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Biochemistry > Exam 1 > Flashcards

Exam 1 Flashcards

1
Q

what is biochemistry

A

study of molecules of life and their chemical reactions in living systems

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2
Q

Cellular architecture falls into two categories

A

Prokaryotes
Eukaryotes

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3
Q

Prokaryote

A

single-celled
includes bacteria, eubacteria, archaea, and cyanobacteria

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4
Q

Eukaryote

A

Contain a well defined nucleus surrounded by a nuclear membrane
can be single celled or multicelled
Mosaic character

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5
Q

All living things make use of the same types of biomolecules, and use energy to make them. What is the result of this

A

all living things can be studies using the methods of biochemistry

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6
Q

What are the most common elements in the cell

A

Carbon
Oxygen
Hydrogen
Nitrogen
(phosphorus)

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7
Q

Biomolecules are ___ based

A

carbon

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8
Q

Covalent bonds

A

the glue that holds compounds together

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9
Q

C

A

carbon

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10
Q

CO

A

carbon monoxide

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11
Q

CO2

A

Carbon Dioxide

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12
Q

H2CO3

A

Carbonic Acid
product of CO2 and H2O

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13
Q

How many bonds does carbon make

A

4

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14
Q

How many bonds does H make

A

1

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15
Q

How many bonds does O make

A

2

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16
Q

How many bonds does S make

A

2

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17
Q

How many bonds does N make

A

3

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18
Q

How many bonds does P make

A

5

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19
Q

Chirality

A

Alpha carbon has 4 different groups attached

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20
Q

Large biomolecules are generally polymers of

A

simpler biomolecular units
monomers

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21
Q

Monomeric biomolecules

A

Nucleotide
Amino acid
Carbohydrate
Acetyl group

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22
Q

Biopolymers

A

Nucleic acids/DNA/RNA
Proteins
Polysaccharides
Lipids

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23
Q

Amino acids contain

A

an amino group
a carboxylic acid group
a side chain

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24
Q

Amino acids are the monomers of

A

Proteins

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25
Q

Carbs are a monomer of

A

Polysaccharides

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26
Q

Nucleotides are monomer of

A

Nucleic Acids
DNA
RNA

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27
Q

Acetyl group is monomer of

A

Lipids

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28
Q

ATP contains

A

Triphosphate
Ribose sugar
Nitrogen base-Adenine

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29
Q

A single monomer in a polymer is called a

A

residue

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30
Q

Functions of proteins

A

Major- Enable metabolic reactions
support cellular structures
Minor- store energy

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31
Q

Functions of Nucleic Acids

A

Major-encode information
Minor- enable metabolic reactions
support cellular structures

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32
Q

Functions of Polysaccharides and Lipids

A

Major- Store energy
Support cellular structures

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33
Q

Macromolecules

A

a molecule with a large number of atoms

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34
Q

Information is passed on from one molecule to another by

A

Sequence of DNA-> RNA->Protein->3D shape of protein molecule->Function of the proteins

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35
Q

Where do cells get their energy

A

Light from the sun
Photosynthetic organisms use light energy to make carbs
non-photosynthetic organisms consume these carbs
some archaebacteria us chemical or geothermal energy

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36
Q

Enthalpy

A

the heat content of a system

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37
Q

Entropy

A

a measure of the system’s disorder or randomness

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38
Q

Gibbs free energy

A

a measure of the free energy of a system based on enthalpy and entropy

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39
Q

Low entropy means

A

work is needed to organize
less likely to occur
higher in energy invested

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40
Q

High entropy

A

More likely to occur, favorable
lower in energy

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41
Q

Gibbs free energy equation

A

Change in G= Change in H- T times change in S
H=enthalpy
S=entropy

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42
Q

When change in G is less than 0 (negative)

A

the reaction is spontaneous or exergonic

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43
Q

When change in G is more than 0 (positive)

A

the reaction is nonspontaneous or endergonic

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44
Q

G less than 0 is

A

favorable

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45
Q

Reduction

A

gain of electrons

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46
Q

Oxidation

A

loss of electrons

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47
Q

The most essential nutritional component needed for life

A

water

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48
Q

Why is water important

A

the solvent for biological systems
to understand biochem it is essential to understand water and its interactions

