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Malika Biochem MCAT > Chapter 1&3 > Flashcards

Chapter 1&3 Flashcards

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1
Q

What are amino acids?

A

Molecules that serve as the building block for proteins. Contain an amino group and carboxylic acid group. Their properties are determined by the R group (side chain) they have.

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2
Q

What does being amphoteric mean?

A

It means the molecule can act as an acid or as a base. Meaning it can either donate or accept a protein depending on the situation.

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3
Q

Which amino acid is achiral?

A

Glycine

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4
Q

Are all the amino acids in eukaryotes L-amino acids or D-amino acids?

A

L-amino acids. This means the amino group has to be drawn on the left in a Fisher Projection.

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5
Q

Name the nonpolar amino acids.

A

Glycine, alanine, valine, isoleucine, leucine, methionine, phenylalanine, proline, tryptophan

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6
Q

Name the polar amino acids.

A

Serine, threonine, tyrosine, cysteine, asparagine, glutamine

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7
Q

Name the basic amino acids.

A

Lysine, histidine, arginine

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8
Q

Name the acidic amino acids.

A

Glutamate (glutamic acid) and aspartate (aspartic acid).

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9
Q

Which amino acids are hydrophilic?

A

The ones that are charged, meaning they can ionize in water.

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10
Q

If the pH < pKa, the group will be _____.

A

Protonated

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11
Q

If the pH > pKa, the group will be _____.

A

Deprotonated

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12
Q

What is the pKa for a carboxyl group?

A

2

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13
Q

What is the pKa for an amino group?

A

9-10

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14
Q

At very acidic pH values, amino acids tend to be _________ charged.

A

positively

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15
Q

At very basic pH values, amino acids tend to be _________ charged.

A

Negatively

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16
Q

At what pH are the zwitterion form of amino acids favored?

A

At neutral pH around 7

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17
Q

What are zwitterions?

A

This is when the amino acid carries a neutral charge because the COOH group is deprotonated and the amino group remains protonated

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18
Q

How is a peptide bond formed?

A

It is formed when the amino group attacks the electrophilic carbon on the COOH group. This allows a water molecule to be removed making the reaction a “dehydration synthesis” reaction.

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19
Q

How is a peptide bond broken.

A

This occurs via the addition of an H2O molecule. The amide bond breaks by adding an H atom to the amide nitrogen and an OH to the carbonyl alpha carbon.

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20
Q

Define primary structure of a protein.

A

It is the sequence of amino acids, which are stabilized by peptide bonds.

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21
Q

Define secondary structure of proteins.

A

This is the local folded structures that form due to intermolecular hydrogen bonding between nearby amino acids.

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22
Q

What are the two types of secondary structures of proteins?

A

Alpha helix and beta pleated sheets.
The alpha helix is a rod like structure where peptide chains coil clockwise around a central axis. The R groups point away from the core.
Beta pleated sheets can be parallel or anti-parallel rippled rows that are held together by intermolecular hydrogen bonding on adjacent chains. The R groups point above and below the plane.

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23
Q

What makes up a protein’s tertiary structure?

A

A proteins 3-D shape is determined by noncovalent interactions between R groups such as ionic bonding, hydrogen binding, dipole-dipole interactions, and London dispersion forces. A covalent bond called a disulfide linkage, occurs between sulfur atoms on cysteine amino acids. Hydrophobic interactions between nonpolar amino acid R groups inside the protein are also important.

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24
Q

Tertiary structure can also involve noncovalent bonds via R groups holding together alpha helices and beta strands that would otherwise be far apart from each other.

A
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25
Q

What happens during denaturation of a protein?

A

The protein loses its higher order structure, but maintains its primary structure, that is the amino acid sequence. Sometimes this process is reversible and sometimes it isn’t.

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26
Q

What happens in protein folding in terms of entropy?

A

During protein folding the hydrophobic residues shift to the inside of the proteins, while the hydrophilic residues go to the exterior coming in contact with nearby water molecules. They form hydrogen bonds which increase the entropy of water. This stabilizes the protein structure itself, causing a decrease in entropy for the protein.

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27
Q

If a protein is denatured the protein unfolds, this causes the overall deltaG to become (positive/negative)

A

Positive because protein unfolding is a nonspontaneous process.

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28
Q

What determines a proteins quaternary structure?

A

This happens when multiple polypeptide chains or multiple subunits come together. This is favorable because it reduces the surface area, making the protein more stable and bringing closer together the catalytic sites. Not all proteins have a quaternary structure.

