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BIOL 107 > Chemistry and Macromolecules > Flashcards

Chemistry and Macromolecules Flashcards

1
Q

Of the 92 elements known, about__are required for organisms to survive.

A

¼

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2
Q

these elements make up >96% of living matter

A

C, H, O, P, S, N

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3
Q

Calcium, Phosphorus, potassium, sulphur, sodium, chlorine, magnesium

A

Trace elements

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4
Q

The discrete shells that electrons can occupy, have a specific capacity. The
closest shell can only hold___ electrons

A

2

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5
Q

The second shell can hold___ electrons

A

8

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6
Q

What does this image represent

A

Represents a probability map of where the electrons will be (not exactly orbiting nucleus)

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7
Q

Electrons try to____

A

Avoid each other and stay in their own zone

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8
Q

The properties of the atom are determined primarily by the number of______these are the_____

A

number of electrons in
the outermost shell, valence electrons

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9
Q

. Atoms with the _____of valence electrons behave _______

A

same number, similarly in chemical reactions.

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10
Q

An atom with
a____valence shell will be____

A

“full”, unreactive (inert).

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11
Q

The atomic number defines the number of_____ present in that particular element.

A

protons,

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12
Q

Because electrons are____, when an element is in its _____
it will have the same number of_____

A

negatively charged, neutral state, protons as electrons.

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13
Q

Every atom of boron contains___ protons

A

5

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14
Q

sharing of a pair of valence electrons by two atoms
Two or more atoms held together by____

A

covalent bonds = a molecule

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15
Q
A

Single pair of
electrons shared

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16
Q
A

Two pairs are shared
between two atoms:
= double bond

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17
Q

Covalent bonds can be_____

A

Nonpolar or Polar

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18
Q

Covalent bonds can be Nonpolar or Polar (determined by the_____of the atom, i.e., the________ of an atom for electrons of the other atom in the covalent bond).

A

electronegativity, attraction
strength,

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19
Q
A

Single bond, non polar

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20
Q
A

Double bond, polar, the electrons spend more time with the oxygen atom.

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21
Q
A

Dipole= separation of 2 opposite charges within the same molecule.

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22
Q
A

e.g., Carbon’s electrons would be dispersed in a “6-pointed structure, but
when bound to H, four pairs of electrons are shared and the s and p
orbitals rearrange to occupy 4 equidistant regions, which form a
tetrahedron

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23
Q

The formation of______ results in a rearrangement of,___________

A

Covalent Bonds, orbitals
in the valence shell.

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24
Q

When two atoms with a very different_____ the electron is transferred from______ leaving
the two atoms with a______ The oppositely charged_________ form an_____.

A

affinity for valence
electrons combine, one to the other, net change in their charge. cations and anions, ionic bond.

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25
Q

what does this represent?

A

The change in charge forms
the ionic bond.

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26
Q

Ionic bonds are relatively weak______

A

aqueous environments.. Salts dissolve in
water, i.e., the ions separate and
become surrounded by water molecules

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27
Q

very important in biology, as these interactions
can be reversible, or modified by changes to the molecule.

A

Weak chemical bonds

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28
Q

when hydrogen forms____ with an_____ atom, like(__________). It will have a positive ______which allows it to
interact with________.

A

covalent bond, electronegative, oxygen or nitrogen, charge, another negatively charged atom.

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29
Q

Because of the random positioning of electrons in the orbitals, net displacements
can occur, creating brief charge differences. This dynamic charge distribution allows
molecules to stick to each other if they are very close. Different molecules can
exhibit different “stickiness” depending on the arrangement of respective atoms.

A

Van der Waals interactions:

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30
Q
A

The distribution of electrons changes over time.

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31
Q
A

One dipole can also induce a
dipole in a neighboring atom.
Although these attractions are
often very weak, they can have a
large cumulative effect.

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32
Q

Water: a __________

A

polar molecule

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33
Q
A

Cohesion of water molecules because of hydrogen bonds.

