Chapter 4 Flashcards
What is a ligand?
a molecule that binds to a specific receptor on a cell
What is the difference between mRNA, rRNA, and tRNA and their functions?
mRNA- Carries the RNA template outside of the cell
rRNA- It reads the amino acids and links them together
tRNA- It delivers amino acids to the ribosomes
Where are triplets, Codons, and anticodons located?
Triplets- In DNA
Codons- mRNA
Anticodons- tRNA
What do triplets, Codons, and Anticodons code for?
Triplets- Specific single amino acid
Codons- Codes for a single amino acid
Anticodons- Codes for a single amino acid
What is AUG in an amino acid sequence?
They start codon for the amino acid sequence
Why is it important for a gene to have a specific sequence of nucleotides?
Because that sequence determines how the protein functions. And we need specific proteins to do certain functions for us to live and function properly
How does a cell only have 20,00 genes but 100,000 proteins? (4 ways)
- RNA cut and spliced in different ways
- alternate polypeptide interactions (getting cut and binding to different polypeptides)
- Carbs or lipids binding to alter function
- Posttranslational modification
What is splicing?
It is where the introns get cut out from a sequence but the exons are left and combine IN THE SAME SEQUENCE/PROTEIN
What is alternative splicing?
Exons from the multiple genes are joined in DIFFERENT combos/ DIFFERENT PROTEINS leading to different related proteins
What is a protein isoform?
Proteins that are related whose functions are similar but their ligands differ
What is an example of a protein isoform? (hemoglobin)
Infants have different hemoglobin protein isoforms that absorb more oxygen than hemoglobin in adults
When OGEN is at the end of a word what can be assumed the molecule is?
An inactive enzyme
What is the function of the chaperone protein?
They guide each protein as it takes on secondary and tertiary structure (help fold correctly
What is protein specificity and some examples?
The ability of a protein to bind to a specific ligand or group.
Examples sucrase- only catalyzes sucrose into glucose and fructose
What is protein affinity?
The strength to which a protein is attached to a ligand
What is protein reversibility?
When proteins bind to other molecules non covalently, they are reversible
What is protein activation?
When a protein is inactive in the cell the enzyme chops off a portion or two of the molecule to make it active again
What is a protein agonist and antagonist?
Agonist- A substance that supports or mimics the actions of a ligand to make a response
Antagonist- It inhibits the function of the ligand
What is the difference in competitive, non-competitive, and uncompetitive inhibition in enzymes?
Competitive- When the inhibitor binds to the binding site of the protein before the ligand gets there
Non-competitive- When the inhibitor binds to the allosteric site (or another site) on the protein and it decreases the ability of the ligand to bind properly to the binding site
Uncompetitive- When the inhibitor just binds to the protein and doesn’t effect the ligand at all
What is a reactant called when an enzyme is required to produce products?
A substrate
What are the 5 factors that contribute to the probability of a chemical reaction to occur?
- Chemical nature of the reacting substance
- State of subdivision (one large lump of reactants vs small particles of them)
- Temperature of reactants (the hotter they are the more likely it is to occur)
- Concentration of reactants (how many there are)
- Presence of a catalyst (something that speeds up the process like a ligand or substrate)
Explain why most chemical reactions in the body cannot occur without an enzyme.
Because the body needs a catalyst (enzyme) to speed up the reaction process at lower temperatures and lower the activation energy. Without it the body would get too hot and wouldn’t be able to do the processes fast
Define activation energy of a reaction. Does this energy encourage or discourage a reaction?
Activation energy is the minimum energy required for the reactants to engage in a reaction. So it discourages a reaction since it is like a wall in the reactants way
What are the contributing factors to activation energy? (4)
- Collision theory ( the odds of 2 molecules colliding
- Placing reactants in proper position for a reaction to happen
- Breaking bonds between reactants
- Removing water from reactants
Why is heat not considered a catalyst?
Because it becomes part of the reaction. And it has negative effects on cells (kills them)
Heat can affect chemical reactions; however, the body does not depend on temperature to carry out vital functions. Why is an enzyme used in place of heat?
