Midterm prep Flashcards
(259 cards)
1
Q
4/2 He = What is the mass number and the atomic number.
A
4 is the mass number which is number of protons and neutrons
2 is the atomic number thats number of protons
2
Q
What is an isotope?
A
Same number of protons different number of neutrons -> making it more unstable
3
Q
What are the 6 essential elements to life (bonus points for the 3 key salt making elements)
A
CHOPNS (Na, Cl, Mg)
4
Q
What is the electronegativity order for some of the most recurring elements in bio (H, N, O, and C)
A
H<C<N<O
5
Q
What does hydrophilic mean?
A
Water-loving. Polar and ions dissolve in water.
6
Q
What does hydrophobic mean?
A
Water fearing. Non-polar molecule do no dissolve in water.
7
Q
What does hydrophobic interactions mean?
A
Water forces non-polar molecules together to minimize the disruption to the H-bonding in the water.
8
Q
Rank the inter/intramolecular forces as seen in bio
A
- Covalent bonding
- Hydrogen bonding (ITS FON TO HYDROGEN BOND)
- Ionic Bonding (in the case of bio this occurs mainly inside protiens and is on the relatively weaker side)
- Hydrophobic Interactions
- Van der Waals forces (dipole-dipole, LDFs)
9
Q
What are acids (provide an example of a strong and weak acid)
A
Acids release H+ ions in a solution. Strong acids (ei HCl) dissociate completely whereas weak acids (Carboxyl groups (-COOH) dissociates partially and reversibly.
10
Q
What are bases (provide an example of a strong and weak base)
A
Bases accept H+s in a solution and releases OH-. A strong base (ei NaOH) ionizes completely to form to ions. A weak acid (ei amino group (-NH2) by partially and reversibly accepting H+ to form NH3.
11
Q
What is a buffer?
A
makes the overall solution resistant to pH change as they react with both acids and bases. It is made of a weak acid and its conjugate base at a 1/2 equivilance point. They are at equimolarity!
12
Q
What are the the functional groups discussed in class and which are the 3 most important?
A
The 3 most improtant are hydroxol (OH), Carboxyl (O-C=O), and amino (-NH2). The other groups are Carbonyl (=O-H), Phosphate (PO4), and sulfyd groups (SH)
13
Q
What are macromolecules provide examples?
A
Macromolecules are large molecules (ei proteins. nucleic acids, lipids, and carbohydrates).
14
Q
How are proteins made?
A
Monomers are added together via a condensation reaction (water is released) forming a polymer
15
Q
How are proteins broken down?
A
They are broken down via hydrolysis where the monomers are split apart within the polymer using water.
16
Q
Characteristics of proteins
A
Polymers of amino acids
proteins range in size from a few amino acids (ei peptide) to thousands (ei titan)
There are ionized and non-ionized amino acids
17
Q
How many amino acids are there?
A
20 in life
18
Q
What is protein folding determined by?
A
- IMFs
- Sequences of aas
19
Q
What is the R group and how does it vary in ionized/non-ionized aas?
A
R determines the identity of the amino acid. It can be C/H for any non polar amino acids. Charged (ei NH2, or HO-C=O). Or polar (ei O)
20
Q
What is the general amino acid shape and what differs.
A
R differs but the general structure is amino group and carboxyl group
21
Q
What is a peptide bond?
A
A special covalent bond between two monomers (aas) between the C and N of the 2 adjacent monomers. Due to the sharing of the electrons, a peptide bond is a half double bond and thus doesnt rotate along the bond.
22
Q
What is a polypeptide chain?
A
- Primary structure
- Starts with an amino group and ends with a carboxyl group (will be on exam)
- All starts with a Methionine/Met (AUG)
- Is important in determining how the protein folds and its function
23
Q
What are the steps of protein folding?
A
- Primary structure -> polypeptide chain
- Secondary structure -> % alpha-helix, beta-pleated sheet, or neither
- Tertiary structure -> smaller interactions (ei H bonds, hydrophobic ints) depending on the polarity of the protein. Determines final folding.
24
Q
What does the primary structure of a protein determine?
A
It determines how the protein folds and its function
25
Describe the steps of the secondary structure:
- H-bonds form between the peptide chains -> the creation of the secondary structure
- These bonds can either form an alpha helix structure, a beta pleated sheet, or neither
26
Describe the characteristics of an alpha helix structure:
- Very stable
- 3.6 amino acids per turn
- Every 4th amino acid forms H-H bonds
side chains always point away from the alpha helix structure
27
Describe the characteristics of a beta pleated sheet:
- H- bonds between the ends to stabalize
- Side chains point upwards or downwards from the pleated sheet
- The COO- groups point in opposite directions
28
Describe the characteristics of proline and what makes it unique:
Proline or Pro or P
- Cannot be alpha helix or beta pleated sheet
- this is due to its ring like structure
- it would break the chain
29
What dictates the tertiary structure of protein folding?
The smaller interactions (ei with/within the side chain) determines the final folding of the protein
30
What are examples of side chain interactions?