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34
Q

Because of the high density of hydrogen bonds,____________________

A

Water has a high heat of vaporization:

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35
Q

Water contributes to______, as liquid evaporates from the
surface______ the liquid that remains behind

A

evaporative cooling, cools down

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36
Q

Water (solid) is_____than Water (liquid).

A

less dense,

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37
Q
A

This arrangement makes ice
about 10% less dense than
liquid (ice floats on water)

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38
Q

Water is an_____

A

Important solvent

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39
Q

Polar molecules
are soluble in water____

A

“hydrophilic”

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40
Q

Non-Polar molecules
are not soluble in water____

A

“hydrophobic”

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41
Q
  • organic molecules consisting
    of only H and C
A

Hydrocarbons:

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42
Q

What hydrocarbon is this?

A

Methane
CH4

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43
Q

What hydrocarbon is this?

A

Ethane
C2H6

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44
Q

what hydrocarbon is this?

A

Ethene
C2H4

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45
Q

hydrocarbons are not prevalent in most living organisms, but some_______ contain regions that have only________

A

organic
molecules, C and H. e.g. fats, (lipids)

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46
Q

Carbon chains can vary in:

A

Length

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47
Q

Carbon chains can vary in:

A

Branching

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48
Q

Carbon chains can vary in:

A

Double bond positioning

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49
Q

Carbon chains can vary in:

A

Presence of rings

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50
Q

Structural (or constitutional) isomers

A

can have a different bond
order of atoms

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51
Q

What kind of Stereoisomer is this?

A

trans

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52
Q

What kind of stereoisomer is this?

A

cis

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53
Q

A double bond restricts
rotation of the two atoms
with respect to each other

A

Stereoisomers

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54
Q

When 4 different atoms (or groups of atoms) bind to Carbon,
an asymmetric arrangement occurs. If the two molecules are mirror images,
and cannot be superimposed on each other,

A

Enantiomers:

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55
Q
A

Effective enantiomer

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56
Q
A

Ineffective enantiomer

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57
Q

A few chemical groups are very important in biological molecules
Seven functional groups
that are most important for
biological molecules are:
Carbon frequently forms covalent bonds with

A

H, O, and N. infinite varieties of molecules that can form

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58
Q

Seven functional groups
that are most important for
biological molecules are: hydroxyl

A

hydroxyl, OH

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59
Q

Seven functional groups
that are most important for
biological molecules are: carbonyl

A

carbonyl, C=O

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60
Q

Seven functional groups
that are most important for
biological molecules are: Carboxyl

A

Carboxyl, COOH, (contains carbonyl groups)

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61
Q

Seven functional groups
that are most important for
biological molecules are: AMINO

A

AMINO, NH2 (NH3+) (Ionized form)

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62
Q

Seven functional groups
that are most important for
biological molecules are: sulfhydryl

A

sulfhydryl, SH

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63
Q

Seven functional groups
that are most important for
biological molecules are: phosphate

A

phosphate, PO43- (found in DNA/ Nucleac acids_)

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64
Q

Seven functional groups
that are most important for
biological molecules are: methyl

A

Methyl, CH3

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65
Q

large molecules that make up living cells:

A

Macromolecules

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65
Q

Carbohydrates
Proteins
Nucleic acids

A

addition of small monomeric subunits, to make polymers

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66
Q

Polymers form via

A

dehydration reactions

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67
Q

Dehydration

A

Removes a water molecule forming a new bond

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68
Q

Polymers are disassembled into monomers by the
reverse reaction, or:

A

hydrolysis.

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69
Q

Hydrolysis

A

adds a water
molecule, breaking a bond, enzymes are involved to catalyze reaction

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70
Q

Adding different monomers together allows for the formation of polymers with:

A

distinct properties, proteins are made from an “alphabet” of 20 different amino acids. Many
proteins are over 200 amino acids long; the potential for variety is huge.

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71
Q

added to build disaccharides and polysaccharides

A

Monosaccharides

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72
Q

Most common biological monosaccharides contain
either_______ Carbon atoms.

A

3, 5, or 6

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73
Q

Molecular formulas
for monosaccharides
are usually multiples
of

A

CH2O

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74
Q
A

Contains 3 carbons

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75
Q
A

Contains 5 carbons

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76
Q
A

Contains 6 carbons

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77
Q

glucose, fructose contain:

A

structural isomers.

