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MCAT-Biochemistry/Biology Flashcards

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1
Q

What are the four different tissue/cell types?

A

Epithelial
Muscle
Neuronal
Connective

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2
Q

Epithelial tissue is classified according to and ______ of cells

A

Shape and arrangement

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3
Q

Shapes of epithelial cells?

A

Squamous
Cudoidal
Columnar

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4
Q

What are the arrangements of epithelial cells?

A

Simple

Stratified

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5
Q

Do epithelial cells have a high turnover rate?

A

Yes

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6
Q

What are the 3 main types of filaments that make up the cytoskeleton?

A

Microtubules
Microfilaments
Intermediate filaments

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7
Q

What is epithelial tissue

A

Covers the surface of the body which contacts the environment

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8
Q

What is the extra cellular material that separates all connective tissue?

A

Matrix

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9
Q

What is connective tissues function?

A

Supports and connects all other tissues

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10
Q

What are the 3 types of connective tissue cells?

A

Fibroblasts
Mast cells
Macrophages

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11
Q

What are the two types of fibroblast cells?

A

Collagen based

Elastic

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12
Q

Where are mast cells found and what is their function?

A

Near blood vessels and secrete various substances into the blood.

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13
Q

What is the function of macrophages?

A

Specialized in phagocytosis of foreign particles pathogens.

Important in defense against infection.

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14
Q

What are the 5 different types of connective tissue?

A 
Blood and lymph
Bone
Loose connective
Dense connective
Cartilage
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15
Q

What is the function of loose connective tissue?

A

Attaches epithelium to organs

Adipose tissue is an example

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16
Q

What is the function of dense connective tissue?

A

Makes up tendons and ligands.

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17
Q

What is the name for bone cells?

A

Osteocytes

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18
Q

What are the three types of muscle tissue?

A

Skeletal muscle
Cardiac muscle
Smooth muscle

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19
Q

Where is nervous tissue found?

A

Brain and spinal chord

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20
Q

Skeletal muscle has what appearance?

A

Striated

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21
Q

Cardiac muscle has what appearance?

How is it controlled?

A

Striated

Involuntarily

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22
Q

Smooth muscle has what appearance?

How is it controlled?

A

Not striated, smooth

Involuntarily

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23
Q

What do neurons do?

A

Transmit electrical impulses

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24
Q

Glial cells have what function?

What is another name for glial cells?

A

Support, insulate and transport nutrients to neurons

Schwann cells

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25
Q

All cells in the soma have a _________ across all membranes?

A

Electric potential

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26
Q

The intercellular space has what kind of net charge?

A

Negative

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27
Q

The intracellular space has a high sodium or potassium concentration versus the extra cellular space?

A

Potassium

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28
Q

What is the resting potential of cells?

A

-70 mv

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29
Q

What system uses active transport to maintain electrochemical potential of cells?

A

Sodium potassium pump

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30
Q

What type of channels facilitate ion flow in and out of membranes down their concentration gradients?

A

Gated channels

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31
Q

An action potential is followed by what event?

Is the cell excitable during this time?

A

Refractory period

Depends on if it is an absolute or relative refractory period

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32
Q

What are microtubules made of?

A

Tubulin

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33
Q

Which of the three filaments of the cytoskeleton form the mitotic spindle?

A

Microtubules

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34
Q

What are the component proteins of microfilaments?

A

Actin and myosin

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35
Q

The nucleus contains what three structures?

A

Nucleolus
Nuclear envelope
Chromosomes

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36
Q

What is the function of the nucleus?

A

Sequesters DNA from enzymatic reactions in cytoplasm

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37
Q

Describe the rough endoplasmic reticulum

A

Attached to cytosolic side of the ER, is studded with ribosomes

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38
Q

What is the function of the smooth endoplasmic reticulum?

A

Plays a role in lipid synthesis

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39
Q

What is the function of peroxisomes?

A

Vesicles with digestive function. Breaks down fatty acids and amino acids. H2O2 is produced as a byproduct, is converted to alcohols and water.

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40
Q

Describe the function of the Golgi apparatus

A

Augment lipids and proteins and package into vesicles for delivery to extra cellular space.

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41
Q

Describe the role and functions of lysosomes

A

performs intracellular digestion. Aids in endocytosis via breaking down material from outside the cell
Contain enzymes that breakdown ALL biomolecules,

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42
Q

What does Avogadro law state?

A

Volume of a gas is directly proportional to number of moles of gas

At constant temperature and volume

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43
Q

What is the trend for the van der waals correction factors?

A

Increase in both correction factors values with increase in mass and complexity of structure

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44
Q

Graham’s law of effusion

A

Effusion rate is inversely proportional to the square root of the molecular mass of gas

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45
Q

Gases have substantial or negligible intermolecular/ attractive forces versus liquids and solids?

