Lectures 2-12 (test 1) Flashcards
(209 cards)
1
Q
4 types of macromolecules
A
lipids, proteins, polysaccharides, nucleic acids
2
Q
what are lipids
A
heterogeneous structure, hydrophobic (ex phospholipid)
3
Q
Lipid: fatty acid vs triacyglycerols vs phospholipids
A
fatty acid: carboxylic acid w/ aliphatic chain, which is saturated (straight) or unsaturated (bent, bc of double bond)
triacyglycerols: made of 1 glycerol & 3 fatty acids
phospholipids: hydrophilic head (phosphate group+glycerol) & 2 hydrophobic tails (fatty acids)
4
Q
what have aromatic rings (lipids)
A
steroids (multiple rings) & terpenes (1 ring)
5
Q
define amphipathic. example?
A
having both hydrophilic & hydrophobic parts; phospholipid (makes up PM)
6
Q
PM consists of
A
2 layers of oppositely oriented phospholipid molecules; heads exposed to liquid, tails into middle of membrane (cholesterol must be here)
7
Q
what are polysaccharides
A
(sugars) long-chain polymeric carbohydrates composed of monosaccharide units bound together by glycosidic bonds
8
Q
what are disaccharides
A
2 monosaccharides joined by glycosidic bond (ex: maltose = glucose + glucose; lactose = galactose + glucose)
9
Q
what can be storage or structural molecule
A
polysaccharides (store starch in plants; glycogen in muscles of naimals)
10
Q
what is cellulose considered
A
structural polysaccharide of cell wall (repeating glucose units)
11
Q
what is chitin
A
long-chain polymer of N-acetylglucosamine (main component of insect exoskeleton)
12
Q
what does protein shape matter for
A
protein shape matters for function
13
Q
what is an amino acid
A
organic molecule w/both an amino group & carboxyl group, w/variable side chain (monomer for proteins)
14
Q
how many amino acids make up protein
A
20
15
Q
types of side chains
A
Nonpolar (hydrophobic), polar side chains (hydrophilic), electrically charged side chains (hydrophilic; - = acidic, + = basic)
16
Q
what are amino acid polymers
A
polypeptides (peptide bonds hold together chain of amino acids)
17
Q
4 levels of protein structure
A
- primary: sequence of amino acids
- secondary: alpha helices & beta-strands (regions stabilized by hydrogen bonds)
- tertiary: subunit/folded shape; overall shape of polypeptide resulting from interactions between amino acids
- quaternary: overall structure resulting from aggregation of more than 1 polypeptide subunits
18
Q
example of quaternary structure
A
hemoglobin (4 heme subunits together)
19
Q
what are nucleic acids
A
macromolecules that exist as polymers called polynucleotides (DNA & RNA); monomers are called nucleotides
20
Q
structure of nucleotide
A
a nitrogenous base, 5 carbon sugar, 1 phosphate group
21
Q
2 families of nitrogenous bases
A
pyrimidines (1 ring) & purines (2 rings)
22
Q
DNA vs RNA
A
Deoxyribonucleic acid (cytosine, guanine, thymine, adenine)
Ribonucleic acid (cytosine, guanine, uracil, adenine)
23
Q
DNA structure
A
2 polynucleotide chains that coil around each other to make double helix
24
Q
nucleotides are joined to one another by what bonds
A
phosphodiester bonds
25
what end of chain has phosphate? sugar?
5' end has phosphate group
3' end has sugar
26
what are steps of taking info from genes to make proteins
Transcription: RNA polymerase uses DNA template to make pre-mRNA
Translation: ribosome makes protein (polypeptide) from mRNA
27
what could cause sickle-cell disease
a single amino acid substitution in hemoglobin
28
proteins are
chains of amino acids with 3D structure
29
What is central dogma
DNA -->(transcription -in nucleus)--> RNA -->(translation -in cytoplasm)--> Protein
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membranes of nucleus
Inner and outer membranes
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what is compact DNA called
chromatin
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what encodes ribosomal RNAs
nucleolus
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what catalyzes chemical reactions that synthesize RNA from DNA template
RNA polymerase
34
Different types of RNA polymerases
RNA polymerase I: rRNA genes
RNA polymerase II: mRNA, miRNA, snRNA, snoRNA genes
RNA polymerase III: tRNA & 5S rRNA genes
35
what is in the active site of RNA polymerase
2 DNA strands & RNA strand (2 DNA strands form helix at top, RNA polymerase separates the 2 DNA strands in middle & builds RNA strand, 2 DNA strands come back together
36
what is the TATA box
DNA sequence of T & A nucleotides (30 nucleotides b4 transcription start site) -TATA binding proteins recognize the TATA box
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RNA Polymerase II requires what proteins? what do they do?