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78
Q

Monosaccharide names end with___ and can be grouped into general
categories based on the_____

A

“-ose”, number of Carbons. e.g., trioses, pentoses, hexoses.

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79
Q

Simple monosaccharides have a
linear structure with a______ and multiple_____.

A

carbonyl group
(C=O), hydroxyl groups, OH.

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80
Q

Glucose is:

A

Hexose

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81
Q

Many monosaccharides change dynamically between

A

linear molecules and and rings.

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82
Q

Glucose: chemical equilibrium between linear and ring structures greatly
favors

A

ring formation. Only about 6% of molecules are in the linear form.

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83
Q

Monosaccharides like glucose are a major_____. Cells can
extract energy from glucose via_______. In addition, the _______ that are broken down can be, reused to form other molecules like _________.

A

Nutrient for cells, Cellular respiration, carbon from sugars, fats and proteins

84
Q

Disaccharide forms when a_______ reaction joins two
monosaccharides

A

dehyration

85
Q

What glucose ring is this?

A

Alpha Glucose

86
Q

What glucose ring is this?

A

Beta glucose

87
Q

Amylopectin is a
branched starch. It
branches via_____. The structure of
amylopectin is not as_______

A

alpha 1-6
linkages, helical because of the
branching of the chain.

87
Q

Starch: glucose polymers, each monomer is joined by _______ like ______, with all monomers in
the______A simple starch_______ is _________.

A

1-4 glycosidic linkages, maltose, alpha configuration, amylose, unbranched and helical

88
Q

What starch is this?

A

Amylopectin, with alpha 1-6 linkage

89
Q

What starch is this?

A

Amylose with alpha 1-4 linkage

90
Q

_______ Animals store glucose in this polysaccharide form, which is
structurally similar to_________ But with a more frequent _________.

A

Glycogen, Amylopectin, alpha 1-6 linkage.

91
Q

Cellulose: Like starch, it is a ________but the
covalent 1-4 linkages involve the_______ of glucose rings.

A

Polymer of Glucose, beta form

92
Q

Cellulose forms______ that ______ It is _______ because some ____________ between different polymers lying________.

A

straight polymers, never branch, very strong, OH groups are free to hydrogen-bond, parallel

93
Q

What structural polysaccharide is this? And What linkage?

A

Cellulose, Beta 1-4 linkage,

94
Q

This is a structural polysaccharide used by arthropods (insects,
spiders, crustaceans), to build their exoskeletons.

A

Chitin

95
Q

What is in the blue circle

A

Acetyl amine group. this allows for increased hydrogen
bonding between adjacent polymers,
giving chitin increased strength.

96
Q

Chitin contains

A

N-acetylglucosamine monomers,
a derivative of glucose (2-(acetylamino)-2-deoxy-D-glucose)

97
Q

Lipids are_____ because they consist mostly of______ which are,______

A

hydrophobic, hydrocarbons, nonpolar

98
Q

Lipids Classes:

A

Fats, phospholipids and steroids

99
Q

Fats are not_______ but they are built from_____________ that
are added by_________

A

polymers, monomers, dehydration reactions

100
Q

What is this?

A

Glycerol, an alcohol. And each of the three C’s has an OH group

101
Q

A fatty acid has a long chain of____with
a____ on the end.

A

16-18 carbons, carboxyl group

102
Q

In a fat ____ fatty acids are joined to_____ by an ___________. creating a ________ or ____________.

A

three, glycerol, ester linkage, triacylglycerol, triglyceride

103
Q

Fatty acids _____ and the
number and location of_______

A

vary in length, double bonds

104
Q

Saturated fatty acids do not
have

A

double bonds

105
Q

If no double bonds exist between Cs of a chain,
and all Cs are bonded to ____ then it is saturated
with ______ and thus a saturated fat.

A

H, Hydrogen,

106
Q

true or false, saturated fats are solid in room temperature

A

true

107
Q

Unsaturated fatty acids have one or more ______

A

double bonds

108
Q

Plant fats and fish fats are usually _________

A

unsaturated.

