week 4 Flashcards
(117 cards)
1
Q
What is the significance of electron shells in atoms?
A
Electron shells determine how atoms will interact with each other; the first shell holds 2 electrons, the second and outer shells can hold up to 8 electrons each.
2
Q
How does the electron configuration of an atom influence its reactivity?
A
Atoms with outer shells that are not filled are more reactive, tending to form chemical bonds to achieve a full outer shell.
3
Q
How do atoms form molecules?
A
Atoms can form molecules by sharing electrons, or by losing or gaining electrons, resulting in bonded atoms.
4
Q
What is the octet rule and its relevance to chemical bonding?
A
The octet rule is the tendency of atoms to form stable molecules by having eight electrons in their outermost shells.
5
Q
What are chemical bonds?
A
A chemical bond is an attractive force that links atoms together to form molecules. There are several kinds of chemical bonds.
6
Q
what is a covalent bond?
A
atoms share one or more pairs of electrons, so that the outer shells are filled
7
Q
what is a polar covalent bond?
A
A polar covalent bond results when electrons are drawn to one nucleus more than to the other, because one atom has more electronegativity
8
Q
what is an ionic bond?
A
When one atom is so electronegative that it removes an electron from another atom to form an ionic bond.
9
Q
what are isomers?
A
molecules with the same chemicalformula, but atoms are arranged differently
10
Q
what are structural isomers?
A
differ in how their atoms are joined together
11
Q
what is an optical isomer?
A
Optical isomers occur when a carbon atom has four different atoms or groups of atoms attached to it.
- Some biochemical molecules that can interact with one optical isomer are unable to “fit” the other
Optical isomers result from asymmetrical carbons.
12
Q
Describe hydrophobic and van der Waals interactions in terms of their interaction basis and bond energy.
A
Hydrophobic interactions occur between nonpolar substances in the presence of polar substances, especially water, with bond energies of 1-2 kcal/mol. Van der Waals interactions are due to the interaction of electrons of nonpolar substances with a typical bond energy of about 1 kcal/mol. Both types of interactions contribute to the stability and folding of proteins, albeit weaker than covalent or ionic bonds.
13
Q
What characterizes a covalent bond and what is its bond energy range?
A
A covalent bond is characterized by the sharing of electron pairs between atoms. The bond energy for covalent bonds typically ranges from 50 to 110 kcal/mol, making them quite strong and stable under physiological conditions.
14
Q
How do ionic bonds and hydrogen bonds differ in their basis of interaction and bond energy?
A
Ionic bonds are based on the attraction of opposite charges and have a bond energy between 3-7 kcal/mol, whereas hydrogen bonds are formed by the sharing of a hydrogen atom and also have bond energy between 3-7 kcal/mol. Despite having similar bond energies, ionic bonds result from electrostatic attractions, while hydrogen bonds are due to polarity within molecules.
15
Q
what is an ionic bond?
A
When one atom is so electronegative that it removes an electron from another atom to form an ionic bond
16
Q
what is biochemical unity?
A
Biochemical unity: there are four kinds of macromolecules in living things, which are present in roughly the same proportions in all organisms, and have similar functions.
17
Q
What Are the Chemical Structures and Functions of Proteins?
A
- Proteins are polymers of 20 different amino acids.
- Polypeptide chain: single, unbranched chain of amino acids.
- The chains are folded into specific three dimensional shapes defined by the sequence of the amino acids.
- Proteins can consist of more than one type of polypeptide chain.
18
Q
What role do enzymes play among protein functions?
A
Enzymes are catalytic proteins that speed up chemical reactions in the body without being consumed in the process.
19
Q
What are defensive proteins and give an example?
A
Defensive proteins are those that protect the body from foreign pathogens. Antibodies are a key example, as they bind to specific foreign particles, such as viruses and bacteria, to neutralize them and prevent disease.
20
Q
are amino acids acidic or basic?
A
Amino acids have carboxyl and amino groups—so they function as both acid and base
21
Q
How do hormonal and receptor proteins function in the body?
