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DPC > Group 8/14/19 > Flashcards

Group 8/14/19 Flashcards

1
Q

Learning issues and look ups

A

Here are our learning issues for Friday:
Biochemistry of amino acids (Marks’ Ch6)
Biochemistry of protein structure (Marks’ Ch7)
Innervation from the wrist down

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2
Q

functions of proteins in the body

A 
transport hydrophobic compounds
attach cells to each other and ECM
hormones that carry signals 
ion channels in lipid membranes
enzymes to speed up reactions
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3
Q

primary structure

A

linear sequence of amino acids that determines the unique characteristics of a protein

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4
Q

genetic code

A

sequence of 3 bases (nucleotides) in DNA that contains the information for the linear sequence of amino acids in the polypeptide chain (its primary structure)

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5
Q

mutations

A

changes in the nucleotides of a gene that result in a change in the products of that gene that might be inherited

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6
Q

general structure of an amino acid parts

A

carboxylic acid group: COO-
amino group: H3N+
hydrogen atom
side chain

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7
Q

what configuration is the alpha carbon of an amino acid in?

A

L-configuration, characteristic of all mammalian proteins’ amino group

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8
Q

what is the name for a free amino acid at physiological pH? Characteristic?

A

zwitterion, has positively charged amino group and negative carboxylate

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9
Q

zwitterion

A

ion in which the amino acid is positively charged and the carboxylate group is negatively charged

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10
Q

what joins amino acids?

A

amino acids are joined by peptide bonds to form polypeptide chains.

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11
Q

how are amino acids grouped by the polarity of the side chain?

A

charged, nonpolar hydrophobic, or uncharged polar

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12
Q

how are amino acids grouped by structural features?

A

aliphatic, cyclic, aromatic

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13
Q

what characteristic do nonpolar hydrophobic proteins share?

A

they’ll cluster together and exclude water

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14
Q

what characteristic do the uncharged polar amino acids share?

A

participate in hydrogen bonding

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15
Q

which amino acid forms disulfide bonds?

A

cysteine, contains a sulfhydrl group

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16
Q

which amino acids are acidic, what characteristic do they share?

A

aspartate and glutamate are negatively charged and acidic

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17
Q

which amino acids are basic, what characteristic do they share?

A

lysine, arginine, and histidine, are positively charged and they are basic (arginine most basic)

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18
Q

what determines the charge on the amino acid?

A

the pKa (- log of the Ka, the dissociation constant)

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19
Q

polymorphism and example

A

a polymorphism is a genetically determined variation in primary structure
example is hemoglobin in humans

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20
Q

what is the relationship between pKa and the acidity

A

the pKa will be low for things that are acidic

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21
Q

what is the connection between pKa and pH?

A

if the pH is lower than the pKa, the acidic groups will be protonated, meaning they’ll have a positive charge

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22
Q

name the two terminals of the side chains

A

carboxyl terminal: last amino acid in chain, has free carboxylate group
amino terminal: first amino acid in the chain, has free amino group

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23
Q

hydropathic index and interpretation

A

a scale used to denote the hydrophobicity of the side chain

more positive means more hydrophobic

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24
Q

nonpolar, aliphatic amino acids names

A

glycine, alanine, proline, valine, leucine, isoleucine

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25
Q

aromatic amino acids names, and their polarity

A

phenylalanine (nonpolar hydrophobic), tyrosine (polar), tryptophan (polar)

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26
Q

polar, uncharged amino acids names

A

asparagine, glutamine, serine, threonine

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27
Q

sulfur-containing amino acids names

A

methionine, cysteine

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28
Q

charged amino acids names

A

aspartate, glutamate, arginine, lysine, histidine

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29
Q

glyine structure and function

A

R: H

not a lot of steric hindrance, usually in bends or chains

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30
Q

structure of aliphatic, polar, uncharged amino acids

A

contains amide group: asparagine, gluatmine
contains hydroxyl group: serine and threonine
hydrogen bonding, with each other or other polar compounds
usually found on surface of water-soluble globular proteins

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31
Q

cysteine structure

A

R: CH2-SH (sulfhydryl group)

can form disulfide bonds with each other

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32
Q

methionine structure

A

R: CH2-CH2-S-CH3
nonpolar, bulky hydrophobic side chain, doesn’t form disulfide bonds. Important metabolic role is to transfer terminal methyl group to other compounds.

