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BSCI 111 > Test 1 > Flashcards

Test 1 Flashcards

1
Q

microscope

A

Instrument that provides a magnified image of a tiny object

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2
Q

cell theory

A
  1. All organisms are composed of one or more cells
  2. The cell is the structural unit of life
  3. Cells can arise only by division from a preexisting cell
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3
Q

in vitro

A

In culture, outside of the body

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4
Q

metabolism

A

The sum total of the chemical reactions in a cell

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5
Q

organelles

A

Cell’s internal structures

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6
Q

prokaryotic

A

Without a nucleus, structurally simpler cells which include bacteria

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7
Q

eukaryotic

A

structurally more complex cells which includes protists, fungi, plants, and animals

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8
Q

nitrogen fixation

A

The conversion of nitrogen (N2) gas into reduced forms of nitrogen that can be used by cells in the synthesis of nitrogen-containing organic compounds, including amino acids and nucleotides

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9
Q

differentiation

A

Process through which specialized cells are formed

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10
Q

model organisms

A

Organisms that are supposed to be representative–build a larger body of knowledge from studies of them

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11
Q

micrometer (µl)

A

10 ^ -6 meters

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12
Q

nanometer (nm)

A

10 ^ -9 meters

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13
Q

angstrom (˚A)

A

1/10 of nm, commonly used for atomic dimensions

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14
Q

hematopoietic stem cells (HSCs)

A

cells in the bone marrow that can proliferate and restock the patient’s blood-forming bone marrow tissue

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15
Q

embryonic stem cells

A

stem cell isolated from very young mammal embryos

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16
Q

stem cells

A

Undifferentiated cells that (1) are capable of self-renewal (2) are multipotent, aka capable of differentiating into tow or more mature cell types

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17
Q

viruses

A

Pathogens smaller and simpler than bacteria; have rna units and do not multiply on their own

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18
Q

virion

A

Virus outside of a living cell; contains a small amount of genetic material surrounded by a protein capsule (capsid)

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19
Q

procirus

A

Viral DNA that is inserted (integrated) into the DNA of the host cell’s chromosomes

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20
Q

viroid

A

Pathogens even simpler than viruses–lack a protein coat

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21
Q

endosymbiont theory

A

Theory that eukaryotic cells emerged from smaller prokaryotic cells that took up residence in the cytoplasm of a larger host cell

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22
Q

covalent bonds

A

Bonds in which pairs of electrons are shared between pairs of atoms

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23
Q

electronegative atom

A

Atom in which shared electrons of a covalent bond are closer to because of its greater attractive force (O and N are very)

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24
Q

nonpolar

A

Molecules that lack electronegative atoms and strongly polarized bonds

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25
Q

ions

A

Charged atoms

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26
Q

anion

A

Ion that receives an electron and therefore has a negative charge

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27
Q

cation

A

Atom that loses an electron and therefore has a positive charge

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28
Q

noncovalent bonds

A

Do not depend on shared electrons but rather on attractive forces between atoms having an opposite charge; weaker

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29
Q

free radicals

A

Atoms or molecules that have orbitals containing a single unpaired electron tend to be highly unstable

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30
Q

ionic bond

A

Electrostatic attraction between positively and negatively charged ions

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31
Q

hydrogen bonds

A

Weak attractive interaction between partially charged hydrogen atom in a covalent bond and ion

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32
Q

hydrophilic

A

“Water loving” describes polar molecules such as sugars and amino acids

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33
Q

hydrophobic

A

“water fearing” describes nonpolar compounds

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34
Q

hydrophobic interaction

A

The aggregation of nonpolar molecules to minimize their exposure to polar surroundings

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35
Q

van der Waals force

A

weak attractive force between transitory/flickering forces of charge (dipoles) in a molecule at a distance of 3-4 å

