Unit 2: Cell Chemistry Flashcards
1
Q
lWhat are the reactants and products of a catabolic reaction?
A
Catabolic reaction: where a complex molecule breaks down into simpler molecules
2
Q
What atoms are lipids composed of? What 2 types of molecules create a triglyceride when synthesized?
A
C, H, and O (not in a fixed ratio)
There is 1 glycerol molecule (the backbone of the lipid), and 3 fatty acid chains.
3
Q
FILL IN THE BLANK: Catabolic reactions result in the ____ of energy.
A
(net) loss/(net) release
4
Q
Name the 5 functions of lipids and examples of each.
A
S- Storage of energy for long term use (triglycerides)
H- Hormones structural component (steroids, such as estrogen and testosterone)
I- Insulation (both thermal (triglycerides) and electrical (sphingolipids)
P- Protection/cushion of internal organs (triglycerides and waxes)
S- Structure of cell membranes (Phospholipids and cholesterol)
→ Chemical signals are diffused: cholesterol range
5
Q
What are ester bonds? Explain how they are formed.
A
Ester bonds are bonds between glycerol and fatty acids, through condensation reactions (dehydration synthesis.)
The H2O is removed between the glycerol and each fatty acid, and the oxygen of the glycerol bonds with the carbon of the fatty acid chain.
6
Q
What are phospholipids? Describe their structural components.
A
Phospholipids are a variation of a triglyceride in a cell membrane. The top fatty acid chain is replaced by a phosphate group (PO4). PO4 is negatively charged, making a polar (hydrophilic) head with nonpolar (hydrophobic) fatty acid tails.
They are amphipathic (have polar and nonpolar traits)
7
Q
What 6 elements are main components of most living things?
A
Carbon
Hydrogen
Nitrogen
Oxygen
Phosphorus
Sulfur
Mnemonic: CHNOPS/CHONPS
8
Q
Define saturated fats, as well as:
- their shape
- their state at room temperature and why
- their melting point
A
Saturated fats are when all carbons have the maximum number of hydrogen atoms bonded to them. There are no double carbon bonds and no kinks.
They are linear in shape when packed together. Their tight packing makes them solid at room temperature, with high melting points.
As well, the tight packing of the layers means more London Dispersion forces can act upon them, holding the fatty acids together.
9
Q
FILL IN THE BLANK: An organism’s metabolism is the ____ ____ of all anabolic and catabolic reactions
A
net sum
10
Q
Define unsaturated fats, as well as:
- their shape
- their state at room temperature and why
- their melting point
A
Unsaturated fats have double bonds of carbon, as not all carbons are fully saturated (has kinks, less hydrogens).
There are bends due to the repulsion of the hydrogens, since they are not balanced on each side of the fatty acid. They are more commonly liquid with lower melting points due to less London Dispersion forces and looser packing.
This also means they are more fluid, such as in cell membranes.
11
Q
State the two types of metabolism reactions.
A
Condensation (aka dehydration synthesis) and hydrolysis
12
Q
Define a condensation reaction, in the context of metabolism. State its alternate name.
A
Two molecules are covalently bonded through the loss of water. AKA dehydration synthesis
13
Q
State the difference between monounsaturated and polyunsaturated fats.
A
Monounsaturated: only one double bond between carbons (1 carbon not fully saturated)
Polyunsaturated: more than one double bond, several carbons not fully saturated
14
Q
Define a hydrolysis reaction, in the context of metabolism.
A
Covalent bond between two molecules is broken through the addition of water
15
Q
Draw a diagram of saturated, monounsaturated, polyunsaturated, trans fats.
A
🤯 good job!
16
Q
Define monomers, polymers and polymerization. Give an example of a monomer and a polymer.
A
Monomers: similar subunits that bond together to form polymers, e.g. amino acids
Polymers: chains of monomers, e.g. proteins
Polymerization: chemical reaction in which monomers react into polymers
17
Q
State the four main kinds of macromolecules.
A
Carbohydrates
Proteins
Lipids
Nucleic acids
18
Q
Explain how London Dispersion forces work.
A
- Intermolecular forces, electronegativity of different atom’s electron clouds
- Electron density is instantaneous in an atom’s orbitals; slightly positive and negative regions
- Causes a brief electrostatic attraction between two molecules
- Instantaneous dipoles react to form induced dipoles, with the negative charge of the atom attracting he partial positive charge of an atom in another molecule, temporarily
- electrons move to another point and the bond breaks
19
Q
Define a monosaccharide and a disaccharide. Name the bond between two monosaccharides.
