Chapter 1 Flashcards
1
Q
An element is
A
a pure substance that cannot be broken down into simpler substances using ordinary chemical or physical techniques
2
Q
the smallest particle of an element is an _________. Elements differ from one another in their ________ __________
A
atom, atomic structure
3
Q
Atoms bind together in fixed numbers and ratios to form _____________
A
molecules
4
Q
A chemical compound is
A
a stable combination of different elements that are held together by chemical bonds
5
Q
what are organic compounds?
A
compounds that contain carbon & hydrogen bonds (akhtar & google!
6
Q
organic compounds in living organism are primarily composed of
A
carbon, hydrogen, and oxygen. they often include nitrogen as well
7
Q
about ___ elements made up living organisms
A
25
8
Q
what elements make up 96% of the weight of living organisms?
A
Carbon, Hydrogen, Oxygen, Nitrogen
9
Q
Most of the remaining 4% of the weight of living organisms is made up of only 7 other elements:
A
Calcium, Phosphorus, Potassium, Sulfur, Sodium, Chlorine, & Magnesium
- these elements often occur as ions or in inorganic compounds in organisms
(Polly Poppy Came Surfing. Super Cool & Majestic)
10
Q
Trace Elements
A
the remaining of the 25 elements are found in such small amounts (<1%), they are called trace elements
- Ex. Iodine & Iron (Fe)
- deficiency in any trace elements=health problems
11
Q
atoms are
A
the smallest units that can retain the chemical and physical properties of a particular element
- rmr atoms don’t have a charge, ions do
12
Q
electrons are not included in the mass number cuz
A
their mass is negligible compared to the mass of protons and neutrons
13
Q
Isotopes
A
are different forms of the same element, with different atomic masses
- since they have the same # of p+ & e-, the behave the same in a chemical reaction
14
Q
a radioisotope is
A
a radioactive isotope of an element
-they generally behave the same way in cells as non-radioactive isotopes
15
Q
Radioactivity
A
the nuclei of some isotopes or an element are unstable and tend to break down (decay), giving off matter that can be detected as radioactivity
- the radiation from isotopes may damage living cell molecules
GOOGLE: the release of energy from the decay of the nuclei of certain kinds of atoms and isotopes.
16
Q
Carbon-12 accounts for __% of all carbon in nature
A
99
17
Q
Radioactive Decay of Carbon-14
A
C-14 is an unstable isotope of carbon.
- it decays, giving off particles & energy.
- as it decays, 1 neutron splits into a high-energy electron & a proton. –> it then has 7 neutrons & 7 electrons & protons.
- this is characteristic of the most common form of nitrogen.
- the decay of C-14 transforms carbon atom into nitrogen atom
18
Q
the rate of decay of a radioactive isotope is _______________ of chemical reactions or environmental conditions
A
independent
19
Q
Radioactive decay occurs at a _________ _______, with a constant proportion of radioactive breakdown during a given interval of time
A
steady rate
20
Q
Radioactive tracers
A
are radioisotopes that are used to follow a specific chemical through a chemical reaction
- used because radioactive isotopes give off a radioactive signal as they decay that is easily detectable in cells.
- using the particles emitted as a signal, specialists can trace the the path of the radioisotope as it moves to different parts of the body
- this way, radioactive isotopes have found many applications in biological, chemical, & medical research
21
Q
Scientist Melvin Calvin
A
- pioneer in photosynthesis study
- used carbon-14 labelled molecules to determine sequence of reactions in photosynthesis
22
Q
Uses of Radioactive isotopes
A
- study biochemical reactions
- perform basic techniques like DNA sequencing
- since most biological molecules contain C & H, carbon-14 & hydrogen-3 (aka tritium) as used as tracers in research
- used in new field of nuclear medicine to help diagnosis & treatment of diseases–> ex, thyroid gland produces hormones that affect growth & metabolism–> it’s the only gland that absorbs iodine. –> if pt’s symptoms indicate an abnormal level of thyroid hormone output, the doc may inject a small amount of radioactive iodine-131 into pt & use a photographic device to scan the gland–> the radioactivity will produce an image like an x-ray, which helps identify the cause
23
Q
the arrangement of electrons determines the __________ _________ of an atom
A
chemical properties
- cuz only electrons are usually involved in a chemical reaction
24
Q
An orbital is
A
a region of space that 1 or 2 electrons can occupy
- most stable & balanced condition occurs when the orbital contains 2 electrons
25
electrons orbitals are grouped into ____________
energy levels aka energy shells
26
How many electrons can be found in each energy level
1st=2
2nd=8
3rd=18
27
The 1st electron shell orbitals
is the 1s orbital shell
- contains a single spherical orbital
- both hydrogen & helium only have 1s electron orbital
(see page 11 in textbook)
28
The 2nd electron shell orbitals
contains on 2s orbital and three 2p orbitals
- the 2s orbital is spherical in shape
- each 2p orbital shape looks like 2 balloons knotted together --> the three 2p orbitals bisect in the centre at right angles to each other, giving orbitals their overall shape
29
the farther the electron from the nucleus....
the greater its energy.
30
the ______ that is occupied by an electron is what determines its energy level
orbital
the balloon-like 2p orbitals contain electrons that are further away from the nucleus that electrons in the 2s orbital, & therefore hold the electrons with a higher energy level
- in large atoms, some higher energy electrons occupy d & f orbitals, which are more complex
31
all the elements in living organisms have _________ valence shells
unfilled
- thus, they participate in chemical reactions
32
Hybridized electron orbitals are
orbitals that result from the sharing of electrons between atoms
- in these orbitals, there is a direct overlap of the valence electron orbitals of the 2 atoms, so the orbital is combo of 2 different orbitals
33
___________ _____________is the most common way for atoms to bond & form biological molecules
sharing electrons
34
a chemical bond is
a stable attraction between atoms
35
there are 4 types of chemical bonds important in biological molecules
- ionic bonds
- covalent bonds
- 2 types of intermolecular bonds
36
ions are very strongly attracted to ____________________
water molecules
- therefore ionic compounds tend to dissociate & dissolve in water, forming hydrated ions
37
The strength of a covalent bond depends on the ________________ of the atom's attraction for additional electrons
electronegativity
38
Electronegativity is
the measure of an atom's attraction for additional electrons.
