Term
| To what must a sugar attach in order to be used as a substrate for polymerization? |
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Definition
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Term
| Show the reaction whereby glu-1-P is activated for polymerization into glycogen |
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Definition
| glu-1-P + UTP <---> glucose + UDP +PPi |
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Term
| What 3 enzymes are involved in glycogen synthesis from UDP-glucose? What does each do? |
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Definition
Glycogenin- provides a polymer
Glycogen synthase- extends chain
Glycogen branching enzyme-makes branches via alpha(1->6) linkages |
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Term
| In order to be used for fatty acid synthesis, acetyl CoA must be shuttled across to the cytosol. What 6C molecule is used to carry it across? Show the rxn that incorporates the acetyl group into this carrier. Where have we seen this reaction before? |
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Definition
Citrate shuttles it across.
Acetyl CoA + OAA ---(gives off CoA)->cit
Seen before in TCA cycle. |
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Term
| Before it can be used for fatty acid synthesis, acetyl CoA must be converted into a 3C molecule precurser. What is the name of this precurser? What molecule donates the CO2 to the acetyl CoA to form it? |
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Definition
| The precurser is malonyl CoA. Acetyl CoA carboxylase donates the CO2. |
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Term
| Fatty acid synthesis occurs on an enzyme called Fatty Acyl Synthase. Before synthesis begins, the 2 starting components must be loaded onto the enzyme. What are the 2 components and to which kind of group on the enzyme do they attach? |
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Definition
Components- acteyl CoA, malonyl CoA
Attach to thiol |
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Term
| To begin the 2nd cycle in the synthesis of a fatty acid, a _________ group becomes attached to the enzyme. What rearrangement must occur on the enzyme in order for this to occur? |
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Definition
Malonyl group
F.A. chain must move to position 1, which opens up position 2 |
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Term
| 7 cycles in the synthesis of a fatty acyl synthesis results in a FA chain with ___ carbons. This fatty acyl chain is then released as the fatty acid called ________. Is this F.A. saturated or unsaturated? |
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Definition
| 16 carbons Palmitate-saturated |
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Term
| In the synthesis of cholesterol, 2 3C molecules undergo a series of reactions to produce a 6C molecule called mevalonate. What are the names of the 2C molecules? What is the name of the enzyme that catalyzes the last step in their conversion to mevalonate and how is this enzyme affected by statins? |
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Definition
2 3C molecules- Acetyl CoA Enzyme- HMG CoA reductase. The enzyme is inhibited. |
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Term
| The committed step in the synthesis of cholesterol is catalyzed by the enzyme HMG CoA reductase. This enzyme is regulated by the hormones insulin and glucagon. What is the effect of each of these hormones on the activity of the enzyme? |
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Definition
| Insulin activates it, glucagon inhibits it |
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Term
| An atherosclerotic plaque forms within the arterial wall. An important component of these plaques are foam cells. Describe how a foam cell develops from a WBC. |
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Definition
| Macrophage engulfs an altered LDL |
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Term
| Name a type of cell that is involved in the formation of the fibrous cap during the progression of an athersclerotic plaque. What happens when the fibrous cap ruptures? |
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Definition
Muscle cells
When fibrous cap ruptures, plaque bursts through and heart attack/stroke can occur |
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Term
| Why is it that the reaction for N fixation, which is exergonic, is so rare in nature? |
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Definition
| Ea to break the bonds is 942KJ/mol |
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Term
| Give an example of a molecule derived from an amino acid. Which amino acid is it derived from? |
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Definition
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Term
| All amino acids are derived from intermediates in 3 important metabolic pathways. What are they? |
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Definition
| TCA cycle, glycolysis, Pentose-phosphate pathway |
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Term
| How do insulin, glucagon and epinephrine affect glycogen breakdown? Glucagon also affects the enzyme "glycogen synthase." Would you expect it to activate or inhibit this enzyme? |
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Definition
Insulin- inhibits glycogen breakdown
Glucagon- activates glycogen breakdown (inhibits glycogen synthase)
Epinephrine- activates glycogen breakdown |
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Term
| Draw a diagram showing the cycle of nitrogen in the biosphere. What happens to most of the ammonia produced? |
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Definition
| Most of the ammonia is used by plants to make amino acids and nucleotides. |
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Term
What organ or tissue is being described in each of the following statements?