A
Hormonal and regulatory proteins control physiological processes by acting as messengers that coordinate the activities of different cell types. Receptor proteins receive and respond to molecular signals, initiating a cellular response to various stimuli, such as the presence of a hormone or a change in the environment.
22
Q
What is the function of storage proteins?
A
Storage proteins store amino acids for later use.
23
Q
A
24
Q
What role do structural proteins play in an organism?
A
Structural proteins provide physical stability and support for cells and tissues.
25
How do transport proteins contribute to cellular function?
Transport proteins carry substances within the organism, such as hemoglobin, which transports oxygen in the blood.
26
What is the function of genetic regulatory proteins?
Genetic regulatory proteins control when, how, and to what extent a gene is expressed.
27
What is the significance of the alpha carbon in amino acids?
The alpha carbon atom is asymmetrical, making amino acids optically active and leading to two isomeric forms: D-amino acids and L-amino acids.
28
What are the two isomeric forms of amino acids and which one is found in organisms?
The two isomeric forms are D-amino acids (dextro, "right") and L-amino acids (levo, "left"), with the L-form being the one found in organisms.
29
How are amino acids categorized?
Amino acids are grouped based on their side chains, or R-groups, which can have various functional groups.
30
What special role does methionine play in proteins?
Methionine initiates chains of amino acids, typically being the first amino acid in a newly synthesized protein.
31
How does proline affect the structure of proteins?
Proline causes kinks in chains of amino acids due to its unique structure, influencing the folding of proteins.
32
What is the function of cysteine in proteins?
Cysteine links
33
What is the role of cysteine in forming disulfide bridges?
The terminal -SH group of cysteine can react with another cysteine side chain to form a disulfide bridge (—S—S—), which is critical for protein folding.
covalent bond
34
Why are disulfide bridges important in proteins, and where are they most commonly found?
Disulfide bridges are important for stabilizing the three-dimensional structure of proteins and are most commonly found in extracellular proteins, which are exposed to more stress outside of the cell.
35
How are amino acids linked together in a protein?
Amino acids are linked together by peptide bonds formed during a condensation reaction, which is a covalent bond between the amino group of one amino acid and the carboxyl group of another.
36
What is the nature of the peptide bond in proteins?
The peptide bond is inflexible, meaning no rotation is possible around it, which contributes to the protein's structure.
37
: What is the primary structure of a protein?
The primary structure of a protein is the sequence of amino acids that determines its higher levels of structure, including secondary and tertiary forms.
38
How does the amino acid sequence influence protein structure?
The sequence of amino acids dictates the secondary and tertiary structures of the protein, essentially determining how the protein will fold.
39
What does the diversity of proteins indicate about amino acid sequences?
The enormous number of different proteins that can be made from 20 amino acids indicates the vast array of functions and structures that proteins can have.
40
What defines the primary structure of a protein?
The primary structure of a protein is defined by its sequence of amino acids, which determines its higher-level structures and ultimately its function.
41
What are the two types of secondary structures commonly found in proteins?
The two common secondary structures are the alpha helix, a right-handed coil resulting from hydrogen bonding between N-H groups on one amino acid and C=O groups on another, and the beta pleated sheet, where two or more polypeptide chains align and are connected by hydrogen bonds.
42
What is the tertiary structure of a protein?
The tertiary structure is the overall three-dimensional shape of a protein, determined by interactions like disulfide bridges, hydrogen bonds, hydrophobic interactions, van der Waals forces, and ionic bonds.
43
How does the tertiary structure relate to protein functionality?
The tertiary structure’s intricate folding allows for a diversity of functional groups on the outer surfaces of the protein to interact with other molecules, enabling specific biological functions.
44
What demonstrates the information to specify protein shape is contained in the primary structure?
The fact that a denatured protein can refold into its normal tertiary structure upon cooling indicates that all information required for folding is contained within the primary sequence of amino acids.
45
What happens to a protein when it is denatured, and what does this demonstrate about protein structure?