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29
Q

What is a conjugating protein?

A

It is a protein that derives part of its function from prosthetic groups that covalently attached to it. Examples of prosthetic groups, include vitamins, cofactors, ions, lipids, carbohydrates, nucleic acids.

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30
Q

How do you calculate PI for an acidic amino acid?

A

You add the pKa of the R group and the pKa of the COOH group and then divide it by two.

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31
Q

How do you calculate PI for a basic amino acid?

A

You add the pKa of the amino group in the pKa of the R group and then divided by two.

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32
Q

What is the isoelectric point of an amino acid?

A

It it is the pH at which the amino acid carries a neutral charge.

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33
Q

How do you calculate the pI of a long polypeptide?

A
  1. Find the max charge of the polypeptide.
  2. Count the number of steps to get to a 0 charge.
  3. Use that number of steps to cross off each pKa value starting from lowest .
  4. Look to see the pKa before and after the 0 charge step.
  5. Use those two before and after pKa’s and divide by 2 to get the pI of the polypeptide.
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34
Q

What is the role of collagen?

A

It’s role is to provide strength and flexibility in connective tissue.

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35
Q

What is the structure of collagen?

A

It is a trimer with three polypeptide chains wound together to form a triple helix. The helices assemble into cable-like fibers; which are strengthened by covalent cross-link bonds on adjacent collagens.

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36
Q

What is the function of elastin?

A

It’s primary role is to stretch, and then recoil like a spring, restoring original tissue shape.

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37
Q

What are the two main structural proteins found in connective tissue?

A

Collagen and elastin

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38
Q

What are intermediate filament proteins?

A

They are proteins, such as keratin that contribute to the mechanical integrity and structural support of the cell. They withstand a lot of tension and are involved in cell-cell adhesion. These proteins are permanent meaning they don’t change length and have a diameter of 10 nm.

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39
Q

What are microfilament proteins?

A

They are proteins made up of twisted chains of actin polymers. They are 7 nm in diameter and they are polar meaning they have a positive and negative side, which allows motor proteins to travel along them. They are also dynamic meaning they lengthen and shorten during actin polymerization and depolymerization.

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40
Q

What are microtubules made out of?

A

They are made of alternating sheets of alpha and beta tubulin dimers that form a protofilament. 13 protofilaments make up 1 microtubule (a hollow tube).

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41
Q

What are some functions of microtubules?

A

They provide structural support, aid in chromosome separation in mitosis and meiosis, and intracellular transport with kinesin and dynein.

42
Q

What are some characteristics of microtubules?

A

They have a diameter of 25 nm and they are polar. They have a negative end which anchors the microtubule organizing center and a positive end close to the periphery where dimers are added.

43
Q

Name three types of microtubules.

A

Kinetochore microtubules, interpolar microtubules, Astral microtubules

44
Q

What is the function of kinetochore microtubules?

A

They attach to chromosomes to help pull them apart.

45
Q

What is the function of interpolar microtubules?

A

They are responsible for pushing centrioles apart and allowing movement of kinesin proteins. They are intertwining between 2 MTOCs like kinetochore microtubules, but don’t actually connect to the chromosome.

46
Q

What is the function of astral microtubules?

A

They emanate from the centrosome/centrioles and go out word, and bind to the cell membrane. Their function is to help position the plane of cytokinesis.

47
Q

What is a myosin protein?

A

It is the primary motor protein that interacts with actin. It is responsible for the power stroke of sarcomere contraction.

48
Q

What is a kinesin protein?

A

It is a motor protein that is responsible for vesicle transport in the cell towards the positive end of the microtubules. It plays a role in aligning chromosomes during metaphase and depolymerizing microtubules during anaphase of mitosis.

49
Q

What motor protein is involved in bringing a neurotransmitter towards the synaptic terminal?

A

Kinesin

50
Q

Which protein brings recycled neurotransmitters towards the soma?

A

Dynein

51
Q

What is a dynein protein?

A

It is a motor proteins involved in vesicle transport towards the negative end of a microtubule. It is also involved in the sliding movement of cilia and flagella.

52
Q

What are cell adhesion proteins?

A

They are integral membrane proteins, found on the surface of most cells that aid in binding the extracellular matrix of one cell to the extracellular matrix of another cell.

53
Q

Name three types of cell adhesion proteins.

A

Cadherins, integrins, selectins

54
Q

What are cadherins?

