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Biochemistry > Exam 1 Review > Flashcards

Exam 1 Review Flashcards

1
Q

What is the first law of thermodynamics?

A

Energy is never lost or created

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2
Q

What is the second law of thermodynamics?

A

Entropy is always increasing

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3
Q

What is an ATPase?

A

A protein that uses ATP

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4
Q

What is an energy charge?

A

A measure of the energy status of cells between 0 and 1.

1 = all ATP; 0 = all AMP; usually around .8-.9

Energy Charge = (ATP + 1/2 ADP)/(ATP + ADP + AMP)

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5
Q

Explain the role of Mg2+ in ATP

A

Mg2+ binds to the phosphate groups by accepting their electrons in order to stabilize the molecule.

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6
Q

List the major functions of proteins

A 
Establish and maintain structure
Transport
Protection
Catalysis
Movement
Storage
Communication
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7
Q

What are the four most common elements?

A

H, N, O and C make up 99% of animals’ bodies

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8
Q

Why are membranes important for the functioning of cells?

A

They allow for unique environments inside and outside of the cell, which creates potential energy in the form of gradients.

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9
Q

Can you calculate/determine the 3D structure of a protein from its primary sequence?

A

No

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10
Q

What is a domain?

A

A region of a protein with unique folding and function that can forms unction, and exist independently of the protein molecule.

Domains are units of protein structure.

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11
Q

What amino acid is the first in any peptide sequence?

A

Methionine

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12
Q

Which amino acid enantiomers are found naturally?

A

Only L-amino acids are found in the body

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13
Q

What is an isoelectric point?

A

The pH where the net charge of the amino acid (or peptide chain) is equal to zero.

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14
Q

As the pH of a solution increases, does the net charge on a protein increase or decrease?

A

Net charge decreases as the molecule is deprotonated in basic solutions with higher pH.

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15
Q

List the amino acids and explain why they are essential.

A

Valine, leucine, isoleucine, methionine, tryptophan, phenylalanine, threonine, and lysine (and histidine for fetal development)

Essential amino acids must be ingested in the diet because the body cannot synthesize them.

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16
Q

Hydrophobic side chains

A

Gly, Ala, Pro, Val, Leu, Ile, Met, Trp, Phe

Non-polar amino acids usually found on the inside of folded proteins

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17
Q

Why is proline important for 3D protein structure?

A

The proline ring forces turns because it is rigid and prevents many rotations from being possible.

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18
Q

Where are valine and leucine often found?

A

In transmembrane proteins functioning as anchors

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19
Q

What is unique about tryptophan?

A

It is the only amino acid with only one codon

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20
Q

Amino acids with polar side chains

A

Ser, Thr, Tyr, Asn, Gln, Cys

Interact with environment and substrates

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21
Q

What role does serine often play in active sites of proteases?

A

It makes active sites even more active when it is deprotonated by a nearby histidine residue.

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22
Q

What special role does cysteine play in protein folding?

A

It can form disulfide bonds (“cystine”), linking two portions of the protein chain

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23
Q

Amino acids with positively charged side chains

A

Lys, Arg, His

Found on surface of proteins
pKas can vary significantly based on the neighboring residues (micro environment)

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24
Q

What is unique about histidine?

A

Histidine can bind and release protons at physiological pH

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25
Q

Amino acids with acidic side chains

A

Asp, Glu

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26
Q

Ionizable side chains and their pKas

A 
Terminal carboxyl groups............3.1
Asp, Glu.........4.1
His........6.1
Terminal amino group ........ 8.0
Cys......... 8.3
Lys......10.8
Tyr.......10.9
Arg.......12.5
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27
Q

What is the 21st amino acid?

A

Selenocysteine, which is important as am antioxidant

Formed from serine by replacing OH with SeH

Coded by a stop codon UGA

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28
Q

Describe a peptide bond

A

Links amino acids together

Rotation about bond is restricted to planar formation because of resonance between the carbonyl group and the amino group of the next AA

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29
Q

What are the dihedral angles?

A

Phi is the angle between the alpha carbon and nitrogen

Psi is the angle between the two carbon molecules

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30
Q

What is a Ramachandran plot?

A

It plots the dihedral angles phi and psi against each other in order to show possible rotation angles for peptides. Green areas represent feasible folds.

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31
Q

Describe the alpha helix secondary structure.

A

A helix that is stabilized by intrastrand H bonds between every fourth residue. The R groups stick out from the coil perpendicular to the backbone and can act as transmembrane anchors.

Most are right-handed

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32
Q

Describe a beta sheet secondary structure.

A

Stabilized by interchain H bonds between beta strands. Often found in middle of globular proteins.