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36
Q

acid

A

Molecule capable of releasing (donating) a hydrogen ion

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37
Q

base

A

Any molecule that is capable of accepting a proton

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38
Q

buffers

A

Compounds that react with free hydrogen or hydroxyl ions, thereby resisting changes in pH

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39
Q

biochemicals

A

Compounds produced by living organisms

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40
Q

functional groups

A

Particular groupings of atoms that often behave as a unit and give organic molecules their physical properties, chemical reactivity, and solubility in aq. solutions

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41
Q

ester bonds

A

Form between carboxylic acids and alcohols

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42
Q

amide bonds

A

form between carboxylic acids and amines

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43
Q

macromolecules

A

highly organized molecules that form the structure and carry out the activities of cells
4 types: 3 polymers, 1 monomer
1. carbs/polysaccharides
2. lipids (not actually a macromolecule, bonds aren’t covelant aka are weak)
3. proteins
4. nucleic acids

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44
Q

metabolic pathway

A

Each series of chemical reactions to form a particular molecule

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45
Q

carbohydrates (or glycans)

A

function primarily as stores of chemical energy and as durable building materials for biological construction; include simple sugars (monosaccharides) and all larger molecules constructed of sugar building blocks

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46
Q

glycosidic bonds

A

Formed by reaction between carbon atom C1 of one sugar and the hydroxyl group of another sugar; –C–O–C– linkage

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47
Q

oligosaccharids (oligo=few)

A

Sugars linked together to form small chains; most are covalently attached to lipids & proteins

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48
Q

glycogen

A

Insoluble of glucose found in liver tissue; branched polymer containing only glucose

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49
Q

polysaccharide

A

Polymer of sugar units joined by glycosidic bonds

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50
Q

starch

A

polymer of glucose where plants bank their surplus chemical energy; mixture of 2 different polymers–amylose and amylopectin

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51
Q

cellulose

A

Major component of plant cell walls; consists solely of glucose molecules; tough durable structural material

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52
Q

glycosaminoglycans (GAGs)

A

group of polysaccharides that has a more complex structure; –A–B–A–B– A and B = 2 different sugars

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53
Q

fats

A

glycerol molecule linked by ester bonds to three fatty acids

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54
Q

triaclyglycerol

A

composite molecule in a fat

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55
Q

fatty acids

A

long, unbranched hydrocarbon chains with a single carboxyl at one end(chain=hydrophobic, carboxyl group = hydrophilic)

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56
Q

amphipathetic

A

molecules having both hydrophobic and hydrophilic regions

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57
Q

saturated

A

fatty acids that lack double bonds

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58
Q

unsaturated

A

fatty acids possessing double bonds (in the cis formation); produce kinks in a chain

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59
Q

oils

A

Fats that are liquid at room temperature

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60
Q

specificity

A

the ability to interact selectively with other molecules

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61
Q

polypeptide chain

A

long, continuous, unbranched polymer of amino acids

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62
Q

peptide bonds

A

Link carboxyl group of one amino acid to the amino group of its neighbor, with the elimination of a molecule of water

63
Q

side chain (or R group)

A

Bonded to the alpha-carbon, highly variable & gives proteins their diverse structures and activites

64
Q

Four categories of amino acids

A
  1. Polar, charged
  2. Polar, uncharged
  3. Nonpolar
  4. The other 3 contain unique properties that separate them from the others–glycine, proline, & cysteine
65
Q

general formula for sugars

A

(CH2O)n important ones have n from 3-7

66
Q

carbonyl group

A

C==O in sugars

67
Q

ketose

A

carbonyl in a sugar is internal

68
Q

aldose

A

carbonyl in a sugar is located at the end

69
Q

stereoisomer/enantiomer

A

structures that cannot be superimposed because they have 4 different groups and are therefore mirror images; will be either D or L (if OH projects left it is L; right it is D); most cells are 1 or the other–> amino acids=L, sugars=D

