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Biochemistry Flashcards

1
Q

What is a non polar bond?

A

A covalent bond formed between two atoms that have the same electronegativity. The electrons are shared equally between the two atoms.

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2
Q

What is a polar bond?

A

A covalent bond that is formed between two atoms with different electronegativities. In this bond, the bonding electrons are not shared equally, and more of the negative charge will be found closer to one of the atoms. So the term “polar” means uneven distribution of charge. A dipole is formed.

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3
Q

Why is CO2 a nonpolar molecule but H2O is polar?

A

The two molecules have different geometries: the CO2 is a linear molecule and thus is not polar, H2O has a tetrahedral geometry and thus has a dipole.

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4
Q

What are the two shapes that amphipathic molecules can form?

A

Micelle: where the individual units are wedged shaped (head is bigger than tail).
Bilateral: where’d individual units are cylindrical shaped (cross section of head = that of the side chain).

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5
Q

What is an ionic bond?

A

An ionic bond, or salt bridge, is an electrostatic interaction that occurs between groups of opposite charge.

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6
Q

What is a hydrogen bond?

A

A hydrogen bond is an electrostatic noncovalent interaction. It is electrostatic in nature because the interaction occurs between an atom (the H) that has a partial positive charge and an atom (the A) that has a partial negative charge.

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7
Q

What are dipole-dipole interactions?

A

This is another type of electrostatic noncovalent interaction. It is electrostatic in nature because the interaction occurs between an atom that has a partial positive charge and an atom that has a partial negative charge.

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8
Q

Water is essential to biological systems, not only because it is present in large quantities, but because of the following two reasons:

A
  1. Biological molecules like proteins assume specific 3-D shapes due to the chemical and physical properties of water. Their specific 3-D shapes are tied directly to their functions.
  2. Water can ionize to H+ and OH-. Due to this, it can participate as a key reactant
    in many reactions that occur in biological systems.
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9
Q

What are London dispersion forces?

A

London dispersion forces are van der Waals interactions. They are the weakest type of noncovalent interaction. They occur when non-polar atoms are very close together in space. They originate from very, very small induced dipoles generated in atoms by the random movement of negatively-charged electrons around a positively-charged nucleus

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10
Q

What is the hydrophobic effect?

A

water’s tendency to minimize its contact with hydrophobic molecules by organizing itself around hydrophobic molecules that become clumped together. Hydrophobic molecules clump together so that fewer organized water molecules are necessary. The further organization of the hydrophobic molecules is outweighed by the fact that fewer organized water molecules are present. Overall, this is more favourable and the entropy is higher.

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11
Q

What is a property of strong acids?

A

Strong acids like HCl become completely deprotonated when placed in water. So, for example, if you place 100 molecules of HCl in water, you would quickly see 100 Cl- and 100 H+. Strong acids do not have a strong affinity for their proton(s).

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12
Q

What is a property of weak acids?

A

Weak acids do not automatically become completely deprotonated when placed in water. Weak acids have a strong affinity for their proton(s) and don ’t want to release them.
The degree to which a weak acid will become deprotonated is expressed through its dissociation constant Ka.

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13
Q

What is a property of a strong base?

A

Strong bases like NaOH have a high affinity for protons and will quickly bind to them in solution.

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14
Q

What is a property of a weak base?

A

Weak bases have a weaker affinity for protons and don’t always bind to them in solution.

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15
Q

What is pH?

A

pH is a measure of the acidity of a solution. It is the logarithmic value of the free proton concentration ([H+]) in solution. It is calculated using the following equation:
pH = -log[H+]
When [OH-]=[H+], the pH is 7 and the solution is neutral.

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16
Q

What is a buffer?

A

A buffer is a substance that prevents drastic changes in pH by preventing changes in free [H+] due to the addition of acid or base.

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17
Q

What are the components of a buffer?

A

A buffer consists of a weak acid (A) and its conjugate base (CB).

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18
Q

What happens when a strong acid is added to an unbuffered solution?

A

Adding a strong acid like HCl to an unbuffered system like pure water will result in the [H+] rising. When a buffer is present, the conjugate base can prevent changes in pH by binding to the protons that are being added to the system:
A = CB + H+

I

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19
Q

What substances can act as good buffers?

A

Strong acids cannot be buffers since they completely ionize leaving no A behind. Water cannot be a buffer since it does not ionize sufficiently. Weak acids are best! They sufficiently ionize and allow us to see A and CB.

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20
Q

When do we see 50% acid and 50% conjugate base in solution?

