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Molecular Cell Biology (Gamze Bulut) > Exam 1 (lectures 1-9) > Flashcards

Exam 1 (lectures 1-9) Flashcards

1
Q

How small is an average protein?

A

3-6 nm

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2
Q

Plasma membrane

A

controls movement of molecules in and out of the cell and functions in cell-cell signaling and cell adhesion.

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3
Q

Mitochondria

A

which are surrounded by a double membrane, generate ATP by oxidation of glucose and fatty acids.

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4
Q

Lysosomes

A

which have an acidic lumen, degrade material internalized by the cell and worn-out cellular membranes and organelles.

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5
Q

Nuclear envelope

A

double membrane, encloses the contents of the nucleus, the other nuclear membrane is continuous with the rough ER

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6
Q

Nucleolus

A

nuclear sub-compartment where most of the cell’s RNA is synthesized

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7
Q

Nucleus

A

filled with chromatin composed of DNA and proteins; site of mRNA and tRNA synthesis

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8
Q

Smooth ER

A

contains enzymes that synthesize lipids and detoxify certain hydrophobic molecules

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9
Q

Rough ER

A

functions in the synthesis, processing, and sorting of secreted proteins, lysosomal proteins and certain membrane proteins

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10
Q

Golgi Complex

A

processes and sorts secreted proteins and membrane proteins synthesized on the rough ER

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11
Q

secretory vesicles

A

store secreted proteins and fuse with the plasma membrane to release their contents

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12
Q

peroxisomes

A

contain enzymes that break down fatty acids into smaller molecules used for biosynthesis

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13
Q

cytoskeletal fibers

A

form networks and bundles that support cellular membranes

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14
Q

microvilli

A

increase surface area for absorption of nutrients from surrounding medium

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15
Q

cell wall

A

composed largely of cellulose, help maintain cell’s shape

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16
Q

vacuole

A

stores water ions and nutrients

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17
Q

chloroplasts

A

carry out photosynthesis

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18
Q

plasmodesmata

A

tube-like cell junctions that span the cell wall and connect the cytoplasms of adjacent plant cells

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19
Q

each cell in your body is a ____ cell of your _____?

A

daughter, zygote

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20
Q

Central Dogma

A

different genes are expressed and make a unique repertoire of RNA and proteins in each cell, DNA->RNA->Protein

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21
Q

Prokaryotic vs Eukaryotic cell differences

A

Flagella, Pili, Peptidoglycan, size, lack of nucleus, one chromosome, binary fission instead of mitosis, etc.

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22
Q

4 major concepts

A

Molecular complementarity, chemical building blocks, chemical bond energy, chemical equilibrium

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23
Q

molecular complementarity

A

fit between molecular shape, charges and other physical properties

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24
Q

chemical building blocks

A

polymerization of small molecules form larger cellular structures like DNA

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25
Q

Chemical equilibrium

A

chemical reactions are reversible, reflects the relative amounts of products and reactants at equilibrium

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26
Q

Chemical bond energy

A

energy driving many cellular activities reactions is derived from hydrolysis of the high energy phospho-anyhdride bond linking in ATP molecules

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27
Q

Covalent bonds

A

two atoms share a single pair of electrons

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28
Q

polar covalent

A

unequal electron sharing

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29
Q

non polar covalent

A

equal electron sharing

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30
Q

ionic bonds

A

noncovalent bond, between + and -, electron completely transferred, 0.25 nm

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31
Q

hydrogen bonds

A

noncovalent bond, interaction between a nonbonding electron pair and hydrogen, usually stronger than van Der Waals, 0.17 nm

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32
Q

van der Waals interactions

A

noncovalent bond, weak transient dipole interactions, usually stronger than thermal energy, 0.35 nm

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33
Q

hydrophobic

A

noncovalent bond, reduces contact with water

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34
Q

protein

A

polymer: polypeptide, monomer: amino acid

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35
Q

DNA/RNA

A

polymer: nucleic acid, monomer: nucleotide

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36
Q

Sugar

A

polymer: polysaccharide monomer: monosaccharide

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37
Q

cell membrane

A

polymer: lipid bilayer, monomer: phospholipid

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38
Q

Purines

A

Adenine and Guanine, pair of fused rings

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39
Q

Pyrimidine

A

Cytosine, Thymine (DNA), and Uracil (RNA), single ring

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40
Q

Post translational modifications

A

Phosphorylation, acetylation, disulfide bond, ubiquination, methylation etc. Amino acid R groups being covalently modified

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41
Q

Yanamaka factors

A

process/factors to go from patient’s cell to iPS cell

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42
Q

how to culture animals cells?