A

They are a group of glycoproteins that mediate calcium dependent cell-cell adhesion through the formation of bridges in the extracellular space between cells. There are many different types of cadherins.

55
Q

What are integrins?

A

They are a group of proteins independent from Ca that are characterized by having 2 membrane spanning chains (alpha and beta). They bind molecules such as fibronectin, collagen, vitronectin.

56
Q

What are selectins?

A

They are a group of Ca dependent glycoproteins that recognize and bind to specific arrangements of oligosaccharides projecting from other cell surfaces. They are involved in cell-cell adhesion, inflammation, and white blood cell migration.

57
Q

What are immunoglobulins?

A

They are proteins produced by the B cells of the immune system that function to neutralize harmful targets in the body and recruit other cells to help eliminate the harmful antigens.

58
Q

What is the structure of an immunoglobulin protein?

A

It is a Y-shaped proteins made of two identical heavy chains and two identical light chains which are held together by disulfide linkages and non-covalent interactions. The protein contains a V domain where the specific antigen binds.

59
Q

What are the three ways in which an antibody response to an antigen?

A
  1. Neutralizing the antigen
  2. Opsonization - marking the pathogen for destruction by other WBCs immediately
  3. Agglutination - clumping the antigen and antibody together into a large insoluble protein that can be digested by macrophages
60
Q

What is the function of integrins in the body?

A

They play an important role in cell, signaling, promoting cell division, apoptosis, white blood cell migration, and stabilization of the epithelium on the basement membrane.
More importantly, they bind substrates in the ECM which allows for transmission of a signal to the inside of the cell.

61
Q

How is the relationship between solute concentration and rate of solute movement different for simple diffusion and facilitated diffusion?

A

For simple diffusion, this relationship is strictly linear. However, for facilitated diffusion as the solute concentration increases the rate of solute movement eventually approaches saturation (Vmax).

62
Q

How does water travel through the plasma membrane?

A

It travels via facilitated diffusion through aquapourin channels.

63
Q

Characteristics of an aquapourin protein channel.

A

This protein channel is made up of alpha helices. It can diffuse up to 1000,000,000 water molecules, However, each H2O molecule passes through this transmembrane protein, one by one.

64
Q

What is a GPCR?

A

G protein coupled receptor, integral membrane protein made of 7 alpha helices, involved in signal transduction pathways. Has three parts: extracellular domain, membrane spanning region, & intracellular domain.

65
Q

Steps of GPCR mediated signal transduction

A
  1. Extracellular ligand binds to the GPCR and cause a conformation change.
  2. The heterotrimeric G protein interacts w/ the GPCR and GDP gets exchanged for GTP.
  3. This activates the alpha subunit that GTP is attached to and causes the beta/gamma subunit to dissociate.
  4. The alpha subunit goes on to bind to an effector molecule such as adenlyl cyclase which produces many 2nd messengers.
  5. To turn the system off, the GTP on the alpha subunit is hydrolyzed back to GDP, deactivating the alpha subunit.
  6. The beta/gamma subunit then reassembles and the trimeric G protein dissociates from the GPCR.
66
Q

What are the 3 types of alpha G proteins subunits?

A

Gs - activates adenylyl cyclase effector molecule
Gq - activates phospholipase C beta
GI - inhibits adenylyl cyclase effector molecule

67
Q

What is an enzyme linked receptor?

A

Also known as a catalytic receptor where the binding of an extracellular ligand causes enzymatic activity on the inside of the cell.

68
Q

What are the 3 parts that make up an enzyme linked receptor?

A

Extracellular ligand binding domain, membrane spanning domain, catalytic domain

69
Q

Name an example of an enzyme linked receptor.

A

Receptor tyrosine kinase

70
Q

Define flagella.

A

They are whip like projections from the cell body that are used for locomotion. They are made of microtubules. In humans, sperm cells are the only cells that have flagella.

71
Q

Define cilia.

A

Whip like protrusions from the cell body which create a beating pattern that move fluid or extra cellular material past the cell. They aren’t involved in moving the actual cell.

72
Q

In which human cells are cilia located?

A

Ependymal cells that line the ventricles of the brain and inner spinal cord, epithelial cells that line the respiratory tract, and cells that line the fallopian tubes which move the egg towards the uterus.

73
Q

Compare eukaryotic vs. prokaryotic flagella.

A

Eukaryotic - produce a whip-like motion, made of microtubules
Prokaryotic - produce spinning & rotating motion, made of flagella protein

74
Q

How are the microtubules in eukaryotic cilia and flagella organized?