When a protein is heated, its secondary and tertiary structures break down, a process known as denaturation. If the protein refolds to its normal structure upon cooling, it demonstrates that the primary structure contains all the information necessary to specify the protein's shape.
46
What is the quaternary structure of a protein?
The quaternary structure of a protein results from the interaction of subunits through hydrophobic interactions, van der Waals forces, ionic bonds, and hydrogen bonds. Each subunit maintains its own unique tertiary structure within the larger complex.
47
How do proteins achieve specificity in binding to other molecules?
Proteins bind noncovalently with specific molecules with high specificity, which is determined by the protein's shape—there must be a general "fit" between the 3-D shapes of the protein and the other molecule, and the chemistry—R groups on the protein surface interact with other molecules through ionic bonds, hydrophobic interactions, or hydrogen bonds.
48
What conditions can affect the secondary and tertiary structures of a protein?
Conditions that can affect protein structure include high temperature, pH changes, high concentrations of polar molecules, and the presence of nonpolar substances.
49
What underlies the transformation of energy in biological systems?
The transformation of energy is a hallmark of life, with energy being the capacity to do work or the capacity for change. Energy transformations in biological systems are closely linked to chemical transformations within cells.
50
How are different forms of energy categorized?
Energy is categorized into potential energy, which is stored energy found in chemical bonds, concentration gradients, and charge imbalances, and kinetic energy, which is the energy of movement.
51
What are the laws of thermodynamics and how do they apply to biological energy transformations?
The laws of thermodynamics, which include the concepts that energy cannot be created or destroyed and that energy transformations are never 100% efficient, apply to all matter and energy transformations in the universe and help explain how cells harvest and use energy.
52
What is the first law of thermodynamics?
The first law of thermodynamics states that energy is neither created nor destroyed. When energy is converted from one form to another, the total amount of energy before and after the conversion remains the same.
53
What is the second law of thermodynamics?
The second law of thermodynamics states that when energy is converted from one form to another, some of the energy becomes unavailable to do work. No energy transformation is 100 percent efficient due to the increase in entropy.
54
What is entropy and how does it relate to energy and order?
Entropy is a measure of disorder within a system. It takes energy to impose order on a system; without energy input, a system will tend towards a more randomly arranged or disordered state.
55
What is the hallmark of life in terms of energy?
The transformation of energy is a hallmark of life.
56
What is energy in a biological context?
Energy is the capacity to do work, or the capacity for change.
57
How are energy transformations linked to cellular processes?
Energy transformations are linked to chemical transformations in cells.
58
What is energy in a biological context?
Energy is the capacity to do work, or the capacity for change.
59
How are energy transformations linked to cellular processes?
Energy transformations are linked to chemical transformations in cells.
60
What are the two categories of energy?
Potential energy (stored energy) and kinetic energy (energy of movement).
61
What is metabolism?
Metabolism is the sum total of all chemical reactions in an organism.
62
What are anabolic and catabolic reactions?
Anabolic reactions build complex molecules from simpler ones, requiring energy input. Catabolic reactions break down complex molecules into simpler ones, releasing energy.
63
How do enzymes lower the energy barrier of reactions?
Enzymes lower the energy barrier by bringing reactants together, orienting them correctly, and straining their bonds to facilitate the transition to the reaction products
64
in a catalysing reaction. how do enzymes work?
In catalyzing a reaction, an enzyme may use one or more mechanisms:
– Orientation of the substrate molecule
– Physical strain of the substrate molecule
– Chemical change of the substrate molecule
65
what are exergonic and endergonic reactions?
Exergonic reactions release free energy(–ΔG): Catabolism; complexity decreases(generates disorder)
Endergonic reactions consume free energy(+ΔG): anabolism; complexity (order)increases.
66
what is a catalyst?
Catalysts speed up the rate of a reaction.
* The catalyst is not altered by the reactions.
* Most biological catalysts are enzymes (proteins) that act as a framework in which reactions can take place.
67
what is activation energy?
Some reactions are slow because of anenergy barrier—the amount of energy required to start the reaction, called activation energy (Ea)
68
What equation represents the total energy in any system?
