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BIO 2600 > Chapter 4 > Flashcards

Chapter 4 Flashcards

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1
Q

peptide bonds

A

C-N (bond carboxyl group with amino group through condensation rxn)

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1
Q

protein backbone sequence

A

N-C-C; hydrophilic (H-bonds with itself)

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2
Q

primary structure of proteins

A

amino acid sequence

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3
Q

secondary structure of amino acids

A

alpha helix and beta sheet folding caused by hydrogen bonding of the backbone

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4
Q

tertiary structure of proteins

A

specific folding caused by side chains, final shape

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5
Q

quaternary structure

A

2 or more polypeptide chains arrangement

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6
Q

alpha helix

A

secondary structure caused by hydrogen bonding between O-H of carboxyl and amino groups 4 amino acids away
can cross lipid bilayer if side chains (exterior) are nonpolar

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7
Q

beta sheet

A

held together by hydrogen bonds between adjacent strands in picket fence organization
parallel or antiparallel

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8
Q

three types of noncovalent bonds that contribute to protein shape/stability

A

ionic/electrostatic bonds
Van der Waals forces
hydrogen bonds

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9
Q

hydrophobic forces

A

nonpolar molecules repel water and force nonpolar side chains together

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10
Q

disulfide bonds

A

covalent bond between adjacent cysteine side chains by oxidation rxn
takes place in ER only (NOT form in cytosol)
important for secreted proteins to maintain function

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11
Q

protein domain

A

segment of polypeptide chain that fold independently into compact stable structure

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11
Q

protein motif

A

simple combinations of secondary structures, not stable by itself, can’t fold by itself

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12
Q

coiled-coil

A

protein motif
2 a-helices coiled around each other with hydrophobic in center and hydrophilic parts exposed

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12
Q

protein subunit

A

separate polypeptide chain of a protein that assembles with other polypeptide chains to form a protein complex

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13
Q

hemoglobin structure

A

made of 2 alpha globin and 2 beta globin subunits, becomes functional at quaternary stage
denatured: loses quaternary, tertiary, and secondary structures

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14
Q

myoglobin

A

made of 1 polypeptide chain, functional at tertiary structure
denatured: loses secondary and tertiary structures

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15
Q

globular proteins

A

one binding site, form dimers

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16
Q

filamentous proteins

A

multiple binding sites, form long helical filament

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17
Q

ring

A

formed when 2 binding sites of identical proteins are disposed appropriately to each other

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18
Q

actin filament

A

helical structure formed by many identical subunits

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19
Q

collagen

A

fibrous protein
triple helix formed by 3 polypeptide chains
bone, cartilage, skin
cross-linked in ECM to form collagen fibrils

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20
Q

elastin

A

fibrous proteins
cross-linked by covalent bonds to form elastic fibers, stretchy protein
important in stretchy tissues, lungs, bladder, some blood vessels

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21
Q

Fibrous protein molecules

A

keratin, elastin, collagen, actin(polymer)

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22
Globular protein molecules
lysozyme, hemoglobin, actin(monomer)
23
serine proteases
family of protein-cleaving (proteolytic) enzymes that include digestive enzymes (chymotrypsin, trypsin, elastase) and proteases involved in blood clotting
24
chaperons
proteins that help other proteins fold, many are heat-shock proteins or isolation chambers
25
denaturation
unfolding due to changes in temp, pH, chemicals, usually reversible
26
protein aggregation
occurs with misfolded proteins in the nervous system, causes neurodegenerative diseases (Alzheimer's, Huntington's)
27
prion
pathogenic misfolded protein that can pass shape to other proteins, "mad cow" disease
28
ferritin
storage protein that stores iron in the liver
29
insulin
signal protein that controls blood glucose levels
30
receptors
proteins that detect signals and transmit to cell's response machinery
31
hemoglobin/myoglobin
transport proteins that carry O2 and CO2 in blood and muscles, respectively
32
collagen/keratin
structural proteins that form cartilage, hair, and nails
33
actin/myosin
motor proteins that allow muscles to contract
34
immunoglobins(antibodies)
defense proteins that recognize foreign organisms and cancer cells
35
transcription factors
regulatory proteins that regulate gene expression
36
Green fluorescent proteins (GFP)
special-purpose protein from jellyfish that emits green light
37
Binding sites
allow proteins to bind to specific ligands, many covalent bonds
38
biochemical pathway
multiple chemical reactions that occur at the same area and the product of one enzyme becomes the substrate of the next (Enzymes work in sets)
39
statins
drug that blocks enzyme activity of HMG-CoA reductase
40
nuclease
breaks down nucleic acids by hydrolyzing bonds between nucleotides
41
protease
breaks down proteins by hydrolyzing peptide bonds between amino acids
42
kinase
catalyzes the addition of phosphate groups to molecules. protein kinases are an important group of kinases that attach phosphate groups to proteins
43
phosphatase
catalyzes the hydrolytic removal of a phosphate group from a molecule
44
structure of an antibody
2 identical heavy chains and 2 light stabilized by S-S bonds constant domain base, variable domain at the top antigen binding site forms where VH and VL come together at "Y" tips
45
ways to homogenize (pop) cells/tissues
high frequency sound force thru small hole/high pressure mild detergent shear cells in vessel with close fitting rotating plunger
46
centrifugation
separates pellet if denser and larger materials
47
differential centrifugation
progressively higher speeds of centrifugation separates based on size
48
SDS Page
added to break S-S linkages, gives proteins a negative charge and unfolds them so that they migrate through the gel at a rate that reflects their molecular weight
49
affinity chromatography
collect protein of interest by pouring sample through column with antibodies that attach to protein. Antigen can then be eluted from column to get pure sample.
50
Gel Exclusion (size exclusion) chromatography
smaller proteins retained in the column longer, longer retention time
51
ion exchange chromatography
charged column attracts proteins f opposite charge binding strength depends on net charge of the protein
52
cation exchanger charge of resin
negative
53
anion exchanger charge of resin
positive
54
allosteric enzymes
have 2 or more binding sites that increase or decrease activity for the others
55
phosphorylation controls protein activity by causing a
conformational change
56
feedback inhibition
late product of the pathway inhibits enzyme early in pathway can be positive reversible
57
When GTP (guanosine triphosphate) is bound to proteins,, they are
active
58
GTP is hydrolyzed by
releasing Pi (inorganic phosphate), becomes GDP, inactive reactivation involves dissociation of GDP and replacement by GTP
59
PTM
post translational modifications covalent modifications that change protein properties
60
ubiquitination (PTM)
tags a protein for degradation
61
Phosphorylation
phosphorylation by protein kinases can increase or decrease activity conformational change reversible
62
ATP hydrolysis
used by motor proteins, separation of chromosomes during mitosis, movement within cells ATP Binding (conformation A-B) ATP hydrolysis (B-C) release ADP and Pi (C-A)
63
Scaffolds
proteins that interact with other macromolecules and bring them together to facilitate function unstructured and structured regions
64
Intracellular condensates
biochemical subcompartments in the cell formed by weak interactions between macromolecules (I.e. nucleolus) can fuse and separate

BIO 2600 (15 decks)

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