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49
Q

Hydrophilic

A

water loving

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50
Q

examples of hydrophilic compounds

A

Polar
Ionic

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51
Q

Hydrophobic

A

water fearing

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52
Q

Examples of hydrophobic compounds

A

non-polar
oils and fats

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53
Q

water has what type of bonds

A

polar

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54
Q

In polar bonds,

A

electrons are unequally shared, more negative charge found closer to one atom (the more electronegative one. In water it is the Oxygen molecule)

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55
Q

Electronegativity

A

tendency of an atom to attract electrons

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56
Q

Covalent bond examples

A

Non-polar bonds-electrons are shared equally between atoms of the same electronegativity
Polar bonds-Electrons are Not shared equally between atoms of different electronegativity

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57
Q

amphipathic

A

polar on one end and non-polar on the other end

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58
Q

Ionic compounds readily dissolve in water because of the

A

ion-dipole interactions

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59
Q

Non-ionic compounds dissolve in water because of the

A

dipole-dipole interactions

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60
Q

Hydrogen bond

A

a dipole-dipole bond that exists between and electronegative atom and a hydrogen atom

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61
Q

A hydrogen bond is _____

A

non-covalent
weak bond, but strong with lots of them present

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62
Q

Strength of bonds from strongest to weakest

A

Covalent bonds
-OH
-HH
-CH
Non-covalent bonds
hydrogen bond
ion-dipole interactions
hydrophobic interaction
Van der Waals interactions

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63
Q

H bonds provide what to macromolecules while still being _____

A

Organization
weak enough to be readily broken

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64
Q

Which are longer- H bonds or covalent bonds

A

Hydrogen bonds (2) Longer
Covalent bond (1) Shorter

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65
Q

Acid

A

a molecule that behaves as a proton donor which occurs as a result of its ionization

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66
Q

Base

A

a proton acceptor

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67
Q

Strong acid

A

a compound that completely ionizes in aqueous solution

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68
Q

Weak acid

A

a compound that is incompletely ionized in aqueous solution

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69
Q

Water is a ____ acid and a ____ base

A

weak acid and weak base

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70
Q

Kw

A

the ionization constant of water

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71
Q

pH is

A

-log10[H+]

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72
Q

pH is what type of log scale

A

negative

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73
Q

Because the pH scale is logarithmic, a difference of one pH unit is equivalent to

A

a 10-fold difference in [H+]

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74
Q

Something more acidic on the pH scale has

A

more H+

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75
Q

Something more basic on the pH scale has

A

more OH-

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76
Q

Acid dissociation constant (Ka)

A

numerical value for the strength of an acid
[H+][A-] over [HA]

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77
Q

The larger the Ka value the

A

stronger the acid

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78
Q

pKa=

A

-log Ka

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79
Q

Buffer

A

a weak acid whose pH resists change upon addition of either more acid or more base

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80
Q

A buffer consists of

A

a weak acid and its conjugate base

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81
Q

How do buffers resist changes in pH

A

able to resist changes in free H+ by either binding H+ when an acid is added, or releasing H+ when a base is added

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82
Q

The maximum buffering capacity of a buffer is when

A

pKa is equal to the pH, the acid is 50% dissociated
[HA]=[A-]

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83
Q

If pH is below the pKa

A

more protons are on the acid
[HA]>[A-]

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84
Q

If the pH is above pKa

A

more protons are off the acid
[HA]<[A-]

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85
Q

The Henderson-Hasselbalch equation

A

pH=pKa + log of [A-] over [HA]

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86
Q

The Henderson-Hasselbalch equation tells us

A

if the concentration of [A-] is higher than [HA], the pH is higher than the pKa
if the concentration of [A-] is lower than [HA], the pH is lower than the pKa

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87
Q

A buffer is effective in a range of about

A

1 pH unit above or below the pKa of the weak acid

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88
Q

Principle buffer in cells

A

H2PO4-/HPO42-

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89
Q

Buffer in blood

A

H2CO3/HCO3-

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90
Q

Hyperventilation can result in

A

increased blood pH

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91
Q

Hypoventilation can result in

A

decreased blood pH

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92
Q

Carbon dioxide in water is

A

an acid
Carbonic acid

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93
Q

Amino acids are

A

building blocks of proteins
monomers of proteins

94
Q

Most amino acids are _____

A

chiral
are L in proteins

95
Q

What distinguishes one amino acids from another

A

R group

96
Q

There are how many amino acids

A

20
10 essential

97
Q

What is the only non-chiral amino acid

A

Glycine
has two hydrogens

98
Q

Proline is really a ____ since it has a secondary amine

A

an imino acid

99
Q

Classifications of amino acids

A

polar/non-polar
charged/uncharged
acidic/basic
aromatic (has a 6-carbon ring structure)