Total energy = usable energy + unusable energy. This is also represented as enthalpy (H) = free energy (G) + entropy (S), or H = G + TS (where T = absolute temperature).
69
How can change in energy be measured?
Change in energy can be measured in calories or joules.
70
How is the change in free energy (ΔG) calculated in a reaction?
ΔG = ΔH – TΔS, which is the difference in free energy of the products and the reactants.
71
What does a negative ΔG indicate in a reaction?
If ΔG is negative, free energy is released.
72
What does a positive ΔG indicate in a reaction?
If ΔG is positive, free energy is consumed.
73
What happens if free energy is not available for a reaction?
If free energy is not available, the reaction does not occur.
74
Who formulated these principles of thermodynamics and when?
Josiah Willard Gibbs formulated these principles. He lived from February 11, 1839, to April 28, 1903.
75
What factors determine the magnitude of ΔG in biological energy transformations?
The magnitude of ΔG depends on ΔH (total energy added or released) and ΔS (change in entropy). Large changes in entropy make ΔG more negative.
76
What does a positive ΔS in a chemical reaction indicate?
A positive ΔS indicates an increase in entropy, meaning the products will be more disordered. Example: In the hydrolysis of a protein into its component amino acids, ΔS is positive.
77
What physical principle indicates that chemical reactions can run in both directions and achieve a state where ΔG = 0?
At chemical equilibrium, ΔG = 0, meaning forward and reverse reactions are balanced. The direction favored depends on the concentrations of the reactants and products.
78
How does the equilibrium point of a reaction relate to ΔG and the directionality of the reaction?
Every reaction has a specific equilibrium point. ΔG is related to this point: the further towards completion the equilibrium is, the more free energy is released. ΔG values near zero are characteristic of readily reversible reactions, indicating the directionality of the reaction based on reactant and product concentrations.
79
What determines the specificity of an enzyme for its substrate?
The shape of the enzyme's active site allows a specific substrate to fit according to the lock and key model. The binding of the substrate to the active site depends on hydrogen bonds, the attraction and repulsion of electrically charged groups, and hydrophobic interactions.
80
How do enzymes change upon binding to their substrate?
Many enzymes change shape when they bind to the substrate, a process known as induced fit. This change in shape helps to catalyze the reaction more efficiently.
81
Name an enzyme that acts as an antibiotic and describe its function
Lysozyme, found in egg white, saliva, and tears, acts as an antibiotic. It catalyzes the cutting of polysaccharide chains in bacterial cell walls, causing them to rupture. It catalyzes a hydrolysis reaction that is spontaneous but not instantaneous.
82
How are chemical reactions organized within cells?
Thousands of chemical reactions occur in cells simultaneously and are organized in metabolic pathways. Each reaction within a pathway is catalyzed by a specific enzyme, and these pathways are interconnected. Regulation of enzymes and thus reaction rates is crucial for maintaining internal homeostasis.
83
What is the commitment step in metabolic pathways?
The first reaction in metabolic pathways is the commitment step, which determines that other reactions will then happen in sequence. This step often regulates the entire pathway.
84
How does feedback inhibition work in metabolic pathways?
The first reaction in metabolic pathways is the commitment step, which determines that other reactions will then happen in sequence. This step often regulates the entire pathway.
85
How does feedback inhibition work in metabolic pathways?
In feedback inhibition (end-product inhibition), the final product of a metabolic pathway acts as a noncompetitive inhibitor of the first enzyme in the pathway, effectively shutting down the pathway to prevent the overproduction of the final product.
86
How does pH affect enzyme activity?
Every enzyme is most active at a particular pH level because pH influences the ionization of functional groups. For example, at low pH (high H+ concentration), —COO– may react with H+ to form —COOH, which is no longer charged, affecting the enzyme's folding and thus its function.
87
What effect does temperature have on enzyme activity?
Every enzyme has an optimal temperature. At high temperatures, noncovalent bonds begin to break, leading to the loss of tertiary structure and resulting in the enzyme becoming denatured.