A

When pH = pka (the inflection point)

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21
Q

At what pH values is each given weak acid/conjugate base pair a good buffer?

A

The optimal buffer zone is found when the pH = pKa ± 1.

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22
Q

What are the three main ways to make buffers?

A
  1. Start with A and add a strong base until you reach a pH that is within pKa ± 1.
  2. Start with CB and add a strong acid until you reach a pH that is within pKa ± 1.
  3. Use the HH equation to calculate how much CB and A you need to add to get a solution at a certain pH.
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23
Q

What are the 2 assumptions that are made in this course for the protonation states of functional groups?

A

When the pH is 1 unit BELOW the pKa, we will assume that the functional group with an acidic proton is completely protonated. When the pH is 1 unit ABOVE the pKa, we will assume that the functional group with an acidic proton is completely deprotonated.

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24
Q

What does 1 equivalent of base mean?

A

Adding an amount of base that is equivalent to the amount of acid that we started with.

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25
Q

What is a half equivalence point?

A

An amount of base that is half the amount of acid we started with (causes pH = pka).

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26
Q

What are the three main buffer systems in the body?

A

Carbonic acid/bicarbonate buffer (HCO3-)
Phosphate buffer (H2PO4 -/HPO4 2-)
And proteins

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27
Q

When athletes run they breathe in more oxygen which increases the amount of metabolic acids in the blood which in turn lowers pH. How is this buffered?

A

As carbon dioxide is exhaled and leaves the body, carbonic acid is used up. This shifts the equilibrium to the left. More protons are used up, decreasing [H+] and preventing the pH from decreasing.

ie. H+(up) + HCO3- = H2CO3 = CO2 + H2O (exhaled)
- reaction shifts to the right

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28
Q

Where are D-amino acids occasionally found?

A

In bacterial and fungal peptides

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29
Q

How are amino acids linked?

A

through a linkage known as a PEPTIDE BOND or AMIDE LINKAGE (joined covalently)

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30
Q

What catalyzes the formation of peptide bonds?

A

The ribosome and other enzymes catalyze the formation of peptide bonds to form peptides and proteins.

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31
Q

What type of reactions form peptide bonds?

A

Condensation reactions.

ie. Produces H2O

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32
Q

What is an important convention when talking about amino acids?

A

An amino acid covalently attached to others via peptide bonds is called a residue.

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33
Q

What influences of proteins ability to act as a buffer?

A

A protein’s ability to act as a buffer depends on the number of acidic protons it has. The more acidic protons it has, the better the buffer it will be.
If it ONLY contains diprotic amino acids, the protein will titrate as a diprotic acid (H2A).
If it contains triprotic amino acids, the protein will titrate as a polyprotic acid H3A, H4A, etc.

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34
Q

What is the primary structure of a protein, and what does it tell us?

A

The primary structure consists of the sequence of amino acid residues in a protein. It is typically reported using amino acid 1-letter codes.
The primary structure tells us the number of each type of amino acid and their order.

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35
Q

Why is the primary structure of a protein important?

A

The physicochemical properties of proteins depend on their constituent amino acids. Moreover, the primary structure contains all of the information needed for a protein to achieve its tertiary structure.

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36
Q

What are the two main parts of the protein’s primary structure?

A
  • main chain (or backbone): consists of the amino acid skeletons joined together via peptide bonds. The only difference between the backbone of different proteins is the length.
  • side chains: The side chains are what give proteins their personalities or physicochemical properties.
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37
Q

What is the secondary structure of a protein?

A

Regular local conformations of the BACKBONE mainly stabilized by hydrogen bonds between peptide carbonyl oxygen atoms and amide hydrogen atoms – these hydrogen bonds form H-BOND NETWORKS

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38
Q

What are the two types of secondary structure?

A
  • the alpha-helix; and
  • beta-strands.
    Both types of secondary structure elements are held together via hydrogen bonds between peptide carbonyl oxygen and amide hydrogen groups.
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39
Q

What is a tertiary structure?

A

Tertiary structure refers to the overall 3-D conformation of an entire polypeptide chain. In the tertiary structure, we keep track of the conformation of both the backbone AND the side chains.

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40
Q

How do tertiary structures form?

A

To form tertiary structure, the elements of secondary structure pack together. The tertiary structure of proteins is layered, resembling what is seen in a micelle.

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41
Q

What are 2 types of proteins?

A

Globular proteins and membrane proteins.

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42
Q

What characterizes a globular protein?

