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