Unit 1 Exam Flashcards
Lectures 1-10
Explain what lipids are? Define fatty acids.
- Lipids are an heterogeneous structure group which are broadly defined as hydrophobic
- fatty acid is a carboxylic acid with an aliphatic chain (no rings), which is either saturated or unsaturated (kink).
Explain the structure of a cell membrane?
cell membranes consist of two layers of oppositely oriented phospholipid
molecules, with their heads exposed to the liquid on both sides, and with the tails directed into the membrane.
Describe the four structures of protein?
- primary structure is the sequence of amino acids
- secondary structure is hydrogen bonds between amino acids, forming Alpha helices and beta-sheets.
- Tertiary structure is the overall shape of a polypeptide resulting from
interactions between the various amino acids (single polypeptide chain) - Quaternary structure is the overall structure that results from more than one polypeptide subunits joining (protein complex)
Explain what you know about DNA
- composed of two polynucleotide
chains that coil around each other to
form a double helix - nucleotides are joined to one another in a chain by phosphodiester bonds
- 5’ end of the chain has a phosphate group. The 3’ end has a sugar
Transcription vs Translation?
Transcription:
- RNA polymerase uses DNA as a template to produce a pre-mRNA (transcript)
- occurs in nucleus
Translation:
- A ribosome builds the
protein molecule (polypeptide) from
a mature mRNA
- occurs in cytoplasm
Overall:
- Proteins are encoded in DNA
DNA→mRNA →Protein
What causes sickle cell disease?
- A single amino acid substitution in hemoglobin
- Hydrophobic interactions between sickle-cell hemoglobin proteins lead to their aggregation into a fibre; capacity to carry oxygen is greatly reduced.
- Fibres of abnormal hemoglobin
deform red blood cells into a sickle shape.
Considering the chemical characteristics of the amino acids valine and glutamic acid, propose a possible explanation for the dramatic effect on protein function that occurs when valine is substituted for glutamic acid?
Glutamic acid has a negative charge that allows it to stick to positively charged amino acids, holding the protein’s shape. Valine can’t stick to positively charged amino acids, so a protein with this substitution won’t be shaped correctly.
What is RNA polymerase’s job? Explain its active site?
Job:
- catalyzes the chemical reactions
that synthesize RNA from a DNA template.
ie:
- Two DNA strands form a double helix at the top
- RNA polymerase separates the two DNA strands in the middle and builds an RNA strand
- the two DNA strands come back together
Active site:
- has two DNA stands and an RNA strand
Name the four different types of RNA molecules and the functions they serve
mRNAs messenger RNAs
- code for proteins
rRNAs ribosomal RNAs
- form basic structure of ribosome
- catalyze protein synthesis
tRNAs transfer RNAs
- adaptors between mRNA and amino
acids
snRNAs small nuclear RNAs
- function in nuclear processes
What does RNA polymerase recognize to initiate transcription? Describe.
- RNA pol II recognizes the TATAAA box (at promoter - DNA region) and binds to its proteins
- large multiprotien transcription factors (TFIID) start the process of transcription, recruiting additional transcription factors. (constructs a large protein complex)
Where does mRNA leave nucleus from?
- mRNA leaves the nucleus through the Nuclear Pore Complex (NPC)
- Particle movement by the NPC is controlled (opens/closes)
- mRNA, ribosomes, and proteins leave the nucleus through the NPC
- Protein import also happens through the NPC
nucleus –> NPC —> cytoplasm
After leaving the NPC, what reads the mRNA? What is the process?
- ribosome reads mRNA and translates the information into a polypeptide
process:
1. The two subunits lock together with a mRNA trapped inside
2. The ribosome then walks down the
messenger RNA and translates the
nucleotides into amino acid chains
3. Three nucleotides (codon) = one amino acid
Explain what you know about Ribosomes?