109
Q

Cis double bond causes______

A

bending

110
Q

True or False unsaturated fats are liquid at room temperature

A

True

111
Q

Major function of fat is _______ but it can also serve
as_____.

A

energy storage, insulation

112
Q
  • Humans and other mammals store their fat in
A

adipose cell

113
Q

Adipose tissue cushions________________

A

vital organs and insulates the body

114
Q

A diet rich in saturated fats may contribute to

A

cardiovascular disease

115
Q

may contribute more than saturated fats to
cardiovascular disease

A

Trans fats

116
Q

they are unsaturated fats
-vast majority consumed by humans are
produced by the food processing industry

A

What are “trans” fats?

117
Q

Finish

A

Saturated by adding H atoms

118
Q

Make plant oils solid at room temp
Can be used as a butter substitute
BUT, the process also creates a lot of trans fat as a by-product

A

Process of making Trans fat

119
Q

= two fatty acids and a
phosphate group attached to glycerol

A

Phospholipid

120
Q

in phospholipids Phosphate group
is

A

hydrophilic

121
Q

in phospholipids the Two fatty
acid tails are

A

hydrophobic

122
Q

Phospholipids are

A

amphipathic molecules

123
Q

Because of their amphipathic nature, when phospholipids are
added to water, they can

A

rearrange into various structures

124
Q

What phospholipid structure is this?

A

Micelle

125
Q

What phospholipid structure is this?

A

Lipid bi layer

126
Q

What phospholipid structure is this?

A

Liposome

127
Q

lipids with a carbon skeleton consisting of
four fused rings

A

Steroids

128
Q

provides strength and flexibility to animal cell membranes

A

Cholesterol- a steroid

129
Q

Although cholesterol is essential in animals, high levels in blood may
contribute to

A

cardiovascular disease

130
Q

Proteins are involved in

A

every biological task

131
Q

Proteins are polymers of

A

amino acids

132
Q

Proteins vary extensively

A

in their structure

133
Q

What is this structure?

A

Structure of an amino acid

134
Q

Amino acids can exist as different enantiomers,
but all proteins use

A

L-enantiomers.

135
Q

What amino acid groups are they?

A

Non polar side chain; hydrophobic

136
Q

What amino acid groups are they?

A

Polar side chains: Hydrophillic

137
Q

What amino acid groups are they?

A

Electrically charged side chains; hydrophillic, Acidic (Negatively charged)

138
Q

What amino acid groups are they?

A

Electrically charged side chains; hydrophillic, Basic (Positively charged)

139
Q

Amino Acids are
linked by

A

peptide bonds

140
Q

A polypeptide is
a polymer of

A

amino acids

141
Q

Four levels of protein structure:

A

Primary, Secondary, Tertiary, Quaternary

142
Q

Primary protein structure:

A

the linear sequence of amino acids.

143
Q

NH3+-Ala-Lys-Arg-Arg-Asn-Met- …. –COO-
NH3+-Met-His-Ser-Ala-Gly-Ala- …. –COO-

A

The order of the amino acids in the chain, Length can vary, (Longest chain in our bodies known as titan)

144
Q

Polypeptides have an_____ and a ______ and they can be composed of a few to more than a thousand_______

A

NH3+ (amino) end, COO- (carboxyl) end, monomers

145
Q

Primary (1o) structure is

A

determined by inherited genetic information.

146
Q

Secondary (2o) structure = the formation of ______
Due to ______ between the ________ and the_________.

A

a-helices or b- pleated sheets, hydrogen bonding, O of carbonyl group, H of the amino group.

147
Q

Depending on how the amino acids line up

A

different structures will form.

148
Q

What formation is this? How does it bond?

A

Alpha helix secondary formation, hydrogen comes from the nitrogen in the core element.

149
Q

What formation is this? How does it bond?

A

b-pleated sheet, forms when peptide sequences lie next to each other in antiparallel orientation (shown here) or parallel orientation

150
Q

Tertiary (3o) structure the arrangement of the _______ due to interactions________ that gives the protein its distinctive shape.