A

Negligible

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46
Q

What holds together a network solid?

A

Covalent bonds

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47
Q

What holds together a molecular solid?

A

Intermolecular forces

Example is solid H2O

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48
Q

Solvation shell of water stabilized what type of amino acids?

A

Charged

Aspartate 
Glutamate 
Lysine
Arginine
Histine
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49
Q

What are the charged amino acids?

A 
Asp
Glu 
Lys 
Arg 
His
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50
Q

What stabilizes primary structure of proteins?

A

Peptide bond

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51
Q

What is the primary structure of proteins?

A

Linear polymer

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52
Q

Types of secondary structures of proteins

A

Alpha helix
Beta pleated sheets
Coils and loops connections

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53
Q

What stabilizes secondary protein structures?

A

Backbone interactions composed of hydrogen bonding

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54
Q

What stabilizes tertiary structure of proteins?

A

Side chain interactions

Hydrophobic interactions
Van der waal forces
Disulfide bonds

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55
Q

Where do charged amino acid residues occur in tertiary protein structure?

A

On the outer part of protein exposed to water

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56
Q

In TLC what is RF

A

Rise of compound /length of tlc glass

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57
Q

Cation exchange resin has what kind of charge on the resin?

A

Negative

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58
Q

What kind of charge does anion exchange resin have?

A

Positive

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59
Q

If using cation exchange resin, if pH of mobile phase is lower than the isoelectric point of protein, will the protein be retarded on the stationary phase?

A

Yes

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60
Q

If using cation exchange resin and the pH of the mobile phase is higher than the isoelectric point of the protein, will the protein be retarded on stationary phase?

A

No, protein has a net negative charge, will be repelled by the anionic charge of resin.

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61
Q

If using a anionic exchange resin, if pH of mobile phase is lower than the isoelectric point of protein, will protein be retarded on the stationary resin?

A

No, protein will have net positive charge and will be repelled by positive charge on resin.

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62
Q

What kind of stationary phase does an HPLC have?

Will polar or non-polar compounds elute first?

A

Non-polar

Polar

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63
Q

Which particles elute first on size-exclusion chromatography?

A

Large particles

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64
Q

Affinity chromatography is used to separate what?

A

Proteins and nucleus acids

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65
Q

How does affinity chromatography work?

A

Recombinant proteins have affinity tags (HIS tags) which bind to nickel bonded to stationary phase. Elute isolated protein via a buffer wash.

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66
Q

Gas chromatography separates compounds based on what?

A

Volatilities

More volatile species elute faster

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67
Q

Simple distillation works best for what scenarios?

A

Removing trace impurities

Separating mix of liquids with a significant difference in boiling points

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68
Q

Fractional distillation works best for what scenarios?

A

Mixture of liquids with similar boiling points.

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69
Q

What two atoms have naturally occurring isotopes in relative abundance dance that allow for identification via mass spec?

A

Cl yields a main peak and a second less abundant peak 2 amu heavier with 1/3 the abundance

Br yields 2 major peaks with equal abundance

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70
Q

Maximum wavelength is proportional to what via uv-vis spec?

A

Conjugation

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71
Q

What is the IR stretch for a carbonyl group?

A

1680-1730

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72
Q

What is the stretch for an OH group?

A

3200-3600 broad

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73
Q

What is the IR stretch for a carbon carbon triple bond?

A

2100-2300

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74
Q

What is the IR stretch for a N-H?

A

2500-3100

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75
Q

What is the proton NMR shift for a aromatic proton?

A

6-8 ppm

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76
Q

What is the proton NMR shift for a alkene proton?

A

5-6 ppm

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77
Q

What is the proton NMR shift for a alcohol proton?

A

2-5 ppm

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78
Q

What is the proton NMR shift for a carboxylic acid proton?

A

10-13 ppm

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79
Q

What is the proton NMR shift for a aldehyde proton?

A

9-10 ppm

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80
Q

What is the proton NMR shift for a proton next to an electronegative atom?

A

2.5-4

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81
Q

The secondary enzyme used in an ELIZA bonds where?

A

The constant region of the antibody that is specific to the antigen interested in.

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82
Q

How does a radio-immuno assay differ from an ELIZA?

A

Uses radio labeled antigens to detect antibodies.

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83
Q

What are the different types of blotting and how do they differ?

A

Southern- detects DNA

Northern- detects RNA

Western- detects proteins- works similar to ELIZA

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84
Q

What does the term transformation mean?

A

The process of implementing modified plasmids into bacterial cells via heat shocking.

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85
Q

What is cDNA?

A

Produced using mRNA ( post-transcriptionally modified) via Reverse Transcriptase

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86
Q

Potassium ions move from where to where via potassium leak channels?

A

Move from intracellular to extra cellular down concentration gradient.