A
Monosaccharide: aka simple sugar, is the most basic unit from which carbohydrates are built
Disaccharide: two monosaccharides bonded together by a glycosidic bond
20
Q
How do London Dispersion Forces help geckos “defy gravity”?
A
- Their toes are padded with tiny, hair like structure called setae, which have even tinier hairs called spatulae
- Creates more surface area, which means more LDF between the gecko feet and walls
- Is miniscule force on its own, but has ~2 billion LDF
- Slightly changing the angle allows the gecko to let go, escaping in a frenzy
21
Q
Define hydrogenation.
A
The process of adding hydrogen to unsaturated fatty acid chains, getting rid of double carbon bonds
- leads to more saturated fatty acid
- plant oils are artificially hydrogenated to make them solid (e.g. margarine, PB&J)
- process results in the creation of partially saturated lipids
22
Q
Define trans fats.
A
Partially saturated/hydrogenated lipids that still have double carbon bonds but exhibit the characteristics of saturated fats.
23
Q
What are qualities of trans fats? Why are they liked/used?
A
- Linear
- Tightly packed
- Solid at room temp
- Difficult to break down by enzymes
- Good taste
- Higher melting point/more stable at higher temperatures
- Last longer
24
Q
(Niche) Why do the components of a disaccharide not follow the same ratio of the components of a monosaccharide?
A
One water molecule is lost from when two monosaccharides are bonded through a condensation reaction (aka dehydration synthesis)
25
Distinguish between cis and trans fats.
- Are both unsaturated fats
CIS:
- hydrogens on same side
- causes kink or bend in fatty acid
- lower melting point
- good for health
- naturally occurring (most common natural double bond)
- can consume as per required
TRANS:
- hydrogens on opposite side
- linear fatty acid
- body does not effectively break down this molecule
- higher melting point
- detrimental to health (lowers good cholesterol [HDL], increases bad cholesterol [LDL])
- Less naturally occurring, thus produced artificially by partial hydrogenation of polyunsaturated fatty acids
- Found in processed food, fast foods, butter/milky products, small red meat
- Occurs naturally in small amounts in red meat/dairy
- no more than 1% of total calories per day
26
Why are some cities/countries banning/taxing foods with trans fats?
They are artificially made and implemented into consumable foods, despite having a highly unhealthy nature.
27
What are polysaccharides composed of?
3 or more monosaccharides
28
Define Urea and its purpose, as well as a secondary application.
- Organic compound CO(NH2)2
- Purpose: excrete nitrogen
- Use: fertilizer to increase crop production
29
2. Who discovered urea, and what did that discovery disprove? What is this kind of discovery called?
- First discovered accidentally by Friedrich Wöhler in 1828
- Synthesis of an organic compound from two inorganic olecules was possible
- Disproved the theory of vitalism (organic compounds can only be synthesized by living organisms as they possess a "life spark"/divine principle that non-living things did not have
- Serendipity!
30
What are Urea's 2 key traits?
- Non-toxic, highly soluble
- Artificially synthesized due to its helpful qualities
31
Name the two uses of polysaccharides. Give two examples of each usage.
Energy storage (e.g. starch - in plants - and glycogen - in animals) and structural use (cellulose - in plants - and chitin - in fungi and arthropods)
32
What are the five elements that appear the most in proteins?
Carbon
Hydrogen
Oxygen
Nitrogen
Sulphur (in some side groups)
Mnemonic: CHONS
Note that phosphorus is not included, unlike in the 6 basic elements of most living things
33
FILL IN THE BLANKS: All amino acids (AAs) have the same basic ____ but they differ in the ____ ____ they have that is attached to the basic ____
structure/components; side/variant/R group; structure/components
34
What determines if an amino acid is essential or nonessential? How many amino acids exist? How many are essential? Nonessential?
Essential AAs: the body cannot make them on its own and therefore must obtain them via consumption; there are 11 essential AAs
Nonessential AAs: the body can make them on its own and does not need to obtain them via consumption; there are 9 AAs
There are 20 AAs
35
Name the five (5) basic functions of proteins. Provide a brief description of each and an example.