- the more electronegative an atom, the more strongly it attracts e-
- electronegativity is strongly influenced by the atomic # & the distance between the valence e- and the nucleus of an atom
- electronegativity increases as distance between nucleus & valence e- decreases --> Ex O has high electronegativity as the valence e- are close to the nucleus, but hydrogen is less electronegative cuz it has a small atomic number. The greater the number the protons, the higher the positive charge of the nucleus and the greater ability the atom has to attract shared electrons. --> so even though the e- get close in a H atom, the nucleus is small and has weaker attraction
39
what indicates shared electrons between atoms?
a dash or a pair of dots
Ex, H-H or H:H
40
Valence Shell Electron Pair Repulsion theory
aka VSEPR theory
- created by Canadian chemist Ronald J. Gillespie
- it states that becuz e- are negatively charged, valence electron pairs repel one another & move as far apart from one another as possible.
- Ex, in a H2O molecule, there r 2 e- spaces in available on the O2 molecure that the H e- fill up, forming H20
- the theory also takes into account non-bonding electrons in its valence shell--> O has 2 pairs of non-bonding e- in its valence shell. Their negative charge repels the pairs that make up the O-H bonds, so the O-H bonds arrange themselves @ an angle of 104 from each other
41
due to their high electronegativity, both _________ & __________ form polar bonds with atoms of most other elements
oxygen, nitrogen
42
difference of <____ can be considered non-polar
0.4
43
polarity
partial positive or negative charge at the ends of a molecule
44
molecules as a whole can have a charge
rmr the arrow thingy from chem grade 11 (page 40 - chapter 3)
45
Polar molecule properties
- they attract and align themselves to other polar molecules & tend to be soluble in water (which is also polar)
- they tend to exclude non-polar molecules, such as oils and fats --> non-polar molecules have very low solubility in polar liquids
46
Intermolecular forces are
aka van der Waals forces
forces of attraction between molecules
- extremely important becuz they influence the physical properties, such as solubility, melting points, & brittleness, of a substance.
- they act between similar molecules as well as between different types of molecules
- the strength of these forces is dependent on the size, shape, and polarity of molecules
47
van der Waals forces are
are very weak attractions between two molecules or parts of two molecules when they are close together
48
Hydrogen Bond
the attractive force between a partially positively charged hydrogen atom and partially negatively charged atom in another molecule
- hydrogen bonds may form between same or different molecules
- strongest & most biologically significant form of van der Waals forces
- Individual hydrogen bonds are weaker compared with ionic & covalent bonds, but they can be very significant & strong when they occur in large #, and they lend stability to the three-dimensional structure of large molecules, such as proteins
- most strongest bonds in living organisms are covalent, weaker hydrogen bonds are crucial to the function of cells & cellular processes
49
The hydrogen bonds that exist between water molecules are responsible for many of the properties that make water a uniquely important molecule for all living organisms. some of these properties include....
- very high heat capacity
- high melting & boiling points
- cohesion -> trees depends on cohesion to transport water through xylem tissue up from roots.
- adhesion -> adhesion of water to the xylem cells walls of a plant helps to counteract gravity
-surface tension -> help give water unusually high surface tension
50
Hydrogen bonds begin to break extensively as temperatures rise above __ degrees celcius. At ___ degrees celcius, hydrogen bonds in water are overcome
45, 100
- rmr they are easier to break than ionic & covalent cuz they weaker
51
Other van der Waals forces
are even weaker and result from the momentary attraction of the electrons of one molecule to the nuclei of another (london dispersion forces)
- occur between all molecules but are only significant when stronger bonds aren't present--> like between non-polar molecules or between regions of slightly positive and negative charges within a single molecule
- 1 bond=very weak, many bonds= can stabilize the shape of a large molecule, like a fat
52
The ________ and _________ of a molecule influences the number & strength of van der Waals forces of attraction. Along side these 2 factors, the strength of these forces is also dependent on ________ of molecules
shape, size,
SHAPE - a larger molecule has larger forces of attraction --> ex, small molecule methane = gas @ room temp cuz the van der Waals forces aren't able to hold them 2gether, whereas large octane molecules are liquid cuz of the cumulative effect of many van der Waals forces between the larger molecules
SIZE - linear molecules can more align more easily with other molecules & therefore the van der Waals forces are stronger
- these influences of size & shape also apply to interactions that involve hydrogen bonds
POLARITY - the intermolecular attraction between polar molecules is obviously greater than attraction between non-polar molecules. rmr creates Dipole-dipole forces = attractive forces between the positive end of one polar molecule and the negative end of another polar molecule
53
Polar molecules can also experience van der Waals forces between....
the positive & negative ends of interacting molecules
54
Polar molecules can also experience van der Waals forces: Which molecules have strong van der Waals forces and which ones have weaker
- the effect is strong in long linear cellulose molecules, which have numerous OH functional groups & r able to form very strong fibres
- globular shaped molecules like starches have fewer accessible atoms for van der Waals forces & therefore form less rigid solids
55
All chemical reactions involve...
the breaking and formation of chemical bonds, thereby changing the arrangement of atoms & ions
56
There are 4 major types of chemical reactions that are common in biological processes:
Dehydration, Hydrolysis, Neutralization, & Redox reactions
57
Dehydration reactions
aka condensation reactions
- consist of the removal of an -OH and an - H from 2 reactant molecules (the O and H is usually removed from one molecule, and an H is removed from another i think)
- the removed -OH and -H from H2O and the 2 reactants are joined together to meet valence needs (synthesis reaction)
- most common method used by cells to join smaller molecules & assemble extremely large macromolecules, like complex carbs & proteins
58
Hydrolysis Reactions are
the revers of dehydration reactions.