70
Q

alpha-pyranose

A

OH group of 1st carbon projects down

71
Q

beta-pyranose

A

OH group of 1st carbon projects above plan

72
Q

disaccharides

A

molecules composed of only 2 sugar units; readily available energy stores (sucrose and lactose)

73
Q

3 major cell domains

A

eubacteria, archaebacteria (prokaryotes)

eukaryotes

74
Q

DNA

A

genetic blueprint used to build body plans

75
Q

Common features of all living creatures

A

Composed of one or more cells
Genetic info stored, copied, and used in the same fashion
Similar membrane structures
Similar metabolism or biochemistry

76
Q

induced pluripotent stem cells (IPS cells)

A

You can take an adult cell and dedifferentiate it back into a pluripotent stem cell

77
Q

What does 98% genetic identity mean? (w chimps/monkeys)

A

on average, the sequence of nucleotides (GATC) making up our genomes has 2 nucleotide differences for every 100 nucleotides

78
Q

How many genes do humans have?

A

25,000 (same as mouse, plant, and chimp)
6000 in yeast cell
20,000 in microscopic worm
3,200 in bacteria

79
Q

Time line?

A 
4 BYA life evolved
2.3-2.5 Oxygen in atmosphere
2 BYA eukaryotes
200 MYA 1st mammals!
5 MYA separated from chimps
200,000 HUMANS AYE
80
Q

How big are cells?

A

Eukaryotes–5-100 micrometers

Prokaryotes about 1 micrometer

81
Q

Characteristics of prokaryotes

A

little to no internal membranes
no organelles
most abundant life on earth

82
Q

Distinguishing features of eukaryotes

A
  1. Size
  2. Internal membrane bound organelles
  3. Cytoskeletal filaments (extremely plastic)
83
Q

Cytosol

A

protein-rich, aqueous region outside of organelles; contains the following:

  1. ribosomes
  2. cytoskeletal proteins
  3. glycolytic enzymes
  4. enzymes involved in metabolism
  5. lipid droplets that store fat
  6. glycogen granules that store glucose
  7. ions
  8. ATP and other nucleotide triphosphates
84
Q

What’s the big whoop about internal compartments and structural filaments?

A

They allow larger size and striking morphological variation in eukaryotes yay

85
Q

Archaebacteria

A

mostly anaerobic, extreme halophiles, thermophiles

86
Q

condensation reactions

A

a water molecule is released as one product

87
Q

hydrolyctic reactions (hydrolysis)

A

consume one water molecule (when macromolecules are usually broken down)

88
Q

nucleotide triphosphate precursors

A

ATP CTP GTP UTP

89
Q

What does ATP actually do?

A

Major energy currency of the cell, providing energy formost of the energy-consuming activities of the cell
Monomer used in the synthesis of RNA, and after conversion to deoxyATP (dATP), DNA
Regulates many biochemical pathways

90
Q

nucleic acids

A

polymers of nucleotides: RNA & DNA

91
Q

What distinguishes RNA from DNA?

A

2’ OH in RNA, 2’ H in DNA

92
Q

Nucleotides consist of….

A

a sugar (deoxyribose/ribose), a phosphate, and a nitrogen containing base (will be GATorC; U replaces T in DNA)

93
Q

phosphodiester linkage

A

Two ester linkages w a phosphate

94
Q

Biological roles for carbohydrates

A
  1. Energy storage and distribution (glycogen/glucose in bloodstream in mammals, starch/sucrose in sap of plants)
  2. structural support–most cells surround themselves w a protective coat of carbs, they arepolar & attract water to cell surface to prevent dehydration)
  3. Recognition–many cell-cell contacts & cell-pathogen contacts are mediated by carbs
95
Q

characteristics of hydroxyl

A

polar and nonionizable

96
Q

sialic acid

A

terminal carb of oligosaccharides attached to mammalian cell surface proteins. Many human pathogens invade by first attaching to sialic acid–different in humans

97
Q

Glycogen

A

Glucose polymer
Short-term glucose storage in the liver of mammals
Chains of alpha1>4 linked glucose w alpha1>6 branges

