Unit 1: Biochemistry Flashcards
1
Q
What is biochemistry?
A
Biochemistry is the science that bridges biology and chemistry through the study of the properties, activities and interactions between biologically important molecules. Biochemistry is the chemistry that makes life possible.
2
Q
What are macromolecules and what are they made up of?
A
Macromolecules are larger type molecules that are made up of monomers joined together forming polymers.
3
Q
What are the 4 types of macromolecules?
A
- Proteins
- Carbohydrates
- Lipids (fats)
- Nucleic Acids (DNA and RNA)
4
Q
What are enzymes made up of and what are catalysts?
A
Enzymes are made up of proteins.
Catalysts are enzymes that speed up chemical reactions.
5
Q
How many naturally occurring elements are there and how do the other elements exist?
A
There are 92 naturally occurring elements.
The rest have been synthesized (human/lab made).
It is believed that there are still gaps in the periodic table.
6
Q
What 6 elements are the chemical foundation for the diversity of life?
A
nitrogen, phosphorus, oxygen, sulfur, hydrogen, carbon
7
Q
What elements make up the weight of living things?
A
C, H, O, N make up 96% of the weight of living things
Around 4% is made up by Ca, P, S, K, Na, Cl, Mg
Less than 1% is made up by trace elements including Fe and I
**If there are deficiencies then it is important to take nutrient supplements since deficiencies cause problems
8
Q
What are isotopes?
A
Elements that have the same number of protons and different numbers of neutrons
9
Q
What are radioisotopes? What are they used for?
A
Isotopes that are unstable and decay over time. Doctors use radioisotopes as a diagnostic tool in a technique called radioisotope tracing.
As an example, radioisotopes are used in Positron Emission Tomography (PET) Scans:
In the scan, tumours will appear yellow/orange
Tumorous cells break down the injected radioactive glucose at a faster rate than normal cells do.
PET Scans can be used to detect cancerous tumours
10
Q
What are molecules?
A
Molecules are substances composed of 2 or more atoms COVALENTLY bonded together.
11
Q
What are organic molecules?
A
Organic molecules are most molecules of life that contain carbon and are almost always bonded to each other and hydrogen.
12
Q
What are intramolecular forces?
A
Intramolecular forces are the forces WITHIN molecules that hold atoms together. They involve the chemical bonds that hold 2 atoms togethor.
13
Q
What are 2 examples of intramolecular forces? Explain them.
A
- Ionic Bonds- force of attraction between oppositely charged ions, Occurs between a metal and non-metal and involves the transfer of electrons for atoms to become stable. Metal atoms give up electron(s), giving an electron(s) to a nonmetal atom.
- Covalent Bonds- the electron shells of 2 nonmetal atoms overlap allowing the valence electrons to be shared for the atoms to become stable.
14
Q
What is a polar covalent bond?
A
A covalent bond between 2 non-metals in which the electrons are not shared equally, causing charge imbalances. This is due to one atom having a higher electronegativity and therefore attracting the electrons more.
15
Q
What is electronegativity?
A
The measure of an atoms ability to attract a shared pair of electrons when participating in a covalent bond.
EN 0-0.4= pure/non-polar covalent bond
EN 0.4-1.7= polar covalent bond
EN 1.7-4.0=ionic bond
16
Q
What are non-polar molecules?
A
When the atoms in a covalent bond equally share the electrons. These molecules are symmetrical, have equal charge distributions, and no charge imbalances.
17
Q
What are intermolecular forces?
A
Interactions between atoms from different molecules. They are weaker than intramolecular forces.
18
Q
What are the 3 types of intermolecular forces? (weakest-strongest)
A
- London Forces
- Dipole-Dipole forces
- Hydrogen bonds (special type of dipole-dipole)
19
Q
What are london forces?
A
London forces are the weakest intermolecular force. They exist between all atoms and molecules and are formed by the temporary uneven distribution of electrons.
20
Q
What are dipole-dipole forces?
A
This force involves the attraction between polar molecules when partially positive ends of one molecule are attracted to the partially negative ends of another molecule. Dipole-Dipole forces are stronger than london forces but weaker than hydrogen bonds.
21
Q
What are hydrogen bonds?
A
Hydrogen bonds are the strongest type of intermolecular force. This is a special type of dipole-dipole force that forms between N, O, or F of one molecule and H of another molecule that is attached to N, O, or F. Hydrogen bonds are also present between water molecules.
22
Q
Describe the hydrophobic effect.
A
The hydrophobic effect is the natural clumping of non-polar molecules away from water molecules. This plays a central role in the formation of cell membranes and helps determine the 3D shape of biological molecules including proteins.
23
Q
Describe the importance of ions in biological systems.
A
Ions including Na+, K+, Cl- play important roles in the body.
For example:
H+ ions are critical in biological processes including cellular respiration.
Na+ ions are part of transport mechanisms that enable specific molecules to enter cells.
24
Q
What are hydrophobic molecules?
A
Hydrophobic molecules are “water fearing.” Non-polar molecules are hydrophobic since they do not form hydrogen bonds and do not dissolve in water. They are immiscible and insoluble in water.
25
What are hydrophilic molecules?
Hydrophilic molecules are "water loving" molecules. They are polar molecules that form hydrogen bonds, are miscible and are soluble in water.
26
How much of the body's weight is water?
~60-70% of the human body weight is water.
70% of the brain is water
90% of lungs is water
22% of bone tissue is water
27
Why is water a universal solvent?
Water is a universal solvent because more substances dissolve in water than in any other substance.
28
Describe the density of water and how it affects water.