General transcription factors; they start transcription
38
Where does RNA polymerase & general transcription factors assemble
at promoter (TATA box)
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what is bigger: gene or protein it makes
gene
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how does mRNA leave nucleus
nuclear pore complex (controls export and import into nucleus)
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What do ribosomes do
read mRNA & translate info into polypeptide (2 subunits trap mRNA inside, ribosome reads & translates into amino acid chains)
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what is codon
3 nucleotides = 1 amino acid
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Which ribosome subunit has catalytic site? what does it do?
large subunit; makes new peptide bonds
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what does ribosome small subunit do
finds mRNA strand & ensures each codon pairs w/anticodon
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what does tRNA do
transfer RNA translates mRNA into amino acid (has anticodons & brings matching codons to mRNA trapped in ribosomes)
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what is the start codon
methionine (AUG)
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what is translation termination factor
a protein that stops translation (UAA, UAG, UGA)
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pros of bacteria not having nucleus
proteins made faster
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what does RNA splicing acheive
removes untranslated regions from mRNA (splices out introns)
50
Introns vs exons (mRNA)
Introns: region in gene that doesn't remain in final mature mRNA (in pre-mRNA & spliced out)
Exons: RNA that codes for proteins (stays in mature mRNA to be exported)
51
what does spliceosome do
cut exons & reconnect them to produce mRNA
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What does splicing allow us to do
encode multiple proteins in a single gene
53
T or F all cells make lipid
true, some more than others
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what is TAG
triacylglycerols (glycerol & 3 fatty acids)
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what can TAG be made from? what does this?
1. Acyltransferases make TAG from monoacylglycerols (cut fatty acid from 1 molecule & paste in another molecule/transfer of fatty acids)
2. Glycerol-3-phosphate make TAG
56
what are acyltransferases
enzymes that move fatty acids
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Where is TAG made
smooth ER
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where does TAG accumulate
lipid droplets
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what are lipid droplets? located where?
storage organelles; between PM of ER (they are in the tails of the phospholipids)
60
what membrane do lipid droplets have
single membrane
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what assists lipid droplet budding from ER
seipin
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describe structure of lipid droplet
hydrophobic core of lipids, phospholipid monolayer
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what are perilipins
family of proteins that coat lipid droplets (on cytoplasmic side, outside)
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3 steps to make lipid droplet
1. TAG synthesis & lens formation (cell separates 2 layers of ER membrane)
2. emergence & nascent lipid droplet formation (still attached)
3. lipid droplet budding & growth (cleaved, free to move)
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where does TAG synthesis occur (step 1 of LD formation)
between the smooth ER bilayer
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What facilitates the budding of lipid droplet (step 2 of LD formation)
Seipin is recruited to lens structure (beginning of LD) & facilitate growth out towards cytoplasm - w/o seipins, LDs would form in & out of ER
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what side does budding of LDs happen towards
cytoplasm side (seipin push LDs this way)
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How does LD grow (step 3 of LD formation)
bud from ER & grow through fusion (w/other LDs) or local lipid synthesis (making more TAG)
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what do LDs do in cytoplasm
fuse/interact w/ other organelles via membrane proteins (mitochondria make energy out of lipids)
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What is the branchpoint between store TAG & making membrane lipids
Phosphatidic acid (smallest phospholipid)
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how to manipulate phosphatidic acid to become: TAG vs phospholipids
TAG: remove phosphate group
Phospholipids: keep phosphate
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where are the enzymes kept that metabolize phospholipids
in all membranes (never in cytosol); different organelles have diff phospholipids
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structure of PIP2
2 fatty acids, glycerol, 3 phosphate groups (2 extra specific to PIP2)
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3 kingdoms
bacteria, archaea, eukaryotes
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What does bacterial cell keep DNA in
nucleoid, in cytoplasm, compact structure of folded DNA
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what do bacterial & archaeal cells lack that eukaryotes have
internal membranes
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What does plant cell have that animal cell does not
cell wall, vacuole, chloroplast, granum (stack of thylakoids)
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what provides energy for cells
mitochondria (TCA/Krebs cycle / electron transport chain -> makes ATP) & chloroplasts (photosynthesis / CO2+light=sugars)
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structure of mitochondria
inner & outer membranes, cristae (invagination of membrane), matrix (has mtDNA, enzymes, where KREBS cycle occurs)
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chloroplast structure
3 membranes (outer, inner, thylakoid membrane), stroma (matrix which has cpDNA, enzymes), thylakoids (stack = granum; photosynthesis, chlorophyl)
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what is endomembrane system? steps?