- Ribosome is composed of a large catalytic subunit and a small subunit
Large subunit
- Contains the active site of the ribosome: the site that creates the new peptide bonds when proteins are synthesized
Small subunit
- Finds a messenger RNA strand and ensures that each codon pairs with the
anticodon
Describe the role of tRNA (transfer RNA)?
- Transfer RNA (tRNA) translate the mRNA into amino acids
- serves as a link between the mRNA molecule and the growing chain of amino acids.
- Anticodons and codons
Why do cells need a nucleus?
nucleus controls and regulates the activities of the cell (e.g., growth and metabolism) and carries the genes, structures that contain the hereditary information.
RNA splicing does what? Where does it occur? Describe introns/exons.
- splicing removes untranslated regions from mRNA (common in eukaryotes) in nucleus
- Splicing allows multiple proteins to be encoded in a single gene
- Exons: part of the RNA that code for proteins
- Introns: regions that resides within a gene but does not remain in the final mature mRNA
- Mature mRNA is exported by the nuclear pore complex
Explain what you know about TAG (triacylglycerol)?
Hints: -ases, enzymes, donors, etc
- make triacylglycerol (TAG) from monoacylglycerols using Acyltransferases
- Acyltransferases are enzymes that move fatty acids
- Acyl-CoA is the fatty acid donor
- Cells also make TAG from glycerol-3-phosphate
- TAG is made in smooth ER, accumulates only in organelles called lipid droplets
What do you know about lipid droplets, and perilipins.
Lipid Droplets
- originate at the ER and are storage organelles
- have a single layer membrane (phosopholipids, since can’t interact with H2O must be hydrophilic membrane)
- no LDs in those that lack TAG synthesis enzymes (yeasts)
Perilipins
- family of proteins that coat lipid droplets
- associate with the lipid droplet
membrane at the cytoplasmic side
What are the three steps in making a Lipid Droplet?
- TAG synthesis & Lens formation
- TAG synthesis occurs at the smooth ER bilayer
- triacylglycerol synthesis (and cholesterol ester synthesis) enzymes deposit neutral lipids in between the leaflets of the ER bilayer - Emergence and nascent lipid droplet formation
- protein complex forms in the ER side to push the LD out
- seipin and other lipid droplet biogenesis factors are recruited to the lens structure and facilitate the growth of the nascent lipid droplet
Note:
- Budding on the cytoplasm side
- Seipin push from the ER side
- Asymmetry in protein recruitment from the cytosol side, and in phospholipid composition
- Lipid droplet budding and growth
- lipid droplets bud from the ER and grow through fusion or local lipid synthesis
- LD fuse and interact with other organelles via membrane
proteins (proteins are always on
cytoplasmic side)
Why is phosphatidic acid is the branchpoint between store TAG
make membrane lipids?
- vital cell lipid and starting point
- smallest phospholipid
choice:
- Remove phosphate group = make TAG
- Keep phosphate = phospholipids
What are the 5 factors needed for Phosphatidylinositol 4,5-bisphosphate (PIP2) to be at the cell membrane?
- two fatty acids
- phosphate group (from being a
phospholipid) - inositol molecule
- two extra phosphates (specific to PIP2)
- glycerol
Explain the fluid mosaic model with respect to membranes?
fluid mosaic model envisions the membrane as a fluid bilayer of lipids with a mosaic of associated proteins
What do you know about membranes?
- define boundaries & are permeability barriers (separating ribosomes for regulated translation)
- contain several classes of lipids (ex: phospholipids, glycolipids & sterols)
- vary in lipid composition
- lipid bilayer is fluid and asymmetric (phospholipids can diffuse)
- Proteins at the membrane must have hydrophobic amino acids (compose the hydrophobic region of membrane proteins)
Membranes contain integral, peripheral, and lipid-anchored proteins. Describe each.