Ice is a solid that is less dense than its liquid form. Ice is 10% less dense than water since the H-bonds in ice form larger lattice space then they do in water (air pockets in ice). This allows fish and aquatic organisms to survive in water under the ice. The constant breaking and reforming gives water its "fluid" property. Most molecules the same size are gases (H2, O2, CO2, HCl, H2S)
29
Describe cohesion and adhesion.
Cohesion is the fact that water molecules tend to stick together. This is related to surface tension (how hard it is to break the surface of water). This explains why insects are able to walk on water.
Adhesion is the fact that water tends to stick to other polar substances. As an example water can rise up a plants xylem against gravity. This is related to capillary action-involves root pressure (the push) and transpiration (the pull).
30
Describe the specific heat capacity of water.
Due to the strong polarity in water molecules, it takes a lot of heat to separate the intermolecular forces (H-bonds in water, H-bonds are the strongest intermolecular force).
Water has a high boiling point, water is liquid from 0-100 degrees celsius. If there were no hydrogen bonds between water molecules, the boiling point of water would be -86 degrees celsius.
31
Describe solubility of other compounds in water.
Water can dissolve ionic and polar compounds by surrounding and interacting with the ions and molecules forming aqueous solutions. Salts dissolve and dissociate into their ions when in water.
32
What is a molecular formula?
A molecular formula shows the type of atoms and number of atoms of the element/the number of atoms of specific elements in a compound.
33
What is a structural formula?
A structural formula shows how atoms are bonded together. This is a 2D representation of 3D structure.
34
What does the 3D shape of molecules influence? How does this apply to methane (CH4)?
Molecules are 3D and their shape influences their behaviour and function.
As an example, methane (CH4) has a tetrahedral shape because the negatively charged electron pairs in the covalent bonds repel each other and move as far away as possible.
The 4 bonds in methane give methane its tetrahedral shape.
35
What is organic chemistry?
Organic chemistry is the chemistry of life. It is based on carbon's ability to form a variety of structures.
36
What are hydrocarbons?
Hydrocarbons consist of carbon and hydrogen atoms bonded together. They are non-polar, flammable, most are fuels and consist of gases and liquids.
37
What are first class hydrocarbons/alkanes? What are their prefixes?
Alkanes consist of single bonds between C atoms and H atoms.
Suffix for alkanes: -ane
Prefixes:
1 carbon: meth-
2 carbons: eth-
3 carbons: prop-
4 carbons: but-
5 carbons: hept-
6 carbons: hex-
7 carbons: hept-
8 carbons: oct-
9 carbons: non-
10 carbons: dec-
38
What elements do organic compounds consist of?
In organic molecules, carbon atoms form 4 bonds mostly with hydrogen atoms or other carbon atoms.
Sometimes the carbon atoms bond to O, N, S
or to halogens F, Cl, Br
39
Describe the properties of carbon.
Carbon is the backbone of biochemistry. Carbon atoms bonded with hydrogen atoms form hydrocarbons. Hydrocarbons are non-polar.
Carbon has 4 valence electrons, allowing for 4 covalent bonds.
These bonds can branch in a variety of directions: rings, branches, triple bonds
Only single, double or triple bonds.
In organic molecules, carbon bonds to H, N, O, S, P
40
What are isomers?
Isomers are when compounds have the same chemical formula but different 3D structures and properties. This is due to variation in carbon skeleton.
An example is C4H10 (Butane and Isobutane)
41
What is the importance of functional groups?
Functional groups contribute to molecular diversity by giving a molecule unique properties.
42
What are saturated hydrocarbons?
Saturated hydrocarbons are stable and unreactive. They are the backbone of C atoms bonded to H atoms. They consist of single covalent bonds allowing for the maximum number of H atoms possible.
43
What is the hydroxyl functional group?
In the hydroxyl group, a hydrogen atom from the saturated hydrocarbon is replaced by -OH.
This functional group is polar and can form hydrogen bonds.
It is found in carbohydrates and alcohols.
44
What is the carbonyl functional group?
In the carbonyl group, an oxygen atom is double bonded to a carbon atom. This group is found in lipids and sugars. This functional group is polar.
45
What is the difference between a ketone and an aldehyde? What functional group are ketones and aldehydes found in?
Ketones and Aldehydes are part of the carbonyl group.
A ketone is when the double bonded oxygen is attached to an inner carbon.
An aldehyde is when the double bonded oxygen is attached to an outer/terminal carbon atom.
46
What type of isomer are ketones and aldehydes an example of?
Ketones and aldehydes are structural isomers. This means they have the same chemical formula but different bonding.
47
What is the carboxyl functional group?
The carboxyl group contains -COOH. It is polar and found in proteins and amino acids. This group is also known as carboxylic acids or organic acids. This functional group can also be found in cells in its ionized form called the carboxylate ion or acetate ion with a 1- charge.
48
Why does the carboxyl group have acidic properties?
The carboxyl group has acidic properties because the covalent bonds between oxygen and hydrogen is so polar. As an example, this group is found in acetic acid which is what gives vinegar its sour taste.
49
What is the amino functional group?
The amino group contains -NH2. It is polar and can be found in proteins and amino acids. The amino group acts as a base meaning it can pick up H+ ions from its surrounding solution. It is ionized with a 1+ charge under cellular conditions.
50
What is the phosphate functional group?