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87
Q

Sodium ions flow from where to where via voltage gated sodium channels?

A

Sodium flows from extra cellular space to intracellular space down its concentration gradient. It depolarizes the cell during an action potential to positive values.

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88
Q

What do Schwann cells create?

A

The myelin sheath

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89
Q

Are myelinated parts of axons able to conduct action potentials?

A

No, no ions are able to penetrate in or out of the myelin sheath.

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90
Q

Where do action potentials occur on an axon?

A

Nodes of ranvier

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91
Q

Outline the 3 steps that occurs during the repolarization after an action potential.

A
  1. Voltage gated sodium channels close
  2. Voltage gated potassium channels open (K flows out of the cell) until the electric potential of the overshoots resting potential and acquires valley of -90 mv. Then they close.
  3. Na/K pump along with with potassium leak channels raise the electric potential of cell from -90 mv to resting potential.
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92
Q

Is a cell capable of an action potential during the absolute refractory period?

A

No

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93
Q

Is the cell capable of conducting an action potential during the relative refractory period?

A

Yes, but a greater stimulus is required because the cell is hyper polarized and is attempting to lower the electric potential from -90 mv to resting potential.

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94
Q

Where do electrical synapses occur?

A

Cardiac muscle and smooth muscle

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95
Q

What structure facilitates the spreading of action potentials in electrical synapses?

A

Gap junctions

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96
Q

What does a chemical synapse do?

A

Converts an action potential to a chemical signal (neurotransmitter).

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97
Q

What kind of voltage gated ion channels are utilized in the presymnaptic knob to release NT’s?

A

Voltage gated Calcium

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98
Q

What type of NT depolarizes a cell?

A

Excitatory

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99
Q

What type of NT hyperpolarizes a cell?

A

Inhibitory

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100
Q

Can a single synapse initiate an action potential of a post synaptic neuron?

A

No, an action potential is generated an determined via the summation of all synapses acting on the post synaptic neuron.

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101
Q

What is temporal summation?

A

Build up of Epsp’S or Ipsp’s from a singular neuron

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102
Q

What is the term Spatial summation

A

The summation of all pre synaptic neurons acting on a post synaptic neuron.

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103
Q

Muscles and glands carry out integrative info from CNS and are called?

A

Effectors

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104
Q

The PNS is responsible for carrying out what functions?

A

Sensory and motor function

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105
Q

What type of neurons carry info toward the CNS?

A

Afferent neurons

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106
Q

When the parasympathetic system is activated the body is prepared for?

A

Rest and digestion

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107
Q

When the sympathetic system is activated the body is prepared for?

A

Fight or flight

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108
Q

The somatic division of the PNS deals with?

A

Conscious voluntary movement of skeletal muscle.

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109
Q

The autonomic division of the PNS deals with?

A

Non-conscious, involuntary processes such as digestion, metabolism and perspiration.

110
Q

List the 4 components of the CNS

A

Spinal chord

Brain

111
Q

List the sub divisions of the brain

A

Forebrain
Mid brain
Hindbrain

112
Q

Equilibrium occurs when delta G equals?

A

0

113
Q

What does the term spontaneous reaction mean?

A

It has a negative delta G value

One that occurs without a net addition of energy

114
Q

How would someone produce more transition state intermediates of a reaction?

A

Lower the activation energy barrier of the reaction.

115
Q

How does a catalyst lower the Ea of a reaction?

A

It stabilizes the transition state intermediate

It makes the existence of the intermediate more thermodynamically favorable

116
Q

Enzymes have what kind of role?

A

Kinetic role

117
Q

What amino acid is a readily available proton donor AND acceptor at physiological pH?

It is prevalent in the active sites of enzymes.

A

Histidine His H

118
Q

Polar amino acids are capable of what?

A

Hydrogen bonding

119
Q

What is the abbreviations of phenylalanine?

A

Phe

F

120
Q

What is the abbreviations of tryptophan?

A

Trp

W

121
Q

What is the abbreviations of asparagine ?

A

Asn

N

122
Q

What is the abbreviations of glutamine?

A

Gln

Q

123
Q

What are the two sulfur containing amino acids?

A

C

M

124
Q

Disulfide bonds can form only on this amino acid?

A

Cys

125
Q

What are the two types of covalent bonds formed in proteins?

A

Peptide bonds and disulfide bonds

126
Q

What is the function of a protease?

A

Cleave peptide bonds

127
Q

What is the name of the resulting residue when two cysteine residues form a disulfide bond?

A

Cystine

128
Q

What two properties of proline cause issues in polypeptide chains?

A
  1. When introduced into a polypeptide it no longer has an amino hydrogen, thus does not participate in hydrogen bonding
  2. The conformational strain of the ring r group kinks the poly peptide chain
129
Q

What amino acid is never found in alpha helixes?