- integral
- have hydrophobic region
- permanently embedded within the plasma membrane
- movement of molecules & transduction of energy and signals - peripheral
- associate though another membrane protein
- temporarily attached to the cell
- allowing them to detach and reattach at specific times, with specific signals (coordination & communication)
- form weak and reversible associations to the membrane, typically through binding to integral membrane proteins
ex:
- Enzymes that metabolize membrane lipids
- Regulatory subunits of transmembrane protein
- lipid-anchored proteins
- bind fatty acids which gets inserted into the membrane
- on the surface of the cell membrane, covalently bonds to fatty acids lipids or isoprenyl groups
ex: Trehalase
note:
- post-translational modification (results in attachment of
hydrophobic prenyl groups anchoring the small GTPAse proteins to intracellular membranes)
Explain the roles of membrane proteins
- detect and transmit electrical and
chemical signals (signals bind to membrane receptors) - mediate cell adhesion and cell-cell communication (cadherin to cadherin binding keep cells together)
- move ions across cell membranes (change conform. and pass in/out)
What are two most common integral proteins?
a) transmembrane Proteins (Cross
the membrane) - most common
b) Monotopic Proteins
Note on Monotopic proteins:
- embed into a single face of the membrane
- Irreversible
- rxns involving hydrophobic or amphiphilic substrates not readily soluble in water
Explain glycosylation and its relationship with proteins/lipids.
- Proteins and lipids in the outside of the membrane are glycosylated
- process by which a carbohydrate is
covalently attached to a target macromolecule
Explain simple/facilitated diffusion.
- protein mediated movement down the gradient
- does not require energy (ATP)
- only moves molecules from high to low concentrations
- Channels (pores) and Carriers mediate facilitated diffusion
ex: glucose
Explain carrier proteins in facilitated diffusion.
- Carrier proteins undergo a conformational change as the solute moves
- alternate between 2 states
- highly specific to solute
- transport either one or two molecules
Explain channel protein(s) role in facilitated diffusion. Give 3 examples.
Role:
- form hydrophilic transmembrane channels
Ex:
1. Ion channels (specific to certain ions)
2. Porins (not specific, only in bacteria & mitochondria, chloroplast)
3. Aquaporins (specific to H2O)
Explain ion channels further.
(facilitated diffusion)
- Ion channels are gated & open when stimulated by voltage, ligand binding, temperature, and pressure
- Potassium channels allow potassium ions to pass, but block smaller sodium ions
Why is passing ions important? Name 3 factors that affect voltage.
- Cells read the change in voltage and use it as an intracellular signal
Ex:
1. Membrane potential
- difference in the concentrations of ions on opposite sides of a membrane.
(–70 mV to –40 mV)
2. Depolarization
- interior voltage becomes less negative ( –70 mV to –60 mV)
3. Hyperpolarization
- interior voltage becomes more negative ( –70 mV to –80 mV)
Ligand-gated ion channels do what? What are examples of ions that use these channels?
What do voltage-gated channels do? High vs low voltage difference?
Ligand gated ion channels
- convert a chemical signal into the cell
- ex: Na+, K+ and Ca2+
Voltage-gated sodium channels
- transmit signals in a wave through the nervous system.
- voltage difference high = channels are tightly closed
- voltage difference is low = channels open and allow sodium ions to pass
What do you know about ATP? How does it get to where it’s needed (VDAC)?
- main energy storage molecule
- made of nucleoside triphosphate, consisting of a nitrogenous base (adenine), a ribose sugar, and three serially bonded phosphate groups
- negative charge
- made in the mitochondria
- can’t pass through the membranes
- uses voltage-dependent anion channel (VDAC) to get from mitochondria to the cytoplasm
Note:
- VDAC mediates exchange of negatively charged metabolites
TP → ADP (releases energy)
ADP → ATP (requires energy)
.
What is active transport, direct vs indirect?
Direct
- using ATP to directly pump a
solute across a membrane against its electrochemical gradient
Indirect
- transport of a solute in the direction of its increasing electrochemical potential coupled to the facilitated diffusion of a second solute (usually an
ion)
Note:
- Both use symporters and antiporters
Using active transport (direct & indirect), explain amino acid absorption.