Structural: proteins act as major structural components of cells and issues, for example, in muscles, actin plays a large role in maintaining cell structure and formation
Hormones (or messengers): proteins create hormones, e.g. insulin
Immunity: proteins form the antibodies of your immune system, e.g. antibodies
Transport: proteins form channels that assist in the transportation of molecules across cell membranes, e.g. transport proteins/protein channels
Proteins also assist in the transportation of molecules through the blood, e.g. hemoglobin (or haemoglobin) is responsible for transporting oxygen from lungs into blood to other areas
Enzymes: some proteins are enzymes; aid in the breakdown of materials, e.g. lipase, which helps break down fats in food to be absorbed through intestines
Mnemonic: SHITE
36
Describe the process in which proteins are formed.
DNA (more specifically, genes) undergo transcription to create mRNA
mRNA undergoes translation with the help of ribosomes to create a polypeptide
Polypeptide is modified to form a protein
37
"One gene will code for one polypeptide." Give three exceptions to this rule.
Genes may be alternatively spliced to generate multiple polypeptide variants; one gene --> multiple polypeptides
Genes encoding tRNA sequences may be transcribed but never translated --> one gene --> no polypeptides
Genes may be mutated (alteration of base sequence) and thus produce a new and unique polypeptide sequence (and by extension, protein); one gene --> multiple polypeptides
38
What are the four levels of protein structure?
Primary, secondary, tertiary, quaternary
39
Describe primary protein structure. What bond(s) maintain the structure?
Primary protein structure: sequential chain of amino acids; amino acids are held together by peptide bonds (which are covalent)
Peptide bonds form between the nitrogen atom of the amino and the carbon atom of the carbonyl; single-bonded oxygen and two hydrogens are lost due to dehydration synthesis reaction
40
Describe secondary protein structure. What are the two shapes it can take? What attraction(s) maintain the structure?
Secondary protein structure: several instances of primary protein structures held together with hydrogen bonds
Can take on the form of either an alpha helix (spiral-shape) or beta sheet (zigzag pleated sheet); the hydrogen bonds between amino acids and hydrogen dictate what shape it will take
Note: the shape is never random, as the same protein will take the same shape
40
Describe tertiary protein structure. What attraction(s) maintain the structure?
Tertiary protein structure: a long chain of alpha helices and beta sheets, pulled into a complex, globular, 3D structure
Maintained through the following attractions:
- Disulfide bridges: two sulfides attract each other
- Ionic interactions: where positively and negatively charged R groups attract
- Hydrophobic interactions: R groups fold toward center to avoid water
- Hydrogen bond: when hydrogen bonds with a highly electronegative atom (e.g. oxygen, fluorine, sulfur), and is near a lone pair of electrons belonging to either oxygen, fluorine, or nitrogen, the hydrogen and lone pair can form a hydrogen bond, which is a type of strong dipole-dipole attraction. Note that a hydrogen bond is NOT a bond, but rather an intermolecular attraction.
41
Describe quaternary protein structure. What attraction(s) maintain the structure?
Quaternary protein structure: consists of several tertiary protein structures pulled together; more than one polypeptide chain/amino acid chain. Same attractions are present here as in the tertiary protein structure (disulfide bridges, ionic interactions, hydrophobic interactions, hydrogen bonds, van der waals)
42
When is a compound transported through blood plasma?
If the compound is soluble (in most cases)
43
Why is transportation in large multicellular organisms necessary?
Molecules like oxygen, glucose, and minerals are needed to be transported to every cell throughout the body
44
When is a compound transported through lymph vessels?
If the compound is insoluble (in most cases)
45
Describe the polarity and solubility of glucose in water, and if it is transported through the blood plasma.
Polar; soluble; yes
blood glucose concentration needs to be strictly maintained due to its osmosis within the cell membranes (homeostasis)
46
Describe the polarity and solubility of amino acids in water, and if it is transported through the blood plasma.
negatively or positively charged; mainly soluble; yes
- solubility varies depending on size and R group
- Hydrophobic --> insoluble, will be transported in lower concentrations in the blood
- Hydrophilic --> soluble, will be transported in blood
47
Describe the polarity and solubility of fats in water, and if it is transported through the blood plasma.
nonpolar; insoluble; no
- transported in structures called lipoproteins (single layer of phospholipids with proteins embedded along the molecules surrounding the fat)
48
Describe the polarity and solubility of cholesterol in water, and if it is transported through the blood plasma.
hydrophobic, insoluble, no
- need for synthesis of many biologically important molecules, and is a component of membranes
- transported through lipoproteins
49
Describe the polarity and solubility of oxygen in water, and if it is transported through the blood plasma.
nonpolar; is small enough that it can limitedly be soluble in water; yes
- needs to bind to protein hemoglobin to move through the plasma
50
Describe the polarity and solubility of sodium chloride in water, and if it is transported through the blood plasma.
ionic compound (charged attraction); soluble; yes
- breaks down into soluble ions of Na+ and Cl-
51
Describe 3 properties of fibrous proteins. Provide an example.