- For polar side chains -> its hydrogen bonds
- For non polar side chains -> its hydrophobic interactions
- For ionic bonds -> its between the carboxyl and amino group
- For covalent bonds -> its a disulfide bond *NOT IN EVERY PROTEIN
31
Describe characteristics of the SH group (ei Cysteine)
If 2 cysteines are close (spatially after the secondary structure) via a redox reaction a disulfide bond/bridge will form covalently.
- the purpose of the bond is to provide structure (ei as seen in keratin)
32
What are hydrophobic interactions?
They are the most important determinate of protein folding. It will reorder hydrophobic molecules/proteins away from water so to minimize the destruction of H bonds
33
Describe the coiled coils found in keratin
- made of multiple alpha helixes bound around each other
- Hydrophobic interactions at every 4th position
- gives rise to many fibrous proteins
34
How to determine if coiled coils are tertiary or quaternary structures?
It can be tertiary if both alpha-helices are from the same polypeptide if they are from dif polypeptides it would be quaternary.
35
Do primary, secondary, and tertiary release or require energy?
Primary structure (ei peptide bond formation) requires energy, but secondary & tertiary folding releases energy (ei happens simultaneously)
36
What are quaternary structures?
They indicate several polypeptides interacting to form a bigger protein complex ei hemoglobin (4 individual polypepties).
37
Do all proteins have a quaternary structure?
Not necessary, many proteins only consist of one polypeptide and are fully folded after the tertiary structure.
38
What does a mutation in the amino acid sequence of hemoglobin cause?
A single amino acid mutation in hemoglobin changes its shape, leading to sickled red blood cells.
39
How does temperature affect protein folding?
At high temperatures, proteins denature (unfold), but they can renature (refold) when the temperature is lowered, demonstrating that primary structure is sufficient for proper protein folding.
40
What is protein turnover and why is it important?
Protein turnover refers to the process by which proteins have a half-life ranging from minutes to weeks (average 2 days). It is important because proteins can be damaged by various factors like fever or pH changes.
41
How do chaperones help proteins?
Chaperones assist proteins in folding correctly after synthesis or after stress-related unfolding.
42
What are nucleotides made of?
Nucleotides consist of a 5-carbon sugar, a nitrogenous base, and a phosphate group.
43
What are the four nucleotides in RNA?
The four nucleotides in RNA are cytosine, uracil, guanine, and adenine.
44
How do nucleotides polymerize in RNA/DNA?
Nucleotides polymerize via phosphodiester linkages, where the 3' hydroxyl group of one nucleotide bonds with the 5' phosphate group of the next.
45
What direction does RNA/DNA polymerization occur?
RNA/DNA polymerization occurs in the 5' to 3' direction.
46
How are the two strands of DNA oriented?
The two strands of DNA are antiparallel, meaning one strand runs 5' to 3' while the other runs 3' to 5
47
What pairs with what in DNA?
Purines can only bond with pyrimidines. Guanine (G) pairs with cytosine (C) (3 bonds) and adenine (A) pairs with thymine (T) (2 bonds).
48
What is the structure of DNA?
DNA is a double helix with a sugar-phosphate backbone on the outside and nitrogenous bases on the inside, arranged like rungs on a ladder.
49
What is the significance of the major groove in DNA?
The major groove in DNA allows DNA-binding proteins to recognize bases, which is crucial for processes like transcription.
50
What came first in evolution, RNA or DNA?
RNA came first in evolution because it can both store and execute information. Furthermore, it can also self replicate!
51
How does RNA catalyze reactions?
RNA can catalyze reactions because it can fold into 3D structures, similar to proteins, that allow it to function as an enzyme.
52
What is a common RNA structure and its function?
The stem-loop structure is common in RNA and plays a role in regulating mRNA function.
53
What makes DNA more stable than RNA?
Base pairing and the double
helical structures makes DNA much more stable than RNA
54
What is metabolism?
Metabolism comprises all chemical reactions in a cell, divided into anabolism (energy-consuming) and catabolism (energy-releasing).
55
What are anabolic reactions?
Anabolic reactions require energy input and involve processes like DNA replication, protein synthesis, and starch production.
56
What are catabolic reactions?
Catabolic reactions release energy, such as the digestion of food molecules to generate energy.
57
How is energy defined?
Energy is the potential capacity to do work, and it is involved in energy conversions during various processes.
58
What drives energy conversions in chemical reactions?
Energy conversions are driven by the tendency of energy to become more evenly distributed or dispersed over time.
59
What is the second law of thermodynamics?
It states that energy conversions always increase disorder (entropy) and proceed in one direction toward a more disordered state.
60
What does ΔG represent in biochemical reactions?
ΔG represents the change in free energy, which is used to judge the spontaneity of a biochemical reaction.
61
How can a cell release free energy to drive a reaction?
A cell can release free energy by creating disorder in the cell (ΔS) or by releasing heat to the surroundings (ΔH).
62
What is the equation for free energy change?
The equation is ΔG = ΔH - TΔS, where ΔG is the change in free energy, ΔH is the change in heat, and TΔS is the change in entropy.
63
When is a reaction favorable?
A reaction is favorable (spontaneous) when ΔG is negative, indicating that energy is released or dispersed.
64
What is an exergonic reaction?