- Water acts as a reactant to split or "lyse" a larger molecule --> a bond in the molecule is broken & you add the O & H to one molecule to make it stable and and H to the other in a way that all valence needs are met --> creates 2 smaller molecules
- in organisms, it is used to break down large molecules into smaller subunits
59
Neutralization Reaction
occurs between acids & bases to produce salts
- H2O often produced
- rmr chem (double displacement reaction)
60
Redox reactions
- named for "reduction" & "oxidation", electrons are lost from one atom & gained by another atom --> (any reaction that creates a new ionic gain --> no DD reaction but yes SD reaction)
- oxidation=loss of electrons --> the oxidation of one molecule is always linked to the reduction of another
- reduction=gain of electrons
- in redox reaction, the oxidizing agent (agent that causes the oxidization) is molecule or atom that is being reduced (the one that is gaining e-)
- the reducing agent (agent that causes the reduction) is the molecule or atom that is oxidized (the one that is losing --> species that is oxidized=reducing agent)
https://www.youtube.com/watch?v=Va-82jDcOKU
NOTE: "oxidation" also refers to the transfer of entire hydrogen atoms (including their electrons) from less electronegative atoms to more electronegative atoms, (ex, combustion reactions)
61
Why do redox reactions happen?
bcuz the electrons involved are more strongly attracted to the oxidizing agent
--> Ex, in oxidization of methane, the electrons in the C-H bonds are more attracted to the O. as the reaction continues, the weaker forces of the C-H bonds are overcome and the atoms separate and r pulled toward and form strong bonds with O atoms
--> this produces much stronger C--O and O-H bonds, compared to the C-H bonds
- redox reaction essentially involve electrons moving from where they are weakly held to where they are more strongly held
62
Water % in body parts
Human weight=60%
brain=70%
lungs=90%
bone tissue=22%
cytoplasm & cell= more than 90%
63
What is the "universal solvent"
water
- more substances dissolve in water more than any other substance due to its polarity
64
Water molecules are special cuz of their ______, _______, ________________, & _________________________________________________________________________
size, shape, polar structure, ability to associate with each other through hydrogen bonding.
65
The Water Lattice
- hydrogen bonds form readily in water & ice cuz water is a polar molecule, (has a negative and positive end)
- in liquid water, each water molecule molecule forms an average of 3.4 hydrogen bonds with its neighboring water molecules. --> this bonding forms an arrangement called the water lattice
- it is unique --> most particles h20's size are gases @ room temp
- as a liquid, the hydrogen bonds constantly form and break, allowing water molecules to slip past on another, reforming the lattice in new positions. --> gives water its fluid properties
66
Water lattice as Ice
- in ice, water lattice is a rigid structure
- each molecule forms 4 hydrogen bonds with its neighbouring molecules.
- due to the rigid structure, the molecules are stuck further from each other than in liquid lattice, making ice lighter (less molecules in a given area) and 10% less dense than water.
67
Specific heat is
the amount of thermal energy that is required to increase the temp of a given quantity of water by 1 degree Celsius.
68
Water's Unique Properties: Specific Heat capacity
- due to its stabilizing hydrogen bond lattice, water has a high heat capacity
- as thermal energy flows though water, much is absorbed by the process of breaking hydrogen bonds--> thus, the temp of water increases relatively slowly as thermal energy is added
- without the hydrogen bond lattice, water would boil at -81degrees Celsius
WHY H20 IS CALLED A TEMP REGULATOR?
- When temperatures drop, water releases stored heat, which helps moderate cooling. This buffering effect prevents extreme temperature fluctuations in areas near large water bodies
69
Water's Unique Properties: Cohesion
refers to the attrractive force between water molecules --> produced by the hydrogen bond lattice
- the reason behind water's high surface tension--> H20 can form hydrogen bonds on all sides, except the side that faces the air. --> this creates an imbalance in bonding, which puts produces a force that places the surface molecules under more tension and makes them more resistant to separation
- it allow insects to walk on water
70
Surface tension is
the measure of how difficult it is to stretch or break the surface of a liquid
71
Water's Unique Properties: Adhesion
refers to the water's ability to form hydrogen bonds with other polar molecules
72
Water's Unique Properties: Cohesion and Adhesion in plants
in plants growing in soil, water moves up an unbroken column within microscopic tubes of xylem tissue that extend from the roots of the plant to the highest leaves
- cohesion helps H20 molecules stick together as they are transported up the xylem tubes (think of pulling a sting of magnet beads)
- adhesion helps the h20 molecules stick to the cell walls as they are transported
- this helps water move up xylem tubes to replace evaporated water
73
Water molecules are _________ and __________________ - two qualities that allow them to readily surround polar & charged molecules & ions of other substances
small, strongly polar
74
Hydration Shells
the surface coat of h20
- it reduces the attraction between the polar molecules or ions of another substance (ionic compounds) & promotes their separation
- what happens is as the molecules & ions separate, h20 molecules surround them, forming a hydration shell which prevent ions from re-associating
- the result is an aq solution
- this is why polar molecules and ionic compounds can dissolve in h20
- similarly, hydration shells surround macromolecules like proteins, sugars, nucleic acids, that have polar or ionic regions on their surface. --> the surrounding h2o reduces the electrostatic interaction between these macromolecules and other molecules.
Electrostatic interaction refers to the attractive/repulsive force between objects with opposite/identical electric charges
75
Hydrophilic Molecules are
(greek= "water-loving)
are polar molecules or charged ions that are strongly attracted to h20
76
Hydrophobic molecules are
(greek= "water-fearing")
non-polar molecules that are not strongly attracted to h20
77
As the solvent in our cells & blood, h20 dissolves thousands of solutes necessary to life, allowing them to ....