88
What are ribozymes made from, and how do they differ from enzymes?
Ribozymes are made from RNA, distinguishing them from enzymes, which are proteins. Both act as biological catalysts. The discovery of a ribozyme in the early 1980s, capable of cutting RNA transcripts, supports the hypothesis of an "RNA world," suggesting that life may have originated with RNA-based catalysis before proteins evolved.
89
What disaccharide is formed from α-D-glucose and fructose, and what type of glycosidic linkage does it have?
Sucrose is formed from α-D-glucose and fructose with an α-1,2 glycosidic linkage.
90
What reaction process forms glycosidic linkages between monosaccharides?
Condensation reactions form glycosidic linkages between monosaccharides, resulting in the release of a water molecule.
91
What disaccharide is formed from two glucose molecules, and what type of glycosidic linkage connects them?
Maltose is formed from two glucose molecules connected by an α-1,4 glycosidic linkage.
92
How are the carbon atoms numbered in the formation of sucrose and maltose?
In sucrose, the bond is formed between the 1st carbon atom of α-D-glucose and the 2nd carbon atom of fructose. In maltose, the bond is between the 1st carbon atom of one α-D-glucose molecule and the 4th carbon atom of another glucose molecule.
93
What are oligosaccharides and their role on cell surfaces?
Oligosaccharides may include various functional groups and are often covalently bonded to proteins and lipids on cell surfaces, where they act as recognition signals. An example of this is the specificity of human blood groups, which is determined by oligosaccharide chains.
94
What are polysaccharides and their functions in living organisms?
Polysaccharides are giant polymers of monosaccharides. They serve various functions such as the storage of glucose in plants (starch), storage of glucose in animals (glycogen), and providing stability for structural components (cellulose).
95
are animal fats and plant oils usually saturated?
animal fats tend to be saturated and packed together tightly - solid at room temperature
plant oils tend to be unsaturated, the kinks prevent packing; liquid at room temperature
96
What are lipids and what forces hold them together?
Lipids are nonpolar hydrocarbons. They are held together by weak but additive van der Waals forces when they are close together. They are not considered polymers in the strict sense because they are not linked by covalent bonds
97
What roles do various lipids play in biological systems?
Fats and oils are used to store energy.
Phospholipids play a structural role in cell membranes.
Carotenoids and chlorophylls capture light energy in plants.
Steroids and modified fatty acids act as hormones and vitamins
98
What constitutes fats and oils, and what are their components?
Fats and oils are triglycerides, also known as simple lipids. They are composed of fatty acids and glycerol. Glycerol has three —OH groups (making it an alcohol), and a fatty acid consists of a nonpolar hydrocarbon with a polar carboxyl group. The carboxyl group bonds with the hydroxyl group of glycerol in an ester linkage.
99
How are saturated and unsaturated fatty acids different?
Saturated fatty acids have no double bonds between carbon atoms and are saturated with hydrogen atoms.
Unsaturated fatty acids contain double bonds within the carbon chain.
Monounsaturated: one double bond
Polyunsaturated: more than one double bond
100
What does it mean that fatty acids are amphipathic, and what are their chemical properties?
Fatty acids are amphipathic, meaning they have both hydrophilic and hydrophobic properties. The carboxyl group at one end can ionize to form COO–, making it strongly hydrophilic, while the hydrocarbon chain is hydrophobic.
101
What are phospholipids and why are they considered amphipathic?
Phospholipids consist of fatty acids bound to glycerol, where one fatty acid is replaced by a phosphate group. The phosphate group (the “head”) is hydrophilic, while the fatty acid chains (the “tails”) are hydrophobic. This dual nature makes phospholipids amphipathic, suitable for forming cell membranes with distinct inside and outside environments.
102
What is the role of ATP in biochemical energetics?
ATP (adenosine triphosphate) captures and transfers free energy. It releases a large amount of energy when hydrolyzed and can phosphorylate, or donate phosphate groups to, other molecules, which is crucial in cellular processes and energy transfer.