98
Q

starch

A

Glucose polymer
Glucose storage in plants
Chains of alpha1>1 linked glucose w few branches
coiled structure prevents higher order packing
dif between starch & cellulose is linkage

99
Q

Cellulose

A 
glucose polymer
chains of beta1>4 linked glucose no branches
most abundant organic material on earth
few creatures can digest
linear--tight packing
100
Q

Chitin

A

N-acetylglucasamine (GlcNAc) polymer
Extremely abundant & tough organic material
Found in exoskeletons

101
Q

Primarily exist as monoatomic ions

A

Ca, Mg, Na, K, Cl

102
Q

valency

A

of electrons required to fill outer shell

103
Q

bond energy

A

measure of the strength of a chemical bond; is described as the amount of heat required to breat the bonds in a mole of molecules

104
Q

Calorie

A

kcal/mol

thermal energy @ body temp=0.6 kical/mol

105
Q

Covalent bonds between carbon atoms

A

double bonds constrain geometry (constrained to a plane)
single bonds can rotate freely around bond axis
85 Calories needed to break carbon-carbon bond
tetrahedral bc of 4 bonds

106
Q

polar

A

electrical charge separation

107
Q

important characteristics of water

A

universal solvent
can hydrogen bond w 4 other water molecules–constantly break & reform
lots of energy required to increase temp/vaporize
would rather stick to itself than hydrophobic substances
hydrophobic effect
buffer for temp change
solid state less dense than liquid

108
Q

noncovalent bonds

A

electrons not shared by interacting atoms
weak, easily broken, but additive (can be strong)
Types:
Ionic
Hydrogen
van der Waals interactions
Hydrophobic interactions

109
Q

electronegativity

A

draws electrons to it (ions that only need 1-2 electrons)

110
Q

amphoteric

A

can serve as acid or base (as in water!)

111
Q

Molarity (M)

A

Moles/liter and is a measure of concentration (# of molecules per unit volume)

112
Q

pK

A

the pH at which
50% of an acidic or basic functional group is ionized
50% is un-ionized
acids lose protons aboce their pK values to form - charges
bases gain protons below their pK values to form positive charges

113
Q

elements of protein structure

A

primary–sequence of amino acids
secondary–alpha helix & beta sheet
tertiary–3D conformation of a polypeptide
quaternary–subunit composition

114
Q

N-terminus, C-terminus

A

Stands for Nitrogen & Carbonyl; endings of alpha helix

115
Q

pattern in alpha helix

A

NCC (nitrogen, alphacarbon, carbonyl carbon)

116
Q

4 ways of depicting tertiary structure of protein

A

backbone, ribbon, wire (ball and stick), space filling

117
Q

amphipathic helix

A

has hydrophobic side chains spaced every 3-4 amino acids along helix; places hydrophobic side chains on the same face of helix to generate hydrophobic stripe

118
Q

subunits

A

each polypeptide in quaternary structure of protein
often symmetrically arranged
sometimes identical–homodimer, homorimer, heterotrimer, etc.
no covalent bonds holding them together
monomer (single chain), dimer, trimer, tetramer etc

119
Q

how can proteins become unfolded?

A

pH extremes

ionic detergents

120
Q

what do enxymes do?

A

Catalysts!
increase reaction rates
don’t alter equilibrium
lower activation energy

121
Q

affinity

A

Strength of the interaction KsubscriptD

122
Q

specificity

A

Preference for certain ligands (compare affinities)

123
Q

ligand

A

protons -> macromolecules

124
Q

Rate

A

max velocity for catalyst in chemical reactions

125
Q

active sites

A

complementary in shape, charge, and hydrogen bonding; corresponding in hydrophobicity

126
Q

induced fit

A

changes conformation on binding substance

127
Q

competitive enzyme inhibitors

A

resemble substrates, bind to active site

128
Q

noncompetitive inhibitors (allosteric)