A

tissue culture, animal cells need special culture medium (rich in nutrients), incubated, antibiotics and anti fungal reagents to keep free of contaminations, cells passaging/splitting is done in special biosafety cabinets

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43
Q

human fetal fibroblasts divide about ___ times before they _____

A

50, senesce

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44
Q

immunoblotting/western blotting

A

incubating with a mixture containing antibody against the protein of interest, detects what size is your protein of interest

45
Q

phosphomimetic

A

study importance of phosphorylation on an amino acid by mutating it to another amino acid which mimics the phosphorylated form (usually changes to D or E amino acid)

46
Q

acetylmimetic

A

changes an acetylated amino acid to one that mimics the acetylated form (usually Q)

47
Q

DNA vs RNA structure

A

DNA is double stranded, has a sole H in the 2’ spot, RNA is single stranded, has hydroxyl group in 2’ spot

48
Q

GC has ____ hydrogen bonds

A

3

49
Q

AT has ____ hydrogen bonds

A

2

50
Q

ATP vs ADP in structure

A

ATP has three phosphate groups, ADP has 2 phosphate groups

51
Q

ATP -> ADP

A

creates energy available to drive energetically unfavorable reactions

52
Q

ADP -> ATP

A

needs energy from sunlight or from breakdown of food

53
Q

How do nucleic acids connect, what bond is created

A

through dehydration, creates a phosphodiester bond

54
Q

which way is DNA synthesized and how

A

5’ -> 3’, uses dNTP precursors

55
Q

where are the phosphodiester bonds formed?

A

between the 3’ oxygen of the growing strand and the phosphate of a dNTP

56
Q

Monosaccharides function and examples

A

energy source; glucose, galactose, fructose

57
Q

disaccharides function and examples

A

transport form; lactose, sucrose, maltose

58
Q

polysaccharide function and examples

A

storage forms, cellulose glycogen, starch

59
Q

glycogen vs starch vs cellulose

A

glycogen: highly branched and long polymer of glucose Starch: moderately branched, primary storage, cellulose: unbranched, major constituent of plant cell walls

60
Q

N-acetyl glucosamine

A

modification on proteins, removal of mannose and addition of n-acetylglucosamine, occur in the cis medal cisternae

61
Q

phospholipid structure

A

hydrophilic head group composed of polar group, phosphate, and glycerol, hydrophobic fatty acyl tail composed of fatty acid chains (double bond makes the acid unsaturated; causes a kink)

62
Q

4 major head groups

A

Phosphoatidylcholine, Phosphoatidylethanolamine, Phosphoatidylserine, Phosphoatidylinositol

63
Q

cis vs trans fats

A

cis C=C bond creates rigid kink, trans C=C is much more linear, trans fats have no health benefits and no safe level of consumption and is banned in the USA

64
Q

how many proteins in an eukaryotic cell

A

~7.9 x 10^9 proteins, 10,000 different proteins

65
Q

what could impact proteins folding

A

hydrophobicity, amino acid size, flexibility, chemical interactions/bonds, environment, enzymes

66
Q

2 principles for folding

A

fold to reach lowest functional free energy, hydrophilic residues will be often exposed while hydrophobic will be buried in the core

67
Q

Primary structure

A

linear covalent attachment of amino acids

68
Q

peptide size vs polypeptide size

A

20-30 amino acids: peptide
200-500 amino acids: polypeptide

69
Q

three secondary structures

A

alpha-helix, beta-sheet, beta-turn

70
Q

alpha helix

A

each amino acid makes hydrogen bonds with amino acid 3/4 acids apart, proline is usually not found, one turn has average of 3.6 residues, promoted by longer skinnier amino acids: M, A, L, K, R, helical propensity value <0.3

71
Q

Coiled coil

A

alpha helix variation where each turn has 3.5 residues

72
Q

Beta-sheets

A

5-8 residues line up in each strand, hydrogen bonds are formed in between separate strands, can be parallel (all facing same way) or anti-parallel (some face the other way), usually contains large aromatic amino acids (Y, F, W) to prevent backbone from bending

73
Q

beta-turn

A

composed of 4 residues, makes sharp U-shaped bend, reverses the direction, 1-4 makes hydrogen bond, usually glycine and proline (G is super flexible, P is super rigid)

74
Q

super secondary structures

A

commonly found structural motifs (eg. Luecine zippers [repeating 7 amino acids unit called Heptad], calcium binding hand motif [helix-loop-helix], zinc finger [1 alpha + 2 beta = finger like bundle])

75
Q

domain vs motifs

A

motif is a chain like structure made up of secondary structural elements while a domain is an independent folding unit of the three dimensional protein structure

76
Q

Tertiary structure

A

overall 3D conformation, makes up function, structural and topological domain

77
Q

What structure do transporters at the cell membrane have

A

alpha helical structures

78
Q

dsiulfide bonding in tertiary structures

A

disulfide bonds are added to help secreted or extracellular side facing protein survive the conditions outside (not needed inside the cell, lighter conditions)

79
Q

quaternary structure

A

proteins bump into each other to create a new low free energy stat using q. structures, interact via binding sites, members are called subunits

80
Q

Dimer, trimer tetramer

A

quaternary structure where the proteins bumping are the exact same

81
Q

what do chaperones do

A

help proteins fold properly, inside the cell is very chaotic, exposed hydrophobic regions can cause clumps and insoluble masses, chaperons bind giving the protein time to fold properly

