exam 2 study guide Flashcards
(61 cards)
1
Q
Describe the R group of an amino acid, and discuss the relevance of R groups to protein shape.
A
- The R group dictates the chemical properties of the amino acid. The folding of amino acids is due to the interactions of R groups.
2
Q
Describe the 4 levels of protein structure, and explain the importance of the 3-dimensional shape of proteins for functions.
A
- Primary structure is the sequence of amino acids.
- Secondary structure results from interactions of nearby amino acids.
- Tertiary structure is the 3-dimensional shape of a polypeptide.
- Quaternary results from interactions of polypeptide subunits.
- The three dimensional shape determines which molecules can bind to it, allowing for specific interactions with molecules within the cell.
3
Q
Define protein denaturation.
A
- Process of changing a proteins shape.
4
Q
How is the genetic code read? What or codons & how are they utilized? What is a reading frame? What are start & stop codons?
A
- A codon chart.
- Codons are sets of 3 nucleotides that specifies a particular amino acid. They instruct cells to create protein chains by specifying the order of amino acids.
- Reading frame is a way a sequence is divided into groups of 3.
- Marks in genetic codes that indicate the beginning and end of protein synthesis.
5
Q
List the different types of RNA utilized during translation and describe functions of each.
A
- mRNA carries genetic code from DNA to ribosome as a template for protein synthesis.
- tRNA brings specific amino acids to ribosome based on codon sequences.
- rRNA assist in binding mRNA.
6
Q
Describe in detail the stages of translation.
A
- Initiation is where ribosome assembles around mRNA and first amino acid.
- Elongation is where the polypeptide chain grows by adding new amino acids.
- Terminations is where the completed protein is released from the ribosomes when stop codon is reached.
7
Q
Explain the importance of the codon/anticodon relationship in translating sequences of nucleotides into sequences of amino acids.
A
- They ensure the correct amino acids are added to the growing peptide chain (Anti-codon is complementary to codon).
8
Q
Discuss what occurs at A-site, P-site, and E-sites of the ribosome during translation.
A
- A site is where tRNA bringing in new amnio acid is located.
- P site is where tRNA with growing peptide is located.
-E site is where tRNA without amino is ejected.
9
Q
Define protein sorting.
A
- Process of directing proteins to specific destinations in and out of the cell.
10
Q
Define energy and differentiate kinetic energy from potential energy.
A
- Energy is the capacity to do work.
- Kinetic is energy of motion & potential is stored energy.
11
Q
Describe the first and second law of thermodynamics.
A
- First is energy cant be created nor destroyed, but only change form.
- Second is the disorder centrophyl in the universe is continuously increasing.
12
Q
Describe the free energy and differentiate exergonic and endergonic chemical reactions.
A
- Free energy refers to the amount of energy actually available to do work.
- Endergonic requires an input of energy. (needs positive)
- Exergonic releases free energy. (needs negative)
13
Q
Describe the structure of ATP.
A
- Consists of a nitrogenous base (adenine), a ribose sugar, and three phosphate groups binded together.
14
Q
Describe coupling of exergonic and endergonic reactions, such as the oxidation of glucose, ATP production, and the coupling of ATP breakdown to cellular endergonic reactions.
A
- Coupled reaction proceeds because G is negative and P is shared between two reactions.
- ATP construction is not anabolic.
- ATP is synthesized during catabolic reactions.
- ATP is hydrolyzed to release energy for anabolic reactions.
- Metabolism = anabolism + catabolism.
15
Q
Describe the activation energy of a chemical reaction.
A
- Extra energy required to destabilize existing chemical bonds in reactions and initiate chemical reactions.
16
Q
Define catalyst and enzyme.
A
- Catalyst is a substance that lowers the activation energy.
- Enzymes carry out most catalysts in living organisms.
17
Q
Describe the process by which enzymes speed up chemical reactions.
A
- Enzymes lower the activation energy needed to start causing the speed up of chemical reactions.
18
Q
Describe the active site of an enzyme and the interaction of the active site to the substrate and subsequent formation of products.
A
- Most enzymes are globular proteins with one or more active sites, substrates bind to the enzymes active site forming an enzyme-substrate complex.
19
Q
Explain enzyme specifically.
A
- Its unique 3-D shape enables an enzyme to stabilize a temporary association between specific substrates.
20
Q
Describe the effects that PH and temperature have on an enzyme activity.
A
- Temperature is increasing collisions between enzyme and substrate(s) and enzymes denature from loss of tertiary structure.
- PH is enzyme excessively protonated active site not at optimum shape and enzyme excessively deprotonated active site not at optimum state.
21
Q
Describe activators and inhibitors.
A
- Inhibitors bind to an enzyme and decrease activity of an enzyme.