synthesis of proteins for variety of cellular destinations; steps: mRNA leaves nucleus, translates into protein in ribosomes of ER, goes to Golgi, sorted or secreted
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structure of ER
tubular membranes & flat sacs, cisternae & lumen
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Rough Er vs Smooth ER (function)
rough: ribosomes, synthesis of proteins
smooth: synthesis of lipids & steroids
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Golgi & secretory vesicles
vesicle enters Golgi at cis, leaves trans side; sugar coats on vesicles allows for protein to sort by coat
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lysosome
enzymes degrade/digest molecules, acidic (low pH), inside membrane is glycosylated
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what is the peroxisome
breaks fatty acid chains, catalase converts hydrogen peroxide into water & oxygen, works with oxidizing agents in cell
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Extracellular matrix vs cell wall
both outside PM
Extracellular matrix: collagen fibrils, proteoglycans (proteins w/many disaccharide units)
Cell walls: cellulose (polysaccharide)
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integrin connects what
cytoskeleton & extracellular matrix (collagen, laminin, proteoglycans)
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what does ECM do
glue cells and tissues
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different classes of lipids in membrane
phospholipids, glycolipids, sterols
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lipid bilayer is
fluid & asymmetric (phospholipids diffuse laterally /move around side they are on, transverse diffusion/flip-flop, rotate (proteins block these movements)
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what are translocases
proteins that move phospholipids between layers & maintain lipid asymmetry
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types of translocases & function
Flippase: moves lipids from outside to inside
Floppase: moves lipids back outside
Scramblase: moves lipids both ways to ensure asymmetric
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what was FRAP used to test
movement of membrane proteins
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what must membrane proteins have
hydrophobic amino acids (pass through membranes)
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types of membrane proteins
integral (single or multi pass)
peripheral (on one side of PM, anchored to integral membrane protein)
lipid-anchored (on one side of PM, bind to fatty acid in membrane)
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membrane proteins mediate what? example
cell adhesion & cell-cell communication; cadherin-cadherin binding in intercellular space keeps cells together/catenin is part inside cell)
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what are integral monotopic proteins
rare proteins that are only on one side of membrane
99
how are lipid-anchored proteins bound to fatty acid? example?