A

Proline

130
Q

Tertiary structure of proteins is governed by what effect?

A

Hydrophobic effect

131
Q

Denaturing agents destabilize what bonds?

A

Hydrogen bonds

132
Q

How do quarter art disulfide bonds differ from tertiary?

A

Quat ds bonds form between two different peptide chains.

133
Q

What does a phosphates do?

A

Removes a phosphate group from a molecule

134
Q

What does a phosphorylase do?

A

Adds a phosphate group to a molecule from inorganic phosphate

135
Q

What does a kinase do?

A

Transfers a phosphate group to a molecule from a high energy carrier (ATP)

136
Q

What does a lyase do?

A

Breaks chemical bonds via methods other than hydrolysis or oxidation.

Ex: pyruvate decarboxylase

137
Q

What does a ligase do?

A

It forms chemical bonds

138
Q

What does a hydrolase do?

A

It hydrolyzes chemical bonds

Ex: ATPase

139
Q

Where is the linear portion of the velocity vs substrate concentration?

A

Up to 1/2 V max

140
Q

What is the definition of Km?

A

Substrate concentration where velocity equals 1/2 Vmax

141
Q

What type of curve is created with enzyme cooperativity?

A

Sigmoidal

Rate increase once enzyme has affinity for substrate is greater than linear!

142
Q

Cooperativity is relevant to what kind of enzymes?

A

Multi-subunit enzymes

143
Q

What is allosteric regulation?

A

Binding of small molecules to sites on an enzyme that are distinct from the active site.

144
Q

What are relaxed and tense states of active sites?

A

Tense states are when the active site has a low affinity for substrate

Relaxed state is when the active site has a high affinity for substrate due to cooperativity

145
Q

What is the main differentiator between allosteric regulation and cooperativity?

A

Cooperativity deals with all substrates binding to different active sites in multi-subunit enzymes.

Allosteric regulation occurs at sites other than active sites

146
Q

Competitive inhibitors resemble what?

A

Substrate, but effective competitive inhibitors actually structurally mimic the transition state intermediate

147
Q

How can a substrate outcompete an inhibitor?

A

Increase the substrate concentration

148
Q

The Km of of a reaction is impacted how by the presence of a competitive inhibitor?

A

The Km is increased. More substrate is need to acquire Vmax of non inhibited enzymatic reaction

149
Q

Is Vmax impacted by competitive inhibitors?

A

No, still achieve Vmax but with more substrate.

Km is increased

150
Q

What values are and are not impacted by non competitive inhibitors?

A

Vmax is decreased

1/2 Vmax is decreased

Km is not impacted

151
Q

How is vmax and Km impacted by uncompetitive inhibitors?

A

Km and Vmax is decreased

152
Q

How is Vmax and Km impacted by mixed inhibitors?

A

Vmax is decreased and Km is varied.

153
Q

What is another term for non competitive inhibition?

A

Allosteric inhibition

154
Q

What kind of plot is the line weaver burke plot?

A

Double reciprocal

Y axis is velocity, lower values on y axis correspond to higher velocity (1/velocity)

X axis is substrate concentration with lower values corresponding to higher substrate concentrations (1/sub conc)

155
Q

What is the definition of the slope on a line weaver Burke plot?

A

Slope= Km/Vmax

156
Q

What is the definition of the y- intercept on a LWB plot?

A

Y intercept= 1/Vmax

157
Q

What is the definition of the x intercept on a LWB plot?

A

X intercept = -1/Km

158
Q

Why does Km decrease when an uncompetitive inhibitor is present?

A

Since inhibitor bonds to the E-S complex and sequesters enzyme, the inhibitor increases the enzymes affinity for the substrate.

159
Q

How are enzymes that breakdown sugar named?

A

By the disaccharides they hydrloyze.

160
Q

Glycogen has what kind of glycosidic finds?

A

Alpha glycosidic bonds

161
Q

What type of glycosidic bonds do cellulose have?

A

Beta, most mammals lack the ability to hydrolyze beta glycosidic bonds.

162
Q

Is glycolysis inhibited or increased with a the presence of a high concentration of ATP?

A

Glycolysis is slowed down and inhibited. ATP is an allosteric inhibitor for regulation steps in glycolysis.

Goes against le chatliers principle

163
Q

Where does oxidative phosphorylation occur in prokaryotes?

A

Cell membrane

164
Q

What transports the NADH from glycolysis in cytoplasm into the inner membrane of the mitochondria?

A

Glycerol phosphate shuttle

Sends electrons directly to ubiqiunone or complex 2 in ETC

There is a reduction in ATP yield similar to FADH2, only 1.5 ATP made vs 2.5 ATP

165
Q

What reaction is commonly used to drive less favorable reactions? ATP not relevant.

A

Oxidative decarboxylation

166
Q

Gluconeogenesis can be thought of how?

