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Content Review > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

Amino acids contain which two functional groups

A

amino group (-NH2) and carboxyl group (-COOH)

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2
Q

For all amino acids, the alpha carbon is chiral, except for ______

A

glycine

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3
Q

Central dogma is that ____ makes __________ which makes ___________

A

DNA, RNA, Protein

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4
Q

Reverse transcription is…

A

the flow of information from RNA to DNA via reverse transcriptase (generates cDNA from an RNA template), used for retroviruses

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5
Q

tRNA and rRNA are referred to as

A

ncRNA (noncoding RNA), they are not used in protein synthesis

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6
Q

Peptide bonds are formed by the nucleophilic addition-elimination reaction between

A

-the carboxyl group of one AA and the amino group of the other AA

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7
Q

There IS/IS NOT much rotation around a peptide bond

A

IS NOT

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8
Q

The amino ground at the end of a polypeptide is known as the

A

N Terminal

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9
Q

Breaking a peptide bond occurs through

A

Hydrolysis

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10
Q

Put a polypeptide chain in with a strong acid and some heat and you will get

A

The cleaved peptide bonds

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11
Q

Proteases are used in

A

cleaving peptide bonds in a very specific spot

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12
Q

Histidines pka is

A

6.5

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13
Q

If the pH is less than the pKA the AA will exist in a

A

protonated form

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14
Q

If the pH is more than the pKa, the AA will exist in a

A

deprotonated form

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15
Q

Glycine and Proline are known as ______ ______ _____

A

Alpha Helix Breakers

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16
Q

Antioxidants are found IN the cell, and therefore, the inner cell would favor a _____ environment

A

reducing (H’s are present)

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16
Q

What happens if you shoot plane polarized light at a chiral carbon?

A

It would rotate that light

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17
Q

Mirror image molecules that are not superimposable (cannot slide it over and have it be the same)

A

enantiomers

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18
Q

In an L-amino acid, the amino group is to which side of the chiral carbon in a fischer projection?

A

Left (L for left)

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19
Q

What form of amino acid is the only kind you will find in the human body?

A

L- Amino Acid

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20
Q

What is called when an amino acid is at a neutral state?

A

Isoelectric point

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21
Q

When a molecule has both a positive and a negative charge present, this is known as

A

a zwitterion

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22
Q

On average, what is the pKa of the amino group?

A

9

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23
Q

On average, what is the pKa of the carboxylic acid group?

A

2

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24
Q

Which amino acids have alkyl groups as side chains?

A

Glycine
Alanine
Valine
Methionine
Leucine
Isoleucine
Proline

*all nonpolar, hydrophobic

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25
Q

Which amino acids have aromatic groups as side chains?

A

Phenylalanine
Tryptophan

*all nonpolar, hydrophobic

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26
Q

Which amino acids have neutral side chains?

A

Serine
Threonine
Asparagine
Glutamine
Cysteine
Tyrosine

*all are polar, and these AA all contain a sulfur or oxygen atom which likes to hog the electrons to create a localized negative charge, but with a positive charge over the rest of the side chain, hence creating a neutral atom

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27
Q

Which amino acids are considered “Acidic”

A

Aspartic Acid
Glutamic Acid

  • both are polar, hydrophilic, if they have donated their hydrogens, then they are aspartate and glutamate
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28
Q

Which amino acids are considered “basic”?

A

Histidine
Lysine
Arginine

*they all have nitrogen atoms, and nitrogen is a very willing proton acceptor, and therefore that is why these ones are basic

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29
Q

Amyloid is

A

clumps of misfolded proteins that can interfere with the neurons ability to send messages

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30
Q

The secondary structure of protein folding is determined by…

A

backbone structures (specifically Hydrogen bonds)
-think alpha helix and beta sheet

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31
Q

How does a tertiary protein structure remain intact and maintain conformational stability?

A

vanderwaals, hydrophobic packing and disulfide bridges

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32
Q

denaturation disrupts what structures of protein folding?

A

secondary, tertiary, and quartenary

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33
Q

This type of reaction is the breakdown of a single compound into two or more simpler substances

A

A decomposition reaction (i.e. AB = A + B)

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34
Q

What is the direction in which mRNA is read?

A

5’ —> 3’

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35
Q

A negative sense genome (CAN or CANNOT) be used directly for translation

A

Cannot (it must first be transcribed)

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36
Q

A bronsted lowry base is

A

a proton acceptor

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37
Q

a bronsted lowry acid is

A

a proton donor

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38
Q

a lewis base is

A

an electron pair donor

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39
Q

a lewis acid is

A

an electron pair acceptor

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40
Q

A right shift on the hemoglobin/oxygen saturation curve is signified with an (increased or decreased) Hb-O2 affinity?