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33
Q

isoelectric point (pI) and significance in testing

A

pH at which the net charge on the molecules in the solution is 0
molecules will not migrate in an electric field toward the positive pole (cathode) or negative pole (anode)

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34
Q

electrophoresis

A

technique used to separate proteins on the basis of charge

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35
Q

variant regions

A

regions of the primary structure that are noncritical and thus variations are tolerated

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36
Q

hypervariable

A

region of primary structure where different amino acid residues are all tolerated at one position

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37
Q

invariant regions

A

regions that form binding sites or are critical for forming a 3D structure. Will have exactly the same amino acid sequences between individuals.

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38
Q

polymorphism

A

variation of an allele (alternate forms of gene at same place on chromosome) that occur with a significant frequency in the population

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39
Q

paralogs

A

divisions of a protein family that are considered to be different proteins and have different names, because they have different functions

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40
Q

isoforms/isozymes

A

different forms of a protein/enzyme that have different properties of the amino acid structure, and may have different locations in the body.
They all have the same function (isoforms) or catalyze the same reactions (isozymes)

41
Q

Hemoglobin (Hb) isoforms

A

Good example of protein that has isoforms. Expressed as fetal isozyme HbF during development, then replaced with HbA.
Proteins have different structures, making functions different, HbF has higher affinity for O2

42
Q

posttranslational modification

A

after protein synthesis, usually when the protein is folded, amino acid residues in primary structure may be further modified by reactions that add a chemical group, oxidize, etc.
examples are trimming and covalent alternations (phoshorylation, glycosylation, hydroxylation, methylation, acetylation, ubiquitination)

43
Q

glycosylation and types

A

the addition of carbohydrates to a molecule

types: O-glycosylation and N-glycosylation

44
Q

fatty acylation

A

the addition of lipids to a molecule

usually for membrane proteins, lipid group will interact hydrophobically with the other membrane lipids

45
Q

phosphorylation

A

protein kinase takes a phosphate group from an ATP to phosphorylate a hydroxyl group
introduces large, negatively charged group that can alter structure and protein activity

46
Q

ADP-ribosylation

A

transfer of an ADP-ribose from NAD+ to arginine, glutamine, or cysteine residues on target protein in membrane
regulates the activity of the proteins

47
Q

secondary structure of proteins

A

local regions of polypeptide chains formed into structures that are stabilized by repeating patterns of hydrogen bonds, e.g. alpha-helices and beta-sheets

48
Q

what determines the types of secondary structure that can occur?

A

rigidity of the peptide backbone

49
Q

tertiary structure of proteins

A

involves folding of the secondary structural elements into an overall 3D conformation.
Can allow ligands to bind, allow diffusion of elements in and out, flexibility, changing positions, and puts important residues on surface

50
Q

quaternary structure

A

only some proteins have this. Involves a combination of two or more subunits, each composed of a polypeptide chain.
These can allow cooperative binding of ligands, binding sites for other molecules, or increase the stability of a molecule
General examples include dimers, tetramers, oligomers (refers to number of subunits that make up protein)

51
Q

quaternary structure of fibrous proteins

A

their polypeptide chains are aligned along an axis, have repeating elements, and are linked to each other through hydrogen and covalent bonds

52
Q

what conformation does a protein fold into for tertiary structure?

A

folds into its stable/native conformation

53
Q

chaperonins*

A

helps the protein fold into its stable conformation by helping to overcome kinetic and thermodynamic barriers

54
Q

prion proteins

A

act as a template for protein misfolding and cause neurodegenerative diseases. Can get prion diseases through infection, or may be a normal protein that was misfolded.