A

bind to different site

129
Q

in reactions, what do catabolic & anabolic mean

A

catabolic–break down

anabolic build up

130
Q

intermediates/metabolites

A

molecules that are formed at each step in a pathway in metabolism

131
Q

phototrophs

A

photosynthetic organisms, use photosynthesis

132
Q

chemotrophs

A

energy is derived from metabolizing organic compounds (sugars, fats, proteins) use respiration

133
Q

3 stages of digestion/metabolism

A

Stage I: macromolecules>monomers (hydrolysis) in gut
Stage II: monomers>simpler compounds, pyruvate & acetyle CoA - ATP (glycolysis for sugars, Beta-oxidation for fatty acids)
Stage III: Feed acetyl-CoA into TCA cycle–more ATP energy is harvested

134
Q

oxidation

A

losing electrons (gain O/lose H)

135
Q

reduction

A

gaining electrons (gain H/lose O)

136
Q

enthalpies

A

H bond energies

137
Q

phospohoanhydride bonds

A

high energy bonds (between phosphates in ATP!)

138
Q

NAD+

A

widely used carrier of high energy electrons; acts as conenzyme in many redox reactions; dericed from vitamins

139
Q

NADH

A

when NAD+ accepts 2 electrons & proton

140
Q

Enzymes involved in catabolism use ___

A

NAD+ as electron acceptor

141
Q

Enzymes involved in anabolic reactions use ___

A

NADPH as electron donor

142
Q

catabolism

A

breaking down of glucose or fatty acids

143
Q

anabolic reactions

A

building up sugars or fatty acids

144
Q

coenzyme A (CoA)

A

carrier molecule that can form a high energy (thioester) bond; carries basic 2-carbon building block used for synthesis of many other organic compounds

145
Q

Breakdown of glucose to harvest energy

A

1 glucose = about 36 ATPs (2 from glycolysis in cytosol; 34 from oxidation of pyruvate to CO2 and H2O in mitochondria)
actualy yield=30 ATP, lost as heat, used to drive processes other than ATP synthesis

146
Q

glycolysis

A

net yield 2 atp, 2 NADHs, 2 pyruvates

2 ATPs invested, 4 generated

147
Q

intermediates to know in glycolysis

A

Glucose»>glucose 6 phosphate»>fructose 6 phosphate»>fructose 1, 6 biphosphate (all 6 carbon sugars)»>2 molecules glyceraldehyde 3-phosphate (3 carbon sugar)»>each 1=2 molecules pyruvate

148
Q

kinase

A

an enzyme that transfers phosphate to a molecule
hexokinase can phosphoroylate (add a phosphate to) several hexoses–including glucose, fructose, & mannose
in liver, enzyme is glucokinase (specific for glucose)

149
Q

Step 1 glycolysis

glucose > glucose-6-phosphate

A
  1. Activates sugar
  2. Traps glucose in cell *** (because glucose-6-phosphate cannot bind to glucose transporter in plasma membrane and transfer out of cell)
  3. Irreversable enzyme reaction
150
Q

Step 2 glycolysis
phosphoglucose isomerase
glucose 6-phosphate > fructose 6-phosphate

A
  1. No difference in free energy between reactant and product
  2. Readily reversible
    Glucose & fructose–same chemical formula, different bonds
151
Q

Step 3 glycolysis
fructose 6-phosphate > Fructose 1, 6-biphosphate
phosphofructokinase

A
  1. Major regulated step in glycolysis ***
  2. Rate-limiting
  3. Irreversible commitment
152
Q

protein classifications

A 
enzymes
transport proteins
nurtrient storage
contractile/motility
structural
defense
regulatory
other
153
Q

amino acid

A

amine (amino) group
carboxylate group hydrogen
side chain (R)

154
Q

functions of lipids

A

energy storage
structural components of membranes
signaling molecules

BSCI 111 (2 decks)

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