An exergonic reaction is spontaneous, with a negative ΔG, where heat is released, and disorder is increased (e.g., digestion of food).
65
What happens when heat is released and disorder decreases?
This type of reaction may occur at a specific temperature, like protein folding, where heat is released, but disorder decreases.
66
What is an example of a reaction where heat is used and disorder increases?
Anabolic reactions are endergonic, requiring heat and causing decreased disorder, so they must couple with exergonic reactions to proceed.
67
How are reactions classified as exothermic or endothermic?
Reactions are classified as exothermic (negative ΔH) when heat is released and endothermic (positive ΔH) when heat is absorbed.
68
What does equilibrium mean in a chemical reaction?
Equilibrium occurs when the forward and reverse reactions happen at the same rate, and ΔG = 0.
69
How do reactant concentrations affect ΔG?
Increasing the concentration of reactants makes ΔG more negative, driving the forward reaction.
70
What role does ATP play in energy transfer?
ATP hydrolysis is an exergonic reaction that releases energy to drive endergonic reactions like polymerization.
71
Why is ATP considered the cell's energy currency?
ATP has an intermediate ΔG that makes it ideal for transferring energy in biochemical processes, like respiration and anabolism.
72
How does the ΔG of ATP hydrolysis differ inside and outside the cell?
The ΔG of ATP hydrolysis is -12 in the cell due to the high ATP concentration and low ADP concentration.
73
Can reactions with a positive ΔG occur?
Yes, reactions with a positive ΔG can occur if they are coupled with a reaction that has a sufficiently negative ΔG.
74
What is activation energy?
Activation energy is the energy required to initiate a chemical reaction, and it is needed to overcome the energy barrier of a reaction.
75
Why do exergonic reactions sometimes occur slowly?
Even though exergonic reactions release energy, they may occur slowly without a catalyst, as the activation energy barrier is high.
76
How do enzymes lower activation energy?
Enzymes lower activation energy by binding substrates at their active sites, inducing a transition state that requires less energy.
77
What happens when the enzyme-substrate complex forms?
The enzyme undergoes a conformational change that helps bring substrates into a transition state, speeding up the reaction.
78
Why is enzyme activity affected by pH?
A different pH can alter the enzyme’s active site, making it inactive if the optimal charge environment is disrupted.
79
What are enzyme cofactors?
Enzyme cofactors are small organic molecules or ions that help enzymes catalyze reactions.
80
What is enzyme saturation?
Enzyme saturation occurs when all active sites are occupied, and increasing substrate concentration will no longer increase the rate of reaction.
81
What is the turnover rate of an enzyme?
The turnover rate is the maximum speed at which an enzyme catalyzes a reaction, which varies depending on the enzyme.
82
What are exergonic reactions?
Exergonic reactions are spontaneous reactions with a negative ΔG, releasing energy, typically seen in catabolic processes.
83
What are endergonic reactions?
Endergonic reactions require energy input, have a positive ΔG, and are seen in anabolic processes.
84
What are the main functions of sugars?
Sugars function in energy storage, as building blocks for nucleic acids, and as structural components (e.g., wood).
85
What is a disaccharide?
A disaccharide is a carbohydrate made up of two monosaccharides. Example: table sugar (sucrose), made of fructose and glucose.
86
What is the general structure of a sugar?
The typical structure of a sugar is a multiple of CH₂O, e.i., C₆H₁₂O₆ (glucose).
87
What are the two functional groups found in all sugars?
A sugar contains one carbonyl group and several hydroxyl groups.
88
What is the difference between aldose and ketose sugars?
Aldose has an aldehyde group (carbonyl at the end), while ketose has a ketone group (carbonyl within the molecule).
89
What are optical isomers (ie stereoisomers)?
Optical isomers are molecules with the same chemical formula but different spatial arrangements, making them non-superimposable, like left and right hands.
90
Give an example of two optical isomers of glucose.
Glucose and galactose are optical isomers of each other.
91
What happens when glucose forms a ring in solution?
Glucose's straight chain forms a ring structure, converting C-1 into an asymmetric carbon, which can result in two isomers: alpha-glucose and beta-glucose.
92
What are glycosidic linkages in polysaccharides?
Glycosidic linkages are covalent bonds that connect monosaccharides in polysaccharides, such as alpha1,4 in maltose or beta1,4 in cellulose.
93
What is the structural difference between starch and cellulose?
Starch has a spiral shape due to alpha1,4 linkages, while cellulose has a straight structure due to beta1,4 linkages and flipped glucose units.
94
What are lipids?
Lipids are a diverse group of molecules that are insoluble in water, including fats, oils, and phospholipids.
95
What are the main components of fats and oils?
Fats and oils are composed of three fatty acids and one glycerol molecule, connected by covalent bonds.
96
What are fatty acids?
Fatty acids are molecules with a carboxyl group and a long hydrocarbon chain. They are amphiphilic, having a hydrophilic carboxyl group and a hydrophobic tail.
97
Why do fats provide more energy than starch?
Fats provide more energy per weight than starch but take longer to mobilize, making them suitable for long-term storage.
98
What are phospholipids?