100
Q

Non-polar amino acids

A

Ala
Val
Leu
Ile
Pro
Phe
Trp
Met

101
Q

Neutral Polar Side chains

A

Ser
Thr
Tyr
Gys
Gln
Asn

102
Q

Acidic Amino Acids

A

Asp
Glu
contain carboxyl groups

103
Q

Basic amino acids

A

Lys
Arg
His
Amine groups

104
Q

All amino acids have at least how many pKas

A

Two

105
Q

Amino group of an amino acid pKa is

A

9.5

106
Q

carboxylic acid group of an amino acid pKa is

A

2

107
Q

when an amino acid is titrated

A

titration curve represents the reaction of each functional group with the hydroxide ion

108
Q

Zwittrion

A

mid point where the amino acid is neutral

109
Q

Many important biological reactions/functions depend on the

A

charge and acid/base properties of proteins

110
Q

Essential amino acid

A

Phenylalanine
valine
tryptophan
threonine
isoleucine
methionine
histidine
arginine
lysine
leucine

111
Q

Peptide bond

A

the special name given to the amide bond between the carboxyl group of one amino acid and the amino group of another amino acid

112
Q

When a peptide bond is formed what is released

A

a water molecule

113
Q

There is little rotation around the peptide bond because

A

it has partial double bond nature

114
Q

peptide bonds are between the carbonyl carbon of the _____ and the N of the _____

A

N-terminal residue
C-terminal residue

115
Q

Peptide

A

realatively short string of amino acid

116
Q

polypeptide or protein

A

longer string of amino acids, often 100 or more

117
Q

N-terminus

A

start, or left end, of a peptide or protein- free amiNo terminus

118
Q

C-terminus

A

end, or right end, of peptide or protein- free Carboxyl terminus

119
Q

Side chains of amino acids contribute most to

A

localized charges on proteins

120
Q

What is the 3-D structure of a protein

A

the final form of a polypeptide chain

121
Q

Why is 3-D structure important

A

form determines function

122
Q

Why is it important to understand ho a protein is formed

A

understanding protein structure allows for understanding of biological processes

123
Q

The final structure of a protein is determined by

A

the amino acid sequence of the protein

124
Q

Primary structure of a protein

A

the amino acid sequence of the protein

125
Q

Secondary structure of a protein

A

the localized arrangement in space of the peptide backbone of a protein

126
Q

Tertiary structure of a protein

A

final 3-D arrangement of all the amino acids

127
Q

Quaternary structure of protein

A

arrangement of separate peptide chains with each other to form an active protein (enzyme)

128
Q

The peptide bond is rigid and does not rotate giving the peptide bond a ____

A

planar configuration

129
Q

Two main types of secondary protein structure

A

alpha-helix
beta-sheet

130
Q

alpha helix

A

polypeptide chain is twisted by the same angle about each of its C atoms

131
Q

The C=O group of one residue will ____ with the N-H group of the 4th amino acid

A

H-bond

132
Q

Amphipathic helix

A

polar on one side, non-polar on the other
common in transmembrane proteins

133
Q

what can disrupt the alpha helix

A

proline
cyclic structure does not allow for rotation of the angle
N in the imino group cannot H bond
terminates the alpha-helix

134
Q

Beta sheet

A

sheet is a straight extension of the polypeptide backbone
H-bonding occurs between neighboring polypeptide chains

135
Q

Beta sheets can be

A

Parallel or Anti-Parallel

136
Q

Parallel

A

both polypeptide chains run in the same direction

137
Q

Antiparalled

A

polypeptide chains run in opposite directions with respect to N and C terminus

138
Q

Tertiary structure of proteins

A

the 3-D arrangement of a protein
the folding of regions of secondary structure
is stabilized by interactions such as H-bonding and disulfide bonds

139
Q

Proteins fall into two categories

A

Globular or Fibrous

140
Q

Globular proteins

A

folding of the peptide backbone to form a spherical shape
most proteins are globular
water soluble
shape allows for amino acids that are far apart in primary structure to be close in tertiary structure