float around and collide with each other, enabling chemical reactions to occur
78
Autoionization is
the process in which a molecule spontaneously dissociates into ions
79
Autoionization of Water
pure water=more than h20
- any given sample of h20 @ 25^C = mixture of h20 molecules, OH- ions, H3O+ ions --> @ 25^C about 2 in 550 million h20 molecules react with one another--> 1 molecule transfers an H+ ion to the other, forming an hydronium ion (the H3O+) & a hydroxide ion (the OH-)
- this autoionization always produces = # of hydronium & hydroxide ions--> other dissolved substances can unbalance this
80
Acidic solutions are characterized by
a sour taste, ability to conduct electricity, & turn blue litmus paper red
81
What happens when u dissolve acids in h20
it increases the H30+ ion concentration, giving the solution acidic properties--> rmr for an acid to show its properties, it needs to be ionized, therefore it needs to be separated into ions which occurs upon dissolving acids in h20
- in high concentrations, it will cause a chemical burn
- acids contain at least 1 ionizable hydrogen ion in their chemical structure. Ex, reaction of Hydrogen Chloride with water to produce Hydrochloric acid: HCl(g) + H2O(l) → H3O+(aq) + Cl-(aq)
- while strong acids like HCI completely ionize in h20, weaker bases may only partially ionize (like HAc)
82
Properties of a base
a bitter taste, slippery feel, ability to conduct electricity, changes red litmus paper blue
83
What happens when u dissolve bases in h20
it increases the OH- ion concentration, giving the solution base properties--> rmr for a base to show its properties, it needs to be ionized, therefore it needs to be separated into ions which occurs upon dissolving bases in h20
- in high concentrations, bases are caustic (corrosive) & will cause a painful chemical burn upon skin contact
- the release of OH- ions will happen in one of 2 ways
1) strong bases (like NaOH) may contain an OH group that will dissociate in water, releasing OH- ions
2) Other bases combine directly with H+ ions. Ex, NH3 (ammonia) which is a weak base will combine directly with h20 molecule. A H+ ion from water binds to ammonia, forming an ammonium ion NH4+ and an OH- ion
84
The pH scale
scientists measure the acidity of a solution using a numerical scale from 0 to 14= the pH scale
- pH = −log10[ H +] --> google to see proper
---> [ H +] represents the concentration of H+ or H30+ ions in an aq solution
- each whole # on the pH scale represents a 10-fold difference in pH --> a change of 1 is a great difference
- concentration of pure h20 @ 25^C is 1.0 x 10^-7
- solutions <7=acidic (coffee), solutions >7=basic (ex egg whites)
85
pH in cells
- both the pH within cells and the pH of the external environment are important for the optimal functioning of life
- a change of 0.1 or even 0.01 in the pH level of a cell can drastically affect biological reactions
- correct blood pH levels are essential for maintaining good health
- the pH levels in the stomach are also critical for proper digestion & defense against microorganisms
- small pH change around some proteins causes structural changes that can alter or destroy the functions of proteins
86
pH of water in environment
- critical for the survival of most organisms on earth
- the changing pH of freshwater bodies and oceans has a serious impact on ecosystems that depend on these water supplies for food or habitat
- pH of oceans=8
- burning of fossil fuels= more co2 in atmosphere = more co2 in oceans & fresh water= more carbonic acid in water= water is more acidic= destruction of coral reefs & marine ecosystems
87
Strong & Weak Acids & Bases
- acids & bases can be classified as strong or weak
- the strength depends on the degree to which it ionizes when dissolved in h20. --> a strong acid like HCl and a strong base like NaOH are completely dissociated in aq
- a weak acid & a weak base only partially ionize in water. --> Ex, only 10% ammonia, a weak base, froms ammonium ions in water. Only 1.3% of acetic acid, a weak acid, dissociates in water, 98.7% stays intact
88
The reaction of a weak acid or base is a _____________ action
reversible
- this means that the molecules can dissociate in h20 to form a weak acid or base, & the ions can re-associate once in solution
- Ex, when placed in h20, acetic acid molecules begin to form hydronium & acetate ions. But as the concentration of these ions increases, the reverse reaction occurs more frequently. --> when about 1.3% of the acetic acid molecules have ionized, equilibrium is reached
- the forward & backward reaction rates are the same, so the concentration of all entities of the solution remain constant
- most acids & bases involved in biochemical reactions r weak
89
A buffer is
a chemical that compensates for relatively small pH changes by absorbin or releasing H+ ions.
- living organisms use them to control cell pH
- When a biological reaction releases excess H+ ions buffers combine with the H+ ions so that they are no longer free in the solution
- they release OH- ion if concentration too low
- since weak acids dissociate in a reversible action in h20, most buffers are weak acids, bases, or a mixture
90
Buffering mechanism in human example
- a buffering system that is based on carbonic acid, a weak acid, helps to maintain proper blood pH levels in the range of 7.35 to 7.45
- in aq, carbonic acid dissociated into bicarbonate ions, HCO3- & H+. --> like other weak acids, this reaction is reversible
- if there is a large concentration of hydrogen atoms in a solution, these atoms will collide frequently with the bicarbonate ions causing a reaction, & the H+ ions will be absorbed as carbonic acid molecules are formed.
- if there are very few H+ ions, they will not collide & cause a reaction with the bicarbonate ions & the reversal reaction will occur @ a slower rate than the forward reaction, and this causes the release of more H+ ions.
91
Carbon atoms mainly bind to
hydrogen, nitrogen, oxygen, sulfur
92
carbon atoms bind to each other to form ______________, __________, _____________________
long chains, rings, or branched structures
93
Hydrocarbons are
molecule consisting of only hydrogen & carbon
- they are non-polar
94
the smallest hydrocarbon is ____________
methane
- CH4
95
carbon skeleton
the chain of carbon atoms in a biochemical molecule = carbon skeleton (see page 25)
- carbon skeleton can be linear, or branched, or form a closed ring shape like the cyclohexane
96
many carbon-containing rings can join to produce __________
polymers
- ex, string of sugar molecules that make up a complex chain
GOOGLE: Polymer= long chain molecule made from small molecules linking together
97
Are hydrocarbons frequently used by living organism??
no
- the molecules of living organisms usually contain other elements in addition to C & H
98
4 major molecule groups in living organisms based on function:
carbs, lipids, proteins, & nucleic acids
99
carbs, lipids, proteins, & nucleic acids undergo _______________ & ________________ in living organisms through interactions between small reactive groups of atoms that are, themselves, a part of these large groups. These small reactive groups are called __________________
synthesis, degradation, functional groups
100
A Functional group is
a group of atoms in a molecule that affects the function of a molecule by participating in chemical reactions
- unlike non-polar hydrocarbons, they are usually ionic or strongly polar
- Functional groups on large molecules interact with other molecules & introduce different types of bonding
101
Most functional groups are ionic or strongly polar. What affect does this have?
- this makes them very attracted to other ionic or polar molecules, including h20 molecules--> thus the chemical or physical properties of large biological molecules are influenced by the polar & ionic characteristics of its functional groups
- these makes functional groups vital for chemical reactions as non-polar molecules do not attract other molecules and thus don't easily react with them
102
Polar groups help molecules interact with others. Give an example
Some polar functional groups are strongly attracted to h20 & can therefore be dissolve in the cytosol of a cell.