Phospholipids are molecules with a hydrophilic head and two hydrophobic fatty acid tails, essential for forming cell membranes.
99
How do phospholipids form lipid bilayers?
Phospholipids self-assemble into lipid bilayers with the hydrophobic tails pointing inward to avoid water exposure.
100
What is the advantage of lipid bilayer formation?
Lipid bilayers form globular compartments, reducing exposure of hydrophobic parts to water, which is energetically favorable.
101
How do phospholipids contribute to the formation of cell membranes?
Phospholipids form lipid bilayers, which are the structural basis for cell membranes, creating a barrier between the cell and its environment.
102
What causes the fluidity of lipid bilayers?
The fluidity of lipid bilayers results from the constant lateral motion of phospholipids within the bilayer.
103
What is the role of unsaturated fatty acids in lipid bilayers?
Unsaturated fatty acids have kinks due to double bonds, increasing the fluidity and permeability of the membrane.
104
Why is butter solid at room temperature?
Butter is solid at room temperature because it contains mostly saturated fatty acids, which can pack closely together.
104
Why are oils liquid at room temperature?
Oils are liquid at room temperature because they contain many unsaturated fatty acids, which have double bonds causing kinks that prevent tight packing.
105
How do fish and plants maintain membrane fluidity in varying temperatures?
Fish and plants adjust the proportion of unsaturated fatty acids in phospholipids to keep membrane fluidity stable across temperature changes.
106
What is the key feature of fatty acids that make them amphiphilic?
Fatty acids have a hydrophilic carboxyl group and a hydrophobic hydrocarbon chain, making them amphiphilic.
107
Why are membranes fluid?
Membranes are fluid to allow proteins (integral or transmembrane) to interact with each other and to move laterally within the membrane
108
How are membrane proteins integrated into the lipid bilayer?
Membrane proteins are typically integrated by alpha-helices, with hydrophobic amino acids in the helix interacting with the lipids.
109
What is an example of secondary active transport?
The sodium-sugar cotransporter, which uses sodium ion gradients to transport sugar into cells, such as in the gut cells for nutrient uptake.
110
What is the main function of membranes in cells?
The main function of membranes is to serve as a barrier and to selectively transport molecules the cell needs or wants to get rid of.
111
What is the sodium-potassium pump and its role?
The sodium-potassium pump moves three sodium ions out and two potassium ions in, establishing ion gradients, controlling osmolarity, and generating the resting potential.
112
What is secondary active transport?
Secondary active transport uses the concentration gradient established by primary active transport to move other molecules against their gradient.
113
What is primary active transport?
Primary active transport directly uses ATP hydrolysis to move molecules against their concentration gradient. An example is the sodium-potassium pump.
114
What is active transport?
Active transport moves molecules against their concentration gradient and requires energy, typically from ATP.
115
How do carrier proteins facilitate passive transport?
Carrier proteins bind the substance on either side of the membrane, causing a conformational change that transports the molecule across.
116
How do gated channel proteins work in passive transport?
Gated channel proteins allow ions to flow along their electrochemical gradient when the channel is open.
117
What is passive transport?
Passive transport is the movement of molecules along their concentration gradient, requiring no energy. Examples include facilitated diffusion via channel or carrier proteins.
118
What does "freeze fracture" reveal about membranes?
Freeze fracture splits membranes into two lipid leaflets because phospholipids are tightly bound to surrounding water molecules by hydrogen bonds, while the two lipid leaflets are held together by weaker van der Waals forces in the frozen state.
119
What molecules pass freely across membranes?
Gases like oxygen and small polar molecules like water pass freely across the membrane.
120
What happens during diffusion?
Diffusion is the passive mixing of substances that results in net transport along the concentration gradient until equilibrium is reached.
121
What is the difference between Brownian motion and diffusion?
Brownian motion refers to the random movement of molecules due to thermal motion, while diffusion is the movement of molecules along a concentration gradient, resulting in an even distribution of substances.
122
What is osmosis?
Osmosis is the diffusion of water across a selectively permeable membrane.
123
What is the difference between hypertonic, hypotonic, and isotonic solutions?
- Hypertonic: Solution with higher solute concentration; water moves out of cells.
- Hypotonic: Solution with lower solute concentration; water moves into cells.
- Isotonic: Solution with equal solute concentration; no net water movement
124
What are the two types of membrane transport?
The two types are passive transport (facilitated diffusion) and active transport.
125
What is facilitated diffusion?
Facilitated diffusion is the passive movement of molecules across the membrane through channel proteins or carrier proteins.
126
What is the difference between carrier proteins and channel proteins?
Carrier proteins transport molecules by undergoing a conformational change, and they can be saturated.
Channel proteins form pores through the membrane and transport ions or molecules along their concentration gradient; they are gated and can be opened in response to stimuli.
127
How do sodium-sugar cotransporters function?
Sodium-sugar cotransporters use the energy from sodium ions flowing into the cell to transport sugar molecules into the cell, particularly in the gut where nutrient uptake occurs.
128
Why is diffusion only effective over short distances?
Diffusion is only effective over small distances because the distance traveled by a diffusing molecule is proportional to the square root of time, meaning it takes longer over larger distances.