141
Q

Myoglobin

A

primary oxygen storage protein in the muscle tissue

142
Q

Heme group

A

a cyclic organic ring containing iron

143
Q

porphyrin

A

a heme group without Fe

144
Q

Quaternary structure

A

the structure associated with the interaction of multiple polypeptide chains

145
Q

individual polypeptides are termed

A

subunits

146
Q

1 sub unit

A

monomer

147
Q

2 sub unit

A

dimer

148
Q

3 sub unit

A

trimer

149
Q

Example of Quaternary structure

A

Hemoglobin
oxygen transport in the blood, compared to storage of myoglobin

150
Q

Positive cooperativity

A

when O2 molecule is bound it is easier for the next to be bound. Changes in subunit interactions increases affinity for the next O2

151
Q

Allosteric

A

changes in one region affect another region

152
Q

O2 binding curve of myoglobin

A

hyperbolic

153
Q

O2 binding curve of hemoglobin

A

sigmoidal due to cooperativity

154
Q

The Bohr Effect

A

As the pH goes down, O2 affinity for hemoglobin decreases
activity respiring cells create acid, this increases the release of O2 from hemoglobin to these cells

155
Q

Sickle Cell Anemia

A

Mutation of a particular Glutamate to Valine occurs
causes RBC to become oblong in shape

156
Q

Polymers of actins are called

A

microfilaments

157
Q

Fibrous proteins

A

highly elongated proteins with secondary structure as dominant structure

158
Q

Two types of fibrous proteins

A

alpha helix
beta sheet

159
Q

Keratin

A

durable, chemically resistant protein
found in higher vertebrates, hair, wool, horn, nails, hooves

160
Q

All the information needed to correctly fold a protein is contained in the

A

one prime sequence

161
Q

Hydrophobic interactions

A

hydrophobic regions of proteins tend to aggregate and dispel water as with membranes.
inner portion of globular proteins

162
Q

Salt (electrostatic) interactions

A

attractive forces between opposite charges (+ and - charges in R groups, N or C terminus, or metal ligands)
acidic amino acids are attracted to basic amino acids

163
Q

disulfide bonds

A

bonds between sulfurs of two different cysteines

164
Q

Forces involved in protein folding

A

hydrophobic interactions
salt (electrostatic) interactions
hydrogen bonds
disulfide bonds

165
Q

Folding in proteins occurs so that

A

nonpolar hydrophobic side chains tend to be on the inside
polar side chains are on the outside and have access to the aqueous environment

166
Q

Liposomes

A

spherical aggregates of lipids arranged so the polar head groups are in contact with water and nonpolar tails are hidden form water

167
Q

Two layers of a globular protein

A

hydrophilic surface
hydrophobic core

168
Q

Misfolding of proteins plays an important part in neurodegenerative diseases

A

alzheimer’s disease
parkinson’s disease
“Prion Diseases” (Mad cow, etc.)

169
Q

APP

A

amyloid precursor protein
in Alzheimer’s disease it is incorrectly clipped by enzymes, aggregated peptide accumulates over decades, killing neurons

170
Q

PrP

A

Prion protein
in prion diseases the infectious agent

171
Q

Ways to increase the rate of chemical reactions

A

increasing the temperature
increasing the concentrations of the reacting substances
adding a catalyst

172
Q

What is the fastest way to increase the rate of chemical reactions

A

adding a catalyst

173
Q

Enzyme

A

a biological catalyst

174
Q

Catalyst

A

something that speeds up a reaction without being used up (changed)

175
Q

Enzymes are considered

A

proteins

176
Q

Enzymes can increase the rate of a reaction by a factor of

A

10 to the 20th power

177
Q

Most enzymes are proteins but a few are made of

A

RNA (ribozymes)

178
Q

Enzymes contains a specific fraction of the structure where reactions take place, this is called

A

the active site

179
Q

Most enzymes work in what type of conditions

A

mild

180
Q

Many chemical enzymes require

A

extremely high temperatures and pressures for optimal performance

181
Q

Activity of many enzymes are

A

regulated so that the organism can respond to changing conditions or follow genetically determined programs

182
Q

Enzymes selectively recognize proper substrates over

A

other molecules

183
Q

Specificity of enzymes is controlled by

A

enzyme structure
the unique fit of substrate with the enzyme controls the selectivity for substrate and the product yield

184
Q

Functional groups on the active site can

A

distinguish its substrates from among many others that are similar in size and shape

185
Q

Reactions that have an energy barrier to overcome called the

A

activation energy or G degree ++

186
Q

Energy states differ between reactants and products this difference gives us

A

the energy change for that reaction termed the Gibbs standard free energy change or delta G degree