Can be parallel or anti-parallel
Parallel: each AA connected to two different AA from otherstrand
Anti-parallel: 1:1 pairing of AA

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33
Q

Collagen

A

A coiled coil fibrous protein found in connective tissue. It functions to resist tensile forces.

Helices are tighter than alpha Helices, and can form interchain H-bonds leading to coiled coil when they wrap around each other

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34
Q

What is quaternary structure?

A

When separate protein chains interact and combine to one functional unit

2= Dimer
4= tetramer
6= hexamer
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35
Q

Explain prion diseases

A

Protein misfolding leads to accumulation of the prion protein into amyloid fibers

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36
Q

What are the five stabilizing factors of proteins?

A

Disulfide bonds, H bonds, ionic bonds, hydrophobic interactions, and van der waals forces

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37
Q

What is the function of urea and B-mercaptoethanol for analyzing proteins?

A

Urea destroys non-covalent interactions between amino acid residues

B-mercaptoethanol reduces disulfide bonds into two disconnected cysteine residues

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38
Q

Does selection work on amino acid sequence or amino acid function?

A

Function

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39
Q

Explain why protein folding is a cooperative process

A

The folding process doesn’t happen all at once. Regions with higher specificity will fold to their preferable position, which will then guide the rest of the folding process.

Folding can occur co-translationally while the ribosomes are still working on translating the protein

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40
Q

What are the two common quaternary structures for insulin?

A

In the blood, insulin is a dimer and used for signalling. It can also exist as a hexamer for storage

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41
Q

Explain dialysis

A

Use concentration gradients and size-exclusion with a semi-permeable membrane in order to purify a solution to a desired concentration

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42
Q

Explain ion exchange chromatography

A

Uses the charges of side chains in folded proteins. Charged beads are suspended in a column which will bind to the target material. All other molecules with different charges will fall through the column, and the target substance can be eluted later.

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43
Q

Explain gel filtration chromatography

A

Separates molecules based on size. The beads have small channels with varying sizes that will slow down the passage of smaller molecules. The big molecules will pass through faster because they will not get held up in the bead pores.

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44
Q

Explain affinity chromatography

A

Much more specific because you need to know what you are looking for. Have target residues on beads and introduce a specific binding protein. Then with addition of target protein, the specific binding protein will bind to the target

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45
Q

Explain polyacrylamide gel electrophoresis

A

Separates proteins by size in a matrix that has electric current running through it. Small proteins will move faster, and large will move slower. Proteins all have negative charge due to treatment with SDS, so they will travel towards the cathode.

46
Q

Explain isoelectric focussing

A

separates proteins based on the pka of their side chains

47
Q

What is salt fractionation?

A

A method used to make proteins more or less soluble
“Salt in” will dissolve the protein, so you’d want to keep the solution
“Salt out” will precipitate the protein, so you’d want to keep the precipitate

48
Q

Explain how to determine the amino acid composition of a polypeptide.

A

Ion exchange chromatography can be used. Different amino acids will fall through the column with different speeds, allowing for elution profiles to be used to determine which amino acids are present in a protein.

49
Q

Why can peptides have very different primary structures, but still have similar function?

A

The tertiary structure and the active site dictate the function, so if the active sites are the same in 2 proteins, they will have similar function as well.

50
Q

Explain Edman degradation

A

Allows you to look at protein sequence 1 amino acid at a time

1) Phenyl isothyiocyanate (PTH) binds to N-terminus
2) Break first bond
3) Determine which AA is bonded to PTH with chromatography
4) Repeat down chain 1 AA at a time

51
Q

What is the shotgun approach for sequencing proteins?

A

Use digestion enzymes such as trypsin or chymostrypsin which cut the protein chain at specific locations. Look for overlapping segments between different fragments in order to determine the overall sequence

52
Q

What is DTT?

A

Dithiothreitol (DTT) functions to reduce disulfide bonds in proteins. It is ‘nicer’ to proteins than B-mercaptoethanol.

53
Q

What are the structural differences between collagen and keratin?

A

Collagen is composed of 3 coiled coils, whereas keratin is composed of two homodimers to form a tetramer.

54
Q

Do monomers have quaternary structure?

A

No

55
Q

Explain what the purpose of a His-tag is.

A

Histags are used to label desired protein products. A chain of 6 histidine residues acts as sticky tape. Imidazole is used to elute proteins with histidine residues from the column.

56
Q

What unit is used to describe the mass of proteins?

A

Daltons
1 Dalton = 1 g/mol
~110AA=12kDaltons

57
Q

Describe the structure of an antibody

A

Antibodies have 2 heavy and 2 light chains that are connected by disulfide bonds to form a Y shape. There are 2 Fab (antigen binding) domains and a Fc domain.
They are made of mostly beta-sheets and loops

58
Q

What is an antigen?