A

Glycolysis in reverse with the 3 enzymes catalyzing the 3 irreversible steps replaced.

Start with pyruvate (3carbons)
Convert to OAA (4 carbons)
To phospho-enol pyruvate (3 carbons)

167
Q

List glycolysis/gluconeogenesis regulation strategies

A

1) energy deficits (high ADP to ATP and NADH to NAD+ ratios) and surpluses ( vice versa)
2) increased concentrations in a pathway serve to decrease the activity of that pathway

3) Fructose 2-6 bus phosphate in glycolysis and gluconeogenesis
Insulin stimulates F,1-6BP formation and activates PFK and stimulates glycolysis

Glucagon triggers breakdown of F,1-6 BP and inhibits PFK and activates F1-6 BPase thereby stimulating glucose biosynthesis

168
Q

List regulation strategies for the Citric Acid Cycle

A

Cellular energy needs
Pathway intermediate concentrations

NOT hormonal regulated

169
Q

Is glycolysis and gluconeogenesis hormonally regulated?

A

Yes

Insulin stimulates glycolysis and glucagon stimulates gluconeogenesis

170
Q

Where does glycogenesis and glycogenolysis occur?

A

Liver and skeletal muscle

171
Q

Phosphorylated glucose must have what occur for glucose to enter the blood stream?

A

Be de-phosphorylated

Skeletal muscle keeps the phosphorus group to prevent the glucose from leaving the sketch muscle

172
Q

How is glycogenesis regulated?

A

Hormonally
by insulin, which stimulates glycogenesis

Glucagon stimulates glycogenolysis

173
Q

What are the 2 main intermediates formed in the pentose phosphate pathway?

A

Ribose-5-Phosphate. Used in nucleotide synthesis

NADPH is formed- used as reducing species in fatty acid biosynthesis -anabolic pathway

174
Q

What are 2 roles of NADPH?

A

Used in fatty acid biosynthesis-acts as a reducing species

Used to neutralize reactive oxygen species

175
Q

Pathways that regulate blood glucose levels are regulated how?

A

Hormonally

Via Cellular energy needs/amount of redox species available

Pathway Intermediate concentrations

176
Q

Why are fats more efficient energy storage molecules than carbs?

A

1) Packing of fats within the cell

2) Are more reduced and thus release more energy via reduced carrier molecules.

177
Q

Unsaturated fatty acids in di-acyl glycerol phosphates (phospholipids) impacts the cell membrane how?

A

Increases the fluidity of the cell membrane.

178
Q

What are the three modulators that increase cell membrane fluidity?

A

Increasing the degree of unsaturated fatty acids

Shorter fatty acid tail length

Cholesterol levels

179
Q

All steroids have the structure of?

A

Tetracyclic ring structure based on cholesterol.

180
Q

Terpenes have the formula of?

A

(C5H8)n

181
Q

Steroid hormones bind where?

A

Steroid receptors are found within the cell since their hydrophobicity facilitates diffusion throughout the lipid bilateral

182
Q

What is the significant sphingolipid in humans?

A

Sphingomyelin found in the myelin sheath of neurons.

183
Q

What are the main fat/lipid structures to know?

A

Fatty acids-saturated and unsaturated

Triglycerides- fat

Phospholipids- usually have another polar group attached to the phosphate

Cholesterol- has the tetracycline ring structure

Steroids- has the tetracyclic ring structure

Sphingomyelin- component of the myelin sheath

Waxes- fatty acids that are esterified to long chain alcohols. Form protective barriers

Fat soluble vitamins
A, K, D, E

Prostaglandins
Derived from 20 carbon fatty acids and have a 5 member ring structure within

184
Q

Where does fatty acid biosynthesis occur?

A

Cytoplasm

185
Q

What enzyme cleaves fatty acids from triglycerides?

A

Lipase

186
Q

What is the priming reaction for fatty acid oxidation?

How many ATP’s are used in this investment stage?

A

Fatty acid is converted to adenylated fatty acid followed by conversion to fatty acetyl CoA

2 ATP’s used to prime fatty acid so it enter mitochondrial outer membrane

187
Q

What are the reactants, products and steps for fatty acid beta oxidation?

A

Fatty acid is primed and converted to fatty acetyl CoA

FA-CoA undergoes elimination reaction between alpha and beta carbon to form a trans double bond

FA-CoA double bond undergoes addition reaction with water to form a beta alcohol

Beta alcohol is oxidized to beta ketone

Carbon carbon bond is cleaved between the alpha and beta carbons to form acetyl CoA and shorter chain Fatty acetyl-CoA

Note: once fatty acid carbon chain is cleaved to 4 carbon chain, it is cleaved into 2 acetylCoA’s

188
Q

How many NADH and FADH2 are made with each round of fatty acid oxidation

A

Each round generated 1 NADH and 1 FADH2

Each acetyl CoA enters the keens cycle and generates 3NADH and 1 FADH2

189
Q

What are the reactants and products of ketogenesis?