Extra: What do enterocytes (columnar cells that form most of the epithelium of the gut intestine) want concentrations to be?
- Direct: ATPase pumps maintain ion gradients
- Indirect: Amino acid symporters move amino acids into the enterocytes
Note:
The enterocytes want to keep:
- High concentration of H+ in the lumen
- High concentration of Na+ in the lumen
- Low concentration of AAs in the lumen
What are the four types of ATPases?
- P-ATPases
- regulated by phosphorylation
- Ca2+/H+
- Na+/K+
- H+/K+ - Vacuolar-ATPase
- Two rotary motors (ATP-driven motor turns an axle, which turns a
second motor that pumps
protons across the membrane)
- pumps H+ ions to increase acidity in specific organelles (vacuoles, lysosomes)
- Not phosphorylated
- V-ATPase is regulated by separating the ATP-powered motor from the proton pumping motor - F-type ATPases
- ATP synthases
- moves (H+) ions with the concentration gradient to produce ATP
- mitochondrial inner membrane - ABC-type ATPases
- mediate ATP-powered translocation of many substrates across membranes
- have two transmembrane domains
(TMDs) that are embedded in the membrane bilayer and two ABCs in the cytoplasm
- Some need a binding protein
- All ABC transporters have a shared
amino acid sequence in the ABC
domain
- transport big molecules (metabolites, drugs, amino acids, sugars, peptides and pigment precursors)
- ex: missing protein in the White mutant fly
- Heterodimerization of ABC ATPases increase the number of solutes
What are the 3 main examples of P-ATPases?
(know)
- Ca2+/H+: Plasma membrane or sarcoplasmic reticulum, eukaryote muscles, keeps Ca2+ low in cytosol
- Na+/K+: PM, animals, maintains membrane potential (-60mV)
- H+/K+: PM, animals, pumps H+ to acidify stomach
What does Na+/K+ ATPase do? Explain.
- maintains electrochemical ion
gradients in all cells - The Na+/K+ ATPase continually pumps Na+ ions out of the cell and K+ ions into the cell
- pumps undergo 2 large conformational changes through the pumping cycle
- Potassium binding sites of the Na+/K+ ATPase are made of oxygens
Note:
- High Na+ outside, high K+ inside
Explain ATP synthase motor briefly.
top part (F0)
- electric motor powered by the flow of H+.
bottom part (F1)
- chemical motor, powered by ATP.
- joins ADP and Pi together by force
the two are connected together by a stator
A relatively small number of ABC transporters move a large number of solutes. How?
binding and hydrolysis of ATP to power the translocation of a diverse assortment of substrates, ranging from ions to macromolecules, across membranes
What are the two types of metabolic pathways?
- Anabolic
- make up large molecules
- Require energy (endergonic)
ΔG>0 - Catabolic
- break down large molecules
- Release energy (exergonic) ΔG<0
What do you know about mitochondria?
- two membranes (inner & outer)
- most metabolic pathways have some connection with them
- cristae (folds of IM, increase in the surface area, more locations for ATP production to occur)
- matrix (enzymes & mtDNA; metabolizes nutrients into by-products)
Oxidation vs Reduction
Oxidation:
- removal of electrons (-)
- cells obtain energy by oxid. of organic molec.
- enzymes catalyze this rxn in series of steps (free energy is transferred in packets to carrier molecules, like ATP and NADH)
Reduction:
- addition of electrons (+)
Explain what you know about NAD and FAD (and therefore NADH and FADH).
- NAD and FAD = coenzymes of redox reactions and electron carriers
- NAD and FAD accept electrons (become reduced) during catabolic steps in the breakdown of organic molecules.
- NADH and FADH2 donate these electrons to some other biochemical reaction normally involved in a process that is anabolic (like the synthesis of ATP).
Why is Glucose is one of the most important oxidizable substrates in energy metabolism? Give two reasons.
- Its oxidation is highly exergonic
- Many polysaccharides break into Glucose
- Ie: Starch, Glycogen, cellulose
What is Glycolysis? Give quick overview of steps.