It is used in place of heat because it can speed up the reaction and lower the activation energy AT LOWER SAFER TEMPERATUREs
What are the 4 benefits of using an enzyme in a chemical reaction?
- Increases the rate of the reaction (makes it go faster)
- Not changed by the reaction (can be used again
- Doesn’t change the nature of the reaction (it could’ve occurred without it)
- Lowers the activation energy
What does the enzyme Synthase do? Name an example
catalyzes synthesis reactions
Example: Synthase takes ADP and adds P to make ATP
What is the enzyme ligase do?
It joins 2 molecules
What does the enzyme synthetase do? Name an example
Catalyzes synthesis reactions but requires ATP
Example:takes ATP and activates the enzyme that then helps the amino acid to be charged and attach to the tRNA
What does the enzyme dehydrogenases do?
It removes hydrogen atoms from a molecule
What does the enzyme hydrolase do? Name an example
It promotes hydrolysis
Example: adding water to sucrose to make glucose and fructose
What does the enzyme isomerases do..?
It rearranges the atoms in a molecule
Is an enzyme capable of synthesis reactions or decomposition reactions? How about rearrangement reactions?
YES AN ENZYME CAN DO ALL OF THOSE (flashcards 29-33)
Describe enzyme specificity.
It is when the enzyme is super picky in choosing a substrate to bind to. So it can carry out a specific reaction
What is the difference between Lock and key, and induced fit enzyme reactions?
Lock and key- Substrates fit into the active sit perfectly like a key in a lock (produce few products)
Induced fit- The substrate doesn’t perfectly fit in the active site initially. So the enzyme changes to better fit the substrate (makes more products)
What does the enzyme kinase do?
Adds a phosphate group
What does phosphatase do?
It removes phosphate groups
Why are kinases and phosphatases so important?
Because they act as the on and off switch for molecules. When kinases add a phosphate group it turns them on and activates them. But when phosphatases remove the phosphate group. Then it turns them off and shuts them down.
How does heat affect an enzymatic reaction? pH? Enzyme concentration (high/low)? Substrate concentration (high/low)?
Heat- Higher the temperature the fast it goes. Until it gets too hot then it slows down the reaction
pH- different pH levels can speed up an enzyme reaction depending on where they are at (stomach enzymes need higher pH to react quicker)
Enzyme concentration- The more enzymes there are the quicker the reaction (depending on how much substrates there are)
Substrate concentration- The more substrates there are the quicker the reaction (depends on how much enzymes there are to fill them with substrates)
Define a cofactor and give examples.
It is a non protein that basically helps the substrate bind to the active site by changing the enzyme active site shape or helps it bind to the active site by binding to it physically to the active site
Example: metals, magnesium, zinc
Define a coenzyme and give examples
They help transport hydrogen atoms and other small molecules between enzymes
Examples: Vitamins
What is a zymogen and why are they important?
It is essentially an inactive enzyme that is activated when needed. A masking sequence stops the active site from being able to be seen and used.
IT is important because they keep the enzyme contained and prevent them from damaging other cells
. Which regulatory processes enable enzymes, and which inhibit enzyme action and which do both?
1. Extracellular signals-
2. Transcription of specific genes-
3.mRNA degradation-
4.mRNA translation on ribosomes-
5. Protein degradation-
6. Enzyme sequestered in subcellular organelles-
7. Enzyme binds substrate-
8. Enzyme binds ligand (allosteric effector)-
9. Enzyme undergoes phosphorylation/dephosphorylation-
10. Enzyme combines with regulatory proteins-
- Extracellular signals- gets a signal from the ligand and makes the enzyme. and if it doesn’t want to make the enzyme then the ligand doesn’t bind. BOTH
- Transcription of specific genes- It transcribes it so ENABLES
3.mRNA degradation- INHIBITS enzyme activity by destroying it
4.mRNA translation on ribosomes- Translates the it so ENABLES - Protein degradation- Tag it with ubiquitin and destroy the enzyme if we don’t want it. INHIBITS
- Enzyme sequestered in subcellular organelles- If we want it but don’t need it right now. INHIBITS
- Enzyme binds substrate- When it binds to the substrate it is ENABLED
- Enzyme binds ligand (allosteric effector)- INHIBITS
- Enzyme undergoes phosphorylation/dephosphorylation- If the enzyme gets phosphorylated then it is enabled. If it gets dephosphorylates then it is inhibited. So BOTH
- Enzyme combines with regulatory proteins- depends on the protein that binds with the enzyme. But it can enable or inhibit it so BOTH
What is allosteric regulation?