A

2 Acetyl CoA’s over 4 steps are converted to acetoacetate

Acetoacetate is converted to acetone and CO2 or beta hydroxy butyrate

Ketone bodies are able to pass through the blood brain barrier

Ketone bodies are converted back to Acetyl CoA once they reach target organ and enter the Krebs cycle

190
Q

What reducing specie is used in fatty acid biosynthesis?

A

2 NADPH’s are oxidized to 2 NADP+’s

Oxidizes reducing species formed in the pentose phosphate pathway

191
Q

How does insulin impact glycolysis and glycogenesis?

A

Insulin stimulates the glycolysis pathway and glycogenesis

192
Q

What are the three reasons why phosphate anhydride bonds store so much free energy?

A

1) the negative charges of the phosphate groups at biological pH repel each other
2) orthophosphate has more resonance structures than linked phosphates
3) ortho phosphate has more favorable interactions will water than linked phosphates

193
Q

What are the two common forms of inorganic orthophosphate in biological systems?

A

Hydrogen phosphate and dihydrogen phosphate

PKAs are 2.1, 7.2 and 12.7 of orthophosphate

194
Q

What energy currency molecule is used in glycogenesis?

A

UTP is used for this specific anabolic pathway

195
Q

Will individual DNA base pairs H bond with each other in water?

A

No, the double helix structure of DNA facilitated proper orientation of the base pairs in 3D space to allow for H bonding with each other.

196
Q

What portion of a nucleotide constitutes the backbone in a polymer of nucleus acids?

A

sugar phosphate backbone

197
Q

The binding specificity of enzymes to DNA is derived from interactions with the sugar phosphate backbone or with the purine /pyrimidine based?

A

Bases because they are the only variable parts of DNA and RNA

198
Q

Name the bases used in DNA and RNA

A

DNA- A, T, C and G

RNA- A, U, C, and G

199
Q

Poly peptide and protein residues are listed how?

A

from the N terminus to the Carboxy terminus

200
Q

Nucleotide sequences are listed how?

A

From the 5’ carbon end to the 3’ carbon end

201
Q

What immediately occurs to pyrophosphate once it is in solution?

A

Hydrolyzes to 2 inorganic orthophosphate. This along with initial cleavage of ATP drives reactions forward

202
Q

Beta pleated sheets structure depends on H bonds between peptide chains in what orientation?

A

Antiparallel, when it is one chain looping to H bonding with itself.

203
Q

State chargoffs rule

A

[A] = [T]

[C] = [G]

[A]+[G]=[T]+[C]

204
Q

What does the term hybridization mean?

A

The annealing of two complementary strands of DNA

205
Q

A G-C rich nucleotide sequence would have a higher or lower Tm than an A-T rich sequence?

A

Higher because G-C base pairs form 3 H bonds in dsDNA

206
Q

What interactions stabilize dsDNA double helix?

A

Van der waals forces and hydrophilic interactions. Once the bases H bond, the dipoles are tied up leaving little polarity left in the structure.

207
Q

What part of the DNA double helix is oriented toward the water and what is oriented towards the interior of the helix?

A

Sugar phosphate backbone is oriented towards the water and the bases are oriented towards the interior.

208
Q

List the differences in genome characteristics btw Eukaryotes, prokaryotes and viruses.

A

Eukaryotes- linear DNA, 43 chromosomes, 23 donated from each parent. Largest Mw of all 3.

Prokaryotes- single circular DNA chromosome

Viruses-linear or circular DNA or RNA

209
Q

What are the proteins used to package DNA? What Ana’s are abundant in these proteins?

A

Histone proteins

N and K, basic r groups are used to attract to the acidic sugar phosphate backbone.

Note at physiological pH the sugar phosphate backbone is deprotonated (have a net negative charge) and the aa side chains are protonated and have a positive charge.

210
Q

Fully packed DNA is called?

A

Chromatin

211
Q

dsDNA helix wrapped around an octet of histone proteins is called?

A

A nucleosome

212
Q

The more compacted/denser regions of chromatin is called?

When stained these regions are darker or lighter?

A

Heterochromatin

Darker

213
Q

The less compacted/less dense parts of chromatin are called?

These regions are darker or lighter when stained?

A

Euchromatin

Lighter

214
Q

List out flow of DNA structure from deoxy ribose sugar to fully packed chromosome

A 
Deoxy ribose sugar
         \+ base 
  Nucleoside
          \+ triphosphate
 Nucleotide
          \+ polymerization with loss of pyrophosphate
Oligionucleotide 
           \+ more polymerization
Single stranded poly nucleotide
            \+ additional ssDNA and H bonding
dsDNA
             \+ coiling
dsDNA helix
              \+ histone protein octet
Nucleosome
              \+ more packing
Chromatin
215
Q

Which part of chromatin has increased gene activity?

