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Biology > Cliff's - Chapter 1- Chemistry > Flashcards

Cliff's - Chapter 1- Chemistry Flashcards

1
Q

Atom

A
  • postively charged protons
  • neutrall charged nuetrons
  • negatively charged electrons oriented around nucleus
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2
Q

molecules

A

two or more atoms conneced by bonds

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3
Q

chemical bonds formed via

A

interaction between their electrons of atoms

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4
Q

electronegativity

A

ability of an atom to attract electrons

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5
Q

chemical bonds

(types)

A
  • ionic
  • covalent
  • polar covalent
  • nonpolar covalent
  • hydrogen
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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

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7
Q

Covalent Bond

A

electrons between atoms are shared

electronegativities of atoms are similar

polar covalent

nonpolar covalent

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8
Q

nonpolar covalent bond

A

electrons shared equally

two atoms sharing electrons are identical - en are identical

e.g. O2

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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

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10
Q

single, double, triple covalent bonds

A

2, 4, 6 electrons are shared, respectively

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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

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12
Q

Properties of Water

(due to H bonding b/w water molecules)

A
  1. water is excellent solvent
  2. water has high heat capacity
  3. ice floats
  4. water has strong cohesion and high surface tension
  5. water has strong adhesion
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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

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14
Q

hydrophilic

A

substances that dissolve in water

“water-loving”

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15
Q

hydrophobic

A

substances that do not dissolve in water

“water fearing”

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16
Q

heat capacity

A

degree to which substances change temperature in response to gain or loss of heat

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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

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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

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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

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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

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21
Q

Organic Molecules

A

have carbon atoms

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22
Q

macromolecules

A

large organic molecules

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23
Q

polymers

A

molecules consisting of a single monomer repeated many times

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24
Q

functional groups

A

in organic molecules

each gives molecule particular property

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25
Q

hydroxyl

(functional group)

A

-OH

alcohols

polar

hydrophilic

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26
Q

carboxyl

(functional group)

A

carboxylic acids

polar

hydrophilic

weak acid

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27
Q

amino

A

amines

polar hydrophilic

weak base

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28
Q

phosphate

A

organic phosphates

polar

hydrophilic

acid

e.g. DNA, ATP, phospholipids

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29
Q

carbonyl

(functional group)

A

ketones, aldehydes

polar

hydrophilic

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30
Q

methyl

(functional group)

A

nonpolar

hydrophobic

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31
Q

Four classes of organic molecules

A

carbohydrates

lipids

proteins

nucleic acids

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32
Q

Carbohydrates

A

classified into 3 groups based on number of sugar (saccharide) molecules present

  • monosaccharide
  • disaccharide
  • polysaccharide
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33
Q

monosaccharide

A

simplest carbohydrate

single sugar molecule

e.g. fructose, glucose

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34
Q

sugar molecule formula

A

(CH2O)n

n = 3,4,5,6,7,8

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35
Q

disaccharide

A

two sugar molecules joined by glycosidic linkage

in joining, water molecule lost

(formula = -H2O)

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36
Q

condensation reaction

A

chem rxn where simple molecule is lost

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37
Q

dehydration reaction

A

chem rxn where water molecule is lost

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38
Q

common disaccharides

A

sucrose = glucose + fructose (table sugar)

lactose = glucose + galactose (sugar in milk)

maltose = glucose + glucose

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39
Q

glycosidic linkage

A

covalent bond

joins hemiacetal group of saccharide to hydroxyl group of another organic compound

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40
Q

polysaccharide

A

series of connected monosaccharides

polymer (repeating units of a monosaccharide)

e.g.: starch, glycogen, cellulose, chitin

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41
Q

starch

A

polymer of alpha-glucose molecules

principle energy storage molecule in plants

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42
Q

glycogen

A

polymer of alpha-glucose molecules

differs from starch by pattern of polymer branching

major energy storage molecule in animals

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43
Q

cellulose

A

polymer of beta-glucose molecules

structural molecule in walls of plant cells

major component of wood

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44
Q

chitin

A

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
Q

alpha-glycosidic linkages vs. beta in digestion

A

easily broken down by humans and other animals

only specialized organisms - bacteria in guts of termites - can break down beta glycosidic

46
Q

Lipids

major groups

A

soluble in nonpolar substances (e.g. ether, chloroform)

  1. triglycerides
  2. phospholipid
  3. steroids
47
Q

triglycerides

A

fats and oils

three fatty acids attached to glycerol molecule

glycerol + 3 fatty acids = triglyceride

48
Q

fatty acids

A

hydrocarbons with carboxyl group at one end

very in structure by number of C and placemtn of single/double bonds

49
Q

types of fatty acids

A

saturated - all single covalent bonds

monounsaturated - one double covalent bond

polyunsaturated - two+ covalent bonds

50
Q

phospholipids

A

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
Q

amphipathic molecule

A

both polar and nonpolar regions

52
Q

steroids

A

backbone of four linked carbon rings

e.g. cholesterol, testosterone, estrogen

(cholesterol is component of cell membrane)

53
Q

Proteins

A

polymers of amino acids

functions are diverse, structures are similar

proteins differ by number and arrangement of amino acids

54
Q

major groups of proteins

A
  1. structural proteins
  2. storage proteins
  3. transport proteins
  4. defensive proteins
  5. enzymes
55
Q

eg of:

structural proteins

storage proteins

transport proteins

defensive proteins

enzymes

A

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
Q

peptide bonds

A

bonds between amino acids

57
Q

polypeptide (peptide)

A

chain of amino aicds, connected by peptide bonds

58
Q

amino acid makeup

A

consists of central carbon atom bonded to amino group, carboxyl group, H, and R group