103
104
is ATP a nucleotide or a nucleoside, and what is the free energy change upon its hydrolysis?
ATP is a nucleotide, not a nucleoside. The hydrolysis of ATP is an exergonic reaction that yields a free energy change (ΔG) of approximately –7.3 to –14 kcal/mol, depending on conditions within the cell.
105
What is the difference between ATP hydrolysis and the formation of ATP in terms of energy?
The hydrolysis of ATP is an exergonic reaction, releasing free energy with ΔG = –7.3 to –14 kcal/mol. In contrast, the formation of ATP is an endergonic reaction that requires an input of energy. The coupling of ATP formation and hydrolysis is central to energy exchange in biological systems, with the hydrolysis of ATP driving endergonic processes like bioluminescence.
106
How does ATP hydrolysis drive bioluminescence?
Bioluminescence is an endergonic reaction that is driven by the exergonic hydrolysis of ATP. In the presence of the enzyme luciferase, ATP hydrolysis transfers energy to luciferin, resulting in the emission of light as a product along with AMP and pyrophosphate (PPi).
107
Why are the formation and hydrolysis of ATP considered coupling reactions?
The formation and hydrolysis of ATP are considered coupling reactions because the energy-releasing process (exergonic hydrolysis of ATP) is often linked to an energy-requiring process (endergonic reaction). This coupling is fundamental in cellular metabolism, allowing cells to perform work and maintain homeostasis.
108
What is an exergonic reaction and what are some examples
An exergonic reaction is one that releases energy. Examples include cell respiration and catabolism.
109
What is an endergonic reaction and what are some examples?
An endergonic reaction requires an input of energy to proceed. Examples include active transport, cell movements, and anabolism.
110
How are exergonic and endergonic reactions coupled in biological systems?
In biological systems, the energy released from exergonic reactions (like the hydrolysis of ATP to ADP and P_i) is used to drive endergonic reactions, demonstrating the principle of energy coupling. This allows for the transfer of energy from catabolic to anabolic pathways, maintaining the cell's energy balance.
111
What are fuels in the context of cellular metabolism, and which is the most common fuel?
In cellular metabolism, fuels are molecules whose stored energy can be released for use. The most common fuel in organisms is glucose, though other molecules can be converted into glucose or intermediate compounds for energy release.
112
What principles govern metabolic pathways in terms of glucose oxidation?
The principles governing metabolic pathways include:
Complex chemical transformations occur in a series of stepwise reactions.
Each reaction within the pathway is catalyzed by a specific enzyme.
Metabolic pathways are conserved across all organisms.
In eukaryotes, metabolic pathways are compartmentalized within organelles.
Each pathway is regulated at strategic points by key enzymes.
113
What are the aerobic pathways of glucose metabolism?
The aerobic pathways of glucose metabolism include glycolysis, the Krebs cycle (also known as the citric acid cycle or TCA cycle), and oxidative phosphorylation in the electron transport chain.
114
How does oxidative phosphorylation form ATP?
Oxidative phosphorylation forms ATP by transferring electrons through a series of membrane proteins in the mitochondria, known as the electron transport chain. As electrons are passed along the chain, energy is released and used to pump protons across the mitochondrial membrane, creating a proton gradient. ATP synthase then uses the energy of the proton gradient to synthesize ATP from ADP and inorganic phosphate.
115
How is energy harvested from glucose in the absence of oxygen?
in the absence of oxygen, energy is harvested from glucose through anaerobic pathways such as glycolysis followed by fermentation. In fermentation, pyruvate from glycolysis is converted into lactic acid or ethanol and carbon dioxide, allowing for the regeneration of NAD+ and the continuation of glycolysis under anaerobic conditions.
116
How are metabolic pathways interrelated and regulated?
Metabolic pathways are interrelated through shared intermediates and are tightly regulated by the control of enzyme activities. Regulation can occur through feedback inhibition, where the end product of a pathway inhibits an enzyme involved in its synthesis, or through other mechanisms such as allosteric regulation, covalent modification, and changes in enzyme synthesis or degradation rates.
117