129
What are prokaryotes known for?
Prokaryotes are known for their metabolic diversity, ability to live in various environments, and their smaller size. Their DNA is stored in a nucleoid, which is not surrounded by a membrane.
130
What distinguishes eukaryotes from prokaryotes?
Eukaryotes have a true nucleus surrounded by a nuclear envelope, and they also possess compartmentalized organelles, which enable them to have larger cells.
131
What are plant cells unique for?
Plant cells have a cell wall, chloroplasts, and a modified lysosome called a vacuole. They do not need a sodium-potassium pump due to the presence of the cell wall.
132
What is the role of the endomembrane system?
The endomembrane system mediates compartmentalization in eukaryotic cells and gives rise to organelles like the nucleus, ER, Golgi, vesicles, and lysosomes.
133
How are the vesicles, Golgi, ER, and cell membrane connected? FIX THIS CARD
The interior of vesicles, Golgi, ER (lumen), is equivalent to the extracellular space. Vesicles bud off from organelles and fuse with the cell membrane, with the membrane's cytosolic side always facing the cytosolic side.
134
What is the function of the nucleus?
The nucleus is surrounded by a nuclear envelope and contains DNA stored as chromosomes. The nucleolus within the nucleus is responsible for ribosome assembly.
135
How are ribosomes involved with the rough ER?
Ribosomes are attached to the rough ER, where they translate membrane proteins. The signal sequence of these proteins targets the ribosomes to the rough ER for immediate insertion into the ER membrane.
136
What does the smooth ER do?
The smooth ER is involved in lipid synthesis, detoxification (including oxidation), and modification of molecules to make them more hydrophilic for excretion.
137
What is the Golgi's role?
The Golgi is a stack of membranes that modifies proteins and lipids, adding sugar side chains, and sorts them for their proper destinations.
138
What is a pulse-chase experiment?
A pulse-chase experiment involves adding radioactively labeled amino acids for a short time (the pulse), then following the movement of proteins through the endomembrane system by electron microscopy during the chase (with unlabeled medium).
139
What is receptor-mediated endocytosis?
Receptor-mediated endocytosis is the process where molecules are recognized by receptors, initiating the budding of a vesicle that transports the molecules into the cell.
140
What is phagocytosis?
Phagocytosis is the process where cells engulf entire organisms or particles, forming a vesicle that may fuse with lysosomes for digestion.
141
What is autophagy?
Autophagy is the process where lysosomal membranes surround and digest damaged organelles or parts of the cytoskeleton, such as muscle fibers, during times of need like damage or starvation.
142
How do proteins get sorted in the endomembrane system?
Proteins are sorted based on their amino acid sequences (tags) which ensure that proteins are sent to specific vesicles, such as those targeted to lysosomes or the cell membrane.
143
Where are ribosomes located, and how do they affect protein synthesis?
All ribosomes are initially cytosolic. Ribosomes that translate membrane proteins become attached to the rough ER, where they help synthesize membrane proteins.
144
How are proteins sorted and directed to their correct destinations?
Vesicles containing membrane proteins and luminal proteins move from the rough ER to the Golgi, where they are sorted based on short amino acid sequences (tags). These tags result in specific protein-protein interactions that ensure the proteins are transported to their correct destinations, such as the lysosome or cell membrane.
145
What is end-product inhibition?
End-product inhibition is when a metabolic pathway is downregulated by its final product to prevent overproduction. This process is similar to just-in-time production in factories.
146
What is cooperativity in enzyme complexes?
Cooperativity occurs when two or more identical enzyme subunits form an enzyme complex. The binding of an inhibitor molecule to one subunit induces a conformation change that helps the binding of more inhibitor molecules to neighboring subunits, leading to a sigmoid inhibition curve.
147
Why are catabolic pathways long and complex?
Catabolic pathways are long and complex to release energy slowly, allowing the cell to capture energy in manageable amounts, unlike burning glucose directly which releases all energy at once.
148
What is the complete oxidation of glucose in cells?
The complete oxidation of glucose releases -686 kcal/mol. Half of this energy is captured as ATP, while the other half is released as heat to drive reactions.
149
What happens during oxidation and reduction?
LEO GER - Oxidation is the loss of electrons or hydrogen atoms, while reduction is the gain of electrons or hydrogen atoms. These processes are always coupled in redox reactions.
150
How is oxidation of glucose characterized?
In the oxidation of glucose, electrons move further from carbon atoms, with the number of C-H bonds decreasing and the number of C-O bonds increasing.
151
How is oxidation energy stored in the cell?
Oxidation energy is stored in NAD+ by reducing it to NADH. NADH serves as a temporary energy carrier in redox reactions.
152
How do you determine whether NADH is oxidized or NAD+ is reduced?
The direction of electron flow depends on the coupled half-reaction. Electrons flow towards NAD+ when coupled with the oxidation of glucose intermediates or flow away from NADH when coupled with oxygen as the electron acceptor.
153
What is the redox potential, and how is it used?
Redox potential measures the voltage between two half-reactions in a redox reaction. Electrons flow from the more negative to the more positive redox potential, which can be used to calculate the change in free energy (ΔG).
154
What are the steps of glycolysis?