A

decreased, marked by higher CO2 and higher acidity, and temperature. This shift is also consistent with higher levels of 2-3BPG, which allows the release of oxygen

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41
Q

weak acids (do/do not) readily give away their protons

A

do not, they stay mostly protonated

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42
Q

a strong acid will have a Ka > or < than 1?

A

> > 1

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43
Q

a weak acid will have a Ka < or > than 1?

A

&laquo_space;1

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44
Q

This type of reaction is when an element undergoes both oxidationa nd reduction in the same reaction

A

Disproportionation

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45
Q

The greater the value of ( rate constant, k), the quicker the rate of reaction.

A
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46
Q

nickel tags are associated with which amino acid

A

histidine tags

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47
Q

Which amino acids are aromatic?

A

Tryptophan
Tyrosine
Phenylalanine

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48
Q

What are cytochrome p450 enzymes?

A

membrane bound proteins that enable oxidation reactions, also knonw as monooxygenase enzymes

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49
Q

When an electron moves to a higher energy state, a photon is …

A

absorbed

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50
Q

When an electron moves to a lower energy state, a photon is…

A

emitted

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51
Q

This chromatography technique is used to separate charged biomolecules (AA, proteins, nucleotides)

A

Ion Exchange Chromtography

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52
Q

In using Ion exchange chromatography, if the resin is postively charged, what charged proteins will bind, and what charged proteins will pass through

A

(-) proteins will bind, allowing (+) proteins to pass through

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53
Q

In size exclusion chomatography, which size molecules will pass through faster?

A

larger ones, since the small ones will go through the beads, whereas the large ones will go around.

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54
Q

This type of chromatography is related to how molecules will bind specifically to a binding partner (think: enzyme/substrate, antibody/antigen)

A

Affinity chromatography

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55
Q

A Nuclear localization signal/sequence is an amino acid sequence that …

A

tags a protein for transport into the nucleus

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56
Q

A signal sequence is a speciific amino acid sequence that …

A

directs proteins in translation to the rough ER & secretory pathway

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57
Q

Negative gene regulation controls the production of genes by

A

turning them off

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58
Q

The method of Flow Cytomtery is one where

A

single cells are stained for certain protein markers using specific antibodies (w/ flouresecene)- emitted light is measured, and we then can see cell size, and how many cells expres the protein markers

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59
Q

Immunohistochemistry is a lab technique that is used

A

uses an antibody to detect a specific protein and measure its expression

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60
Q

In Situ Hybridization is a lab technique that is used

A

to study gene expression in a tissue or embryo; this process can detect where transcripts are expressed

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61
Q

the average weight of an amino acid is

A

110 dA

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62
Q

cytochrome C (a component of the mitochrondria attached to the ETC) is often a driver of…

A

apoptosis

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63
Q

What is a Thymine Dimer?

A

When a Thymine base forms a covalent bond with another Thymine base d/t UV light damage. This can then lead to replication issues

64
Q

Calcitonin is produced (location)

A

the thyroid gland

65
Q

Though oxyocin is secreted by the pituitary gland, it is produced by the _____

A

hypothalamus

66
Q

Surfactant helps to (increase/decrease) surface tension of alveoli

A

decrease the surface tension

67
Q

During inhalation the diaphragm (contracts/relaxes)

A

contracts

68
Q

During inhalation, the volume of the thoracic cavity (increases/decreases)

A

increases, therefore pressure decreases

69
Q

W (watt) is =

A

Joules/second

70
Q

V (volt) is =

A

Joule/ Coloumb

71
Q

A (amp) is =

A

Coloumb/ second

72
Q

____ is the term used to describe the total heat content of a system

A

Enthalpy

73
Q

How does a dielectric impact capacitance in a circuit?