A

A sequence or structure to which an antibody is designed to complementary bind to via non-covalent interactions.

59
Q

Explain what titer is.

A

Titer is the amount of antibody that is in a solution. Titers are measured in terms of a fractional dilution. A high titer is desireable and shows that enough of the antibody is present even in a highly diluted sample.

60
Q

Why do many antibodies form from one protein?

A

Antibodies form specific to many different sites (antigens) on the protein.

61
Q

What are polyclonal antibodies?

A

Many different antibodies that can bind to different surfaces of the same antigen?

62
Q

How are antibodies produced in laboratories?

A

The antigen is injected into an animal and spleen cells are removed from it. The cells are then hybridized with myeloma cells in order to immortalize them. The cells can then be plated and cloned for mass production.

63
Q

Describe an indirect ELISA

A

The walls are coated with antigens which will bind to any of the antibodies preesent in the solution. It detects antibody.
The rate of color formation is directly proportional to the amount of ANTIBODY present

64
Q

Describe a sandwich (direct) ELISA

A

Anibodies coat the wall and will bind any antigens present in the solution. A complementary antibody is introduced that will bind to a different site on the antigen. The rate of color change is directly proportional to the amount of ANTIGEN present

65
Q

Describe a competitive ELISA

A

Antibodies are inserted into a solution and will bind to any antigens present. Then, an enzyme linked antibody is introduced to compete with the antigens. The more antigens that are present, the less there will be to compete for. The rate of color formation is INDIRECTLY proportional to the amount of ANTIGEN that is present.

66
Q

Describe a Western Blot

A

Use a radiolabeled specific antibody to wash over a sheet that went through polyacrylamide gel filtration. If the antibody is present, then a band will be visible on the autoradiogram.

67
Q

Why are secondary antibodies useful for immunofluorescence.

A

They bind to primary antibodies and amplify the fluorescent signal.

68
Q

What is the purpose of protein crystallization?

A

Crystallization is used to determine the 3D structure of proteins

69
Q

What are the three methods for crystallizing proteins?

A

Hanging Drop
Sitting Drop
Microdialysis

They all reduce the amount of liquid in a drop

70
Q

Explain X-ray diffraction

A

Used to determine the 3D structure by creating an electron density map from the diffraction pattern

71
Q

What is an epitope?

A

The structure recognized by an antibody. 1 epitope refers to 1 antibody
A single protein has many epitopes.

72
Q

Which is more evolutionarily conserved, primary or tertiary structure?

A

Tertiary structure is more evolutionary conserved than its primary structure

73
Q

What is divergent evolution?

A

Share a common ancestor, but have evolved apart from each other

74
Q

What is convergent evolution?

A

Two very different proteins that serve similar functions due to them having the same active site.

75
Q

Why is oxygen so important for maintaining life?

A

O2 is the terminal electron acceptor in respiration, so it needs to reach all of the tissues in the body for cells to stay alive.

76
Q

What is the function of hemoglobin?

A

It is the main transporter of oxygen throughout the body

77
Q

What is the pH of blood?

A

7.35-7.45

78
Q

Describe the structure of Hemoglobin

A

It is a heterotetramer composed of 2 alpha and 2 beta subunits. It is made of mostly alpha helices. Each monomer has a prosthetic group called heme, which has an iron atom capable of binding to oxygen.

79
Q

Which form is the iron atom in the hemoglobin molecule?

A

Ferrous form (Fe2+), as opposed to the Fe3+ Ferric form

80
Q

What are the structural differences between oxygenated and deoxygenated hemoglobin?

A

In the deoxygenated state, the Fe atom is not in the same plane as the heme (protoporphyrin), but when oxygen binds to the Fe, it is pulled up into the same plane

81
Q

What role does the distal histidine play in hemoglobin?

A

The distal histidine binds to the oxygen and stabilizes the oxygenated form. It prevents the superoxide ion (O=O-) from escaping

82
Q

What is a homotropic regulator?

A

A molecule that regulates its own binding

83
Q

Explain what fractional saturation is

A

When all available heme groups are bound to O2, fractional saturation = 1

84
Q

What is the difference between the oxygen binding curves of hemoglobin and myoglobin?

A

Myoglobin has a hyperbolic curve, whereas hemoglobin has a sigmoid curve

85
Q

Which binds and releases oxygen easier: Hemoglobin or Myoglobin?

A

Hemoglobin because once one O2 molecule is bound, it is easier for additional O2 molecules to bind (allosteric regulation)

86
Q

Explain the 2 conformations that hemoglobin has

A

T state: Tight, O2 binding is weak
R state: Relaxed, picks up O2 right away

at low pO2, predominately T-state
The R-state is the default conformation

87
Q

What does a right shift signify?

