme affected by pH
* many enzymes operate in specific pH
* most human enzymes at around 7.2
* exception: pepsinogen active only in very acidic pH
* pepsinogen digests proteins in stomach
91
Induced-fit model
describes how enzymes work
enzyme has active site
substrate (reactants) interact with active site due to shape, polarity, etc
interaction bw substrate and enzyme causes shape of active site (enzyme) to adapt
rxn may proceed
after rxn, product is released
92
Cofactors
nonprotein molecules that assist enzymes
93
holoenzyme
union of cofactor and enzyme
94
apoenzyme
enzyme that requires cofactors but does not have one bound
95
coenzymes
* organic cofactors
* donate or accept component of rxn (electrons)
* e.g. some vitamins
96
inorganic cofactors
metal ions
e.g. Fe2+ & Mg2+
97
ATP
adenosine triphosphate
source of Ea for metabolic rxns
composition: adenine nucleotide + 2 phosphate groups
98
ATP energy delivery
energy in last bond delivered to rxn
last phosphate bond broken
ATP ---\> ADP (adenosine diphosphat) + P*i*
99
ATP assembly
| (phosphorylation)
using energy rom energy-rich molecule (i.e. glucose)
-----\>
ADP + P*i* -----\> ATP
100
Enzymes regulate reactions in these ways
1. Allosteric enzymes
2. competitive inhibition
3. noncompetitive inhibition
4. cooperativity
101
Allosteric Enzymes
| (enzymes regulate rxns)
two binding sites:
1. for substrate
2. allosteric site for allosteric effector
* allosteric activator
* allosteric inhibitor
102
allosteric activator
| (allosteric enzymes)
binds to enzyme and induces enzyme's active form
103
allosteric inhibitor
| (allosteric enzymes)
binds to enzyme and induces enzyme's inactive form
104
Feedback inhibition
| (allosteric enzymes)
* end product of series of rxns acts as allosteric inhibitor
* shuts down one of the enzymes catalyzing rxn series
105
competitive inhibition
| (enzymes regulate rxns)
substance mimics substrate
occupies active site ---\> inhibits enzyme
mimic displaces substrate
enzyme cannot catalyze substrate
106
noncompetitive inhibition
| (enzymes regulate rxns)
substance binds to enzyme at location other than active site
inhibitor changes shape of enzyme
disables enzymatic activity
(e.g. toxins, antibiotics)
107
cooperativity
| (enzymes regulate rxns)
one substrate mlc attaches to active site
enzyme more receptive to additional substrate mlc
108
cooperativity occurs in
enzymes with 2+ subunits (quaternary structure)
each subunit has own active site
e.g. hemoglobin (not an enzyme) - binding cap to additional oxygen mlc increases after 1st oxygen binds