Glycolysis starts with energy-consuming reactions (like adding phosphate to glucose), followed by energy-releasing reactions such as the oxidation of glyceraldehyde 3-phosphate and reduction of NAD+, which leads to ATP formation.
155
What is substrate-level phosphorylation?
Substrate-level phosphorylation is the transfer of a phosphate from a substrate directly to ADP to form ATP, as opposed to oxidative phosphorylation where free phosphate is combined with ADP by ATP synthase.
156
How do unfavorable reactions proceed in glycolysis?
Unfavorable energy-consuming steps in glycolysis are driven by the favorable oxidation reactions that follow. Reactions are coupled, and the concentration of products drives the reaction forward.
157
Where does glycolysis occur in the cell?
Glycolysis occurs in the cytosol and ends with the production of pyruvate.
158
What happens to pyruvate after glycolysis?
Pyruvate is further oxidized in the mitochondrial matrix to form acetyl-CoA, which plays a central role in metabolism.
159
Why is acetyl-CoA considered an energy carrier?
Acetyl-CoA contains a high-energy bond (C-S) and allows the transfer of a 2-carbon group to another molecule, which is crucial for starting the citric acid cycle.
160
What roles does acetyl-CoA play in metabolism?
Acetyl-CoA is key for metabolism, as it is the end product of many catabolic processes and serves as a building block for making fats and other metabolites.
161
What is the primary function of the citric acid cycle?
The citric acid cycle completes the oxidation of glucose by converting acetyl-CoA (a 2-carbon compound) into 2 CO2 molecules. It also produces reduced electron carriers (NADH, FADH2) and 1 GTP.
162
Why is FAD used in the citric acid cycle instead of NAD?
FAD is used because the oxidation of succinate (a step in the citric acid cycle) does not release enough energy to reduce NAD, but it can reduce FAD.
163
What happens during the electron transport chain (ETC)?
he ETC involves a series of redox reactions coupled with the transport of protons across the inner mitochondrial membrane into the intermembrane space, creating an electrochemical proton gradient.
164
Why doesn’t NADH deliver its electrons directly to oxygen in the ETC?
NADH cannot deliver electrons directly to oxygen because the reactions must be catalyzed by enzyme complexes. NADH donates electrons to the first complex, ensuring gradual energy release for proton transport.
165
How does FADH2 contribute to the electron transport chain?
FADH2 donates electrons to complex II (succinate dehydrogenase) in the ETC. This releases less energy than NADH oxidation and bypasses the first enzyme complex.
166
What is the role of ubiquinone and cytochrome c in the electron transport chain?
Ubiquinone and cytochrome c are hydrophobic electron carriers that shuttle electrons between enzyme complexes by diffusing laterally in the membrane.
167
What is the proton motive force?
The proton motive force is created by an electrochemical proton gradient across the mitochondrial membrane, with voltage and concentration differences driving protons back across the membrane.
168
How does ATP synthase produce ATP?
ATP synthase uses the flow of protons back through the protein channel to synthesize ATP. About 3 protons are required to produce one ATP molecule. This process is called oxidative phosphorylation.
169
What is the chemiosmotic mechanism?
The chemiosmotic mechanism refers to the formation of ATP (chemi) through the diffusion of protons (osmotic) across the mitochondrial membrane.
170
Can ATP synthase function independently of the electron transport chain?
Yes, ATP synthase can function independently of the ETC, as demonstrated by experiments where ATP is synthesized in vesicles with a proton gradient but without the ETC.
171
What is an example of uncoupling the ETC and ATP synthase?
Uncoupling occurs in brown fat cells in newborns and hibernating animals, where the electron transport chain is coupled to a proton channel to produce heat instead of ATP.
172
How is the glycolysis, citric acid cycle, and ETC regulated?
Glycolysis is inhibited by high ATP levels, the citric acid cycle by high NADH levels, and the ETC by a high proton gradient.
173
What happens when oxygen is absent in the ETC?
In the absence of oxygen, the ETC shuts down because oxygen is the final electron acceptor. This stops ATP synthase and prevents NAD+ regeneration, halting pyruvate oxidation and the citric acid cycle.
174
How does fermentation provide energy under anoxic conditions?
Fermentation allows glycolysis to continue by replenishing NAD+ from NADH, producing small amounts of ATP without oxygen. It is a backup process when oxygen is unavailable.
175
How does fermentation contribute to food production?
Fermentation, assisted by bacteria, is used in food production (e.g., yogurt, cheese, and salami) by preventing bacterial growth through acid production and the absence of oxygen.
176
Why is fermentation considered a step backward?
Fermentation is a step backward because it does not generate additional energy; it simply replenishes NAD+ used in glycolysis, whereas aerobic respiration generates much more energy.
177
Why are fats considered higher energy sources than carbohydrates or proteins?
Fats contain more C-H bonds, and their complete oxidation releases more NADH, providing more energy. The oxidation process is slower, allowing for more efficient energy release.
178
Why does the body store excess food as fat?
The body stores excess food as fat because fat contains the highest energy per unit weight, providing a long-term energy source for the body.
179
Why should sugar consumption be reduced?