Only found in animals
Form long protein filaments; rod/wire-like shapes
Usually structural proteins
Generally insoluble in water due to the hydrophobic R groups that stick out of the molecule
E.g. collagen, keratin
52
Describe 2 properties of globular proteins. Provide an example.
Compact, rounded shapes; literally globular - globe-like
Generally soluble in solution, due to hydrophilic amino acids moving outwards to form dipole dipole attractions with solvent, and hydrophobic amino acids are pulled towards interior to hide from water
e.g. hemoglobin, antibodies
53
Define amphipathic, and provide an example.
When a macromolecule contains both hydrophilic and hydrophobic components, e.g. phospholipids
54
FILL IN THE BLANKS: Chemical reactions occur when two particles ____ with each other with the proper ____ and sufficient ____.
collide; orientation; energy
55
Name 5 ways to increase chemical reaction rates.
Lower container volume: less room for particles to move --> more collisions
Increase amount of particles: more particles --> more collisions
Increase temperature: increases movement of particles --> more likely for sufficient energy
Break up large particles: interior particles are shielded from collisions by exterior particles; breaking them allows all of them to be collided into --> more collisions
Use a catalyst: a catalyst is a substance that speeds up reaction rate without being consumed in the process --> more reactions
56
Define exothermic and endothermic.
Exothermic: a reaction that releases energy; net loss of energy (exo --> exit)
Endothermic: a reaction that gains energy; net gain of energy (endo --> enter)
57
Define activation energy, and how enzymes affect it.
Activation energy: the amount of energy required to start a reaction
Enzymes are capable of lowering the required activation energy, increasing the likelihood of the reaction occurring
58
What is the name of the difference between the initial amount of free energy and the final amount of free energy when a reaction occurs?
Net change in E/△E
59
Define catalyst, and provide an example.
Catalyst: a substance that increases the rate of a chemical reaction without being consumed in the process, e.g. enzymes
60
State and describe the two substrate-fitting-into-enzymes models.
Lock-and-key model: the active site is the exact same shape of its designated substrate(s)
The substrate(s) fits perfectly into its active site
Once the reaction finishes, the product(s) detaches and the enzyme is left unchanged
Induced-fit model: the active site is of a slightly different shape of its designated substrate(s)
When the substrate(s) enters the active site, the active site, being dynamic, undergoes a conformational change to allow the substrate(s) to fit perfectly
This conformational change possibly increases the reactivity of the substrate and might be necessary for the enzyme's catalytic activity
Once the product(s) leaves the active site, it goes back to its original structure (called the native confirmation)
61
FILL IN THE BLANKS: Because enzymes ____ the activation energy (E_a (subscript a)) of a chemical reaction, the ____ of enzymes results in the regulation of chemical reactions
lower; regulation
62
Describe competitive inhibition. Describe what would happen if the substrate concentration were to increase.
Competitive Inhibition: when a molecule (inhibitor) other than the substrate binds to the active site of the enzyme before the substrate is able to
The inhibitor blocks the substrate from entering the active site, preventing it from reacting
Due to the inhibitor being in direct competition with the substrate(s), the effectiveness of the inhibitor would decrease as the substrate concentration increases, until there is nearly no noticeable change between a lack of regulation and competitive inhibition
Note that the first enzyme in the biological pathway is regulated, as it is more resource efficient than regulating, say, the last enzyme
63
Define native conformation.
The state in which the protein is the most active and function
64
Define denaturation (use the word conformational change, specificity)
The process of an enzyme's shape/bonding/characteristics being altered, preventing a substrate from binding/fitting into its active site. This conformational change makes the enzyme lose its specificity to its specific substrate.
This results in a loss of protein activity.
65
Define denaturing agents and the two kinds of denaturing agents.
denaturing agents: conditions that can cause denaturation.
pH: higher or lower amounts of pH than the optimal pH can result in the denaturation of enzymes.
--> R groups of amino acids are charged and can form ionic bonds; pH can change the charges on the groups
temperature: higher temperature than the optimal temperature can cause the enzyme to rapidly change shape/bonding/characteristics, or cause the enzyme to die.
66
define a catalyst.
a substance that increases the reaction rate of a chemical reaction by reducing/lowering the amount of activation energy.
67
define activation energy.
the amount of energy needed to start a reaction.