- Activators bind to an enzyme and increase the activity of enzymes.
22
Q
Define metabolism and differentiate anabolism and catabolism.
A
- The chemical processes that
occur within a living organism in order to maintain life. - Anabolic reactions build things.
- Make energy
- Endergonic
- Catabolic reactions break down things.
- Release energy
- Exergonic
23
Q
Describe biochemical pathways and feedback inhibition.
A
- Biochemical pathways are organizational units of metabolism.
- Feedback inhibition is when a particular product inhibits the ability to produce more (temporarily shit down biochemical pathways when their products are not needed).
24
Q
Describe oxidation reduction reactions.
A
- Electron lost by an atom (oxidation) is gained by another atom (reduction).
25
Differentiate substrate level phosphorylation and oxidative phosphorylation.
- Substrate level phosphorylation directly transfers a phosphate group from a high-energy substrate molecule to ADP to produce ATP.
- Oxidative phosphorylation uses the energy from electron transport along the mitochondrial membrane to create a proton gradient which then drives ATP synthesis through ATP synthase.
26
Distinguish overall processes of aerobic and anaerobic respiration.
- Aerobic is when final electron acceptor is oxygen (O2).
- Anaerobic is when final electron acceptor is not (O2).
27
Describe the structure and function of NAD+/NADH and FAD+/FADH.
- NAD+ accept energy and electrons is reduced. NADH is formed and carries the energy and electrons to a subsequent step in cellular respiration. Then donates energy an electrons and is oxidized to form NAD+. (nicotinamide adenine dinucleotide).
- FAD (faluine adenine dinucleotide).
28
Summarize the overall chemical equation of aerobic respiration with one molecules of glucose, noting which molecules are oxidized and reduced.
- Chemical Equation: C6H12O6 +6O2 ---> 6CO2 +6H2O.
- Oxidized: C6H12O6 +6
- Reduced: O2 ---> 6CO2 +6H2O.
29
Note the eukaryotic cellular respiration and aerobic/anaerobic respiration nature of each of the stages of aerobic respiration.
- Glycolysis (cytoplasm).
- Pyruvate oxidation (mitochondrion).
- After transport from (cytoplasm).
- Citric acid cycle (mitochondrion).
- Oxidative phosphorylation (mitochondrion).
30
List the initial reactants and products of glycolysis.
- Reactants: C6H12O6 +6O2
- Products: 6CO2 +6H2O
31
Distinguish the priming phase from pay off phase of glycolysis.
- First ATP consuming reaction and second ATP consuming reaction (spend).
- First ATP producing reaction and second ATP producing reaction (makes) and generate 2 NADH.
32
Summarize the net yield of ATP and reduced electron carriers at the end of glycolysis
- Start by spending 2, then making 2 more, then making another 2 more, so by the end of glycolysis you gain 2 ATP.
33
List the initial reactants and products of the oxidation of pyruvate.
- Reactants: CH3 - C - C=O
-O
- Products: CH3 - C - CoA
34
Summarize the net yield of ATP and reduced electron carriers at the end of oxidation of pyruvate.
- Electrons are striped away and added to NADH. It loses CO2 and gains coenzyme A along the way. Repeats twice.
35
List the initial reactants and products of the citric acid cycle.
- Reactants: 4 carbon molecule (oxaloacetate)
- Products: 6 carbon molecule (citrate)
36
Summarize the net yield of ATP and reduced electron carriers at the end of the citric acid cycle.
- Oxaloacetate goes through steps by adding 2 carbons to get to citrate. Goes through cycle twice the citrate goes through steps to get back to oxaloacetate. GNAD+ reduced GUADH.
37
Describe the process by which electrons are passed from NADH and FADH2 down the electron transport chain, generating a proton gradient in the process.
- Electrons are passed from NADH+ H+ and FADH2 onto mitochondrial electron carriers; NADH and FADH are converted back into NAD+ and FAD; H2O is produced from O2.
38
Describe the process by which ATP synthesis uses this proton gradient to produce ATP.
- ATP synthase provides a channel for H+ to diffuse back down their concentration gradient. The energy harvested from the gradient is used by ATP synthase to produce ATP.
39
Summarize the net field of ATP and the end of the electron transport chain.
- The F1 subunit used the rotational energy to catalyze the synthesis of ATP. The F0 subunit forms a channel that rotates as protons pass through it (ATP are generated oxidative phosphorylation).
40
Describe fermentation as a means to regenerate oxidized electron carriers.
- By accepting electrons from reduced carriers (like NADH) produced during glycolysis, allowing glycolysis to continue producing ATP even in the absence of oxygen, where the usual electron transport chain is unavailable.
41
Differentiate alcohol fermentation and lactate fermentation.
- Lactate: pyruvate goes to lactic acid.