Excessive sugar consumption disrupts the body's regulatory systems, contributing to health issues such as diabetes. Carbohydrates like starch release sugar more slowly, making them easier for the body to process.
180
How does snacking affect metabolism?
Frequent snacking can reduce or shut down fat catabolism, as the body tends to metabolize glycogen (stored carbohydrates) first. Eating at night also prevents the body from fully utilizing stored fat for energy.
181
Where do photosynthetic reactions occur in plant cells?
n chloroplasts: light reactions in the thylakoid membranes, Calvin cycle in the stroma.
182
What is the overall reaction of photosynthesis?
The reverse of respiration: 6CO₂ + 6H₂O + light → C₆H₁₂O₆ + 6O₂.
183
How are NAD and NADP different in their functions?
NAD accelerates sugar oxidation (high NAD+), while NADPH is used for reductions in photosynthesis (high NADPH).
184
Why is visible light important for photosynthesis?
Visible light has wavelengths that chlorophyll absorbs to excite electrons, driving photosynthesis.
185
What happens when chlorophyll absorbs light?
Energy excites electrons to a higher energy level, initiating chemical reactions in photosynthesis.
186
What are conjugated double bonds in chlorophyll responsible for?
They allow delocalized electrons to be excited by specific wavelengths of visible light.
187
How do the absorption and action spectra relate?
The overlap between the two spectra suggests chlorophyll’s role in photosynthesis.
188
What is the action spectrum of photosynthesis?
It shows the wavelengths at which plants produce the most oxygen, indicating active photosynthesis.
189
Why do leaves change color in autumn?
Chlorophyll is broken down, revealing carotenoids, which cause yellow and red colors.
190
What are the three possible outcomes for an excited electron?
1) Fall back and release heat/light, 2) resonance energy transfer, 3) redox electron transfer.
191
What is the role of the light-harvesting complex?
It absorbs light and transfers energy to a central chlorophyll, which then transfers electrons to the electron transport chain.
192
Why is chlorophyll a 680 nm important?
It acts as an energy sink to receive energy and transfer electrons for the electron transport chain.
193
How does chlorophyll oxidize water?
Chlorophyll, when it loses an electron, oxidizes water, producing oxygen.
194
How does the electron transport chain in photosynthesis work?
It transfers electrons through redox reactions to pump protons (H+) across the thylakoid membrane, generating ATP via photophosphorylation.
195
What is the Z-scheme?
The Z-scheme describes noncyclic electron transport, where electrons move from photosystem II to I, producing both ATP and NADPH.
196
What is cyclic electron transport?
Electrons cycle back to chlorophyll P700 in photosystem I, producing ATP but no NADPH or oxygen.
197
Where does carbon fixation occur?
In the stroma of the chloroplast during the Calvin cycle.
198
What role does Rubisco play in photosynthesis?
Rubisco catalyzes the attachment of CO₂ to RuBP in the first step of the Calvin cycle.
199
What is the outcome of carbon fixation?
It produces 2 3-carbon molecules that are reduced using ATP and NADPH to form sugars.
200
What is photorespiration?
Photorespiration occurs when Rubisco binds O₂ instead of CO₂, wasting energy and not fixing carbon.
201
Why does Rubisco also bind oxygen?
Rubisco is an ancient enzyme that evolved before high oxygen concentrations in the atmosphere.
202
How does the plant reduce photorespiration?
Plants have evolved mechanisms, such as C4 and CAM pathways, to minimize photorespiration under high oxygen conditions.
203
What is the final product of the Calvin cycle?
The Calvin cycle produces glucose and other sugars, which can be used by the plant for energy or stored as starch.
204
Why are mitochondria important for plants?
Mitochondria provide ATP through cellular respiration, especially at night or in winter when photosynthesis doesn’t occur.
205
What is the relationship between mitochondria and photosynthesis?
Mitochondria produce ATP through respiration, while chloroplasts produce it through photosynthesis, providing energy for the plant’s needs.
206
What are traits of heredity?
All organisms come from other organisms, all organisms resemble their parents, and siblings are not identical.
207
What is cell theory?
All organisms consist of cells, cells divide to produce new cells, higher organisms their cells (sperm and egg, pollen and egg) to produce a new organism.
208
What is a chromosome and what are the two types?
A chromosome is a single string of DNA. Either circular (bacteria) and linear (most other organisms).
209
What are chromatins?
When the cell is getting ready to divide, the chromosome condenses by associating with proteins (eg histones). The combination of protein and DNA is called chromatin.
210
What is a karyotype and how do they work?
A karyotype is a way of organizing and identifying chromosomes. Chromosomes are lined up according to banding pattern.
211
What are identical pairs of chromosomes called?
Homologs
212
What is a mitotic chromosome?
It is two chromatids bound by a centromere
213
What is trisomy 21?
Down Syndrome
214
What are the steps in cell division?
1. Chromosome (DNA) replication (S phase)
2. Mitosis
3. Meiosis
4. Cytokinesis
215
What is mitosis?
The process by which somatic cells make identical copies (clones) of themselves by creating daughter cells that inherits one copy of each chromosome
216
What is meiosis?