A

Peptide chain, between R groups,

151
Q

What structure is this?

A

Tertiary (3o) structure, Transthyretin polypeptide

152
Q

label the interactions that are involved when forming tertiary proteins structures distinct folding shapes

A
  1. Hydrogen bonds

2.hydrophobic interactions (pockets that
exclude water and push other amino acids to the outside), van der Waals interactions

3.disulphide bonds (a type of covalent bond between two S atoms from two
different side chains (e.g., two cysteines).

4.ionic bonds

153
Q

Some proteins also exhibit Quaternary (4º) structure_______________________

A

results from the aggregation of two or more polypeptide subunits.

154
Q

what Quaternary (4º) structure is this?

A

Transthyretin
( with 4 identical polypeptides) (builds the final protein with more than 1 polypeptide in the final structure)

155
Q

what Quaternary (4º) structure is this?

A

Hemoglobin with
(2 a and 2 b subunits)

Hemoglobin
Protein
(carries O2 in blood)

156
Q

A change in primary structure can affect a protein’s _______

A

function

157
Q

One form of sickle-cell anemia results from an_________ substitution in hemoglobin

A

amino acid

158
Q

What determines protein structure?
In addition to primary structure__________

A

physical and
chemical conditions can affect structure

159
Q

What determines protein structure? Alterations in __________

A

pH, salt concentration,
temperature, or other environmental factors
can cause a protein to unravel

160
Q

Loss of a protein’s native structure is
called

A

denaturation

161
Q

A denatured protein is _______

A

biologically
inactive.

162
Q

Most proteins probably go through

A

several stages on their
way to a stable, properly folded structure

163
Q

Diseases such as __________________________are associated with misfolded proteins

A

Alzheimer’s, Parkinson’s, and “Mad cow
disease”

164
Q

proteins that assist proper folding of
other proteins

A

Chaperonins

165
Q

A specific protein may or may not require a chaperonin to assist its folding.
Regardless

A

proteins are not functional until they are completely folded.

166
Q

steps of chaperonin actions

A
  1. un unfolded polypeptide enters the cylinder from one end
  2. the cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding polypeptide

3.the cap comes off and the properly folded protein is released

167
Q

Nucleic acids

A

Coded information that cells can transmit to future generations
and the messages that determine protein production.

168
Q

Nucleic acids
There are two types:

A

Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)

169
Q

Nucleic acids, Each polynucleotide is made of
monomers called _______

A

nucleotides

170
Q

label the Nucleic acid

A
  1. 5’ end, sugar-phosphate (on blue background)
  2. 3’ end, polynucleotide, or nucleic acid
171
Q

A nucleotide consists of 3 different molecules joined together

A
  1. phosphate
  2. 5 carbon
    sugar
  3. nitrogenous
    base
172
Q

what is this?

A

nucleotide

173
Q

what is this?

A

nucleoside

174
Q

In _______the sugar is ribose

A

Ribonucleic acid (RNA)

175
Q

In________ the sugar is deoxyribose

A

Deoxyribonucleic acid (DNA)

176
Q

Features of a Nucleotide:

A
  1. 5′ C- attaches to phosphate group
    “five-prime phosphate”
  2. 1′ C - attaches to the base
  3. 2′ C- OH in RNA “two-prime OH”
    2′ C- H in DNA

4.3′ C - OH important for polymer formation:
“three-prime OH

  1. The Carbon atoms in the ribose sugar are numbered with a prime to
    distinguish them from the Carbons in the nitrogenous base ring.
177
Q

Two types of nitrogenous bases:

A
  1. Pyrimidines
  2. Purines
178
Q

What nitrogenous bases is this?

A

Pyrimidines
(single 6-sided ring)

  1. Cytosine
  2. Thymine
  3. Uracil
179
Q

What nitrogenous bases is this?