A

It partially decreases the net field created by the capacitor, and the potential difference across it

74
Q

If the dielectric has a high permitivity

A

it INCREASES the capacitance for any given voltage

75
Q

A dielectric interrupts a circuit, and can also be known as

A

an insulator

76
Q

The total capacitance of capacitors in series is equal to the

A

sum of the inverse of the individual capacitors

77
Q

The capacitance of a single parallel plate capacitor is directly proportional to the

A

surface area of the plates

78
Q

The capacitance of a single parallel plate capacitor is inversely proportional to the

A

distance between the two plates

79
Q

A dielectric can be inserted between two plates and is directly proportional to

A

the capacitance of the capacitor

80
Q

Which of the following is NOT a strong acid?:
A) H2SO4
B) CH3COOH
C) HI
D) HBR

A

B) CH3COOH
Acetic Acid, a weak acid
A is sulfuric acid
C is hydroiodic acid
D is hydrobromic acid

81
Q

List the Strong acids
“So I Brought No Clean Clothes”

A

“So”: Sulfuric Acid (H2SO4)
“I”: HydroIodic Acid (HI)
“Brought”: Hydrobromic Acif (HBr)
“No”: Nitric Acid (HNO3)
“Clean”: Hydrochloric Acid (HCl)
“Clothes”: Perchloric Acid (HCLO4)

82
Q

Describe Pi Stacking interactions

A

A Non-covalent attraction that occurs between pi bonds of aromatic rings

83
Q

How is secondary strucutre of protein held together?

A

Hydrogen bonds
(which create the alpha helix and beta pleated sheets)

84
Q

How is tertiary structure of a protein held together?

A

Side Chain interaction, think hydrogen bonds or dipole interactions, van der waals, and disulfide bridges

85
Q

How is primary structure of a protein held together?

A

Peptide bonds between amino acids

86
Q

Which amino acid makes disulfide birdges?

A

Cysteine

87
Q

The _______ variable is one that you are changing on purpose

A

independent

88
Q

The ________ varibale is one that you are measuring the reponse of

A

dependent

89
Q

Describe the TAID P Method for analyzing graphs/tables

A

T: Title
A: Axes
I: Independent Variables
D: Dependent Variables
P: Patterns

90
Q

Which two amino acids are likely to initroduce kinks and flexibilty into peptide chains

A

Glycine, and proline

91
Q

This technique can amplify small amounts of DNA, very useful in determining cellular mRNA levels

A

PCR (and RT-PCR)

92
Q

This technique measures protein levels in a sample using antibodies

A

Western Blot

93
Q

This technique measures DNA levels

A

Southern Blot

94
Q

This technique measures RNA levels

A

Northern BlotT

95
Q

This technique separates molecules on the basis of size/charge

A

Gel Electrophoresis

96
Q

This technqiue separates denatured proteins on the basis of size

A

SDS-Page

97
Q

This technique separates proteins in their native conformations that allows subunits to remain intact

A

Native gels

98
Q

This technique is used to introduce genetic information into a plasmid for protein expression or genetic manipulation

A

Molecular Cloning

99
Q

If two molecules have the same connectivity, they can/cannot be constitutional isomers

A

they cannot be

100
Q

If molecules were _______, they have equal and opposite rotations (think +40, and -40)

A

enantiomers

101
Q

A racemic mixture is 50% of one ______ and 50% of the other.

A

enationmer. This leads to a specific rotation of 0.

102
Q

Conformational isomers will always have the same specific rotation becaues they are forms of the

A

same compound

103
Q

________ differ in the magnitude of their specific rotations

A

diastereomers

104
Q

The main function of the loop of henle is to

A

reabsorb water and NaCl

105
Q

What occurs during prophase?

A

The chromatin condenses

106
Q

What occurs during M Phase?

A

Chromsomes are segregated into two nuclei and metaphase, anaphase, and telophase occur

107
Q

Cytokinesis (of the division of the cell membrane) yields

A

two daughter cells

108
Q

It is possible to separate diastereomers or enantiomers?

A

Diastereomers (enantiomers cannot be separated from each other)

109
Q

A Transverse (T) tubule is a channel formed within the sarcolemma that

A

brings the depolarized current nearer the sarcoplasmic reticulum (which then induces Ca2+ to be released

110
Q

After Ca2+ is released in muscular contraction, then what occurs?

A

Ca2+ binds troponin, which then allows the actin and myosin filaments of the sarcomere to slide across each other (which shortens the sarcomere) inducing the muscle contraction

111
Q

How does an enzyme function to lower the activation energy

A

They faciliate a more stable transition state, and this more stabilized state leads to a lower actvivation energy

112
Q

How are parathyroid hormone and bone remodeling related?

A

low calcium stimulates PTH, which causes increased activity of osteroclasts

113
Q

How does high amounts of calcium circulating affect hormone levels?

A

high calcium stimulates calcitonin, which causes decreased activity of osteoclasts

114
Q

The boiling point is defined as the point at which the vapor pressure of a solution is equal to the

A

atmospheric pressure

115
Q

What occurs during Beta-minus decay?