The process by which germ cells make non-identical copies of themselves by creating daughter cells that have one of each homolog.
217
What is cytokinesis?
Dividing the cytoplasm in two (optional)
218
What affects checkpoints?
Caffeine disables the checkpoint, and hydroxyurea blocks chromosome replication
219
How do cells know when to divide?
Most cells in your body are not dividing, the cells that are not dividing are usually arrested in the G1 phase of the cell cycle, and often they are waiting for signals from other cells to tell them to divide.
220
How are chromosomes actually separated into the daughter cells?
Mitosis
221
What happens in interphase?
During the S phase of interphase, the nucleus replicates its DNA and centrosomes.
222
What happens in prophase?
Chromatin coils and supercoils, becoming more compact and into visible mitotic chromosomes -> consisting of identical, paired sister chromatids
223
What happens in prometaphase?
The nuclear envelope breaks down, the kinetochore microtubules appear and connect the kinetochores to the poles.
224
What happens in metaphase?
The centromeres become aligned in a plane at the cell's equator
225
What happens in anaphase?
The paired sister chromatids separate, and the new daughter chromosomes begin to move toward the poles.
226
What happens in telophase?
Daughter chromosomes reach the poles. As telophase concludes, the nuclear envelopes and nucleoli re-form, chromatin becomes diffuse, and the cell again enters interphase.
227
Rules for making a metaphase mitotic spindle
Sister chromatids are paired, microtubules become stable when captured by kinetochores, and once a checkpoint senses when all chromatids have been captured by microtubules and then allows the chromatids to separate by dissolving the centromere.
228
Describe cytokinesis in animals
Actin and myosin form a "purse string" that constricts and divides the cell
229
Describe cytokinesis in plants
Vesicles fuse to make cell a membrane and cell plate, which becomes a new cell wall dividing the mother cell.
230
Do all cells undergo cytokinesis?
No. An example is muscle cells that have many nuclei (syncytial).
231
What is sex (genetically)?
Mixing the genetic material of two organisms
232
What is meiosis?
The process by which which haploid are made.
233
What are the general steps of meiosis?
1. Replicate the DNA of a diploid cell
2. Meiosis 1 and Meiosis 2
234
What happens in prophase one?
* DNA begins to compact
* Synapsis: pairing of homologous chromosomes
* Chiasmata form, crossing over.
235
Does meiosis happen very quickly?
Unlike mitosis, meiosis can take a very long time.
236
What happens in prometaphase one?
- the nuclear envelope breaks down
- spindle fibers form
237
What happens in metaphase 1?
- microtubules attach to kinetochores (one per homolog not per chromatid)
- chromosomes line up at metaphase plate held together by chiasmata
238
What happens in anaphase 1?
- separation of homologous chromosomes into separate cells
NOTE: each cell now has 2 copies of each homologous chromosomes - theses chromatids are not identical because of crossing over
239
What about telophase 1?
It is optional
240
What happens in mitosis 2?
It is essentially mitosis except with half the number of homologs. You end up with 4 haploid cells.
241
In what stage of meiosis does trisomy occur?
During anaphase 1 of meiosis, a non-disjunction event occurs, meaning rather than the chromosomes separating equal, both end up in a single gamete and when fused with the extra chromosome ends up with 3.
242
What are the two ways to think of the process of meiosis?
1. A diploid organism divides its chromosomes in the haploid gametes so that when the haploid cells fuse you get back a diploid organism
OR
2. Two haploid cells combine to form a diploid so that the chromosomes can be shuffled before undergoing meiosis to produce another haploid
243
How do the different ploidy replicate?
Even numbered ploidy create gametes via meiosis, odd however can only replicate via mitosis.
244
What are the types of variation in genetics?
Continuous and discrete
245
what is continuous variation?
-> infinite number of traits for a given character fall along a continuous spectrum (ei height and skin colour)
246
What is discrete variation?
There are only two or a few traits for a given character (ei fur colour in mice)
247
What were the results of mendel's true cross pea experiment?
P0 -> SS x ss
F1 -> Ss x Ss
F2 -> SS, ss, Ss, Ss 1:2:1
Further 3/4 were round (S or SS) and 1/4 were wrinkly 3:1
248
know that heredity exists in discrete units that travel through space and time
249
What is a gene?
A gene is a unit of heredity related to a character (ei eye colour)
250
What is an allele?
It is the different traits within a given character ei (wrinkled or round peas)
251
Compare genotype vs phenotype
The genotype is the set of alleles that an organism has and the phenotype is the set of traits the organism displays
252
What is independent assortment?
The alleles of two (or more) different genes get sorted into gametes independently of one another
253
254
What is hemizygous?
Where a gene is missing/deleted from one of the chromosomes.
255
Why is colourblindness more likely to occur in males?
Colourblindness is a sex-linked trait - Males only have one X chromosome thus if the mother is homozygous (its guaranteed) or heterozygous (its a 50/50 chance)
256
What is the mutation for colourblindness?
The gene that makes the protein - opsin that detects green light is mutatueted in some X chromosomes thus the protein cant be made properly
257
What are functional vs defective alleles called?
The functional allele is called wild type and defective are called mutant alleles.
258