The phosphate group consists of 4 oxygens bonded to a phosphorous atom. This group is also known as organic phosphorous and can be found in DNA and ATP. It is polar and negatively charged. It contributes negative charge to the molecule it is a part of. When it is at the end of a molecule, it contributes a charge of 2- and if it is located internally/in the middle of a molecule it contributes a charge of 1-. Additionally, the phosphate group has potential to react with water and thus, releasing energy.
51
Identify the functional group glycerol phosphate is a part of and describe its importance.
Glycerol phosphate is part of the phosphate functional group. Glycerol phosphate takes part in important chemical reactions in cells and provides a backbone for phospholipids. Phospholipids are the most prevalent molecules in cell membranes.
52
What is the sulfhydryl functional group?
The sulfhydryl functional group consists of a sulfur atom bonded to a hydrogen. The sulfur atoms also has 2 lone pairs. This functional group is slightly polar and can be found in proteins.
53
What is the amino acid functional group?
Amino acids consist of the amino group + the carboxyl group + the R group. The general molecular formula of amino acids is: NH2CHRCOOH
54
What are macromolecules and what do they consist of?
Macromolecules are large molecules that consist of polymers which are made from identical repeating subunits called monomers.
55
What is the process in which monomers make polymers?
Monomers make polymers through the process of POLYMERIZATION.
56
What elements do organic compounds contain?
C, H, O, N, S, P
57
What are carbohydrates? Why are they important?
Carbohydrates consist of C, H, O and they are polymers of simple sugars (monosaccharides). Carbohydrates provide short-term energy, they are the sole fuel for the brain. The brain lacks fuel storage and continuously uses fuel for energy, hence it is important to include carbohydrates in diet to ensure fuelling the brain. The carbohydrate the brain uses for energy is glucose. Glucose enters the brain through the blood brain barrier (BBB).
58
What are monosaccharides?
Monosaccharides are simple sugars, consist of one sugar. They are water soluble and therefore polar and hydrophilic, sweet tasting and require no digestion in order to be absorbed in the body since the intestine can absorb simple sugars directly.
59
What functional groups are present in sugar?
Sugar has a carbonyl group (C=O) and multiple hydroxyl groups (-OH).
60
What is the general chemical formula of monosaccharides?
(CH2O)n
where n= # of carbon atoms
61
What are the 3 common simple sugars and where are they found?
Glucose- primary source of energy for cells
Galactose- found in milk
Fructose- found in fruit
62
What are the 3 most common monosaccharides? Give examples of each.
TRIOSE (3 carbons)- ex: glyceraldehyde
PENTOSE (5 carbons)- ex: ribose (in RNA) and deoxyribose (in DNA)
HEXOSE (6 carbons)- ex: glucose, fructose, galactose
63
Explain why glucose, fructose and galactose are isomers?
Glucose, fructose, and galactose all have the same molecular formula (C6H12O6). However, they have differing characteristics and structures.
64
What are structural isomers?
Same chemical formula, different bond.
ex: glucose and fructose
65
What are stereoisomers?
Same chemical formula, "same" bonding, different arrangement.
ex: glucose and galactose
66
What are geometric isomers?
Same chemical formula, similar chemical properties, different physical properties. Can't get the isomer by rotating the molecule.
67
What are the 2 types of geometric isomers? Explain them.
Trans:
the atoms of the same element go across both sides of double bond.
Cis:
atoms of the same element are on the same side of the double bond.
68
What are the 2 major groups of sugars formed as a result of ketones and aldehydes?
Ketoses- contain a ketone
Aldoses- contain an aldehyde
69
Explain how glucose, fructose and galactose are structural isomers.
Glucose vs Fructose: glucose is an aldehyde (C=O on carbon 1), fructose is a ketone (C=O on carbon 2)
Glucose vs Galactose:
glucose- carbon 4: H-C-OH
galactose- carbon 4: HO-C-H
Glucose vs Fructose vs Galactose
glucose: hexose, 6 ring
fructose: pentose, 5 ring
galactose: hexose, 6 ring
70
What is the structure of sugars in the body and why?
~3% of sugars exist in linear form
~97% exist in ring structure form
The rings form because they are more energy efficient for the body.
Ring structures consist of only single bonds. Ring structure forms when carbonyl interacts with hydroxyl.
71
What are the 2 forms of glucose? Explain the difference between them.
1. Alpha Glucose: -OH is pointing down, alpha glucose is found in starches and can be easily digested by humans
2. Beta Glucose: -OH is pointing up, beta glucose is found in cellulose and is indigestible for humans.
72
What are disaccharides?
Disaccharides are a type of simple sugar composed of 2 monosaccharides joined together. Disaccharides must be digested and broken down in order to be used by the body.
73
What is hydrolysis involving monosaccharides and disaccharides?
Hydrolysis is when disaccharides are broken down by adding water to produce monosaccharides.
74
What is a condensation reaction involving monosaccharides and disaccharides?
A condensation reaction occurs when 2 monosaccharides are joined together, forming a disaccharide as well as releasing water.
75
What are the 3 main examples of disaccharides?
1. Maltose
2. Lactose
3. Sucrose
76
What monosaccharides make up maltose? And where is maltose found in?
Maltose = α glucose + α glucose
**maltose has α linkage
Maltose is found in barley, beer, malt vinegar
77
What monosaccharides make up lactose? And where is lactose found in?
Lactose= β glucose + galactose
***lactose has β linkage
Lactose is found in milk
**the enzyme that breaks down lactose is called lactase
78
What monosaccharides make up sucrose? And where is sucrose found in?
Sucrose= α glucose + fructose
** sucrose has α linkage
Sucrose is found in table sugar
79
What a glycosidic bond?
A glycosidic bond is the linkage between 2 monosaccharides.