a) specialized for quick ATP production
b)processing and distribution of nutrients
c) releasing FAs into the bloodstream |
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Definition
a)muscle tissue
b)liver
c)adipose tissue |
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Term
| When sugars enter the liver, what molecule are they immediately converted into? What are 5 possible ways that this molecule can be used? Which one would occur in response to low blood sugar? |
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Definition
-Converted glu-6-P (would occur if blood sugar was low)
-glucose, glycogen, fuel, fats, NTs |
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Term
| Amino acids cannot be stored as is in the liver. What must they be converted into in order for them to undergo short-term storage? Long term storage? |
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Definition
Short term- carbs
Long term- fats |
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Term
| One of the 4 routes taken by FAs in the liver is beta-oxidation to acetyl CoA. What happens when the amount of acetyl CoA produced exceeds that required by the liver? Does it go to waste or can it still be used to get energy? |
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Definition
| Excess acetyl CoA is made into ketone bodies, which go into the TCA cycle |
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Term
| What 2 compounds act as the primary fuel molecules in resting muscle? |
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Definition
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Term
| What is the result of a lack of oxygen to heart muscle? Why does this occur? |
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Definition
| Muscle tissue dies-occurs due to a lack of blood flow caused by a blockage |
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Term
| The brain has a very active respiratory metabolism, producing a large amount of ATP. For what is the ATP used for? |
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Definition
| Used to produce and maintain the electrical potential. |
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Term
| Define hormone. What kind of tissue produces them? |
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Definition
| Produced by endocrine tissues, chemicals that move through the blood to exert their effects at a distant site |
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Term
| What endocrine gland releases the hormone epinephrine? From where does it get its signal to secrete the hormone? |
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Definition
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Term
| What endocrine gland acts as the coordinating center of the endocrine system? To what other endocrine gland does it send its hormonal signals? In what part of the bodies are these 2 glands located? |
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Definition
| Hypothalamus, pituitary glands. Found in the brain |
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Term
| What endocrine tissue responds to changes in the blood glucose levels? What are 2 hormones secreted by it and how do each affect the level of glucose in the blood? |
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Definition
| Pancreas- insulin (lowers), glucagon (increases) |
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Term
| What are 3 classes of hormones mentioned in class? Give an example of each type. |
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Definition
| Amino acid derived- dopAMINE, Peptide-insulin, Steroid- testosterone |
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Term
| Briefly describe the 2 general signaling pathways used by hormones. Which is taken by steroid hormones? by amine hormones? |
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Definition
Steroid- alters transcription of a gene
Amine- alter activity of other enzymes |
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Term
| In the signal transduction pathway taken by epinephrine a "G protein" is activated by epinephrine binding to its beta-adregenic receptor in the cell membrane. What membrane-bound enzyme is subsequently activated by the "G protein" and what reaction does it catalyze? |
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Definition
| Adenylyl cyclase is activated and ATP produces cAMP. cAMP degrades glycogen to glucose. |
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Term
| How does the signal from epinephrine get turned off (2 components)? |
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Definition
| G protein has GTPase activity, converts GTP->GDP. Degrade cAMP to AMP, signal only present as long as hormone is bound |
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Term
| What are the 3 hormones that affect blood glucose levels? What conditions stimulate the release of each? |
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Definition
Insulin- lowers BS, used if BS is high
Glucagon- raises BS, used if BS is low
Epinephrine- increases BS; used under dire circum. |
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Term
| Epinephrine causes both physiological and metabolic effects. Among the metabloic effects are an upregulation of gluconeogenesis and glycolysis. How is a futile cycle between the pathways avoided? Considering what you know about the role of epinephrine, why do you think that both of these pathways are being turned on? |
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Definition
| The pathways occur in different sites. Energy must be made available very fast, so both must be on simultaneously. |
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Term
| What is the effect of glucagon on glycolysis and gluconeogenesis in liver cells? |
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Definition
| Inhibits glycolysis and activates gluconeogenesis |
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Term
| What role does DnaB play in the initiation of replication (& during elongation)? What kind of an enzyme is it? |
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Definition
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Term
| During the elongation process of DNA synthesis, what are the roles of gyrase, helicase and SSBs? What kind of enzyme is gyrase an example of? |
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Definition
Gyrase- relieves topological strain from helicase activity (topoisom. enz)
Helicase- unwinds DNA
SSB- keeps strands apart |
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Term
| Why doesn't DNA Pol III perform all of the polymerization reactions during the DNA synthesis? What other polymer is used? What does it do? |
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Definition
| It cannot destroy RNA primers. DNA Pol I is used- 5'->3' exonuclease |
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Term
| What is the significance of the 3'->5' exonuclease activity of DNA Pols I and III? |
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Definition
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Term