A

Euchromatin because it is less packed and easier for transcription and replication machinery to access DNA

216
Q

Heterochromatin is largely made up of what?

A

Large sections of repetitive DNA

217
Q

Define centromeres and kinetochores

A

Centromeres- region of chromosomes where the mitotic spindle fibers attach during mitosis. Made of heterochromatin.

Kinetochores- act mitotic spindles attach to the centromere via these multi protein complexes that act as anchor sites

218
Q

Telomeres are made up of what?

A

Both ssDNA and dsDNA. Composed of repeat sequences 6-8 bp’s long that are guanine rich.

219
Q

What are the function of telomeres?

A

Function to prevent chromosome degradation and prevent fusion with neighboring chromosomes.

220
Q

Do prokaryotes have telomeres?

A

No, since they have circular chromosome they have no chromosome ends.

221
Q

What are the differences btw RNA and DNA?

A

1) there is a 2’ hydroxyl group on the ribose sugar
2) RNA is single stranded
3) RNA uses the base uracil instead of thymine

222
Q

What is the only coding type of RNA?

A

mRNA

223
Q

What is the premature version of mRNA called?

A

heterogenous nuclear RNA hnRNA

224
Q

Do prokaryotes have mRNA?

A

No backside they do not process their Primary transcripts, thus they only have hnRNA

225
Q

What are the two major noncoding types of RNA?

What are their functions?

A

tRNA- transfer RNA is used in translation, carries an amino acid from the cytoplasm to the ribosome

rRNA- ribosomal RNA is the major component of ribosomes. Has limited catalytic function.

226
Q

What are catalytic RNA’s called?

A

Ribozyme

227
Q

What is the composition of a ribosome?

A

It is made of of rRNA and proteins

228
Q

Acetylcholine is what type of neurotransmitter?

It will depolarize or hyperpolarize a post synaptic membrane?

A

Excitatory

Depolarize

229
Q

GABA dopamine and norepinephrine are examples of what type of neurotransmitter?

Will they depolarize or hyperpolarize a post synaptic membrane?

A

Inhibitory

Hyperpolarize- make more negative

230
Q

Can presynaptic neurons change the type of neurotransmitter they release?

A

No

231
Q

What is the definition of reciprocal inhibition?

A

Simultaneous inhibition/relaxation of one muscle with the excitation/stimulation of another muscle.

232
Q

The vagus nerve is what type of nerve?

What are the target organs of the vagus nerve?

A

Cranial nerve

Heart and GI tract

Lower heart rate and stimulate digestion

233
Q

List the types of sensory receptors

A 
Mechanoreceptors
Thermoreceptors
Nociceptors- pain receptor
Chemoreceptors
Electromagnetic receptor
234
Q

What is the difference between exteroceptors and interoceptors?

A

Intwroceptors recieve sensory stimuli from inside the soma whereas exteroceptors receive sensory information from outside the soma.

235
Q

What is the definition of a hormone?

A

A chemical released into the bloodstream by an endocrine gland which has its effects upon a distant target which has the appropriate receptor.

236
Q

What is the characteristic that differentiates between an endocrine gland and an exocrine gland?

A

Endocrine glands are ductless. They secrete their products into the bloodstream.

Exocrine glands secrete their products to the external environment via gastrointestinal lumen or the external world.

237
Q

Tissue specificity of hormone action is determined by?

A

Whether the cells of a tissue have the appropriate receptor

238
Q

What are examples of hydrophilic hormones?

Where do they bind?

A

Peptides and amino acid derivatives

Receptors are located on the cell surface

239
Q

What are examples of hydrophobic hormones?

Where are hydrophobic hormone receptors located?

A

Steroid hormones

Receptors are located inside the cell

240
Q

Hydrophilic Hormones

Where are they made?

Regulation of release?

Transport in bloodstream?

Specificity

Mechanism of effect

Timing of effect

A

Rough ER

Stored until released

Free

Target cell surface receptors

Secondary messenger cascade- augment enzyme activity

Rapid, short lived

241
Q

Hydrophobic Hormones

Where are they made?

Regulation of release?

Transport in bloodstream?

Specificity

Mechanism of effect

Timing of effect

A

Smooth ER

Synthesized only when needed and then immediately released

Stuck to protein carrier

Cytoplasmic receptors

Change the amount and type of enzymes- alter gene expression

Slow- long lasting

242
Q

What is a tropic hormone?

A

They are hormones that regulate other hormones, not physiological endpoints.

Are also called meta-regulators

243
Q

What are releasing and inhibiting factors(hormones)?

A

These are hormones released by the hypothalamus that regulate tropic hormones.

244
Q

Another name for factor is?