80
What are polysaccharides?
Polysaccharides are made from 3 or more monosaccharides and usually consist of 1000s of glucose monomers linked together. Polysaccharides are complex carbs and must be broken down in order to be used. They are usually stored or some are used for structural support.
81
What are 3 common polysaccharides?
1. Glycogen
2. Starch
3. Cellulose
82
Describe glycogen.
Glycogen is a polysaccharide that consists of α glucose. It is used for short term animal energy storage. Its general structure consists of many branches meaning it is fast to break down.
83
Describe starch.
Starch is a polysaccharide that consists of α glucose. It is used for short term plant energy storage and it can be digested by humans. Its general structure consists of fewer branches meaning it is slower to break down.
84
Describe cellulose.
Cellulose is a polysaccharide that consists of β glucose. It is used for plants structural support. Humans cannot digest cellulose however, cellulose is important in health diet since it is an INSOLUBLE FIBRE. Cellulose is also the most abundant organic molecule on earth. Its general structure consists of long, straight chains of hydrogen bonded to each other.
85
What are lipids?
Lipids (fats) are macromolecules that are not "true" polymers since they do not have repeating subunits. They consist of C, H, and O atoms but have less oxygen and more hydrogen than carbohydrates. They are mostly composed of C and H. Due to the long hydrocarbon chains (which are non-polar) lipids are insoluble in water making them hydrophobic.
86
What are the 4 main types of lipids?
1. Triglycerides (aka fats and oils)
2. Phospholipids
3. Steroids
4. Waxes
87
Describe fats and oils (triglycerides).
Fats and oils are most commonly known as triglycerides. They provide long term energy storage, help protect the internal organs, and insulate the body. They are composed of 1 glycerol molecule and 3 fatty acid molecules. The fatty acid molecules are usually 16-18 carbon atoms long with a -COOH (carboxyl) functional group on one end. The 3 fatty acid molecules are usually different from one another.
88
Describe the solubility of triglycerides.
Triglycerides are composed of long carbon chains. As the carbon chain increases, they become more non-polar and less water soluble. This is because triglycerides contain hydrocarbons which are non-polar. The more hydrocarbons the molecule consists of, the more non-polar the molecule is.
89
Describe fatty acids.
Fatty acids are the structural backbone of most lipids. There are two types of fatty acids; saturated and unsaturated fatty acids.
90
Describe saturated fatty acids.
Saturated fatty acids are linear molecules that have only single bonds between all the carbon atoms. This bonding allows for the maximum number of hydrogen atoms possible. Saturated fatty acids are found in butter, animal fats and lard and they are SOLID at room temperature. Since they are linear, they can stack on top of each other due to stronger intermolecular forces/stronger london forces. Saturated fatty acids are bad for health as they can form atherosclerosis which causes fatty plaques on the blood vessel walls which can lead to coronary heart disease and heart attack.
91
Describe unsaturated fatty acids.
Unsaturated fatty acids contain one or more double bond between carbon atoms. They are healthier fats and can be found in plant and fish oils (ex: canola oil, corn oil, olive oil, cod liver oil). Unsaturated fatty acids are liquid at room temperature and most have "cis" double bonds (H atoms are on same side of double bond. The "cis" double bonds cause a kink/bend in the molecule. This prevents the fats from packing together since there are weaker intermolecular forces/weaker london forces.
92
Describe the formation of a triglyceride.
3 fatty acids bond to one glycerol molecule in a series of reactions. They are bonded together by an ESTER LINKAGE. In this process, a condensation or dehydration reaction occurs which releases 3 water molecules.
93
Differentiate between polyunsaturated and monounsaturated fatty acids.
Polyunsaturated fatty acids have 2 or more double bonds between carbon atoms meaning they have 2 or more kinks.
Monounsaturated fatty acids have 1 double bond between carbon atoms meaning they have only one kink.
94
What does "hydrogenated vegetable oils" mean on food labels?
Trans fats act like saturated fats due to "trans" double bonds. Trans fats are linear, can be solid, and are partially hydrogenated which is not naturally occurring. This is because unsaturated fats have been synthesized and converted into saturated fats by adding hydrogens. This is done with peanut butter and margarine. Trans fats are bad for health, can cause atherosclerosis which causes plaque buildup on blood vessel walls which can lead to heart attack or coronary heart disease.
95
Describe the structure of phospholipids.
Phospholipids are an essential part of cell membranes. They are composed of a glycerol and 2 fatty acids (the fatty acids are non-polar). There is no third fatty acid chain since it is replaced with a phosphate group that has negative charge and is polar. This region can attach to small polar substances and other charged substances.
The phospholipid head is hydrophilic and faces the aqueous environment that is either outside/inside the cell.
The phospholipid tail consists of the fatty acids. The tail is hydrophobic.
Phospholipids have 2 layers which are called the phospholipid bilayers.
96
Describe the hydrophobic effect with the phospholipid bilayer.
The phospholipid bilayer consists of the fatty acid tails and the polar head. The polar heads of phospholipids are hydrophilic and face the aqueous environments. Oppositely, the fatty acid tails are non-polar and therefore insoluble and hydrophobic. Thus, the tails clump together/away from the water molecules.
97
What is extracellular fluid (ECF)?
ECF is fluid found outside of a cell
98
Describe the structure of steroids. What are some examples of steroids?
Steroids are hydrophobic molecules that are composed of 4 carbon rings that are linked together. Different steroids are distinguished by the functional groups that are attached to them. Examples of steroids include cholesterol, testosterone , estrogen and adrenal hormones.