55
Q

denaturation, and common causes

A

denaturation is when the protein unfolds, or refolds and loses their native 3D conformation
can be caused by heat, acid, or other agents

56
Q

globular proteins

A

small irregular balls, usually soluble in aqueous medium. Usually has a densely packed hydrophobic core with polar amino acid side chains on the outside facing the aqueous environment.

57
Q

fibrous proteins

A

linear proteins arranged in single axis, have repeating unit structure

58
Q

transmembrane proteins

A

have one or more regions aligned to cross the lipid membrane

59
Q

alpha helix

A

maximizes hydrogen bonding, highly compact rigid structure
peptide backbone has hydrogen bonding within the same strand. H bonds form between each carbonyl oxygen atom and amide hydrogen of further-down amino acid residue

60
Q

Beta sheets

A

maximizes hydrogen bonding between peptide backbones while maintaining allowed torsion angles
hydrogen bonding between neighboring polypeptide chains arranged parallel to each other, optimal when the sheet is bent/pleated

61
Q

nonrepetitive secondary structures

A

bends, loops and turns of secondary structure do not have a repeating element of hydrogen bond formation.
Usually more flexible than alpha helices and beta sheets, sometimes form hinge regions. Characterized by abrupt change of direction, usually on the protein surface.

62
Q

motifs

A

relatively small arrangements of secondary structure that are recognized in many different proteins

63
Q

structural domains

A

physically independent regions of tertiary structure, usually can be identified visually in large complex proteins, because they can have different structures

64
Q

solubility of globular proteins in aqueous environment

A

most globular proteins are cell-soluble. Usually have hydrophobic core, and charged or polar uncharged amino acids are on the surface/outside.

65
Q

protomer

A

unit structure composed of nonidentical subunits

66
Q

what is Ka vs. Kd in the context of ligand binding?

A

Ka is the association constant for the reaction between the ligand and the protein. Calculated by [LP]/[L][P]
Kd is the dissociation constant, which is reciprocal of Ka

67
Q

how does Ka indicate the binding site’s affinity for the ligand?

A

tighter binding of the ligand to the protein means higher Ka and lower Kd

68
Q

myoglobin vs. hemoglobin structure

A

both oxygen binding proteins with similar primary structure, have heme in hydrophobic pocket, binds to Fe2+
myoglobin is globular protein with single polypeptide chain with one oxygen binding site
hemoglobin is tetramer with 2 different subunit types with oxygen binding sites

69
Q

differences in myoglobin and hemoglobin at different PO2’s

A

when partial pressure of oxygen (PO2) is high, both myoglobin and hemoglobin saturated with oxygen
at low levels of PO2 in oxygen-using tissues, myoglobin binds better than hemoglobin, so myoglobin is more saturated with oxygen at lower PO2

70
Q

heme

A

planar porphyrin ring composed of 4 pyrrole rings linked by methenyl bridges that lie with their nitrogen atoms in the center, and bind to the Fe2+ atom

71
Q

prosthetic group

A

organic ligands that are bound tightly to proteins, such as the heme of myoglobin

72
Q

holoprotein vs. apoprotein

A

holoprotein- protein with its attached prosthetic group

apoprotein- protein without prosthetic group

73
Q

cooperativity of O2 binding in hemoglobin

A

conformational changes take pace in tertiary structure when O2 binds to hemoglobin. Changes from tense to relaxed state when O2 binds, and increases affinity for more O2. Called positive cooperativity, creates sigmoidal oxygen saturation curve of hemoglobin.

74
Q

what degree of structure will determine the folding of a protein?

