Exam 1 (lectures 1-9) Flashcards
(109 cards)
1
Q
How small is an average protein?
A
3-6 nm
2
Q
Plasma membrane
A
controls movement of molecules in and out of the cell and functions in cell-cell signaling and cell adhesion.
3
Q
Mitochondria
A
which are surrounded by a double membrane, generate ATP by oxidation of glucose and fatty acids.
4
Q
Lysosomes
A
which have an acidic lumen, degrade material internalized by the cell and worn-out cellular membranes and organelles.
5
Q
Nuclear envelope
A
double membrane, encloses the contents of the nucleus, the other nuclear membrane is continuous with the rough ER
6
Q
Nucleolus
A
nuclear sub-compartment where most of the cell’s RNA is synthesized
7
Q
Nucleus
A
filled with chromatin composed of DNA and proteins; site of mRNA and tRNA synthesis
8
Q
Smooth ER
A
contains enzymes that synthesize lipids and detoxify certain hydrophobic molecules
9
Q
Rough ER
A
functions in the synthesis, processing, and sorting of secreted proteins, lysosomal proteins and certain membrane proteins
10
Q
Golgi Complex
A
processes and sorts secreted proteins and membrane proteins synthesized on the rough ER
11
Q
secretory vesicles
A
store secreted proteins and fuse with the plasma membrane to release their contents
12
Q
peroxisomes
A
contain enzymes that break down fatty acids into smaller molecules used for biosynthesis
13
Q
cytoskeletal fibers
A
form networks and bundles that support cellular membranes
14
Q
microvilli
A
increase surface area for absorption of nutrients from surrounding medium
15
Q
cell wall
A
composed largely of cellulose, help maintain cell’s shape
16
Q
vacuole
A
stores water ions and nutrients
17
Q
chloroplasts
A
carry out photosynthesis
18
Q
plasmodesmata
A
tube-like cell junctions that span the cell wall and connect the cytoplasms of adjacent plant cells
19
Q
each cell in your body is a ____ cell of your _____?
A
daughter, zygote
20
Q
Central Dogma
A
different genes are expressed and make a unique repertoire of RNA and proteins in each cell, DNA->RNA->Protein
21
Q
Prokaryotic vs Eukaryotic cell differences
A
Flagella, Pili, Peptidoglycan, size, lack of nucleus, one chromosome, binary fission instead of mitosis, etc.
22
Q
4 major concepts
A
Molecular complementarity, chemical building blocks, chemical bond energy, chemical equilibrium
23
Q
molecular complementarity
A
fit between molecular shape, charges and other physical properties
24
Q
chemical building blocks
A
polymerization of small molecules form larger cellular structures like DNA
25
Chemical equilibrium
chemical reactions are reversible, reflects the relative amounts of products and reactants at equilibrium
26
Chemical bond energy
energy driving many cellular activities reactions is derived from hydrolysis of the high energy phospho-anyhdride bond linking in ATP molecules
27
Covalent bonds
two atoms share a single pair of electrons
28
polar covalent
unequal electron sharing
29
non polar covalent
equal electron sharing
30
ionic bonds
noncovalent bond, between + and -, electron completely transferred, 0.25 nm
31
hydrogen bonds
noncovalent bond, interaction between a nonbonding electron pair and hydrogen, usually stronger than van Der Waals, 0.17 nm
32
van der Waals interactions
noncovalent bond, weak transient dipole interactions, usually stronger than thermal energy, 0.35 nm
33
hydrophobic
noncovalent bond, reduces contact with water
34
protein
polymer: polypeptide, monomer: amino acid
35
DNA/RNA
polymer: nucleic acid, monomer: nucleotide
36
Sugar
polymer: polysaccharide monomer: monosaccharide
37
cell membrane
polymer: lipid bilayer, monomer: phospholipid
38
Purines
Adenine and Guanine, pair of fused rings
39
Pyrimidine
Cytosine, Thymine (DNA), and Uracil (RNA), single ring
40
Post translational modifications
Phosphorylation, acetylation, disulfide bond, ubiquination, methylation etc. Amino acid R groups being covalently modified
41
Yanamaka factors
process/factors to go from patient's cell to iPS cell
42
how to culture animals cells?