99
Describe cholesterol.
Cholesterol is a steroid. It is made in the liver but can also be obtained through diet. It is a common component of cell membranes in animals that maintains fluidity of membrane (allows easy/smooth flow). Cholesterol is the precursor to sex hormones (testosterone in males and estrogen in females).
100
Describe waxes.
Waxes are composed of long fatty acid chains that are attached to alcohol or carbon rings. They are hydrophobic and used as waterproof protection on plants/animals.
101
Describe proteins.
Proteins make up 50% of the dry mass of most cells. There are over 10,000 proteins in the body that have vital structural and functional roles. Each protein has a unique 3D shape All proteins are polymers, the monomers of proteins are amino acids, there are 20 different amino acids. Proteins can be found in spider webs, egg whites, antibodies, hair, hormones, hemoglobin, enzymes.
102
Describe the structure of amino acids.
Amino acids are the monomers of proteins. There are 20 amino acids, each amino acid contains C, H, O, N. Each amino acid is made up of a central carbon atom, connected to a hydrogen atom, a carboxyl group, an amino group and a side chain/R-group. The R-group is different for each of the 20 amino acids and it gives the amino acid its characteristics. The R-group can be polar, non-polar, or charged (+ or -).
103
What is a zwitterion? How is this applicable to the proteins/amino acids?
A zwitterion contains a positive and negative charge on the amino acid.
When the amino acid is in solution or in the cell, the carboxyl group (-COOH) loses an H and the amino group gains an H. This causes the amino and carboxyl group to be in their charged form.
104
Differentiate between the essential and non-essential amino acids.
There are 20 amino acids in humans. 11 amino acids are non-essential and are synthesized by the body. 9 amino acids are essential meaning that they are not secreted by the body and must be obtained through our diets. The essential amino acids can be found in nuts, seeds, quinoa, and spirulina.
105
Describe what protein synthesis is.
Protein synthesis is the process of making proteins into polymers called POLYPEPTIDES. In this process, cells make proteins by joining amino acids together. The amino acids are held together by peptide bonds. When there are 2 amino acids joined together, it is called a dipeptide and when there are more than 2 amino acids joined together, it is called a polypeptide. Cells make many different proteins with combinations of the 20 amino acids.
106
What determines the chemical nature of the protein molecule? What determines the function of a protein?
The chemical nature of the final protein molecule is determined by the kind of R-groups/side chains and their sequence. The protein's shape determines its function.
107
What are the 4 levels of protein structure?
1. Primary Structure
2. Secondary Structure
3. Tertiary Structure
4. Quaternary Structure
108
What is primary protein structure?
The primary structure is the linear sequence of amino acids, there are limitless combinations of the primary structure of proteins.
The side chains and types of bonds will determine the proteins secondary/tertiary structures.
109
What is secondary protein structure and what are the two types of secondary protein structure subunits?
The secondary structure is a coiled/folded pattern that results from H-bonding between the amino and carboxyl groups on the repeating polypeptide "backbone" of the protein.
The 2 types of secondary structure are:
1. α-helix: this is the coiling pattern created by H-bonding between every 4th amino acid within a strand. In this pattern, the amino acids are close together. An example of this can be seen with the keratin protein in hair.
2. β-pleating (sheets): this is the folding pattern created when H-bonds form between 2 parts of a polypeptide chain layered on each other. These amino acids are far apart. β-pleating is seen in collagen and in silk.
Different sections of amino acid polypeptides can have α-helix and β-pleating patterns.
110
What is tertiary protein structure? Describe what a disulphide bridge is.
Tertiary protein structure is within the same polypeptide and creates the overall 3D shape of the protein that is stabilized by R-group interactions. A range of bonding occurs between R-groups in amino acids including, H-bonds, ionic bonds, covalent bonds, hydrophobic and nonpolar interactions. These interactions create folds in the protein chains.
A disulphide bridge is a covalent bond between 2 cysteine amino acid R-groups. (-SH + -SH forms a -SS- bond)
111
What is quaternary protein structure? Explain how this applies to hemoglobin.
In quaternary protein structure, 2 or more large polypeptides interact to create the final shape of the protein. The final shape of the protein then gives the protein its function. The same forces are at play as in the tertiary structure (H-bonds, ionic bonds, covalent bonds, hydrophobic and nonpolar interactions).
As an example, hemoglobin is the oxygen binding protein of red blood cells. It contains 4 polypeptide subunits that each contain a "heme" that contains an iron atom that binds with oxygen.
112
What is denaturation? What are causes of it as well as real life examples?
The protein 3D biological function depends on the physical and chemical conditions of the environment. Denaturation occurs when proteins lose their shape or the peptide bonds break. This causes proteins to "unwind" and lose their biological activity.
Causes of denaturation include; acidity and basicity, high temperatures, salty environments and the transfer from aqueous to non-aqueous environments.
Denaturation occurs during cooking, curing meat, and curling hair.
113
What are the monomers of nucleic acids?
Nucleotides
114
What are the 2 types of nucleic acids?
1. DNA - deoxyribonucleic acid
2. RNA - ribonucleic acid
115
What are the 3 parts of a nucleotide?
1. Phosphate group
2. Pentose Sugar: 5-Carbon Sugar (RNA-ribose sugar, DNA- deoxyribose sugar)
3. Nitrogenous Bases (DNA: adenine, thymine, cytosine, guanine. RNA: adenine, uracil, thymine, cytosine)
116
What is the difference between purines and pyrimidines? Give examples and explain their bonding.
Purines are nitrogenous bases with 2 rings. Adenine and guanine are purines.