A

9+2 arrangement; 9 doublets (1 alpha/1 beta in each doublet) surrounding two microtubules in the center.
Looks like a flower

75
Q

What are the main functions of receptor tyrosine kinases?

A

Their main functions are to bind growth factors that aid in cell growth and blood maturation. They also bind hormones like insulin.

76
Q

Describe the process of signal transduction with a receptor tyrosine kinase.

A
  1. A ligand binds to each of the RTK monomers, and these nearby monomers dimerize.
  2. Once in dimer formation, they cross phosphorylate each other’s tyrosine sites on the intracellular side.
  3. Intracellular enzymes attached to the phosphorylated tyrosine sites and are activated.
  4. These enzymes go on to activate other kinases.
77
Q

What are the main functions of GPCR proteins?

A

They regulate a diverse range of functions, such as hormone regulation, smell, vision, cell growth, etc.

78
Q

If an integrant binds to a substrate extracellularly, what kinds of things can occur inside the cell?

A

Kinase, activation, polymerization of actin filaments, activation of gene expression

79
Q

What is the function of microfilaments?

A

They use ATP to generate force for movement by interacting with myosin in muscle contraction and they form the cleavage furrow during cytokinesis in the division of two new daughter cells.

80
Q

Which amino acids are able to be phosphorylated?

A

Tyrosine, threonine, serine (YST neumonic),
histidine (rare)

81
Q

Which amino acids mimic “phosphorylated” amino acids?

A

Remember phosphorylated AAs have a - charge. So Glu and Asp mimic them, bc they already have a negative charge R group.

82
Q

Which amino acid is most commonly acetlyated?

A

Lysine (K)

83
Q

What is the pKa of the side chain in histidine? What is the significance of this?

A

It is about 6. That means it is readily protonated/deprotonated at physiological pH of 7. At this pH, most of the side chains are deprotonated, but small % still have a + charge.

84
Q

What is the pKa (usually) of an acidic R group?

A

4

85
Q

What is the pKa (usually) of a basic R group?

A

11-12

86
Q

Trypsin and chymotrypsin cleave proteins on the (N-terminus/C-terminus).

A

C terminus

87
Q

At which amino acids does trypsin cleave?

A

Arginine and lysine

88
Q

At which amino acids does chymotrypsin cleave?

A

Phenylalanine, tryptophan, and tyrosine

89
Q

Which amino acid is the most basic out of the 3?

A

Arginine

90
Q

Compare definitions of essential vs. nonessential amino acids.

A

Essential AA - Body can’t synthesize it, needs to come from diet.
Nonessential AA - Body can synthesize it naturally on its own.

91
Q

In which protein structure is proline found?

A

At the ending point of turns in beta sheets

92
Q

How do you find the PI of an uncharged polar amino acid (has 3 pkA values)

A

You take the 2pKa values which are closest to the 0 net charge of the amino acid. For example line up all the pKas from lowest to highest. Find max charge and start deprotonating from there until you reach 0. Then find the two pKA values that fall right before and right after the 0.

93
Q

What is the weight of an average amino acid?

A

110 Da

94
Q

What are aliphatic amino acids?

A

Amino acids which are nonaromatic, non polar, and hydrophobic.

95
Q

Which amino acids can be hydroxylated (addition of an OH group)

A

Aliphatic amino acids such as proline, isoleucine, leucine, alanine, valine, methionine, etc

96
Q

Which two amino acids are NOT found in alpha helices and why?

A

Proline and glycine because they disrupt the bonds.D

97
Q

Which amino acids are most commonly found in nature (in our bodies)?

A

L-amino acids

98
Q

Histidine has a _____ in its side chain, while tryptophan has a ______ in its side chain.

A

imidazole, pyrrole (indole group altogether)

99
Q

If pH > pI, then ….
If pH < pI, then ….
If pH = pI

A

pH > pI, majority of protein’s functional groups are deprotonated
pH < pI, majority of functional groups remain protonated
pH = pI, half of functional groups are deprotonated, other half protonated thus the ratio of cations:anions is 1 and net charge is 0

100
Q

Finding Km and Vmax on a Lineweaver Burke Plot

A

Km = -(-1/x-intercept value)
Ex: -(-1/0.05) = 20mM

Vmax = 1/y-intercept
Ex: 1/2000 =

Malika Biochem MCAT (11 decks)

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