Ethane is non-polar & has no functional group. Though it has a lot of PE it can't be used as fuel cuz it's a gas @ room temp & isn't soluble in h20
Ethanol, although has less PE than ethane, has an alcohol functional group (-OH), which gives it polar characteristics & allows it to from hydrogen bonds with h20. It is a liquid at room temp, and is highly soluble (technically miscible, according to google) in h20, allowing it to dissolve in cytosol to be used as fuel
103
The ___________, _____________, & _______________ groups are all ionic functional groups. what is their connection to biological compounds
carboxyl, amino, phosphate
- the carboxyl group, COOH, can release proton, becoming COO+. The release of the H+ in H2O makes it acidic
- the amino group, NH2, can bond with a H+ ion, turning it into NH3+, making it a weak base
- proteins = amino acids --> an amino acid has both an acid (carboxyl) and a base (amino) as its functional groups
- phosphate functional groups are also acidic (lose H+ ions & become negatively charged).
- DNA is an acid cuz it contains a huge number of these phosphate group in its backbone structure, making DNA negatively charged.
104
Dehydration Example: Formation of starches (diagram in notebook)
- dehydration occurs when sugar molecules combine to from a starch molecule
- 2 -OH groups interact with each other, where the oxygen in one, is attracted to the hydrogen in the other, which forms one H2O
- The remaining oxygen forms a bridge as it binds the two molecules together into one
105
Hydrolysis Example: Formation of Sugars (diagram in notebook)
H+ and OH- are added to functional groups to break down a starch molecule into sugar ones
- 2 hydroxyl groups are formed when water is added to the oxygen bridge during this process, and these hydroxyl groups can interact with each other.
106
Functional Groups - Hydroxyl
Alcohols
–OH or HO-
Polar due to O, can attract water molecules which helps dissolve compounds like sugars
names typically end in -ol (ex. ethanol)
107
Functional Groups - Carbonyl
Aldehyde: C=O at end molecule
Ketone: C=O in middle of molecule
- names typically end in -al (aldehydes) or -one (ketones)
- Cinnamaldehyde - gives cinnamon its odor and flavor
Carboxylic Acids
-COOH
Acidic - more than -OH groups
but less than HCl, H2SO4
Amino acids also contain carboxyl groups
Commonly found in fatty acids
names typically end in -oic acid (ex. butanoic acid)
108
Functional Groups - Amino
major class of molecules:Amino Acids
-NH2
Building blocks of proteins
20 diff amino acids
Nonessential (synthesized in our bodies)
Essential (acquired from our diets)
names typically end in -ine
109
Functional Groups - Phosphate
-PO42-
Found in the genetic material
(DNA and RNA) and ATP
High energy group - 4 Os
Part of phospholipids (cell membranes)
Part of nucleic acids
110
Functional Groups - Sulfhydryl
Thiols
-SH
Polar molecules
Strong odor - rotting eggs, skunks
-SH groups stabilize the structure
of proteins by building protein
bridges (ex. curly hair)
111
Carbs & lipids are best known for their role as _____________________ in the body
energy sources
112
Other roles of carbs
- play role in structural support & cell-to-cell communication
- they are the raw material used to build other important molecules like amino acids & nucleic acids
- provide insulation, act as a water barrier (large carbs are non-polar, water is polar) (akhtar!)
113
Other roles of lipids
- structural role: all biological membranes are composed of lipid molecules
- hormones, certain vitamins, & defense mechanisms are based on lipids
- provide insulation for nerve cells & have waterproofing qualities
114
carbs are
a biomolecule that consists of Carbon, Hydrogen, & Oxygen in the ration 1:2:1
- among most common biological molecules on earth
- Carbo means carbon, Hydrate means water
- In photosynthesis, CO2 and H2O are used to build
carbohydrates --> plant & algae produce millions of tonnes of carbohydrates
-are used as building material, cell
communication and as energy sources
115
Monosaccharides are
the simplest form of carbs, consisting of a single sugar unit. (its a monomer) --> its a single building block of the many used to make more complex carbs
- Ex, glucose, fructose
- glucose= the most widely used monosaccharide, produced during photosynthesis
116
What Monosaccharides are the most common in living organisms?
ones that contain 3 carbons (triose), 5 carbons (pentose), & 6 carbons (hexose)
117
Monosaccharide shapes
- all linear
- formed in water, ones with 5 or more C can fold back onto themselves into a ring
- Ex, in glucose, the carbonyl group interacts with a hydroxyl group to from a ring (see page 30)
- carbon atoms in glucose have # assigned to them, that scientist refer when discussing structures of sugars
118
An isomer is
a molecule with the same composition as another but diff arrangement of atoms
119
Glucose isomers
- when glucose form ring, there r 2 possible arrangements of the -OH groups that is bound to carbon at position 1 (far right carbon in middle)
- α-glucose (alpha-glucose): -OH downwards of the carbon
β-glucose (beta glucose): -OH upwards of the carbon
- the diff arrangement of -OH groups on glucose, give dif chemical properties--> α-glucose=easily digestible, β-glucose= not easily digestible (cellulose is made from it)
- glucose, fructose, galactose are isomers of each other
120
Disaccharides are
a carb molecule that is made from 2 monosaccharides that are joined together by a dehydration synthesis reaction
- FUNCTION: energy source
121
Disaccharide examples
- Ex, maltose is forms through linkage of 2 α-glucose molecules at 1-carbon of one glucose and the 4-carbon of the other
- α-glucose + fructose = sucrose (1-carbon to 5-carbon with O in middle)
- Lactose (milk sugar) = galactose + β-glucose (1-carbon to 4-carbon (z shape) with O in middle)
- chemical shorthand to represent glycosidic bond between 1-carbon & a 4-carbon = 1--> 4
- 1-->2, 1-->3, & 1-->6 are common in carb chains
- linkage called α or β based on orientation of -OH on 1-carbon that is being bonded
122
Glycosidic bonds
the bond between 2 monosaccharides
123
Sugar properties
- have many polar functional groups
--> make them very hydrophilic & soluble in H20
- sweet taste= dissolved in H20
- monosaccharides=sweetest
- # of monosaccharides linked increases=sweetness decreases
124
Disaccharide properties
contain same functional groups that make monosaccharides hydrophilic --> easily dissolved in H20
125
sources of sucrose
maple syrup, table sugar & sugar beet
126
Complex Carbs are
a molecule that is composed of hundreds to thousands of monosaccharides linked 2gether
- some important for energy storage= starch & glycogen
- some essential for structural support= cellulose & chitin
127
A polysaccharide molecule is
a chain of monosaccharides with many subunits joined by glycosidic linkages
- polysaccharide=macromolecule assembled by covalent linkage of smaller subunit molecules
- polysaccharides may be linear unbranched molecules or may contain branches of side chain sugars that attach to a main one
- FUNCTION: energy storage, structural support, & cell-to-cell communication
128
Polymerization is
the process in which identical or variable subunits, called monomers, link together in a long chain to form a larger molecule --> this molecule is called a polymer
- dehydration synthesis reactions are an example of polymerization
- many polymers are found in cells, not just polysaccharides. --> Ex, DNA
129
The most common polysaccharides are ...