- metabolic pathway that entails the oxidation of glucose into two pyruvate
- 10 enzymatic rxn process
- occurs in cytoplasm
- stores energy as ATP and NADH molecules
Steps:
1. Add two phosphates and cleave
2. Oxidation and ATP
3. Make Pyruvate and ATP
Glucose → 2 Pyruvate + 2 NADH + 2 ATP
Disaccharides break down into? What about monosaccharides?
- broken into three monosaccharides Glucose, Galactose and Fructose.
- Enzyme names match substrate names (ex: lactase for lactose)
- monosaccharides (eg Fructose and Galactose) are converted into Glycolysis intermediates
Why is pyruvate the branchpoint between aerobic and anaerobic metabolism?
- If high O2, PDH takes pyruvate → aerobic
- If low O2, LDH make lactate → anaerobic
What is the step leading up to TCA Cycle? (Before TCA occurs & acetyl-CoA enters)
Mitochondrial Pyruvate Carrier transports pyruvate into mitochondria (as this is where TCA occurs)
How is Pyruvate converted into acetyl-CoA? Define the enzyme.
Pyruvate dehydrogenase (PDH) converts Pyruvate into Acetyl-CoA
- adds a CoA
- removes a carbon
- releases a lot of energy (-33ΔG)
Pyruvate dehydrogenase (PDH) info:
- multienzyme complex
- metabolizes pyruvate
- It is big ~ 100 subunits
- Multiples of 3 subunits (E1 metabolite binding sites, E2 core of the complex, E3 intermediate enzyme)
- needs a vitamin B1 derivative as cofactor (thiamine pyrophosphate)
What do you know about the Citric Acid Cycle or TCA Cycle? What are the products?
- occurs in mitochondria
- aerobic rxns
- oxidative catabolism for carbohydrates, amino acids, and fatty acids
Acetyl-CoA → 3 NADH* + FADH2* + ATP + 2 CO2
*e- carriers that can be used or oxidized
What happens if there are excess amino acids or the body is starving in the TCA cycle? What about intermediate products?
- amino acids will be converted into TCA cycle metabolites
- TCA cycle intermediates can be lost to cataplerotic pathways that provide precursors for biosynthesis
What is the goal of the Electron Transport Chain (ETC)? What is its power source?
Goal
- use NADH and FADH2 to concentrate H+ protons in the intermembrane space (fueling ATP synthesis)
Power
- electron transport chain uses e-
- hydride ion is removed from NADH (to regenerate NAD+) and is converted into a proton and two electrons (H-→ H+ + 2e -)
- Could use FADH2 (reduced to FAD)
What does the ETC turn the reduction of NADH into?
ETC converts NADH reduction into a gradient of protons
- The electrons start with very high energy and gradually lose it as they pass along the chain.
- electrons pass sequentially from one complex to another until transferred to oxygen
What carriers support the ETC? Define and then give an example.
ETC requires the close association of the electron carriers (prosthetic groups) with protein molecules.
- Prosthetic groups: large non-protein molecules embedded in the protein (not possible with amino acids)
Ex:
heme is the prosthetic group in hemoglobin and is is necessary for oxygen binding
Describe what each of the 4 complexes do in the Electron Transport Chain.
Complex I
- Complex I receives 2 electrons from NADH and passed them to CoQ (coenzyme Q - lipid-like carrier).
- The energy is used to pump 4 H+
Complex II
- receives 2 electrons from succinate passing them directly to FADH2 and then into CoQ.
- Does not pump H+
Complex III
- receives 2 electrons from CoQ and passes them to Cytochrome C.
- The energy is used to pump 4 H+
Complex IV
- receives 2 electrons from Cytochrome C and passes them to Oxygen, which is reduced to water.
- The energy is used to pump 2 H+
What role does Cytochrome C play in the ETC?
- Cytochrome c is a small protein that serves as carrier of electrons (from complex III to IV)
- Has a heme cofactor that allows the carrying of e-
Why do electrons move in a single direction?