A

Decreased O2 affinity

88
Q

What are heterotropic effectors?

A

Molecules such as CO2, H+, and 2,3-BPG that enhance oxygen release, help shift the curve right

89
Q

Describe the two models for cooperative binding in hemoglobin.

A

Concerted model: Hb exists either in T or R state and the equillibrium shifts depending on the pO2. This explains the exponential part of the curve

Sequential model: Different rate constants between the T and R state depending on the pO2, explains the linear part of the curve

90
Q

Which helix in hemoglobin is the proximal histidine part of? Distal histidine?

A

Proximal: Helix F
Distal: Helix E

91
Q

What causes R to T conversion of hemoglobin?

A

increasing 2,3-BPG, reducing pO2, increasing pCO2, decreasing pH, increasing temp

92
Q

What role does 2,3-BPG play in the hemoglobin molecule?

A

It binds right in the center of the molecule connecting the 2 beta subunits connected to positively charged amino acids (it has lots of negative charge)

93
Q

Why does fetal hemoglobin have a higher affinity for O2 than adult hemoglobin?

A

Fetal Hb doesn’t have a histine (OR LYSINE????) residue, so BPG cannot bind to the molecule

94
Q

What does a right shift of the oxygen binding curve mean?

A

Decreased affinity for oxygen

95
Q

How many molecules of BPG bind to each hemoglobin molecule?

A

1

96
Q

Explain what allosteric regulation means.

A

The regulating molecule binds to a site different than the substrate, but effects how well the substrate binds

97
Q

How is does altitude effect the concentration of 2,3 BPG?

A

The concentration of 2,3 BPG increases in order to provide more oxygen to the tissue faster in high altitude

98
Q

Explain gas exchange in the placenta

A

Even though there is no direct interaction between the fetal blood and the maternal blood, oxygen is able to diffuse from the maternal hemoglobin to the fetal hemoglobin due to an oxygen gradient and higher oxygen affinity for fetal Hb

99
Q

Approximately when does the fetal Hb switch from gamma to beta subunits?

A

Approximately 6 weeks after birth

100
Q

Why is carbon monoxide poisoning so deadly?

A

CO is a competitive inhibitor of O2 for hemoglobin binding. Hb has a much higher affinity for CO than for O2, so when CO is present, it will trump any O2 in the area. When CO2 binds, it locks the hemoglobin in the R state causing the other O2 bound to the Hb to be locked in, preventing the tissue from receiving O2

101
Q

Explain the Bohr effect

A

describes the effect of pH and CO2 concentration in the tissues on the oxygen binding of hemoglobin. When the pH is reduced, or CO2 is increased, the curve is shifted right, causing more O2 to be released to the tissues.

102
Q

How does a majority of the CO2 travel throughout the body?

A

In the form of a bicarbonate ion HCO3-

103
Q

What role does Carbonic Anhydrase play?

A

It is an enzyme that catalyzes the conversion of CO2 to HCO3 (and the reverse reaction as well)

104
Q

How does the bicarbonate ion leave the RBC?

A

Through a membrane protein called Anion Exchanger 1 (AE1) which is a counter-transporter that brings Cl- in and HCO3- out

105
Q

Explain the path of CO2 from tissue to lungs

A

1) CO2 is produced by tissue cells
2) It diffuses into the blood and is bound to Hb in RBCs
3) CA catalyzes the conversion to a bicarbonate anion
4) HCO3- leaves through AE1, getting exchanged with Cl-
5) HCO3- travels in the blood to the lungs
6) CA converts HCO3- to CO2
7) CO2 is exhaled

106
Q

What effect does sickle cell anemia have on hemoglobin?

A

A qualitative effect
Regular amounts of Hb are produced, but it is defective due to a one AA mutation
The RBCs have reduced O2 carrying capacity

107
Q

Explain the AA mutation in sickle cell anemia

A

Glutamic acid (charged) is replaced by valine (hydrophobic). This valine residue interacts with a Phe and Val causing the T-state conformation. Hb forms insoluble HbS fibers

108
Q

Explain Thalassemia

A

A quantitative trait in which subjects lack 1 or more of the 4 Hb subunits. Alpha-thalessimia is the most severe, and delta is the least

109
Q

What do enzymes do?

A

The speed up the rate of reactions

110
Q

How are food and oxygen involved in the production of ATP by enzymatic reactions?

A

Food is broken down into NADH which enters the electron transport chain in the inner mitochondrial membrane. A proton gradient is produced by various transmembrane enzymatic reactions including the conversion of O2 to H2O. This gradient provides the energy for converting ADP to ATP.

Biochemistry (4 decks)

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