A

Hormone

245
Q

Hypophysis is another name for what gland?

A

Pituitary gland

246
Q

What is the name of the miniature circulatory system used by the hypothalamus to deliver releasing and inhibitory factors?

A

The hypothalamus-pituitary portal system

247
Q

Adenohypophysis is what?

How is it controlled?

A

Anterior pituitary gland

It is controlled by the hypothalamus via releasing and inhibiting factors

248
Q

Neurohypophysis is what?

What controls it?

A

Posterior pituitary gland

Hypothalamic neurons

249
Q

Which is a hormone and which is a neurotransmitter?

A

Epinephrine is a hormone secreted by the adrenal gland

Norepinephrine is a neurotransmitter

250
Q

Thyroid hormone is what kind of hormone?

A

Modified amino acid that acts like a steroid

251
Q

What are the 7 major endocrine glands?

A

Hypothalamus
Pituitary gland

Thyroid gland

Thymus

Adrenal glands

Pancreas

Tested/ovaries

252
Q

What are intergenic regions on chromosomes?

A

Non coding DNA

Composed of tandem repeats and transposons

253
Q

What are 4 genomic variations?

A

Single nucleotide polymorphisms- single nucleotide change

Copy number variations- large sections of repeats or deletions

Transposons- mobile genetic elements that jump around the genome

Tandem repeats- repeated sequences

254
Q

What are the two immediate gene products?

A

Non coding RNA and mRNA

255
Q

Stop codons are also called what?

How many stop codons are there?

A

Nonsense codons

3
Start with UA

256
Q

How many nucleotides are actually necessary to code for an amino acid in a codon?

A

Only the first two

257
Q

What is the origin of replication?

A

The point where DNA replication is initiated.

258
Q

What are important DNA replication rules?

A

Polymerization occurs in the 5’ to 3’ direction. This means the template strand is read from 3’ to 5’.

DNA polymerase requires a RNA primer. It can only add to an existing nucleotide chain.

DNA requires a template strand/parent strand

Leading strand polymerization is continuous

Lagging strand is dis-continuous-form Okazaki fragments

259
Q

What are the three major enzymes involved in DNA replication?

A

DNA polymerase (DNA pol III, DNA pol I)

Helicase- unwinds DNA at origin of replication

Topoisomerase - cut DNA strands to unwrap the helix and release tension.

260
Q

All amino acids have what configuration?

A

L configuration

261
Q

What are the pKas for the carboxylate and amine groups of all amino acids at physiological pH?

A

Carboxylate pKa is 2.00

Amine pKa is approx. 10.00

262
Q

What are the pKas of the side chains of the charged polar amino acids?

A

Asp- pKa 4.00
Glu- pKa 4.00

His- pKa 6.00

Lys- pKa 11-12 above amine pKa

Arg- pKa 11-12 above amine pKa

Note that the carboxylate pKa’s are 2.00 and the amino pKa’s are 9- 10

263
Q

What are the letter code abbreviations for

Arginine
Asparagine

A

Arginine- R charged polar

Asparagine- N polar

264
Q

Fatty acids are transported in the bloodstream via what protein?

A

Albumin

265
Q

What must occur to a fatty acid before it can enter the mitochondria to undergo fatty acid oxidation?

A

It must be primed ( utilizes 2 equivalents of ATP/cleaves two high energy phosphate bonds) and converted into a fatty acid-CoA

266
Q

What is the equation to determine the number of rounds of fatty acid beta oxidation based on the carbon length of the fatty acid?

A 
# of rounds of oxidation= (carbon tail length/2)-1
B/c once tail is 4 carbon's long it cleaves in half to make 2 acetyl-CoA's
267
Q

Fatty acid biosynthesis occurs where?

Fatty acid catabolism occurs where?

A

In the cytoplasm

In the mitochondria

268
Q

Are reduced or oxidized species formed during biosynthesis reactions?

A

Oxidized species are formed

269
Q

What are the starting and ending components of fatty acid biosynthesis?

How many NADP+’s and mol of CO2 are formed?

A

Acetyl CoA and multiple units of Malonyl CoA (3 carbon chain) converted into C16 fatty acid.

Acetyl CoA is activated via conversion to Malonyl CoA via ATP (1 equivalent) driven carboxylation (addition of CO2).

Each addition of Malonyl CoA to growing fatty acid chain via ACP portion of Fatty Acid Synthase oxidizes 2 NADPH’s to 2 NADP+’s (14 NADP+’s produced per 1 C16 fatty acid).

Note* 1 CO2 is used to make each Malonyl CoA, and 1 CO2 is lost with each condensation of Malonyl CoA to growing fatty acid chain at active site.

270
Q

What redox species is used in fatty acid biosynthesis?

A

NADPH is oxidized to NADP+

MCAT (3 decks)

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