plant starches, glycogen, & cellulose
- assembled from thousands of glucose
- Cellulose= main component of plant cell walls, is most abundant organic molecule on Earth. - is large & straight, & have very large # of polar -OH groups --> enable cellulose to form side by side & form 100s or 1000s of hydrogen bonds, which give cellulose its strength
130
Polysaccharide properties
- very pollar & therefore very hydrophilic
- but since they are huge, they can attract water but won't dissolve in it
--> this is the principle behind paper towels --> made of cellulose, they attract h20, but do not dissolve it them, making them effective
131
Lipids are
- lipid= a general term for a variety of non-polar biological molecules.
- they are composed mostly of hydrogen, carbon, & lesser amounts of oxygen
- smaller than complex carbs= not considered macromolecules & are not polymers cuz they aren't made up of defined monomers
132
Lipids properties
- they are generally non-polar= insoluble in h20 --> enables them to form cell membranes (so they can act a water a barrier)
- some stored by cells as energy source
- some serve as hormones that regulate cellular activities & as vitamins
133
Lipids in living organisms fall into 5 main categories:
fatty acids, fats, phospholipids, steroids, & waxes
134
An ester linkage is
a type of covalent bond formed when a carboxylic acid reacts with an alcohol.
Lipids also may have ester linkages, a type of covalent bond formed between fatty acids and glycerol.
135
Fatty Acids
- structural backbone of most lipids= derived from fatty acids
- fatty acid consists of a single hydrocarbon chain with a carboxyl functional group @ one end --> it gives fatty acids it acidic properties
- fatty acids in humans contains 4 or more carbons in their hydrocarbon chain
- most common forms have even-numbered chains of 14-22 carbons - as length increases, h20 solubility & fluidness decreases
136
Saturated & unsaturated fatty acids
- if the hydrocarbon chain binds the max possible hydrogen atoms & if all carbons are linked together with single bonds, the fatty acid is saturated
- if there are double bonds in the chain it is unsaturated --> the carbons have potential to bind with more hydrogen
- fatty acids with one double bond= monounsaturated
- fatty acids with >1 double bond= polyunsaturated
- the presence of a double bond in an unsaturated fat creates a kink in the molecule, which causes it to bend
137
Fats
- a fat is a lipid that is made from 2 types of molecules: fatty acid & a glycerol molecule
- r nonpolar
- In a fat molecule, 1-3 fatty acid chains are joined to a single glycerol molecule though dehydration synthesis between -OH functional groups on glycerol & the carboxyl on the fatty acids. Bond= ester linkage
- a fat molecule can have identical fatty acid chains or different ones, linked to glycerol
138
Triglycerides are
the most well-know fats
- they contain 3 fatty acid chains
- diff organisms usually have distinctive combos of fatty acids in their triglycerides
--> Ex, fats from animals like butter usually contain only saturated fatty acids, = saturated fats
---> fats from plants like olive oil usually contain more monounsaturated & polyunsaturated fatty acids = unsaturated fats ---> unsaturated fats are usually referred to as oils
139
Triglycerides usually become less __________ as length _______________
fluid, increases
- those with shorter lengths= unsaturated fats = liquid & fluid @ room temp cuz they have kinks that are bent & can't be packed as tightly
- longer & straight lengths= saturated fats= solid @ room temp cuz they can be packed closely together
140
Do living organisms have more saturated or unsaturated fat?
- organism need to be flexible to move, so if they have large amounts of saturated fat (typically solid), they won't be able to move easily
- Warm-blooded mammals & birds are the exception in having more saturated fat, but it is liquid cuz of our relatively high body temp.
- plant seeds usually contain mostly unsaturated fat
- cold-water fish need their bodies to stay flexible so fats in their bodies are mostly unsaturated fish "oils" --> benefit of eating fish
141
Triglycerides function widely as...
stored energy
- gram to gram, they have more than 2x energy as carbs making fats a great source of energy
- storing the equivalen amount of energy as carbs rather than fats would add >45kg to a person
- layer of fat under tissue just under the skin acts as insulation in mammals & birds
142
Which are better? unsaturated or saturated fats?
- most plant fats are unsaturated fats are better for your health & can acc improve ur health
- diets rich in saturated fats can lead to health disease
143
Phospholipids are
a lipid that consists of two fatty acids & a phosphate group bound to glycerol
- cells could not exist without them
- they're the primary lipids of cell membranes
- in most phospholipids glycerol forms the backbone of molecules with 2 fatty acids chains attached to it and 1 phosphate group in opposite direction, which often binds to another polar or charged unit.
- essentially, a phospholipid contains 2 hydrophobic fatty acids @ one end, attached to a hydrophilic polar group aka head group ( glycerol is part of non-polar group, textbook)
- are amphipathic molecules
144
Amphipathic molecules are
molecules that contain both hydrophobic & hydrophilic regions
- the head of an amphipathic molecule is the polar & hydrophilic region
- the tail is the hydrophobic lipid, which is composed of a carbon chain
145
Phospholipids in cell membranes
-they make up the lipid bilayer (a double layer of closely packed atoms or molecules) of cell membranes, an important structural feature of cells.