A

They are water-soluble proteins, the inner layer contains the hydrophobic amino acids; this allows these amino acids to minimize contact with the protein’s aqueous environment. The outer layer contains the hydrophilic and charged amino acids, which can interact with the aqueous environment through a variety of non-covalent interactions such as hydrogen bonds and ionic bonds.

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43
Q

What characterizes a membrane protein?

A

In membrane proteins, their tertiary structure can also resemble a micelle. However, the consistency of the layers is opposite what is seen for globular proteins.

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44
Q

What characterizes a quaternary structure?

A

Quaternary structure consists of the 3-D arrangement of the polypeptide chains in relation to one another. Only proteins made up of more than 1 polypeptide chain have quaternary structure. These proteins are known as oligomeric proteins.

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45
Q

What is an oligomeric protein?

A

proteins made up of more than 1 polypeptide chain

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46
Q

What is a monomer if protein?

A

Proteins that only contain one polypeptide chain.

47
Q

True or false, peptide bonds are POLAR and have a partial double-bond character.

A

True

48
Q

True or false, there is rotation around the peptide bond axis.

A

False, Because of its partial double-bond character, the peptide bonds are planar and there is NO ROTATION AROUND THE PEPTIDE BOND.

49
Q

Where is there rotation around bonds in a peptide backbone?

A

Rotation in the polypeptide backbone is only allowed around two bonds:
(1) around the N-Cα bond: rotation angle is known as Φ – sounds like “first”; rotation angle around N-Cα bond (the first bond you see when you look at an amino acid from N to C)
(2) around the Cα-C bond: rotation angle is known as Ψ – sounds like “second”; rotation angle around Cα-Co bond (the second bond you see when you look at an amino acid from N to C)
Think of the Cα as a “pivot point”. Planes of atoms rotate about Cα.

50
Q

On what axis are phi and psi plotted on a Ramachandran plot?

A

Φ is plotted on the x-axis, while Ψ is plotted on the y-axis.

51
Q

Due to steric hindrance there are only a few places on the Ramachandran plot where specific combinations of phi and psi allow the protein backbone to adopt specific types of secondary structure. Where on the plot are these secondary structures found?

A

right-handed alpha helices typically have phi angles of approximately -60 ± 5 degrees, and psi angles of approximately -50 ± 5 degrees (lower left hand quadrant of the plot).
Beta-sheets, which are made up of beta-strands, on the other hand have phi/psi combinations in the upper left-hand quadrant of the plot.
(Left handed alpha helices are in the top right hand quadrant).

52
Q

What is steric clash?

A

When Sterically forbidden combinations cause two or more atoms to try and occupy the same location at the same time.

53
Q

Peptide bonds are usually trans, because there is less steric hindrance than in the cis conformation, however there is one exception, what is it?

A

Peptide bonds N- terminal of proline are sometimes found in the cis conformation. Because the R- group of proline is covalently attached to the alpha-amino group, it is more difficult to avoid steric clashes when the peptide bond is in either cis or trans conformations. The trans conformation is still favoured, but less favoured than for peptide bonds preceding other amino acids.

54
Q

How do you find the N-terminus in an alpha helix?

A

Look for where the N-groups point

55
Q

How do you determine if a helix is right handed or left handed?

A

Take your right hand and form a fist. Point your thumb towards the C-terminus. If the direction in which your fingers curl matches the direction in which the helix curls, then the alpha-helix is right-handed. This is the most common type of helix.

56
Q

What is the distance of one turn of an alpha helix?

A

One turn or one repeat of the alpha-helix travels a distance of 0.54 nm or 5.4 Å. This distance is known at the pitch or rise of the helix. It consists of 3.6 amino acids. This means that each amino acid travels a distance of 1.5 Å.
Practice: What is the length of a 12-residue α-helix?
12 aa x 1.5 Å/aa = 18 Å

57
Q

Where do the side chains point in an alpha helix and why?

A

The side chains of all amino acids in an alpha-helix point out from the core of the helix.
The reason? The core is full! If you were to look inside the core of an alpha-helix, you would see that there is no space.

58
Q

What are beta strands?

A

A β-sheet is made up of β-strands, which are portions of polypeptide chain.

59
Q

What are the 2 types of beta sheet?

A

Parallel and anti parallel

60
Q

Why are the H-bonds in anti parallel beta sheets stronger than in parallel beta sheets?

A

the H-bonds are stronger because they are linear. In parallel beta-sheets, the H-bonds are weaker because they are not as linear.

61
Q

What is the distance travelled by each amino acid in a beta sheet?

A

Each amino acid in a beta-sheet travels a distance of 3.5 Å, which is much larger than the distance travelled per amino acid in an alpha-helix. This is why amino acids in a beta-sheet are said to be extended.