82
Q

how were chaperones discovered

A

cells were treated with heat shock

83
Q

Hsp70 vs Hsp40 vs BAG1

A

Hsp70 is the chaperone itself, binds to hydrophobic patches, isolating and simplifying folding
Hsp40 is the helper (co-chaperone), increases Hsp70’s capacity to hydrolyze ATP more efficiently by 100-1000 fold, stimulates the binding of substrate
BAG1: co-chaperone, nucleotide exchange factor, helps Hsp70 exchange ADP for ATP (doesn’t add new phosphate, completely exchanges it)

84
Q

Why dose ATP/ADP binding change molecular chaperons shape

A

ATP hydrolysis largely causes changes in conformation due to changes in ionic interaction in addition to energy released, ATP-bound is open

85
Q

chaperonins

A

folding chamber, isolates unfolded/misfolded protein and gives time and space for it to fold (not binded to protein)

86
Q

how does GroEL use ATP

A

addition of ATP adds the GroES cap while hydrolysis of ATP into ADP releases the cap

87
Q

How do scientists know structures?

A

X-ray crystallography, NMR spectrophotometry, cryo electron microscopy

88
Q

what can misfolding and aggregates cause?

A

diseases (Alzheimer’s, scrapie, mad cow disease), loss of function, gain of new toxic function

89
Q

what can plaques and tangles lead to?

A

plaques: loss of action potential, neuron’s can’t send signals off
tangles: misfolding of tau proteins leads to microtubules amyloid precursor protein and tau tangle formations

90
Q

what are amyloid plaques made of?

A

composed of ~42 amino acid long fragments of amyloid precursor protein (APP)

91
Q

what can APP fragments aggregate into

A

insoluble cross beta-sheets when at a high concentration

92
Q

what is the prion protein

A

PrPSC, scrapie associated, mutations cause this protein to fold improperly into beta-sheet aggregates

93
Q

how do we regulate proteins

A

abundance, activity, location, interactions, covalent and noncovalent interaction/modifications

94
Q

allostery

A

ligand binding changes conformation of a protein

95
Q

cooperative binding

A

positive allosteric interactions, oxygen binding to hemoglobin allows for more oxygen to bind as well

96
Q

competitive binding

A

negatively regulated by conformational coupling between two separate binding sites, ampicillin is a irreversible comp. inhibitor to an enzyme important for cell wall synthesis

97
Q

non-covalent interactions regulation

A

binding to GTP through non-covalent bonds, GAP: similar to hsp40 promoting GTP hydrolysis, GEF: guanine nucleotide exchange factor

98
Q

phosphorylation enzymes

A

kinase: phosphorylates the amino acid
Phosphatase: cuts of the phosphate group

99
Q

what does proteases do?

A

degrades proteins, mainly those who are misfolded (autophagy), tagged with polyubiquitin chain

100
Q

different ubiquitin types

A

Mono ubiquitination: one ubiquitin binded, used for histone regulation, protein protein interactions
multi ubiquitination: many ubiq. are binded in different spots, used for endocytosis
poly ubiquitination: many ubiq. are binded in the same spot (chain), used for degradation

101
Q

where is ubiqutin attached to and how big is it?

A

side chain amino group of Lysines (K), small protein (76 amino acids)

102
Q

E1 vs E2 vs E3

A

E1: activation of Ub by the addition of Ub molecule (requires ATP), prime Ub
E2: transfer of Ub molecule to a cysteine residue in a Ub conjugating enzyme (E2)
E3 ligase: covalently links the carboxyl group of the C-terminal glycine 76 to the Ub to the amino group of the side chain of a lysine residue in the target protein creating an isopeptide bond, only one that binds to the substrate through lock-key model

103
Q

lock-key model

A

good fit, complementarity, ionic interactions

104
Q

K63 ubiquitin chain

A

protein kinase activation DNA damage response

105
Q

K48 branched ubiquitin chain

A

proteasomal degradation

106
Q

26S proteasome structure

A

2400 kDa, Core has 6 sites of proteolytic activity (ability to cut acidic, basic and hydrophobic amino acids), has filters that let “tagged” proteins in/peptide fragments out, 19S regulatory subunit has 6 ATPases, 3 Ubiquitin receptors and DUB (deubiquitinase enzyme)

107
Q

who is more likely to get alzheimers

A

People with specific gene alterations:
Mutations in APP
Mutations in beta-secretase or y-secretase leading to hyperactivatijkkDown syndrome patients with elevated levels of APP
Specific ApoE alleles (e4 version bad at clearing plaques)
Old people

108
Q

What mutation causes Scrapie to form

A

alpha helices change to beta sheets

109
Q

autophagy

A

natural, conserved degradation of the cell that removes unnecessary or dysfunctional components through a lysosome-dependent regulated mechanism.

Molecular Cell Biology (Gamze Bulut) (1 decks)

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