covalent bond; trehalase (cuts trehalose into 2 glucose molecules)
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what proteins & lipids are glycosylated
outside the membrane
101
what are 2 types of glycosylation
N-linked glycosylation & O-linked glycosylation
102
what is process of glycosylation
carbohydrate is covalently attached to target macromolecule
103
how can solutes cross membrane
simple diffusion, facilitated diffusion, active transport
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what molecules pass freely vs not
Pass freely: Small uncharged molecules (oxygen, carbon dioxide
Don't pass freely: Large polar molecules/ions (water, hydrogen, glucose, amino acids - all required active transport)
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what is simple diffusion
unassisted movement of solute following concentration gradient
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what is facilitated diffusion
protein mediated movement along concentration gradient (no ATP used) (ex: glucose)
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what are 2 major protein types that mediate facilitated diffusion
channels (pores) & carriers (conformation change = solute moves)
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types of carrier proteins (3)
uniport (move 1 solute), symport (move 2 in same direction), antiport (move 2 in opposite directions)
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3 types of channel proteins (transmembrane channel)
ion channels (specific to ion), porins (not specific), aquaporins (h2o only)
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what are ion channels
transmembrane proteins that allow rapid passage of specific ions
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what can open ion channel (4 types)
voltage, ligand, temperature, pressure
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what do ligand-gated ion channels convert
convert chemical signal into cell
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what does voltage-gated channel transmit
transmit signal in wave through nervous system (amplifies signal)
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what can have porins
mitochondria, chloroplasts, bacteria (allow rapid passage of various solutes)
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what is ATP
main energy storage molecule, negatively charged, made in mitochondria, can't pass through membranes (Adenosine + sugar + 3 phosphate groups)
116
what is a voltage-dependent anion channel (VDAC)
mediates exchange of negatively charged metabolites (ex ATP from mitochondria to cytoplasm)
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what does movement against concentration gradient require
ATP
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indirect vs direct active transport
Indirect: symporters & antiporters; one solute follows conc gradient, this saved energy is used to move another solute against gradient
Direct: ATP used directly to pump a solute across membrane against its electrochemical gradient (protein hydrolyzes ATP)
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what uses both direct & indirect active transport
Amino acid absorption
Indirect: amino acid symporters move amino acids into enterocytes
Direct: ATPase pumps maintain ion gradients
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what are transport ATPases
ATP-driven pumps (they hydrolyze ATP to ADP & P, use the energy released to pump ions or other solutes across membrane)
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Types of transport ATPases
1. P-type pump: phosphorylate themselves during pumping cycle (maintain electrochemical gradients)
2. ABC-type ATPases: ATP-binding cassette transporters, mediate ATP-powered translocation of many substrates across membranes
3. Vacuolar-ATPase: pumps H+ ions to increase acidity (2 rotary motors)
4. F-type ATPases: ATP synthase (moves ions with concentration gradient to produce ATP)
122
P-ATPases to know (3):
1. Ca2+ ATPase/pump / Moves Ca2+/H+: keeps [Ca2+} low in cytosol, in sarcoplasmic reticulum or PM, in muscles
2. Na+/K+ ATPase / Na+/K+: maintains membrane potential (-60mV), in PM, in animals
3. H+/K+: pumps H+ to acidify stomach, in PM, in animals
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what does sarcoplasmic reticulum of muscle cells do
intracellular store or Ca2+; special type of ER that forms network of tubular sacs in muscle-cell cytoplasm (uses ATP to change conformation to move Ca2+)
124
what is role of Na+/K+ ATPase
maintains electrochemical ion gradients in all cells (pumps 3 Na+ out / 2 K+ in)
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structure & function of Vacuolar-ATPase
has 2 motors, ATP-driven motor turns an axle which turns second motor (transmembrane part) that pumps protons across membrane, held together by linker; pumps H+ ions to increase acidity in certain organelles (ex lysosomes)
126
function and structure of F-type ATPases
Function: ATP synthases; moves ions w/conc gradient to produce ATP; moves H+ along gradient to drive ATP synthesis (into mitochondrial inner membrane)
structure: 2 motors (connected by stator); intermembrane motor is powered by H+ flow, other motor is powered by ATP (in mitochondria)
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how does the motor inside the mitochondria in ATP synthase/F-type ATPase join ADP and P
joins together by force
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what are ABC-type ATPases
ATP-binding cassette transporters, mediate ATP-powered translocation of many substrates across membranes; heterodimers that hydrolyze ATP and change conformation (has 2 transmembrane domains, 2 ABC in cytoplasm
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what is ATP-binding cassette
conserved protein domain (all ABC transporters have a shared amino acid sequence in ABC domain)
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how does heterodimerization of ABC-ATPases affect solutes
more solutes can be moved
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2 types of metabolic pathways
Anabolic: make large molecules (require energy)
Catabolic: break large molecules (releases energy)
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Oxidation vs Reduction of organic molecules (resulting effects)
Oxidation: loss of hydrogen, gain of oxygen, loss of electrons
Reduction: gain of hydrogen, loss of oxygen, gain of electrons
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what are NAD & FAD
coenzymes of redox reactions & electron carriers
NAD+ & FAD accept electrons (become reduced) during catabolic steps
NADH & FADH2 donate these electrons to another reaction (usually anabolic, like synthesis of ATP)
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what is an important oxidizable substrates in energy metabolism? reasons?