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
43
human fetal fibroblasts divide about ___ times before they _____
50, senesce
44
immunoblotting/western blotting
incubating with a mixture containing antibody against the protein of interest, detects what size is your protein of interest
45
phosphomimetic
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
acetylmimetic
changes an acetylated amino acid to one that mimics the acetylated form (usually Q)
47
DNA vs RNA structure
DNA is double stranded, has a sole H in the 2' spot, RNA is single stranded, has hydroxyl group in 2' spot
48
GC has ____ hydrogen bonds
3
49
AT has ____ hydrogen bonds
2
50
ATP vs ADP in structure
ATP has three phosphate groups, ADP has 2 phosphate groups
51
ATP -> ADP
creates energy available to drive energetically unfavorable reactions
52
ADP -> ATP
needs energy from sunlight or from breakdown of food
53
How do nucleic acids connect, what bond is created
through dehydration, creates a phosphodiester bond
54
which way is DNA synthesized and how
5' -> 3', uses dNTP precursors
55
where are the phosphodiester bonds formed?
between the 3' oxygen of the growing strand and the phosphate of a dNTP
56
Monosaccharides function and examples
energy source; glucose, galactose, fructose
57
disaccharides function and examples
transport form; lactose, sucrose, maltose
58
polysaccharide function and examples
storage forms, cellulose glycogen, starch
59
glycogen vs starch vs cellulose
glycogen: highly branched and long polymer of glucose Starch: moderately branched, primary storage, cellulose: unbranched, major constituent of plant cell walls
60
N-acetyl glucosamine
modification on proteins, removal of mannose and addition of n-acetylglucosamine, occur in the cis medal cisternae
61
phospholipid structure
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
4 major head groups
Phosphoatidylcholine, Phosphoatidylethanolamine, Phosphoatidylserine, Phosphoatidylinositol
63
cis vs trans fats
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
how many proteins in an eukaryotic cell
~7.9 x 10^9 proteins, 10,000 different proteins
65
what could impact proteins folding
hydrophobicity, amino acid size, flexibility, chemical interactions/bonds, environment, enzymes
66
2 principles for folding
fold to reach lowest functional free energy, hydrophilic residues will be often exposed while hydrophobic will be buried in the core
67
Primary structure
linear covalent attachment of amino acids
68
peptide size vs polypeptide size
20-30 amino acids: peptide
200-500 amino acids: polypeptide
69
three secondary structures
alpha-helix, beta-sheet, beta-turn
70
alpha helix
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
Coiled coil
alpha helix variation where each turn has 3.5 residues
72
Beta-sheets
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
beta-turn
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
super secondary structures
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
domain vs motifs
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
Tertiary structure
overall 3D conformation, makes up function, structural and topological domain
77
What structure do transporters at the cell membrane have
alpha helical structures
78
dsiulfide bonding in tertiary structures
disulfide bonds are added to help secreted or extracellular side facing protein survive the conditions outside (not needed inside the cell, lighter conditions)
79
quaternary structure
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
Dimer, trimer tetramer
quaternary structure where the proteins bumping are the exact same
81
what do chaperones do
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
how were chaperones discovered
cells were treated with heat shock
83
Hsp70 vs Hsp40 vs BAG1
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
Why dose ATP/ADP binding change molecular chaperons shape
ATP hydrolysis largely causes changes in conformation due to changes in ionic interaction in addition to energy released, ATP-bound is open
85
chaperonins
folding chamber, isolates unfolded/misfolded protein and gives time and space for it to fold (not binded to protein)
86
how does GroEL use ATP
addition of ATP adds the GroES cap while hydrolysis of ATP into ADP releases the cap
87
How do scientists know structures?
X-ray crystallography, NMR spectrophotometry, cryo electron microscopy
88
what can misfolding and aggregates cause?
diseases (Alzheimer's, scrapie, mad cow disease), loss of function, gain of new toxic function
89
what can plaques and tangles lead to?
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
what are amyloid plaques made of?
composed of ~42 amino acid long fragments of amyloid precursor protein (APP)
91
what can APP fragments aggregate into
insoluble cross beta-sheets when at a high concentration
92
what is the prion protein
PrPSC, scrapie associated, mutations cause this protein to fold improperly into beta-sheet aggregates
93
how do we regulate proteins
abundance, activity, location, interactions, covalent and noncovalent interaction/modifications
94
allostery
ligand binding changes conformation of a protein
95
cooperative binding
positive allosteric interactions, oxygen binding to hemoglobin allows for more oxygen to bind as well
96
competitive binding
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
non-covalent interactions regulation
binding to GTP through non-covalent bonds, GAP: similar to hsp40 promoting GTP hydrolysis, GEF: guanine nucleotide exchange factor
98
phosphorylation enzymes
kinase: phosphorylates the amino acid
Phosphatase: cuts of the phosphate group
99
what does proteases do?
degrades proteins, mainly those who are misfolded (autophagy), tagged with polyubiquitin chain
100
different ubiquitin types
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
where is ubiqutin attached to and how big is it?
side chain amino group of Lysines (K), small protein (76 amino acids)
102
E1 vs E2 vs E3
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
lock-key model
good fit, complementarity, ionic interactions
104
K63 ubiquitin chain
protein kinase activation DNA damage response
105
K48 branched ubiquitin chain
proteasomal degradation
106
26S proteasome structure
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
who is more likely to get alzheimers
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
What mutation causes Scrapie to form
alpha helices change to beta sheets
109
autophagy
natural, conserved degradation of the cell that removes unnecessary or dysfunctional components through a lysosome-dependent regulated mechanism.