59
Q

structure of a protein

A

primary structure

secondary structure

tertiary structure

quaternary structure

60
Q

primary structure

(protein)

A

order of amino acids

e.g. ADH (antidiuretic hormone)

Cys-Tyr-Phe-Gln-Asn-Cys-Pro-Arg-Gly

61
Q

secondary structure

(protein)

A

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
Q

tertiary structure

A

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
63
Q

disulfide bonds

A

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
Q

globular proteins

A

globe-like

soluble in water

65
Q

quaternary structure

(protein)

A

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
Q

Nucleic Acids

A

genetic information of cell stored in molecules of DNA (deoxyribonucleic acid)

DNA —> RNA —> directs metabolic activities of cell

67
Q

DNA

A

polymer of nucleotides

68
Q

nucleotides

(composition)

A

three parts: nitrogen base, deoxyribose (5-carbon sugar), phosphate group

69
Q

4 nitrogen bases of nucleotides

A

adenine - double ring base (purine)

guanine - double ring base (purine)

thymine - single ring base (pyrmidine)

cytosine - single ring base (pyrimidine)

70
Q

purine

A

adenine and guanine

end with nine

two rings of purine have nine unshared carbon bonds

71
Q

DNA

(composition)

A

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’

72
Q

5’ —> 3’

A

phosphate group attached to fifth carbon of deoxyribose (5’ end)

ends where phosphate of next nucleotide would attach - third deoxyribose carbon (3’)

73
Q

RNA

A

sugar in nucleotides is ribose, not deoxyribose

thymine replaced by uracil

A-U instead of A-T

single-stranded

does not form double helix

75
Q

Activation Energy

A

energy that must be overcome for a chem rxn to take place

76
Q

for a chem rxn to take place

A

molecules or atoms must collide and have sufficient energy to overcome Ea and to form new bonds

77
Q

catalyst

A

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
Q

metabolism

A

chemical rxns that occur in biological systems

  • catabolism
  • anabolism (synthesis)
  • transferring energy from one substance to another
79
Q

catabolism

(metabolism)

A

breakdown of substances

80
Q

anabolism

A

formation of new products

81
Q

Characteristics of metabolic processes

A
  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
Q

Equilibrium

A
  • rate of rxn in forward = rate of rxn in reverse
  • no net production of reactants or products
83
Q

Characteristics of Enzymes

A
  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
Q

e.g. enzyme and substrate

A

enzyme amylase catalyzes breakdwon of substrate amylose (starch)

85
Q

e.g. of substrate specific

A

amylase catalyzes rxn that breaks alpha-glyco linkage in starch but cannot break beta-glyco linkage in cellulose

86
Q

e.g. unchanged as result of rxn

A

can perform repeatedly

87
Q

e.g. catalyzes in forward and backward

A

direction determined by substrate concentration

88
Q

e.g. efficiency of enzyme affected by temperature

A

human body maintained at 98.6 - optimal temp for human enzymes

about 104 - enzymes lose ability to catalyze rxns - become denatured

89
Q

denatured enzymes

A

lose 3D shape

hydrogen bonds and peptide bonds begin to break down

90
Q

e.g. efficiency of enzyme affected by pH

A
  • 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
Q

Induced-fit model

A

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
Q

Cofactors

A

nonprotein molecules that assist enzymes

93
Q

holoenzyme

A

union of cofactor and enzyme

94
Q

apoenzyme

A

enzyme that requires cofactors but does not have one bound

95
Q

coenzymes

A
  • organic cofactors
  • donate or accept component of rxn (electrons)
  • e.g. some vitamins
96
Q

inorganic cofactors

A

metal ions

e.g. Fe2+ & Mg2+

97
Q

ATP

A

adenosine triphosphate

source of Ea for metabolic rxns

composition: adenine nucleotide + 2 phosphate groups

98
Q

ATP energy delivery

A

energy in last bond delivered to rxn

last phosphate bond broken

ATP —> ADP (adenosine diphosphat) + Pi

99
Q

ATP assembly

(phosphorylation)

A

using energy rom energy-rich molecule (i.e. glucose)

—–>

ADP + Pi —–> ATP

100
Q

Enzymes regulate reactions in these ways

A
  1. Allosteric enzymes
  2. competitive inhibition
  3. noncompetitive inhibition
  4. cooperativity
101
Q

Allosteric Enzymes

(enzymes regulate rxns)

A

two binding sites:

  1. for substrate
  2. allosteric site for allosteric effector
  • allosteric activator
  • allosteric inhibitor
102
Q

allosteric activator

(allosteric enzymes)

A

binds to enzyme and induces enzyme’s active form

103
Q

allosteric inhibitor

(allosteric enzymes)

A

binds to enzyme and induces enzyme’s inactive form

104
Q

Feedback inhibition

(allosteric enzymes)

A
  • end product of series of rxns acts as allosteric inhibitor
  • shuts down one of the enzymes catalyzing rxn series
105
Q

competitive inhibition

(enzymes regulate rxns)

A

substance mimics substrate

occupies active site —> inhibits enzyme

mimic displaces substrate

enzyme cannot catalyze substrate

106
Q

noncompetitive inhibition

(enzymes regulate rxns)

A

substance binds to enzyme at location other than active site

inhibitor changes shape of enzyme

disables enzymatic activity

(e.g. toxins, antibiotics)

107
Q

cooperativity

(enzymes regulate rxns)

A

one substrate mlc attaches to active site

enzyme more receptive to additional substrate mlc

108
Q

cooperativity occurs in

A

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

Biology (19 decks)

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