glucose; its oxidation is highly exergonic (releases energy), many polysaccharides break into glucose (starch, glycogen, cellulose)
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what enzymes catalyze oxidation
ATP and NADH
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what is glycolysis
metabolic pathway that entails the oxidation of glucose molecules into 2 pyruvate molecules
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steps of glycolysis (3)
1. prep & cleavage (glucose is phosphorylated twice by ATP, split)
2. Oxidation & ATP generation (the 2 molecules are oxidized, energy is conserved as 2 ATP & 2 NADH molecules are produced)
3. Pyruvate formation & ATP generation (the 2 molecules are converted into pyruvate & this makes 2 ATP)
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what is the net/end result of glycolysis
1 glucose --> 2 ATP & 2 pyruvate & 2 NADH
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summary/short steps of glycolysis
1. add 2 phosphates & cleave
2. oxidation & ATP made
3. Make pyruvate & ATP
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what are disaccharides broken down into (what are the 3 monosaccharides)? They are converted into Glycolysis intermediates
glucose, galactose, fructose
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what are the disaccharides in Glycolysis
Lactose, maltose, sucrose
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what is the branchpoint between aerobic & anaerobic metabolism
pyruvate
If high [O2], PDH takes pyruvate; if low [O2], LDH makes lactate
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aerobic vs anaerobic metabolism
Aerobic: oxygen present, pyruvate -> Acetyl CoA (pyruvate oxidized, NAD+-> NADH, CO2 released, Acetyl CoA made)
anaerobic: lacks oxygen, pyruvate --> either lactate or ethanol & CO2 (NADH oxidized to NAD+)
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how do tumor cells metabolize glucose to lactate
w
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what is Warburg effect
done by tumor cells; perform anaerobic glycolysis, despite having available oxygen
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what is mitochondrial pyruvate carrier
it transports pyruvate into mitochondria (glycolysis happens in cytoplasm, TCA cycle happens in mitochondria, Acetyl-CoA enters TCA cycle)
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what does pyruvate dehydrogenase do
convert pyruvate into Acetyl-CoA (adds CoA & NAD+, removes carbon & NADH, releases energy)
148
what are dehydrogenases
enzymes that remove a pair of hydrogen atoms from a substrate, oxidizing it
149
what is the structure of pyruvate dehydrogenase? cofactor needed?
