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BIO 2600 > Chapter 4 > Flashcards

Chapter 4 Flashcards

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Biology 101 flashcards
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
Q

Globular protein molecules

A

lysozyme, hemoglobin, actin(monomer)

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23
Q

serine proteases

A

family of protein-cleaving (proteolytic) enzymes that include digestive enzymes (chymotrypsin, trypsin, elastase) and proteases involved in blood clotting

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24
Q

chaperons

A

proteins that help other proteins fold, many are heat-shock proteins or isolation chambers

25
Q

denaturation

A

unfolding due to changes in temp, pH, chemicals, usually reversible

26
Q

protein aggregation

A

occurs with misfolded proteins in the nervous system, causes neurodegenerative diseases (Alzheimer’s, Huntington’s)

27
Q

prion

A

pathogenic misfolded protein that can pass shape to other proteins, “mad cow” disease

28
Q

ferritin

A

storage protein that stores iron in the liver

29
Q

insulin

A

signal protein that controls blood glucose levels

30
Q

receptors

A

proteins that detect signals and transmit to cell’s response machinery

31
Q

hemoglobin/myoglobin

A

transport proteins that carry O2 and CO2 in blood and muscles, respectively

32
Q

collagen/keratin

A

structural proteins that form cartilage, hair, and nails

33
Q

actin/myosin

A

motor proteins that allow muscles to contract

34
Q

immunoglobins(antibodies)

A

defense proteins that recognize foreign organisms and cancer cells

35
Q

transcription factors

A

regulatory proteins that regulate gene expression

36
Q

Green fluorescent proteins (GFP)

A

special-purpose protein from jellyfish that emits green light

37
Q

Binding sites

A

allow proteins to bind to specific ligands, many covalent bonds

38
Q

biochemical pathway

A

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
Q

statins

A

drug that blocks enzyme activity of HMG-CoA reductase

40
Q

nuclease

A

breaks down nucleic acids by hydrolyzing bonds between nucleotides

41
Q

protease

A

breaks down proteins by hydrolyzing peptide bonds between amino acids

42
Q

kinase

A

catalyzes the addition of phosphate groups to molecules. protein kinases are an important group of kinases that attach phosphate groups to proteins

43
Q

phosphatase

A

catalyzes the hydrolytic removal of a phosphate group from a molecule

44
Q

structure of an antibody

A

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
Q

ways to homogenize (pop) cells/tissues

A

high frequency sound
force thru small hole/high pressure
mild detergent
shear cells in vessel with close fitting rotating plunger

46
Q

centrifugation

A

separates pellet if denser and larger materials

47
Q

differential centrifugation

A

progressively higher speeds of centrifugation separates based on size

48
Q

SDS Page

A

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
Q

affinity chromatography

A

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
Q

Gel Exclusion (size exclusion) chromatography

A

smaller proteins retained in the column longer, longer retention time

51
Q

ion exchange chromatography

A

charged column attracts proteins f opposite charge
binding strength depends on net charge of the protein

52
Q

cation exchanger charge of resin

A

negative

53
Q

anion exchanger charge of resin

A

positive

54
Q

allosteric enzymes

A

have 2 or more binding sites that increase or decrease activity for the others

55
Q

phosphorylation controls protein activity by causing a

A

conformational change

56
Q

feedback inhibition

A

late product of the pathway inhibits enzyme early in pathway
can be positive
reversible

57
Q

When GTP (guanosine triphosphate) is bound to proteins,, they are

A

active

58
Q

GTP is hydrolyzed by

A

releasing Pi (inorganic phosphate), becomes GDP, inactive
reactivation involves dissociation of GDP and replacement by GTP

59
Q

PTM

A

post translational modifications
covalent modifications that change protein properties

60
Q

ubiquitination (PTM)

A

tags a protein for degradation

61
Q

Phosphorylation

A

phosphorylation by protein kinases can increase or decrease activity
conformational change
reversible

62
Q

ATP hydrolysis

A

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
Q

Scaffolds

A

proteins that interact with other macromolecules and bring them together to facilitate function
unstructured and structured regions

64
Q

Intracellular condensates

A

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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