A

primary structure determines protein folding

75
Q

collagen structure*

A

made from a precursor procollagen, a triple helix with 3 polypeptide chains twisted around each other to form a ropelike structure. They’re linked by hydrogen bonds, and glycine (lacks side chain) is present when the strands come in close contact with each other.
Has lots of hydroxylated residues

76
Q

denaturation through nonenzymatic modifications of proteins

A

Examples are nonenzymatic oxidation or glycosylation. In glycosylation, glucose binds and acculumates advanced glycosylation end products (AGEs)

77
Q

protein denaturation by temperature, pH and solvent

A

proteins can be denatured by changes of pH, temperature, or solvent that disrupt ionic, hydrogen, or hydrophobic bonds

78
Q

steps of protein synthesis*

A

initiation, elongation, and termination

79
Q

initiation*

A

eukaryotic initiation factors (eIFs) find either the 5’ cap or an internal ribosome entry site (IRES)
eIFs help combine the 40s subunit with the initiator tRNA
mRNA and 60s subunit will assemble with the complex

80
Q

eukaryotic vs prokaryotic ribosomal subunits in initiation*

A

eukaryotes: 40S and 60S -> 80S
prokaryotes: 30s and 50s -> 70s

81
Q

which processes of initiation are ATP vs GTP used for?*

A

ATP is used for tRNA activation (charging)

GTP is used for tRNA translocation (gripping and going places)

82
Q

what are the different elongation sites and their function?*

A

A site holds the incoming Aminoacyl-tRNA
P site accomodates the growing Peptide
E site holds the Empty tRNA as it Exits

83
Q

steps of elongation*

A
  1. aminoacyl-tRNA binds to the A site, requiring an elongation factor and GTP
  2. rRNA (ribozyme) catalyzes peptide bond formation, transfer growing polypeptide to amino acid in A site
  3. Ribosome advances 3 nucleotides toward the 3’ end of mRNA, translocation moves the peptidyl tRNA to P site
84
Q

termination process of protein synthesis*

A

a release factor recognizes the stop codon and halts translation. The completed polypeptide is released from the ribosome. Requires GTP.

85
Q

trimming*

A

a posttranslational modification where the N- or C- terminal propeptides are removed from zymogen to generate a mature protein (example: trypsinogen t trypsin)

86
Q

collagen and types*

A

organizes and strengthens the extracellular matrix

type 1, type 2, type 3 and type 4

87
Q

mnemonic to remember the different collagen types*

A

[Be So Totally] Cool, Read Books corresponds to the 4 types of collagen

88
Q

type 1 collagen*

A

Be So Totally: in the Bone, Skin and Tendons, as well as dentin, fascia, cornea, late wound repair

89
Q

type 2 collagen*

A

Cool: located in Cartilage, especially hyaline; also found in vitreous body, nucleus pulposus

90
Q

type 3 collagen*

A

Read: Reticulin, found in the skin, blood vessels, uterus, fetal tissue, granulation tissue

91
Q

type 4 collagen*

A

Books: found in the Basement membrane (type 4 under the floor)

92
Q

collagen synthesis process*

A
  1. synthesis: collagen alpha chains are translated (preprocollagen), usually has Gly-X-Y structure
  2. hydroxylation of some proline and lysine residues, requires vitamin C
  3. glycosylation of pro-alpha-chain hydroxylysine residues and formation of procollagen via hydrogen and disulfide bonds, to form triple helix of collagen alpha chains
  4. exocytosis of procollagen into extracellular space
  5. disulfide-rich terminal regions of procollagen are cleaved to form insoluble tropocollagen
  6. covalent lysine-hydroxylysine cross-linkages reinforce tropocollagen molecules to make collagen fibrils
93
Q

what are the essential amino acids?*

A

PVT TIM HaLL: Phenylalanine, Valine, Tyrosine, Threonine, Isoleucine, Methionine, Histidine, Leucine, Lysine

94
Q

what are the glucogenic amino acids?*

A

I MET HIS VAlentine, she is so sweet: Methionine, histidine, valine

95
Q

glucogenic/ketogenic amino acids?*

A

isoleucine, phenylalanine, threonine, tyrosine

96
Q

ketogenic amino acids?*

A

the onLy pureLy ketogenic amino acids: leucine, lysine

97
Q

elastin location*

A

a stretchy protein within skin, lungs, large arteries, elastic ligaments, vocal cords, ligaments flava (connect vertebrae)

98
Q

elastin structure*

A

rich in nonhydroxylated proline, glycine, and lysine residues
cross-linkage takes place extracellularly, has tropoelastin with fibrillin scaffolding

DPC (11 decks)

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