Pyrimidines are nitrogenous bases with 1 ring. Cytosine, thymine and uracil are pyrimidines.
Purines bond to pyrimidines so that there is an equal width across the whole DNA double helix (3 rings across each bond).
117
Explain the anti-parallel structure of the DNA double stranded helix.
DNA is composed of 2 strands. Each strand has 2 ends, a 5' end and a 3' end. On the 5' end the phosphate group is bonded to carbon 5. On the 3' end the hydroxyl group is bonded to carbon 3. DNA is antiparallel because one strand of DNA runs from 5' to 3' and the other strand runs from 3' to 5'.
118
What is the difference between DNA and RNA.
The difference between DNA and RNA is seen on carbon 2. In RNA an -OH (hydroxyl group) is attached to carbon 2. In DNA a hydrogen is attached to carbon 2.
**"deoxy"=lacking oxygen
119
What is the difference with the structure of DNA and RNA.
DNA is double a double stranded helix and has hydrogen bonding that occurs between complementary base pairs found on opposite strands. RNA is single stranded and therefore has no complementary base pairing. RNA is linear.
120
What are the complementary base pairs in DNA?
Adenine bonds with thymine with 2 hydrogen bonds. Guanine bonds with cytosine with 3 hydrogen bonds.
121
What are the 4 main types of chemical reactions that biological molecules undergo in the cell?
neutralization (acid/base)
oxidation-reduction (aka redox reaction)
condensation or dehydration reaction
hydrolysis
122
How are the macromolecules assembled?
The macromolecules are assembled by hydrolysis and condensation/dehydration reactions.
123
What is a dehydration reaction?
A dehydration reaction combines smaller molecules into a larger molecule and water is lost in the process. An H atom is lost from one monomer and combined with the OH from the other monomer, creating water.
124
What is a hydrolysis reaction?
In a hydrolysis reaction, water is added to separate a polymer into its monomers. A larger molecule is broken down into smaller molecules with the addition of water. An example of this is seen with digestion.
125
Differentiate between catabolic and anabolic reactions.
Catabolic reactions break down larger molecules into smaller molecules and usually release energy. They are known as exothermic reactions.
Anabolic reactions combine simple molecules into larger molecules and usually store energy. They are known as endothermic reactions.
126
What are enzymes?
Enzymes are biological catalysts that are used to speed up reactions in the body. Enzymes function as catalysts without being consumed and without changing the products of the reaction. They are built from amino acids and the tertiary and quaternary protein structures.
127
What is activation energy?
Activation energy is the energy required to begin any chemical reaction. The larger activation energy required, the slower the reaction will take place.
128
Describe the role of catalysts.
Catalysts are substances that speed up chemical reactions by lowering the activation energy of reactions. Cells manufacture specific proteins called enzymes to act as catalysts and increase the rate of reactions. Almost all chemical reactions in organisms are facilitated by enzymes. Each enzyme is specific to each chemical reaction it catalyzes (enzyme specificity).
129
Describe the structure of enzymes and the formation of the enzyme-substrate complex.
Enzymes have globular shapes or indentations on their surfaces known as active sites. The active sites interact with the reactant called a substrate. Specific substrates interact with specific enzymes because enzymes are substrate specific. The active site of the enzyme and the substrate form an enzyme-substrate complex. When the substrate binds to the active site, H-bonds form between the substrate and the active site which cause a slight change in the enzyme shape to occur in order to accomodate for the substrate, this change is called an induced fit.
130
How do enzymes prepare substrates for reaction?
An enzyme prepares substrates for reaction by changing the substrate, its environment, or both and thus, lowering the activation energy of the reaction. Once the reaction has taken place, the products of the reaction are released from the enzyme and the enzyme is able to accept another substrate.
131
Describe the catalytic/enzyme cycle. (4 main steps)
1. An enzyme is available with an empty active site.
2. A substrate binds to the active site of the enzyme with induced fit creating an enzyme-substrate complex.
3. The substrate is converted into the products of the reaction.
4. The products are released from the active site and the enzyme can be reused.
132
What are coenzymes and cofactors?
In some cases additional molecules or ions are required to catalyse a reaction. These include cofactors and coenzymes being required to catalyse a reaction.
Coenzymes are organic molecules derived from water-soluble vitamins.
Cofactors are metal ions and non-protein groups. This includes minerals such as zinc, copper, magnesium, manganese, iron.
As a result, various vitamins and minerals are essential towards enzyme activity and without them cells would not be able to catalyse certain reactions.
133
Describe how surrounding conditions affect enzyme activity.
Enzyme activity is affected by any change in conditions that affects the 3D shape of the enzyme, this includes temperature, pH and substrate concentration. Additionally, the formation of an enzyme-substrate complex will take longer if there are fewer substrates present since the enzyme and substrates will encounter each other less frequently. Enzymes work best at optimal pH and temperatures. For example:
- Trypsin- helps break down proteins in small intestine works best at a temp of around 40 degrees celsius and a pH of between 6-8
- Pepsin- breaks down proteins in the stomach, stomach is an acidic environment, therefore the optimum pH for pepsin is around 2.
134
Describe the process of feedback inhibition.
Many biochemical reactions are grouped and regulated in a process called feedback inhibition. The product of the last reaction of a pathway is a noncompetitive inhibitor of the enzyme that catalyzes a reaction at the beginning of the pathway. This process signals that there is enough of a product and prevents overproduction of the product in the body.
135
What are the two types of inhibition that regulate enzyme activity? How does inhibition affect the rate of a reaction?