A

Purines
(6- and 5-sided rings fused)

  1. Adenine
  2. Guanine
180
Q

Nucleotide monomers can
be added together to form______ VIA __________

A

nucleic acid polymers, a
dehydration reaction

181
Q

RNA
synthesis

A

1.A new nucleotide
gets added to the
free 3′ OH

2.Extra detail: The incoming
nucleotide is a nucleotide
triphosphate, but two phosphates
get removed when it gets added
(more about that later in course)

182
Q

label the polynucleotide chain

A
  1. Phosphate group at this 5′ end
  2. Sugar-phosphate
    backbone
  3. Covalent bond formed is an ester bond
  4. The linkage between nucleotides
    is a phosphodiester linkage
  5. OH group at this 3′ end
183
Q

Structure of DNA- DNA molecules have two______ spiraling
around an imaginary axis,
forming a _______

A

polynucleotides, double helix

184
Q

Structure of DNA- DNA double helix:
two backbones run in _______, an arrangement referred to as______.

A

opposite
5′→3′ directions from each other, antiparallel

185
Q

Structure of DNA - Complementary base pairing- DNA bases pair by ___________

A

hydrogen bonding:

186
Q
A
187
Q

please label this diagram.

A
  1. sugar-phosphate backbones
  2. hydrogen bonds
  3. base pair joined by hydrogen bonding
188
Q

The Structure of RNA- RNA molecules are usually a _________.

A

polynucleotide chain

189
Q

The Structure of RNA- complementary base-pairing
can occur between RNA and:

A

DNA
- other RNAs
- itself

190
Q
A

thymine is only in DNA

191
Q

The Structure of RNA -adenine (A) can pair with

A

uracil (U),

192
Q

The Structure of RNA - guanine (G) can pair with

A

cytosine (C)

193
Q

please label the diagram.

A

base pair joined by hydrogen bonding

194
Q

Nucleic acids - DNA:

A

stores hereditary information
transmits information to cell descendants

195
Q

Nucleic acids - mRNA:

A

(messenger RNA) transmits information within the cell

196
Q

Nucleic acids- please label the diagram.

A
  1. DNA
  2. mRNA
  3. Protein
197
Q

Nucleic acids - please label the diagram.

A
  1. Synthesis of mRNA in the nucleus
  2. Movement of mRNA into cytoplasm via nuclear pore
  3. Synthesis of protein using information carried on mRNA
198
Q

DNA nomenclature: dGMP

A

Sugar- Deoxyribose
Base- Guanine
Nucleoside- Deoxyguanosine
Nucleotide- Deoxyguanosine MP

Nucleotide
abbreviation- dGMP

199
Q

DNA nomenclature: dAMP

A

Sugar- Deoxyribose
Base- Adenine
Nucleoside- Deoxyadenosine
Nucleotide- Deoxyadenosine MP

Nucleotide
abbreviation- dAMP

200
Q

DNA nomenclature: dCMP

A

Sugar- Deoxyribose
Base- Cytosine
Nucleoside- Deoxycytidine
Nucleotide- Deoxycytidine MP

Nucleotide
abbreviation- dCMP

201
Q

DNA nomenclature: dTMP

A

Sugar- Deoxyribose
Base- Thymine
Nucleoside- Deoxythymidine
Nucleotide- Deoxythymidine MP

Nucleotide
abbreviation- dTMP

202
Q

RNA nomenclature: GMP

A

Sugar- Ribose
Base- Guanine
Nucleoside- Guanosine
Nucleotide- Guanosine MP

Nucleotide
abbreviation- GMP

203
Q

RNA nomenclature: CMP

A

Sugar- Ribose
Base- Cytosine
Nucleoside- Cytidine
Nucleotide- Cytidine MP

Nucleotide
abbreviation- CMP

204
Q

RNA nomenclature: AMP

A

Sugar- Ribose
Base- Adenine
Nucleoside- Adenosine
Nucleotide- Adenosine MP

Nucleotide
abbreviation- AMP

205
Q

RNA nomenclature: UMP

A

Sugar- Ribose
Base- Uracil
Nucleoside- Uridine
Nucleotide- Uridine MP

Nucleotide
abbreviation- UMP

206
Q

Nucleotides also can have

A

di- or tri-phosphates attached:

207
Q

MP =

A

monophosphate

BIOL 107 (14 decks)

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