- the hydrophilic end faces outward towards water & the hydrophobic fatty acid tails face inwards towards each other (page 36
146
Steroids are
a lipid that is composed of 4 carbon rings
- differences in side groups that are attached to the rings distinguish one steroid from another
- most abundant steroids= sterols= have 1 polar -OH group @ one end of the ring framework & a complex non-polar hydrocarbon at the other ---> although sterols are almost completely hydrophobic, the hydroxyl gives one end slight polarity, giving sterols dual solubility properties
- FUNCTION: hormone signaling, cell response to the environment, & growth
147
Steroids: Cholesterol
- it's an important component of the plasma membrane that surrounds animal cells & converts into
several compounds like vitamin D--> similar sterols, called phytosterols occur in plant cell membranes
- too much dietary cholesterol = harmful
- high concentration of it in bloodstream & saturated fat rich diet are linked to atherosclerosis- a condition where fat deposits, or plaques form on the inner lining of arteries, restricting blood flow, causing heart attacks ( it builds up in arteries cuz while arteries are thicker, the hole diameter is smaller - Ms.Akhtar)
148
Steroids: Sex hormones
- sex hormones like testosterone, estrogens, & progesterone r also steroids
- they control development of sexual traits & sex cells that are specific to males & females
149
Anabolic Steroids
- steroids that mimic testosterone steroid
- used by some athletes to build muscle mass
- have harmful affects on the body, including high bp, depression, suicidal tendencies, changes in sex hormone levels, & reduced growth in youngsters
150
Waxes are
large lipid molecules that are made when long fatty acid chains are joined to alcohols or carbon rings
- are hydrophobic, extremely non-polar, & r soft solids over a wide range of temp
- make them ideal for waterproof coatings on plants & animal parts
--> ex, one type of wax, called cutin, is produced by plants to form a water resisting coating on the surfaces of stems, leaves, & fruit
--> cutin enables plants to conserve h20, & acts as barrier to infections & diseases. without it, plants wouldn't survive on land
- birds secrete a waxy material that helps to keep their feathers dry.
- bees produce beeswax to make honeycombs
151
A protein is
a large molecule (polymer) that consists of many amino acids that are joined by peptide bonds folded into a specfic 3D shape that specifies its function
152
Proteins are the most diverse group of molecules in living systems, in terms of their _______________ & ______________
structure & function
153
Nucleic acids are
a blueprint for proteins that are synthesized in cells
- stores hereditary info
- genetic info passes from he nucleic acids DNA to the nucleic acid RNA. Chemical info is translated from RNA for protein synthesis.
154
Amino acids
proteins= polymers made from amino acid monomers
- it has a central carbon atom, attached to an amino group, a carboxyl group, & a hydrogen atom
- in solution, the amino group bonds to an H+ while the carboxyl group releases an H+
-attached to the central carbon atom is a side variable group (R group aka side group) which gives each amino acid its distinct characteristics
- side group may be polar or non-polar. --> on polar side, some may carry positive or negative charge, and others act as acids or bases
- r 20 types of amino acids side groups, ranging from 1 hydrogen atom to complex carbon chains or rings --> 1 exception is proline--> has a ring structure that includes the nitrogen & central carbon atoms
155
Many of the amino acid side groups contain a reactive ____________ _____________
Functional group
- they may interact with atoms located in the same protein or with molecules & ions located outside the protein
156
with few exceptions, all proteins in living things are an assembly of various # & combos of ___ diff amino acids. ____ of these are considered essential for humans
20 , 8
157
essential proteins are
the 8 proteins that can only be obtained from diet.
- the rest can be synthesized by cells
- there are also other amino acids like neurotransmitters
158
Proteins are the most ____________ molecules in living organisms
complex
159
Types of proteins , their functions, & examples
- structural= framework support=keratin, collagen
- Defensive=infection fighters=antibodies
- Signal=messenger=hormones
- Carrier=transport of materials=hemoglobin
- recognition & receptor=cellular markers on cell surface= major histocompatibility complex
- enzyme=catalyst=amylase
- motile=give cells & cellular structures ability to move=actin (helps mucles contract) & myosin (drive contraction of a muscle cell and allow bodies to move or perform an action.)
- storage= bean seed proteins
160
Peptide bonds are a
covalent bond that links amino acids together
- formed by dehydration synthesis between NH2 group & the COOH group of another amino acid
- N-terminal end: -NH2 end of amino acid chain
- C-terminal end: -COOH end of amino acid chain
--> In cells, amino acids are only added to COOH end of a peptide strand
161
A peptide is
a chain of amino acid monomers that are connected by peptide bonds
- unlike carbs, no side chains of amino acids in a peptide but can contain small non-amino acid components
162
A polypeptide is
a peptide that has >50 amino acids
- a protein is 1 or more polypeptides that are folded into a precise 3d shape --> only after folding, the protein can function
163
Protein structure parts
- proteins have up to 4 levels of structure, with each level adding diff traits & degrees of complexity
- the levels are: primary structure, secondary structure, tertiary structure, & Quaternary structure
- the shape of protein influences the function
164
Primary structure
= the unique linear sequence of amino acids in each polypeptide chain
- changing even 1 amino acid will alter the overall structure of the protein to some degree--> single change can change or destroy biological function of the protein
- is enormous diversity in the primary structures that can form
165
Secondary Structure
-most polypeptides have sections that repeatedly coil or fold into patterns that contribute to overall protein shape.
- result of hydrogen bonding between diff parts of the same amino acid backbone (usually between electronegative N & O and H)
- common secondary structures are the beta-pleated sheet & the the alpha-helix
- beta-pleated sheet= segments of a polypeptide chain line up next to each other, forming a sheet-like structure held together by hydrogen bonds.--> plays important role in silk strngth
- alpha-helix= delicate coil held by hydrogen bonds btween every 4th amino acid --> found in filamentous proteins & transmembrane proteins
166
Tertiary structure
is the overall 3d shape of a protein due to a range of interactions among the amino acid R groups
--> interactions include hydrogen bonds, hydrophobic interactions, & disulfide bridges
- this structure is critical to function of proteins, especially enzymes
167
Hydrophobic interactions are
the interaction of non-polar side groups (aka R groups) that cluster together in centre as a result of other amino acid R groups interacting with h20.
- hydrophobic amino acids form a cluster in center while hydrophilic ones make an outer coating
168
A disulfide bridge is
the bond that is formed when the -SH groups of two cysteine amino acids line up & react to from an S-S covalent bond --> a strong bond that holds 2 parts of the polypeptide strand 2gether, stabilizing the shape
169
Denaturation is
the loss of structure & (thus) function of protein
- extreme conditions like temp, pH, salinity, can cause it.
170
A. What happens when a protein denatures? * (akhtar)
It loses its primary structure.
It loses its secondary and tertiary structure.
It becomes irreversibly insoluble and precipitates.