A substrate binds to the allosteric site and it changes the shape and activity of the enzyme. It can increase and decrease activity.
Describe oxidation and reduction reactions; what is donated/received?
Oxidation: When an atom or molecule loses electrons (more positive)
Reduction: When an atom or molecule gains an electron (more negative)
What is a reducing agent and an oxidizing agent?
Reducing agent- electron donor
Oxidizing agent- electron receiver
What is cellular respiration, what is required?
It is the breakdown of glucose that REQUIRES OXYGEN
Describe an aerobic process vs an anaerobic process.
Aerobic process- Is a process that requires oxygen to work and produces more energy
Anaerobic process- doesn’t use oxygen to produce energy but it produces less energy
Consider glycolysis, citric acid cycle, and oxidative phosphorylation (electron transport):
a. Which of the processes are endergonic, and which are exergonic?
b. Which of the processes are anaerobic/aerobic?
c. Describe the major substrate(s) and products of each process listed above.
Glycolysis- a. exergonic b. Anaerobic C. Substrates (glucose, 2 ATP, 2ADP, 2NAD+, 2 inorganic phosphate), Products (2 Pyruvate, 2 NADH, 2 H+, 2 H2O, 4 ATP)
Citric Acid Cycle- a. exergonic b. aerobic C. Substrates (Oxaloacetate, Coenzyme A, Pyruvates) they make citric acid Products (oxaloacetate, GTP, 3 NADH, 2 FADH2, 2 ATP, 4 CO2)
Oxidative phosphorylation (electron transport chain)- a. exergonic b.Aerobic c. Substrates (NADH, FADH2, oxygen (O2), ADP, phosphate) Products (ATP, NAD+, FAD and H2O)
How does glucose remain in a cell against its gradient; what enzyme is responsible
It gets phosphorylated to create glucose-6-phosphate so it can’t go against the gradient. The enzyme responsible is Hexokinase
What are the 10 basic steps of glycolysis?
- 1 ATP is used to get glucose to glucose-6-phosphate
2. - 1 ATP is used to phosphorylate fructose-6-phosphate into fructose 1,6 biphosphate. by the enzyme. Phosphofructokinase. Prepares to spit into two
4 &5. fructose 1,6 biphosphate splits into two 3 carbon isomers
- NAD+ is reduced to NADH + H+ which is used in the electron transport chain
- 2 ADP are phosphorylated to form 2 ATP
8.
9.
- 2 more ADP are phosphorylated to form 2 more ATP and the end product of pyruvate
NET GAIN IS 2 ATP and 2 NADH
What two substrates enter the Kreb’s cycle (citric acid cycle) to synthesize citrate; from where is each derived?
acetyle CoA and oxidative phosphorylation. They are both from glycolysis
What is NADH and how is it derived/used during cellular respiration?
NADH accepts 2 electrons and binds to 1 proton. 1NADH = 3 ATP. It is derived from glycolysis, pyruvate, and citric acid cycle
What is GTP and how does it contribute to cell energy?
It donates a phosphate group to ADP to form ATP
What is the purpose of the complexes in the electron transport chain?
When they move the electrons it makes energy. It then creates a proton gradient and pumps the free hydrogens in the cell to the outside of the cell. (complex 1,3, 4 and ATP synthase pump them across)
What is the final electron acceptor in the electron transport chain?