| DNA Pol III acts as a dimer thereby allowing the concurrent synthesis of both leading and lagging strands. How can this work if the strands are moving in opposite directions? |
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Definition
| The lagging strand is looped so that it faces the same direction |
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Term
| DNA ligase is an enzyme that seals nicks between a ____ and a _____. What are the 2 main stages of the sealing acitivity? |
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Definition
3' OH & 5' P
activation of the 5'P in the nick
3' OH attacks the P and releases AMP |
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Term
| When DNA is completed in E. coli, the resulting daughters are intertwined in a catenated state. What type of enzyme separates them? Where in DNA synthesis have we seen this before? |
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Definition
| Topoisomerase; elongation, decatenation |
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Term
| What is represented by +1? by the -35 region? by the -10 region? |
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Definition
+1 = transcription starts
-35 = forms closed complex
-10 = opens duplex/complex |
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Term
| As the initiation of transcrip.proceeds, the RNA pol is bound, noncovalently, to a protein called sigma. What is the purpose of this factor? What happens in its absence? |
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Definition
| It provides specificity in what promoter is recognized. If it was absent, the promoter wouldn't be recognized |
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Term
| What are 2 types of regulators of prokaryotic transcription other than the sigma factor? Describe what each does. |
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Definition
| Repressors-bind regions called operators, inhibit/affect RNA pol binding/movement Activators- enhance binding of RNA pol to promoter |
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Term
| Describe one of the 2 systems by which E. coli terminates transcription (dep. or indep.) |
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Definition
Dependent
-Termination loop forms, RNA pol pauses
-sigma factor causes RNA pol to dissoc.- sigma factor acts as helicase, RNA releases |
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Term
| What polymerase does each RNA pol.synthesize: RNA pol I,II,III |
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Definition
| I- lg rRNA II- mRNA III- tRNA, sm. rRNA |
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Term
| What are the access proteins called that are required for the initiation of transcription in euks? |
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Definition
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Term
| What are 2 processing events that occur on newly synthesized eukaryotic RNAs other than the addition of the 5' cap? |
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Definition
| Splicing of introns and adding the poly-A tail |
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Term
| How did Nirenberg & Matthei determine that the codon for Phe was uuu? |
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Definition
| Poly (u) + E. coli + GTP +a.a.s = poly (Phe), so uuu = Phe |
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Term
| Do all mRNA codons code for amino acids? |
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Definition
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Term
| T/F: The start codon only appears once on an mRNA, in the position that sig. 1st amino acid |
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Definition
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Term
| T/F: Each amino acid is coded by one mRNA codon. |
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Definition
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Term
| What 5 components make up the basic requirements for proteins synthesis? |
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Definition
mRNA
aa-tRNA
ribosomes
factors
GTP (evergy) |
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Term
| Describe how "wobble" is related to the degeneracy of the genetic code? |
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Definition
| The wobble position doesnt allow for precise line-up. This allows flexibility in what can base pair with what. |
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Term
| The E. coli and euk ribosomes are each made of __ subunits. Each subunit is composed of ____ and ____. |
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Definition
2 subunits
rRNA and proteins |
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Term
| What are the 5 steps in producing a functional protein? |
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Definition
1) aa activation
2) initiation
3)Elongation
4)termination/release
5) folding/processing |
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Term
| In the activation of amino acids, what kind of enzyme is used? What kind of linkage attaches the amino acid to the tRNA and activates it? |
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Definition
aa-tRNA synthetase
ester linkage |
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Term
In the initiation step of protein synthesis, in what order do the following add in?
initiating tRNA, 50S subunit,mRNA |
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Definition
1)mRNA
2)Init. tRNA
3)50S subunit |
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Term
| What are the roles for each of the initiation factors (IF 1, IF2, IF3)? |
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Definition
IF1: blocks A site so init. tRNA-aa will go to P site
IF2: binds GTP, hydrolyzes when lg. subunit enters
IF3: Keeps 30S & 50S subunits separated |
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Term
| Concerning the initiation step of protein synthesis, how is the mRNA guided to the 30S subunit such that the AUG codon is aligned in the P site? |
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Definition
| Base pairing between 16S rRNA and Shine Delgarno seq. line up the start codon with the P site. |
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Term
| Of initiation and elongation, which occurs at the P site? the A site? |
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Definition
P- initiation A- elongation |
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Term
| What are the 3 steps of elongation in protein synthesis? What molecule provides the E and in which 2 of the 3 steps is it used? |
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Definition
tRNA-aa enters A site, pep bond forms, translocation
uses GTP in steps 1 & 3 |
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Term
| What reaction is catalyzed by peptidyl transferase? Can this activity by performed by rRNA? |
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Definition
Peptide bond formation
Yes it can |
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