1. Competitive Inhibition
2. Noncompetitive Inhibition
Inhibition slows down the rate of the reaction in order to prevent the overproduction of a product.
136
Describe competitive inhibition.
In competitive inhibition a molecule called an inhibitor competes for the enzymes active site. The inhibitor binds to the active site, preventing the substrate from binding to the active site which prevents/slows down the reaction from occuring.
137
Describe noncompetitive inhibition/allosteric regulation (inhibition).
In noncompetitive inhibition an inhibitor binds to the allosteric site of an enzyme and changes the shape active site which means that due to the changed shape, the active site will no longer accept substrates.
Noncompetitive inhibition is either reversible or irreversible.
Reversible- ex: antibiotics such as penicillin
Irreversible- ex: toxins such as cyanide - irreversible noncompetitive inhibition can cause death
138
Describe enzyme activators/allosteric regulation (activators).
Molecules called activators bind to the allosteric site of an enzyme and increase the enzyme's activity. This increases the active site's affinity to the substrate causing the inactive enzyme to become active. The activator changes the shape of the inactive protein in order to allow for the ligand to bind to the protein. This causes the inactive protein to become active. The purpose of enzyme activators is to speed up the rate of chemical reactions.
139
Describe the fluid mosaic model of the cell membrane.
The cell membrane is made from several molecules that create a fluid mosaic model. It is fluid since the molecules are able to move freely around each other and it is described as a mosaic since the molecules are randomly located throughout the membrane.
The fluid mosaic model features a semi-fluid phospholipid bilayer with a mosaic of proteins, the proteins have non-polar segments that are in contact with the non-polar interior of the bilayer. There are other proteins and molecule that float in or on the bilayer. The 2 layers (leaflets) of the bilayer can slide across each other and individual phospholipids exchange places frequently.
140
What is the function of the cell membrane?
The cell membrane controls the entry and exit of substances in and out of the cell. Since it is semi permeable, it only allows some substances to enter the cell.
141
What affects the fluidity of the phospholipid bilayer?
The degree of fluidity of the phospholipid bilayer is crucial towards the proper functioning of the cell. The fluidity is affected by:
1. TEMPERATURE: if the temp. is too high the bilayer becomes too fluid and pourous, if the temp. is too low the bilayer solidifies becoming a barrier
2. PRESENCE OF DOUBLE BONDS IN FATTY ACID TAILS: more double bonds in fatty acids cause more kinks and bends in the fatty acids. This causes phospholipids to be less tightly packed and more fluid.
3. LENGTH OF FATTY ACID TAIL: the longer the fatty acid tail, the stronger the intermolecular forces holding the fatty acids. This causes the phospholipids to be more packed and less fluid.
4. PRESENCE OF CHOLESTEROL: at room temp. cholesterol molecules reduce fluidity, at lower temps. cholesterol helps keep the bilayer from solidifying.
142
What 4 different molecules make up the cell membrane?
1. Lipids
2. Proteins
3. Cholesterol
4. Glycoproteins and glycolipids
143
How do lipids affect the cell membrane?
Lipids form a phospholipid bilayer creating the phospholipid bilayer. This consists of 2 rows of phospholipids being packed together. The hydrophobic fatty acid tails face inwards/clump together and hydrophilic heads face outwards (involves hydrophobic effect).
144
How do proteins affect the cell membrane and what are the 2 types of proteins?
Proteins float freely throughout the membrane and help stabilize the membrane and link it to the cytoskeleton of the cell. The two types of proteins are:
1. INTEGRAL PROTEINS- the proteins span across the entire membrane, they are embedded proteins.
2. PERIPHERAL PROTEINS- the proteins do not span the entire membrane, they are looser and more temporary and stick out on one side only.
145
What are the functions of the peripheral and integral proteins? (5 functions)
1.Transport
2.Enzymes
3.Chemical signalling
4. Cell recognition
5.Support and intercellular joining
146
Functions of proteins - TRANSPORT
Integral proteins can provide channels for specific chemicals to pass into or out of the cell.
147
Functions of proteins - ENZYMES
Proteins act as catalysts for chemical reactions involving the cell.
148
Functions of proteins - CHEMICAL SIGNALLING
Some chemicals (hormones) can bind to the proteins of the membrane signalling the cell to perform a specific task.
149
Functions of proteins - SUPPORT AND INTERCELLULAR JOINING
Proteins connect to the cytoskeleton inside the cell to help provide shape and support to the cell.
Proteins from one cell can interact with proteins from the adjoining cell binding or holding them together.
150
Functions of proteins - CELL RECOGNITION
Carbohydrate chains from glycoproteins allow cells to recognize each other. This allows cells to identify intruders (ex- disease-causing bacteria)
151
How does cholesterol affect the cell membrane?
Cholesterol maintains the fluidity of the cell membrane.
152
How do glycoproteins and glycolipids affect the cell membrane?
Glycoproteins and glycolipids are sugar molecules attached to proteins or lipids in the cell membrane. They are used for cell recognition and communication (ex- immune responses). They connect to other cells to form tissues and maintain stability.
153
What are the 3 types of passive transport?
1. Simple diffusion
2. Facilitated diffusion
3. Osmosis
154
What is passive transport?
Passive transport is the movement of substances across the cell membrane down their concentration gradient without the use of energy (ATP).
155
What factors affect the rate of diffusion?
The rate of diffusion is affected by:
- molecule size
- molecule polarity
- molecule or ion charge
- temperature and pressure - an increase in temp and pressure causes an increase in the rate of diffusion.