A

a neutron is converted to a proton as an electron is emitted

116
Q

Mass spectrometry can be used to make clear…

A

the structure of a compound

117
Q

Why does hydrogen bonding increase the boiling point of a compound?

A

It takes more energy to break the van der waals and hydrogen bond forces

118
Q

Nitrogen, in its neutral state, has how many bonds/lone pairs?

A

3 bonds, and a lone pair of electrons

119
Q

Oxygen, in its neutral state, has how many bonds/lone pairs?

A

2 bonds, and 2 lone pair of electrons

120
Q

A stereocenter carbon means…

A

it must be sp3 hybridized and bonded to 4 different groups

121
Q

τ = rFsin(θ) is the equation for

A

torque

122
Q

Ka is the acid disassociation constant, and is found with the equation:

A

[H+][A−]/[HA]

123
Q

The smaller the Pka value, the _____ the acid

A

stronger

124
Q

1 µg is equal to

A

1 x 10-6 g

125
Q

According to Newtons Third Law,

A

Every force has an equal and opposite force (think: when earth exerts a gravitational force on your body, your body is also exerting a gravitational foce on the earth)

126
Q

N2 (diatomic Nitrogen) is what type of gas

A

an inert gas (also means a noble gas)- this means that it is not very reactive

127
Q

Is C6H6 or CH a empirical formula?

A

CH (empirical formula is the lowest common denominator among the molecules at the correct ratios)

128
Q

Power is measured in…

A

watts (W)

129
Q

ACcording to Ohms Law, P=

A

IV or V^2/R

130
Q

PCC could be used to

A

oxidize a primary alcohol to an aldehyde (and a secondary alcohol to a ketone)

131
Q

LiAIH4 (a strong reducing agent) could redule a carboxylic acid to a

A

alcohol

132
Q

Kinases and phosphorylases can be grouped into the broader enzyme category of

A

transferases

133
Q

Referring to IR Spectroscopy, a carbonyl spike will be at what number?

A

1700, and it will be a sharp spike

134
Q

Referring to IR Spectroscopy, an alcohol spike will be at what number?

A

3,000, and it will be broad

135
Q

In the electron transport chain, electrons are passed from a species with a ____- positive reduction potential to a species with a _____-positive reduction potential

A

less-positive to more-positive

136
Q

ΔG° < 0 corresponds to a Keq …

A

Keq > 1

137
Q

In regard to light hitting water, how are the angle of reflection and the angle of incidence related?

A

They are always the same (angle of refraction will differ)

138
Q

The more negative the RSE of an element (relative stabilization energy), the more/less stable the compound is

A

more stable (more negative RSE= more stable compound)

139
Q

An electrolytic cell allows for this type of spontaneous reaction

A

redox

140
Q

If all electrons of a molecule are paired, what is the resulting magnetic outcome of the molecule?

A

it is then “diamagnetic”, and the paired electrons will be repelled by the magnetic field

141
Q

If electrons in a molecular orbital are left unpaired, what is the resulting magnetic outcome of the molecule?

A

it is then “paramagnetic”, and the unpaired electrons will be attracted to an external magnetic field

142
Q

In Beta minus decay, the atomic number is _____ by 1

A

increased

143
Q

In Beta plus decay, the atomic number is ______ by 1

A

decreased

144
Q

In alpha decay, the atomic number is _____ by 2, and the atomic mass is _____ by 4

A

decreased, decreased (-2 neutrons, -2 protons)

145
Q

In gamma decay, the atomic number is ____

A

unaffected

146
Q

Electronegativity is the tendency of an atom to (attract / repel) electrons within a bond

A

attract electrons

147
Q

Ionization energy is the energy that that is required to

A

remove an electron from an atom

148
Q

L-DOPA is a precursor to …

A

catecholamines [dopamine, norepinephrine, epinephrine]

149
Q

When two complementary single stranded strands bind together to form a double stranded molecule, this is known as

A

hybridization

150
Q

How many arms of the chromosome does a double crossover event affect?

A

Just one of the arms

151
Q

The Hardy- Weinberg equation is

A

AA + 2Aa + aa = 1

152
Q

_________ structures are those structures that evolved independently to carry out the same function

A

analogous

153
Q

________structures are those that have a similar evolutionary history, arising from the same source, even if they now have separate functions

A

Homologous

154
Q

Sucrose, lactose, and maltose are _______

A

disaccharides

155
Q

Galactose is a monosaccharide or a disaccharide?

A

monosaccharides

156
Q

_____ is a term used in conditioning that refers to small steps being reinforced in order to achieve some larger behavior

A

Shaping

157
Q
A

Content Review (8 decks)

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