(Hint: Redox Centers).
- because Redox centers (electron carriers) are organized from low to high affinity
- redox centers and the H+ pumps are separated in complex (ex: complex I)
What moves H+ through Complex I?
- Structural changes in Complex I direct H+ to move through translocation half-channel
- half-channels are formed by conserved polar residues and polar cavities containing water molecules
Matrix → intermembrane space (via these channels)
What does the flow of H+ back mean?
- The synthesis of ATP can be powered with H+ back
- Ie: power source for the ATP synthase is a difference in the concentration of H+ on opposite sides of the inner mitochondrial membrane.
ADP + Pi + squeezing force = ATP
What do you know of apoptosis?
- mediated cell death
- clears connecting tissue and makes arthropod joints
- apoptotic cells have intact plasma membranes (die neatly, no damage to neighbors while necrotic cells spill their contents into their neighbors)
Note:
Healthy neighbors phagocytose and digest apoptotic cells
Briefly go over work done on c.elegans (flatworms) that help our understanding of apoptosis today.
- lineage of all cells in C.elegans is known
- Follow them in-vivo, saw cells dying
isolated mutants in which the cells remain - reconstructed the apoptotic pathway in worms
- grown easily in large #s
- useful in study of ageing processes, organism passes through several distinct phases of life which can be observed physiologically and genetically
What cascade is apoptosis dependent on? Which enzyme mediates this? What is overall triggered?
Apoptosis depends on a proteolytic cascade mediated by Caspases (Cysteine Aspartate Proteases)
Overview:
1. Once activated they chop up strategic proteins in the cell.
2. they are cysteine proteases that use the sulfur atom in cysteine to perform the cleavage reaction.
3. they cut proteins next to aspartate amino acids
apoptotic signal triggers the assembly of an adaptor-protein complex
Explain Caspases (role in apoptosis).
- synthesized in cell as procaspases (inactive precursors) and are activated by cleavage at aspartic acids by other caspases
- cascade of caspase activations make apoptosis amplifying and irreversible
- they degrade a flippase that keeps Phosphatidyl serine inside the cell
…..In apoptotic cells PtdSer is outside
…..normal cells recognize apoptotic cells because they have PtdSer outside
What catalyzes the hydrolytic cleavage of DNA? On the other hand, how is DNA degraded?
- A caspase activated DNAse (CAD) catalyzes the hydrolytic cleavage of DNA
- Caspase release the brake on DNAses to degrade DNA
Differentiate between the two main activation pathways. Explain how both are initiated.
- extrinsic pathway
- signaled from outside the cell
Initiated by
a) Activation of cell-surface death receptors
b) activated Fas receptors cluster and expose death domains on the receptor tails, which then bind and cluster a small intracellular adaptor protein called FADD
c) FADD clusters recruit multiple copies of inactive initiator caspases, which oligomerize. The large structure is called the death-inducing signaling complex (DISC)
- intrinsic pathway
- signaled from mitochondria inside the cell
- response to developmental signals or to injury (DNA damage)
- release of cytochrome c from the mitochondria into the cytoplasm is the signal that activates it
Initiation process cont’
a) binding of cytochrome c to Apaf1 exposes an oligomerization domain and a caspase recruitment domain
b) oligomerized Apaf1 recruits an inactive caspase-9 monomer, forming the apoptosome. Then, the caspase-9 monomers are activated by dimerization
Note:
Apaf1 = apoptotic protease activating factor 1
What is a line of defense that prevents inappropriate caspase activation?
- caspase inhibitor proteins called inhibitors of apoptosis (IAPs).
- IAPs bind and prevent activation of some procaspases
What is the main regulator of the intrinsic (internal) pathway?
Bcl2 proteins
- Pro-apoptotic Bcl2 proteins: make holes into the mitochondrial membrane
- Anti-apoptotic Bcl2 proteins: inactivate the pro-apoptotic Bcl2