62
Q

What do the side chains in beta sheets do?

A

Side chains in either type of β-sheet alternate up and down.

63
Q

What are the properties of an alpha helix?

A
  • stabilized by H-bonds
  • H-bond rule: C=O of residue i H-bonds with the N-terminus of residue i+4
  • right handed
  • pitch/rise = 5.4 A (angstroms)
  • # of a.a.’s per turn: 3.6
  • distance travelled per a.a.: 1.5 A (angstrom)
  • side chains point away from the core of the helix.
64
Q

True or false, left handed alpha helices are not found in proteins.

A

True, they are not equivalent to right handed proteins.

65
Q

What is the angle between each alpha helix in a helical wheel?

A

100 degrees

66
Q

What are the features of beta sheets?

A
  • Stabilized by H-bonds
  • two types: parallel and anti parallel
  • no H-bond rule
  • distance travelled per aa: 3.5 A (angstroms)
  • side chains alternate up and down.
67
Q

Why do beta sheets twist?

A

Two main reasons:

  1. To avoid steric hindrance
  2. By having the sheets twist the molecules that form H-bonds are better aligned so the H-binds can be stronger.
68
Q

What is a topology map?

A

A 1D diagram that shows how beta strands interact to form beta sheets.

69
Q

True or false, if things are side by side in a sequence then they are arranged side by side in a tertiary structure.

A

False

70
Q

What type of secondary structure elements does Hb have?

A

Alpha helices only.

71
Q

Can we predict whether a segment of a polypeptide chain will form an alpha helix or a beta strand?

A

NO!!!!

72
Q

What are the features of a tertiary structure?

A
  • It is the complete arrangement in 3D of the backbone and the side chains of the polypeptide.
  • built from combinations of secondary structural elements
  • highest level of structure for a monomeric protein.
  • it is layered
73
Q

How are secondary structure elements packaged to yield a tertiary structure?

A

Primary structure = polypeptide folds into local regular and irregular spatial arrangements = tertiary structure.

74
Q

Where do the charges accumulate in an alpha helix?

A

Negative accumulates at the C-terminus and positive accumulates at the N-terminus (due to partial double bond and dipoles in the peptide backbone).

75
Q

How do beta sheets pack together with other beta sheets and alpha helices?

A

Alternating R groups and similar side chains. ie. Polar and polar or nonpolar and nonpolar.

76
Q

How do secondary element structures stick together?

A

H-bonds, ionic bonds, van der wals forces, and the hydrophobic effect (most important for tertiary structure formation).

77
Q

What two factors can stabilize tertiary structures?

A

Disulphides bridges and/or the presence of a cofactor.

78
Q

Where are disulfide bonds formed?

A

Between two cysteine groups

79
Q

What types of proteins are cysteine groups found in?

A

Found in proteins exclusively excreted outside the cell because it forms covalent bonds. These are strong bonds that can take a lot of abuse because outside the cell is a very harsh environment (keeps protein from unfolding).

80
Q

What is a cofactor?

A

Cofactors are inorganic ions or complex organic or metalloorganic molecules. These often help proteins fold into their 3D shape.

81
Q

What are cofactors called when they are covalently attached to proteins?

A

Prosthetic groups. ex. Heme

82
Q

How many chains and heme groups does hemoglobin have?

A

4 chains and 4 heme groups.

83
Q

What is a domain?

A

An individually folded bit of tertiary structure.

ex. 1 chain folds as 2 distinct parts

84
Q

What types of proteins have domains?

A

Multiple domains found in proteins that perform more than 1 job.
ie. Each domain performs a function.

85
Q

What are the features of a domain?

A
  • in some proteins domains are involved in playing very different roles.
  • one domain may bind to a specific bio molecule or may be responsible for the catalysis of a certain reaction.
  • proteins with domains are often said to have a bi- or multilobial appearance.
86
Q

Why are irregular loops found on the outside of the protein?

A

The H-bonding requirements of the polypeptide backbone are not satisfied and so these structures interact with water at the surface.

87
Q

What are three points about quaternary structures?

A
  • only applies to oligomeric proteins.
  • all that applies to tertiary structures in terms of covalent and non covalent bonds also applies to quaternary structures.
  • one advantage: subunits communicate with one another.
88
Q

What does hemoglobin do?

A

Carries O2 and maintains pH

89
Q

True or false, oxygen is polar

A

False oxygen is nonpolar

90
Q

What is the typical partial pressure of O2 in the blood?