Oxygen
Where are hydrogen ions pumped during the electron transport chain and why?
They are pumped from the inside of the cell to the outside. The movement makes an energy gradient for the enzyme ATP synthase which converts ADP to ATP
What is lactate; how and why is it produced.
How: When there is not oxygen to complete the breakdown of glucose NADH gives electrons to pyruvate and makes NAD+ and turns pyruvic acid to lactic acid
Why: It replenishes the NAD+ pool to make energy through glycolysis
How is ATP made during oxidative phosphorylation; what enzyme is responsible?
The ATP has a channel for the hydrogens to go with its gradient. Which then it gives the ATP synthase to phosphorylate and make ATP.
ATP SYNTHASE IS THE ENZYME RESPONISIBLE
Describe the ATP balance sheet from each process (remember that 1 NADH = 3 ATP and 1 FADH2 = 2 ATP)
a. How many usable ATP are produced in glycolysis (per glucose)
b. How many ATP are produced in the citric acid cycle (per glucose)
c. How many NADH are produced as pyruvate is converted to acetyl CoA (per glucose)
d. How many NADH are produced in glycolysis (per glucose)
e. How many NADH are produced in the citric acid cycle (per glucose)
f. How many FADH2 are produced in the citric acid cycle (per glucose)
G. How many NADH are produced when pyruvate is turned into lactate (in fermentation)
A. 2
B. 2
C. 2
D. 2
E. 6
F. 2
G. 0
What is the total ATP derived from 1 glucose molecule during cellular respiration; why is there a theoretical and actual number
The total is 30-32.
There is a theoretical number and an actual number because the theoretical number is how much it should add up to based on how much ATP is produced by each cycle. But there is an actual number because energy needs to be used to move all the ATP out of the mitochondria in the cell. NADH = 2.5 ATP used and FADH2 = 1.5 ATP used. SO that is why we have an actual and theoretical number
What other macromolecules can be used to produce energy in the cells? (5)
Amino acid metabolism (muscle tissue)
Glucose (liver)
Ketone bodies (liver)
Fatty acid metabolism (adipose tissue)
Lactic acid metabolism (muscle tissue)
What is the purpose of the proton gradient?
Basically the hydrogen/energy released from it is used to fuel ATP synthase to make ATP
List the basic steps in transcription and the end product. (3 phases)
Phase 1:
1.The hydrogen bonds between the bases in the DNA are broken and the histone is removed from the promoter
2. The complementary DNA strand separates and RNA polymerase binds to the promoter gene
Phase 2:
1. RNA polymerase gets the complementary bases that go together with the original DNA bases.
- At the stop signal the mRNA and the enzyme detach from the DNA strand and transcription ends
Phase 3:
1. The original DNA strands get back together
- RNA processes the newly transcribed mRNA and removes the introns and combines the exons.
- Then the mRNA leaves
Are protein inhibitors agonists or antagonists?
Antagonists because they either bind to the active site or allosteric site of the enzyme and inhibit activity between the ligand and the enzyme
How many ATP are is NADH and FADH2 are equal to after ATP is trasnferred out?
NADH= 2.5 ATP
FADH2= 1.5 ATP
What does the enzyme phosphofructokinase do?
It phosphorylates fructose-6-phosphate into fructose 1,6 biphosphate
List the basic steps in translation and the end product. (3 phases)
Phase 1 Initiation:
1. mRNA returns to the cytoplasm and binds to a ribosome
2. the ribosome reads the mRNA until it hits AUG (the start codon)
3. the tRNA anticodon UAC binds to the start codon
4. The P site in the ribosome is where the polypeptide building begins
Phase 2 Elongation:
1. Then another tRNA comes and brings more amino acids to the A site in the ribosomes
- Then the tRNA goes into the E site and exits the ribosome and is then able to be picked up again and create another anticodon
Phase 3 Termination:
1. this is where the ribosome reaches one of the three stop codons and the ribosome detaches and leaves the mRNA.
Energy barriers that may prevent a reaction from happening can be called…….
Activation energy barriers