187
Q

Activation energy requires

A

an energy input to start a reaction

188
Q

Enzymes do what to the activation energy

A

lowering it
making the reaction more likely to happen and more favorable
they stabilize the transition state of the reaction

189
Q

A reaction is spontaneous if

A

Delta G degree is negative

190
Q

Delta G degree doesn’t say… and cannot…

A

anything about how fast the reaction will proceed
be altered by a catalyst

191
Q

Delta G degree is negative, reaction is

A

spontaneous

192
Q

Delta G degree is positive, reaction

A

requires external energy input and is not spontaneous

193
Q

The rate of reaction depends on

A

its activation energy

194
Q

Spontaneous

A

characteristic of a reaction or process with a negative free energy change

195
Q

For an enzyme-catalyzed reaction, what must bind to the enzyme

A

substrate

196
Q

The substrate fits in a special pocket of the enzyme called the

A

active site, where the reaction occurs

197
Q

Binding of substrates to the active site is usually

A

non-covalent and reversible

198
Q

Non covalent means

A

H-bonds, ionic bonds, hydrophobic and van der Waals contacts

199
Q

Two models to describe the formation of the enzyme-substrate complex

A

Lock and key
induced fit

200
Q

Lock and key model

A

substrate binds to that portion of the enzyme with a complementary shape

201
Q

Induced fit model

A

binding of the substrate induces a change in the conformation of the enzyme that results in a complementary fit

202
Q

Seven major classifications of enzymes

A

Oxidoreductasis
transferases
hydrolases
lyases
isomerases
ligases
translocases

203
Q

Oxidoreductases

A

enzymes in oxidation-reduction reactions

204
Q

transferases

A

enzymes in transfer of functional groups

205
Q

hydrolases

A

enzymes in hydrolysis reactions

206
Q

lyases

A

enzymes in group elimination to form double bonds

207
Q

isomerases

A

enzymes in isomerization reactions (change the shape of something)

208
Q

Ligases

A

Enzymes in bond formation coupled with ATP hydrolysis

209
Q

Translocases

A

Enzymes in solute transport through the membrane

210
Q

Many enzymes are named

A

after the reaction they catalyze

211
Q

Enzymes often use _____ to aid in catalysis

A

cofactors

212
Q

Two categories of cofactors used by enzymes

A

metal ions
coenzymes- further cut into cosubstrates and prosthetic groups

213
Q

Coenzymes are derived from

A

vitamins

214
Q

Three kinds of chemical catalytic mechanisms used by enzymes

A

Acid-base catalysis
Covalent catalysis
Metal ion catalysis

215
Q

Acid base catalysis

A

a proton is transferred between the enzyme and the substrate

216
Q

Covalent catalysis

A

a covalent bond forms between the catalyst and the substrate during formation of the transition state

217
Q

Metal ion catalysis

A

metal ions mediate oxidation-reduction reactions or promote the reactivity of other groups in the enzyme’s active site through electrostatic effects

218
Q

Amino acids that can be ____ play a role in acid-base catalysis

A

ionized

219
Q

Amino acids that act as covalent catalysts

A

Ser, Tyr
Cys
Lys
His

220
Q

Nucleophile

A

Nucleus seeking atom
slight negative charge
attacks positive charges

221
Q

Electrophile

A

electron seeking atom
has slight positive charge

222
Q

Catalytic triad

A

hydrogen-bonded arrangement of the Asp, His, and Ser residues of chymotrypsin and other serine proteases

223
Q

How does the catalytic triad of chymotrypsin work?

A

Hydrogen-bonded arrangement of Asp, His, and Ser residues
bond cleaved by hydrolysis is between the Ser when the substrate binds to the enzyme
His acts as a base catalysts and abstracts a proton from Ser so the oxygen can act as a covalent catalyst
Asp stabilizes

224
Q

Specifity pocket

A

a cavity on the enzyme surface at the active site that accommodates the residue on the N-terminal side of the scissile peptide bond

225
Q

Rates are measured in

A

units product produced or substrate consumed per time period

226
Q

Unimolecular reaction has a

A

velocity (rate) that is dependent on the concentration of only one substrate

227
Q

Biomolecular reaction has a

A

velocity (rate) that is dependent on two substrate concentrations

228
Q

Km is the

A

concentration of substrate at which half of the enzyme’s active sites are bound to substrate

229
Q

Km measures the

A

affinity of the enzyme for the substrate

230
Q

High Km means

A

low substrate affinity

231
Q

Low Km means

A

high substrate affinity

Biochemistry (14 decks)

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