A

20 torr

91
Q

What is myoglobin analogous to?

A

A tank of oxygen.

92
Q

What 3 factors determine the success of oxygen transport?

A
  1. An efficient way for oxygen to bind to myoglobin and hemoglobin.
  2. Hemoglobin must be able to effectively bind to oxygen at the lungs and then unload it at the tissue area
  3. Myoglobin must be able to effectively bind to any O2 released by hemoglobin, and then release it at the mitochondria.
93
Q

What are the shapes of the lines for myoglobin and hemoglobin?

A

Hyperbolic and sigmoid.

94
Q

Define positive coopertivity

A

When one chain of Hb binds to oxygen it tells the other three chains and changes their affinity.

95
Q

How do hemoglobin and myoglobin differ in structure? How are they the same?

A

Their primary structures are different, their tertiary structures are the same for one of the chains of the hemoglobin and a myoglobin.

96
Q

How does the structure of Hb change when oxygen binds?

A

Oxygen binding changes the position of the iron in the heme group which causes the entire tetramer to change confirmation from the T (tense) state to the R (relaxed) state; dimmer movement causes a 15 degree rotation which breaks existing bonds and forms new ones.
O binds = electron redistribution on the Fe atom and diameter shrinks allowing it to be in plane with the heme; distance moved: 0.6 A

97
Q

Why can Hb adopt 2 different conformations?

A

It is a buffer

ie. Protons and CO2 (allosteric effectors) causes Hb to adopt the T state

98
Q

What are Allosteric effectors.

A

Molecules that bind to Hb and effect the binding and release of O2.

99
Q

When are CO2 and H+ produced by the muscles?

A

During periods of heavy work. They stabilize the T state by binding to deoxy-Hb

100
Q

What is the Bohr effect?

A

Hb has a weaker affinity or oxygen at a higher pH.
- this is important for periods of heavy work because pH of tissue decreases when tissues are starved for O2 and the stabilizing T state allows Hb to unload more oxygen.

101
Q

Where does CO2 bind to the hemoglobin?

A

Binds reversible to the N-terminal amino groups of Hb subunits, changing them from positively charged to negatively charged.
-stabilizes T by forming more ionic bonds

102
Q

Where does H+ bind to hemoglobin?

A

The N on a histidine amino acid turning it from neutral to positively charged.

103
Q

What are the two types of immunity?

A
  1. Cellular immunity: mediated by T lymphocytes or T cells; particularly effective at eliminating virally infected cells.
  2. Humoral immunity: mediated by antibodies (aka immunoglobulins) produced by B lymphocytes or B cells; effective against bacterial infections and extracellular phases of viral infections.
104
Q

How many classes of human immunoglobulins are there are what are they made of?

A
  • 5 classes
  • at least 4 subunits (12 domains in IgG having immunoglobulin fold) with 2 identical 23kDa light chains and two identical 53-75kDa heavy chains each having both constant and variable domains.
105
Q

What are antigens?

A

Foreign macromolecules (often proteins or carbohydrates) that bind to immunoglobulins

106
Q

Why are immunoglobulins flexible?

A

Because antigens come in all shapes and sizes and they need to buy no to them.

107
Q

How many variable domains are there in an igG and what is a variable domain?

A

4; portions of the protein that allow for intentional primary structure amino acid changes. This is needed to make a complimentary domain to the antigen.

108
Q

How is an IgG held together?

A

Held together covalently by 2 types of disulfide bonds: inter-disulfide bonds, and intra-disulfide bonds and noncovalent interactions. ie. Hydrogen bonds.

109
Q

What are hyper variable loops?

A

In IgG, change to adapt to antigens; primary structure amino acid changes are restricted to this area.

110
Q

How are the domains of IgG held together?

A

Two beta sheets are sandwiched together and a disulfide bond holds them together. This is called the immunoglobulin fold.

111
Q

How do you know if your proteins of interest is in a fraction?

A

Test for some unique identifying property of your protein of interest - an ASSAY

112
Q

What is Beer’s law used for?

A

Allows you to determine the total protein concentration that you have in your fraction. ie. Aromatic a.a.’s absorb light at a wavelength of 280nm.

113
Q

What type of positively charged residues are near the center of the hemoglobin tetramer? Why are they important?

A

Lys, His, Arg; this is where 2,3-BPG binds and stabilizes the T state

114
Q

What is the function of 2,3-BPG?

A

Stabilizes the T state; when the concentration of this goes up the Hb’s affinity for oxygen goes down. (Curve shifts right)

Biochemistry (3 decks)

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