156
Describe simple diffusion.
The movement of substances through a cell membrane down their concentration gradients. Net movement proceeds until equilibrium is achieved.
157
Describe facilitated diffusion.
Facilitated diffusion involves the movement of large and charged molecules/ions through a cell membrane down the concentration gradient moving through protein channels in the membrane. These molecules cannot pass through the cell membrane unassisted and are helped through channel or carrier proteins.
158
Describe channel and carrier proteins/their functions.
Channel and carrier proteins are integral proteins that assist with transporting molecules through a cell membrane in facilitated diffusion.
CHANNEL PROTEINS are highly specific, hollow cylinders. Their shape/structure determines what molecules can pass through them. They transport specific ions or polar molecules and are voltage gated.
CARRIER PROTEINS bind to specific molecules, carry them across the membrane and then release them. Carrier proteins are very specific, specific proteins transport specific molecules. Carrier proteins transport larger molecules such as amino acids and glucose.
159
Describe osmosis.
Osmosis is a type of diffusion that involves the movement of water molecules in and out of the cell. Water molecules move down the concentration gradient to balance the concentration of other solutes across the membrane.
160
What is tonicity and what are the 3 possible tonicities of osmosis?
Tonicity refers to the situation that results in osmosis with the movement of water molecules in/out of the cell.
3 possible situations result:
1. ISOTONIC SOLUTION - equal concentration of solutes outside and inside the cell
2. HYPERTONIC SOLUTION - higher concentration of solutes outside the cell vs inside the cell
3. HYPOTONIC SOLUTION - lower concentration of solutes outside the cell vs inside the cell
161
What is active transport?
Active transport involves the movement of a substance through a membrane against the concentration gradient (from low-high concentrations). This type of transport requires energy in the form of ATP.
The hydrolysis of the end of a phosphate group from an ATP molecule releases energy. The direct use of this energy is primary active transport, the indirect use of this energy is secondary active transport.
162
Describe how primary active transport works.
In primary active transport, carrier proteins act as ion pumps directly using ATP energy to pump ions from one side of the membrane to the other.
Example: Sodium-Potassium Pump
163
Describe how secondary active transport works.
In secondary active transport, ATP is used indirectly to move molecules across the cell membrane. In primary active transport, when ion pumps actively move ions across the membrane against the concentration gradient, a charge builds up on one side of the membrane. This charge alone with the electric potential of the membrane creates an electrochemical gradient. In secondary active transport the electrochemical gradient is used to transport molecules or ions.
Example: Hydrogen/Sucrose Symporter
164
Passive transport and protein pumps cannot transport large particles or large amounts of smaller particles through the cell membrane. How do these types of molecules get transported across the cell membrane?
Large particles and large amounts of particles are transported across membranes with bulk transport using vesicles. This is known as membrane-assisted transport. In membrane-assisted transport the cell forms vesicles to surround incoming or outgoing material to transport large large macromolecules, this requires energy (ATP) input.
165
What are the 2 functions of Membrane-Assisted Transport?
1. Endocytosis - to move materials into the cell. Endocytosis involves the cell membrane folding in and pinching off to bring materials into the cell.
2. Exocytosis - to move materials out of the cell.
In exocytosis large molecules and waste leave the cell through vesicles which become part of the cell membrane
166
What are the 3 types of endocytosis?
1. Phagocytosis
2. Pinocytosis
3. Receptor-Mediated Endocytosis
167
Describe phagocytosis.
In phagocytosis, the cell engulfs a large particle along with some of the liquid surrounding it. This type of endocytosis is known as "cell eating."
This is seen with dead cell parts, viruses and foreign particles.
168
Describe pinocytosis
In pinocytosis, the cell engulfs a liquid and the small particles dissolved and suspended in the liquid. This type of endocytosis is described as "cell drinking"
169
Describe Receptor-Mediated Endocytosis
In receptor-mediated endocytosis, receptor proteins in cell membranes bind to specific molecules outside of the cell. The cell membrane folds inwards to create a vesicle containing the bound particles. These vesicles are coated with a protein called clathrin which forms a cage around the vesicle. The coated vesicle may fuse with a lysosome and enzymes can break it down.
170
Describe how exocytosis is used in animal cells
In animal cells exocytosis provides a mechanism to secrete hormones, digestive enzymes and neurotransmitters
171
Describe how exocytosis is used in plant cells
In plant cells exocytosis is a way to excrete the materials necessary to construct the cell wall.
172
What are the different types of active transport?
- Primary Active Transport
- Secondary Active Transport
- Bulk Transport Using Vesicles/Membrane Assisted Transport: Endocytosis (phagocytosis, pinocytosis, receptor-mediated endocytosis) and exocytosis
173
What is an ether bond/when does it form?
Ether bonds form when 2 alcools combine together, common in carbohydrates since there are a lot of hydroxyl groups).
Ether linkage: COC
174
What is an ester bond/when does it form?
Ester bonds form when alcohols and carboxylic acids combine. They are common in lipids.
Ester linkage: OCO
175
What is a phosphate ester/when does it form?
Phosphate esters/phosphoesters form when an alcohol reacts with phosphoric acid. They are common in nucleic acids and are present in one of the most important reactions in biology due to being present in the sugar phosphate backbone.
Phosphate Ester: OPO
176
What are peptide linkages/when do they form?
Peptide linkages form between amino acids in proteins. Proteins are formed from long chains of amino acids joined together by peptide linkages. A peptide linkage forms when an amino end of one amino acid joins to carboxyl end of other amino acid.
Peptide linkage consists of C, O, H, N