- Glucose + 2 ADP --> 2 Lactic Acid+ 2 ATP
- Alcohol: pyruvate to acetaldehyde to ethanol.
- Glucose + 2 ADP +2 P --> 2 Ethanol + 2 ATP + 2CO2
42
Summarize the overall ATP yield of glycolysis followed by fermentation.
- 3 ATP per glucose total.
43
Describe the cellular usage of carbohydrates, proteins, and fats within the overall process of cellular respiration.
- Carbohydrates (primarily glucose), Proteins (broken down into amino acids), and Fats (broken down into fatty acids) are all used as energy sources.
44
Describe aerobic respiration regulation.
- Primarily occurs through feedback mechanisms at steps within the metabolic pathways.
45
Distinguish autotrophs from heterotrophs.
- Autotrophs harvest sunlight and convert radiant energy into chemical energy via anabolism.
- Heterotrophs live off energy produced from autotrophs (expect energy from food via digestion and catabolism).
46
Describe the chemical equation for the summary of photosynthesis, noting which molecules are oxidized and reduced.
- 6 CO2 + 12 H2O --> C6H12O6 + CO2 +6 H2O
- Oxidized: ... 2O --> C6H12O6 + CO2 +6 H2O
- Reduced: 6 CO2 + 12 H2O --> C6 ...
47
Describe the internal structure of the chloroplast and list the locations of photosynthesis processes.
- The internal membranes, thylakoids, and stroma are organized into gland.
- A chloroplast contains a double membrane surrounding a fluid-filled space called the stroma, where stacks of flattened discs called grana are embedded; within each granum are individual thylakoids, which are the membranes where the light-dependent reactions of photosynthesis occur, while the stroma is the site of the light-independent reactions (Calvin cycle) of photosynthesis.
48
Explain the relationship to energy and wavelength regarding the electromagnetic spectrum.
- High energy/shorter wave lengths gamma rays, x-rays, ultra-violet, VISIBLE LIGHT, infrared, micro-waves, radio-waves Low energy/longer wavelengths
49
Describe the visible light spectrum.
- Visible light is only one part of the electromagnetic spectrum, which the human eye can see.
50
Define pigment, and describe pigments in terms of absorption and reflection of visible light.
- Pigments are molecules that absorb light in the visible range. Color we see = wavelength that are not absorbed.
- Absorption spectrum: range and efficiency of photons the molecule is capable of absorbing.
51
List primary and accessory photosynthetic pigments.
- Chlorophyll a: primary pigment in plants and cyanobacteria
- Chlorophyll b & carotenoids: secondary pigments absorbing light
that chlorophyll a does not.
52
List the wavelength ranges and colors of light absorbed and reflected by photosynthetic pigments.
- 400-500-600-700.
- Gamma rays, x-rays, ultra-violet, VISIBLE LIGHT, infrared, micro-waves, radio-waves.
53
List the stages of the light-dependent reactions.
- Charge seperation.
- Electron transport.
- Chemiosmosis.
54
Describe the structure of a photosystem.
- Network of pigments that channels
energy to the reaction center.
55
Describe in detail the noncyclic photophosphorylation associated with photosystems I and II.
- Absorption of light energy by PS II allows electrons pulled from water to enter the photosynthetic electron transport chain.
- A second input of light energy by PS I
produces electron donor molecules capable of reducing NADP+.
56
Account for the ATP and NADPH produced, and H2 O consumed, during the light-dependent reaction
- ATP and NADPH are produced as energy-carrying molecules by harnessing light energy, while H2O is consumed as the source of electrons.
57
Explain the process by which reducing power generated during the light-dependent reactions is used
during the light-independent reactions.
- During light dependent reactions of photosynthesis, light energy is capture and used to generate high energy electrons, which are then transferred to the electron carrier molecule NADP+ to form NADPH, essentially reducing power. NADPH is then transported to the stroma of the chloroplast when light independent reactions occur.
58
Describe carbon fixation.
- The incorporation of CO2 into
organic molecules.
- Uses ATP and NADPH from light-dependent reactions as energy sources
59
Describe the three stages of the Calvin cycle. Account for the relative amounts of CO2 , ATP, NADH consumed, and glucose produced, during the Calvin cycle.
1. Carboxylation: The addition of CO2 to the 5- carbon compound, RuBP, is catalyzed by the enzyme rubisco.
2. Reduction: NADPH transfers high-energy electrons.
3. Regeneration of RuBP: In this multistep process, 3-carbon compounds are reorganized and combined to produce RuBP.
60
Describe the activity of rubisco during the Calvin cycle.
- Catalyzes RuBP.
61
Define photorespiration and describe its impact on photosynthetic yield.
- O2 is incorporated into RuBP rather
than CO2.
- Decreases yields of photosynthesis.