multiples of 3 subunits;
E1 metabolite binding sites
E2 core of complex
E3 intermediate enzyme;
E1 needs vitamin B1 derivative as cofactor
150
what molecule is used in Glycolysis to store energy
ATP & NADH
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What are the names for Citric acid cycle
Citric acid cycle, Tricarboxylic acid cycle, Krebs cycle
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where does KREB cycle occur
matrix of mitochondria
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Steps of KREB cycle (very brief)
1. Glycolysis (only step done in cytosol)
2. Pyruvate oxidation
3. Citric acid cycle
4. Electron transport & Proton pumping
5. ATP synthesis
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what is done in first step of KREB cycle
pyruvate converted to Acetyl CoA by Oxidative Decarboxylation (removal of carboxyl group & releases CO2)
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how does Citric acid cycle begin
entry of acetate as Acetyl CoA
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what are the products of TCA cycle
CO2, ATP, NADH, FADH2
(acetyl-CoA --> 3NADH + FADH2 + ATP + 2CO2)
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what plays a big role controlling citric acid cycle
oxoglutarate dehydrogenase (inhibited by its products, succinyl CoA & NADH, also inhibited by high energy charge in cell; activators: ADP & Ca2+)
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where does NADH bind in TCA cycle
anywhere on pyruvate dehydrogenase but the E1 subunit to inhibit the complex
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what is an allosteric regulator
substance that binds to site on an enzyme separate from the active site (where they bind to substrate); binding changes protein shape & activity (positive or negative feedback)
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what is common between citric acid cycle and electron transport chain
Succinate dehydrogenase (SDH) or respiratory complex II (it is a membrane protein)
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what does Citric acid cycle play central role in
catabolism of fats & proteins
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what is most fat stored as
triacylglycerols
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how does catabolism of triacylglycerols begin
hydrolysis to glycerol & free fatty acids
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how are fatty acids in TCA cycle
fatty acids linked to coenzyme A to form fatty acyl CoAs, which are degraded by beta-oxidation (catabolic process that generates acetyl CoA & NADH & FADH2, reduced forms)
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what free thing can be catabolized for energy
free amino acids
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what does protein catabolism begin with
Proteolysis: hydrolysis of peptide bonds linking amino acids in polypeptide chain (enzymes used to do this are proteases - chop bonds)
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all pathways for amino acid catabolism eventually lead to ...
pyruvate, acetyl CoA, or other intermediates in citric acid cycle (amino acids give up carbons for KREB cycle)
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cataplerotic vs anaplerotic pathways
Cataplerotic pathways provide precursors for biosynthesis (take apart TCA intermediates for this)
Anaplerotic pathways regenerate TCA intermediates
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what feeds into TCA cycle
amino acids, sugars & lipids
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what are the products & play important role in electron transport chain
NADH & FADH2
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What is the goal of electron transport chain
use NADH & FADH2 to concentrate protons in intermembrane space (of mitochondria)
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What happens in outer mitochondrial membrane, intermembrane space, inner mitochondrial membrane, and matrix
outer mito membrane: glycolysis
intermembrane space: high [H+]
inner mito membrane: electrochemical potential generated here
matrix: NADH & FADH2 made here
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what does electron transport chain use for energy
electrons from NADH & FADH2 (H from NADH is removed & converted into 1H+ & 2e-)
174
Electron transport chain for NADH
NADH->NAD+ -gives up 2e- to Complex I, pass 2e- to Coenzyme Q & pump out 4H+, go to Complex III, to Cyt C, to Complex IV, 2e- transferred to oxygen (make H2O)
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What are prosthetic groups (ETC)
electron carriers (associate closely with protein molecules); are large non-protein molecules embedded in protein (ex: iron-sulfur clusters)
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example of prosthetic group in electron transport chain
heme is prosthetic group in hemoglobin & is needed for oxygen binding
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what is Coenzyme Q
lipid-like carrier (aka ubiquinone)
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Electron transport chain for FADH2
Succinate gives FADH2 2e- (associated w/ Complex II), 2e- go to CoQ (no H+ pumped), go to Complex III, 2e- go to Cytochrome C & pump 4H+, 2e- go to Complex IV, go to water & pumps 2H+
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what is cytochrome C
small protein that serves as carrier of electrons; moves e- from Complex III to IV
180
how many directions do electrons move? why?
single direction; bc of redox centers (electron carriers) are organized from low to high affinity
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what complex is a part of FADH2 & not NADH electron transport chain
Complex II
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summary of NADH & FADH2 electron transport chain pathways
NADH: C1, CoQ, C3, Cyt C, C4, O2
FADH2: C2, CoQ, C3, Cyt C, C4, O2
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structure of complex I (how are redox centers & H+ pump structured)
redox centers & H+ pumps are separated in complex (H+ pump is transmembrane; redox centers are attached on outer side)
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what must happen for Complex I to move H+
structural changes in Complex I direct H+ to move through translocation half-channels (aligning of half-channels allows H+ to move)
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in electron transport chain, are complexes apart or together
complexes are clustered together; form supramolecular assemblies/supercomplexes
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what powers ATP synthase
difference in [H+] on opposite sides of the inner mito membrane (motor squeezes ADP + P together = ATP)
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define apoptosis
programmed cell death
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what was an in class example of apoptosis/see a dying cell (animal?)