68
describe the lock and key metaphor.
a door needs a specific key for it to open. enzymes are highly specific (key word SPECIFICITY), meaning they need a highly specific substrate to fit into their active site.
69
define induced fit of enzymes.
sometimes, when a substrate doesn't exactly fit into an enzyme's active site, it alters its shape for it to perfectly fit in. after the reaction is completed and the product is released, the enzyme reverts back to its normal shape.
70
Describe noncompetitive inhibition. Describe what would happen if the substrate concentration were to increase.
Noncompetitive Inhibition: when a molecule (inhibitor) other than the substrate binds to a secondary site of the enzyme
This second site is called the allosteric site
When the inhibitor bonds to the allosteric site, the shape of the enzyme's active site undergoes a conformational change
Due to this change, the active site is no longer the same shape as the designated substrate(s), and the substrate(s) is not able to undergo a reaction
Due to the inhibitor not being in direct competition with the substrate(s), the effectiveness of the inhibitor would not be affected by an increase in substrate concentration
Note that the first enzyme in the biological pathway is regulated, as it is more resource efficient than regulating, say, the last enzyme
71
Describe end-product inhibition. Provide an example of a molecule that uses this form of enzyme regulation.
End-product inhibition: also known as feedback inhibition, this is a special case of noncompetitive inhibition where the inhibitor that binds to the allosteric site is the very product of the reaction being catalyzed by the enzyme
This helps regulate the amount of product being made; if the body feels as though it has a sufficient supply of the product, said product would inhibit further products from being formed by binding to the allosteric site in the enzyme
However, if there is an insufficient supply of the product, the product would not be plentiful enough to stop all reactions from occurring, thusly allowing more product to be made
An example of a product that uses end product inhibition is isoleucine, one of the essential amino acids
72
describe the 4 steps to the enzyme-substrate process.
1. an enzyme and a substrate are in the same area.
2. the random movement of substrates leads the substrate to move into the enzyme's active site.
3. catalysis happens (when the substrate is changed).
4. the enzyme lets go, returning to normal for another reaction. the substrate is now called a product, and is different than it was before (whether synthesis or decomposition).
73
define substrates.
biological molecule that the enzyme will work on.
74
define active site.
the highly specific site that the substrate fits inside in an enzyme for the reaction to occur.
75
define catalysis.
the process of when the substrate is changed through catalyzation.
76
What are the 5 enzyme controls, and how do they affect enzyme activity?
mnemonic: PITAS
1. pH: a higher or lower pH than the optimum pH means the substrates will work less efficiently, or be denatured.
2. inhibitors: whether competitive or noncompetitive, inhibitors will reduce the reaction rate of substrates and enzymes. (either blocking the substrate from binding by occupying that space itself or attaching via allosteric site and causing a conformational change)
3. temperature: higher temperature means more kinetic energy. this means substrates will bump and collide more with each other, increasing the chances of them colliding with the enzyme's active site. however, they can be denatured if the temperature gets too high (past the optimum temperature).
4. activators: attach allosterically, then increase the rate of reaction
5. substrate levels: the more substrates, the more likely one of them will collide (note: reaction rate reaches a plateau/constant once all enzymes are occupied/working as fast as they can)
77
how do enzymes help in terms of activation energy? use a graph.
enzymes are catalysts, so they lower the activation energy for reactions to occur (less energy for the reaction to start).
note that this does not change the difference in energy between reactants and products, it just requires less energy for the reaction to happen, making it easier for it to happen.
78
use a graph to explain how temperature affects enzyme activity.
An increase of temperature means more kinetic energy is applied to the enzyme. This allows the enzyme to work more efficiently, resulting in a higher reaction rate.
However, it will eventually reach the optimal temperature, or the temperature that the enzyme catalyzes most efficiently at/highest reaction rate. Any higher temperatures results in a change in the enzyme shape or bonding, meaning it is denatured; it can no longer fit the substrate in the active site/be as efficient.
79
What are peptide bonds? How are they formed? Draw a diagram using generic amino acids (use the R group)
Peptide bond: a covalent bond formed between two amino acids due to a condensation reaction (aka dehydration synthesis)
Diagram requirements: OH on the carboxyl group bonds with one H in amino group to form a water molecule, peptide bond is formed between C of carboxyl and N of amino
80
List the atoms that compose
Carbohydrates
Lipids
Proteins
Nucleic Acids
CLPn: CHO CHO CHON CHONP
Carbohydrates: C H O
Lipids: C H O
Proteins: C H O N
Nucleic Acids: C H O N P