c. elegans (worm watched in vivo)
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what are methods to execute apoptosis
DNA degradation, corpse engulfment
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what can apoptosis do with tissues
clear connecting tissue & make arthropod joints (e.g. get rid of webbed feet)
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Differences between necrotic & apoptotic cells
Apoptotic have intact PMs, die neatly (shrinks, is eaten by another cell)
Necrotic cells spill their contents into neighbours
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What is the role of caspases in apoptosis
caspases (cysteine aspartate proteases) mediate proteolytic cascade that apoptosis depends on
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what do caspases do (apoptosis)
when activated, chop up strategic proteins in cell, use sulfur atom in cysteine to perform cleavage (cut proteins next to aspartate amino acids)
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Examples of initiator caspases vs effector caspases (apoptosis)
initiator caspases: Caspase 8 & 9
effector caspase: Caspase 3, 6, & 7
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what do initiator caspases do
being apoptosis by activating executioner caspases, which orchestrate apoptosis
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what are caspases synthesized as? how are they activated?
procaspases (inactive precursor); activated by cleavage (by another caspase through dimerization - apoptotic signal triggers assembly of adaptor-protein complex, it brings 2 procaspases close, they cleave/activate each other)
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how are executioner caspases activated
cleaved/activated by initiator caspases
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what amplifies apoptosis signal
cascade of caspase activations
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what does caspase-activated DNAse (CAD) do
catalyzes hydrolytic cleavage of DNA (CADs activated by executioner caspase, CAD cleaves DNA between nucleosomes)
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what are the 2 main activation pathways
extrinsic pathway: signaled from outside the cell
intrinsic pathway: signaled from mito inside the cell
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details of extrinsic pathway
Fas ligand on killer lymphocyte PM binds to Fas death receptor on target cell PM, activated Fas receptors on PM reveal death domains on receptor tails (in cell), bind & cluster small intracellular adaptor protein FADD, clusters of FADD recruit inactive initiator caspases which oligomerize, this large structure is called the death-inducing signaling complex (DISC), caspases cleave & activate, target cell is now apoptotic
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why is intrinsic apoptosis done/started? What is the intrinsic signal?
in response to developmental signals/injury (like DNA damage); release of Cytochrome C from mito into the cytoplasm is signal that activates intrinsic pathway activation
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details of intrinsic apoptosis pathway
binding of cytochrome c to Apaf1 adaptor protein in cytoplasm activates/exposes an oligomerization domain (CARD exposed to recruit more Apaf1) & caspase recruitment domain, Apaf1 recruits inactive caspase-9 monomer forming apoptosome, caspase-9 monomers are activated by dimerization (cleaving each other) --> apoptosis
204
what is apoptosome? what apoptosis pathway is it assocaited with?
oligomerization of Apaf1 and caspases (Apaf1=apoptotic protease activating factor 1, activates caspases by oligomerizing into complex called apoptosome)
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what are inhibitors of apoptosis (IAPs)
caspase inhibitor proteins; they are defense against inappropriate caspase activation (bind & prevent activation of some procaspases)
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what are the main regulators of intrinsic pathway
Bcl2 proteins; pro-apoptotic Bcl2 proteins make holes into mito membrane, anti-apoptotic Bcl2 proteins inactivate pro-apoptotic Bcl2 (no holes made)
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what phagocytoses and digest apoptotic cells? What happens if cells are cancerous?
healthy neighbors apoptose dying cells; cancer cells induced apoptosis to healthy neighbors to make room for more cancerous cells
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what do caspases degrade
flippase that keeps Phosphatidyl serine inside cell (PtdSer must be outside for apoptosis to occur); normal cells recognize apoptotic cells bc they have PtdSer outside
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what is ferroptosis
intracellular iron-dependent form of cell death (distinct from apoptosis & necrosis); not enough iron + too many damaged phospholipids = Ferroptosis (characterized by accumulation of oxidatively damaged phospholipids/lipid peroxidation)