It hydrolyzes into component amino acids.
Its hydrogen bonds, ionic bonds, and peptide bonds are disrupted.
171
Quaternary Structure
Many proteins r composed of 2 or more polypeptides that come together to form the final functional proteins.
- The quaternary structure refers to how multiple polypeptide chains, called subunits, come together to form a complete, functional protein. --> The same bonds and forces that fold single polypeptide chains
into tertiary structures also hold the multiple polypeptide chains together.
--> ex, hemoglobin molecule is made of four polypeptides, each consisting >140 amino acids
172
Protein Prosthetic Groups are
non-protein components many proteins require to function
- ex, In hemoglobin, polypeptides don't bind to 02. O2 is bound to heme groups, which are surrounded and held by the polypeptides. Each polypeptide chain
contains one heme ring where there is a single iron (Fe(2+)) ion. Thus, there r 4 heme groups/hemoglobin, and 4 O2 are carried.
- Many enzymes require prosthetic groups that contain metal ions--> ex, some enzymes involved the process of cellular respiration require Mg(2+) ions.
173
Protein Structure and Functional Relationship
shape of a protein influences and enables its function
- Ex, long linear proteins align to form the strong fibres of silk, collagen, and keratin. This long linear
formation provides the strength.
- Ex, Compact globular proteins, like hemoglobin protein, are good for transport --> its shape enables them to carry O2 efficiently
- Ex, enzymes & antibodies have special pockets that bind specific molecules, allowing these proteins to carry out their function.
174
Chaperonins
Are protein molecules that assist in the proper folding of other proteins
175
Nucleic Acids
Two types of nucleic acids exist: DNA and RNA.
-DNA stores the hereditary info that is responsible for inherited traits in all eukaryotes and prokaryotes and in many viruses.
- Ribonucleic acid (RNA) is the hereditary molecule of some viruses. There are several different forms of RNA involved in protein synthesis in all cells including ours
176
A nucleotide is
the building block of nucleic acids; consists of a 5-carbon sugar, a nitrogenous base, and one to three
phosphate groups
- each nitrogenous base links covalently to a 5-carbon sugar, either deoxyribose (in DNA) or ribose (in RNA).
- The 2 sugars differ only in the chemical group that is bound to the 2ʹ-carbon: deoxyribose has an -H, and ribose has an -OH group (see diagram on page 45 & in notebook)
177
There are two general types of nitrogenous base:
pyrimidines and purines
- Pyrimidine bases= single organic rings
- purine bases= two-ringed organic structures
- Both types of bases have a high nitrogen content
- The 3 pyrimidine bases: uracil (U) --> it replaces thymine in RNA ( which will bind to Adenine with 2 hydrogen bonds) thymine (T), & cytosine (C).
- The two purine bases: adenine (A) and
guanine (G).
178
DNA and RNA are nucleotide _________.
polymers
179
Polynucleotide chains are
chains of nucleotides that make up DNA & RNA, with 1
nucleotide linked to the next by a single bridging phosphate group between the 5ʹ-carbon of one sugar and the 3ʹ-carbon of the next sugar in line. --> this linkage= phosphodiester bond
- arrangement of alternating sugar & phosphate groups forms the nucleic acid chain backbone. The nitrogenous bases of the nucleotides project from this backbone
180
phosphodiester bond is
a link that is formed between nucleotides by a
phosphate bridge
181
DNA vs RNA nucleotide
DNA chain, each nucleotide contains deoxyribose, a
phosphate group, and one of the four bases A, T, G, or C
In an RNA chain, each nucleotide contains ribose, a phosphate, and one of the four bases A, U, G, or C
- DNA is almost always found as a very long double helix but RNA takes on a greater variety of structures.
--> RNA structures include relatively short linear forms and structures that fold back on themselves in clover or hairpin formations
182
DNA VS RNA (Akhtar
DNA
Double stranded helix
N-bases: A, G, C, Thymine
Stores hereditary info
Longer/larger
Sugar: deoxyribose
RNA
Single stranded
N-bases: A, G, C, Uracil
Carry info from DNA to ribosomes
tRNA, rRNA, mRNA
Sugar: ribose
183
DNA molecule structure
is a double-stranded molecule in which the two strands of DNA run antiparallel to each other meaning they are oriented in opposite directions.
--> One strand runs from the 5' to 3' end, while the other runs from the 3' to 5' end, allowing the two strands to align and pair correctly. (SEE PAGE 46)
- end with the phosphate group = 5ʹ end, and end deoxyribose sugar = 3ʹ end
- . G (guanine) forms 3 H bonds
with C (cytosine), and A (adenine) forms 3 H bonds with T (thymine). --> As base pairs form between two strands of DNA, the molecule is twisted into a double helix
184
Which 2 nucleotides are the primary molecules that transport chemical energy from one reaction system to another and regulate & adjust cellular activity?
adenosine triphosphate (ATP) and guanosine triphosphate (GTP)
185
four major types of biological molecules:
carbohydrates, lipids, proteins, and
nucleic acids.
186
An Enzyme is
a biological catalyst, usually a protein, that speeds up a chemical reaction
- about 4000 diff enzymes in typical cell
- one missing or defective enzyme= disastrous results
- Each enzyme has unique 3D shape, and it determines which reaction it catalyzes.
--> For a chem reaction to move forward, it must overcome an energy barrier, and this is where enzymes are important. Enzymes bind a specific reactant or reactants called a substrate --> in doing so, they lower the energy barrier so that the
reaction proceeds at a faster rate than it would without the enzymes
187
2 examples of hydrolysis enzymes
- The enzyme lipase speeds up the hydrolysis of the lipid triglycerides.
-Sucrase speeds up the hydrolysis of
sucrose into glucose and fructose.
188
a substrate is
a substance that is recognized by and binds to an enzyme
189
An enzyme remains ___________ in a chemical reaction
unchanged
190
Each type of enzyme catalyzes the reaction of only...
one type of molecule or one group of closely related molecules
191
Hydrogen peroxide plus enzyme
hydrogen peroxide = a toxic chemical that occurs in cells as a by-product of metabolism. --> To prevent cell
damage, hydrogen peroxide is broken down by the ENZYME CATALASE
2H2O2 --> 2H2O + O2
192
The active site is
usually a pocket or groove that forms when the newly synthesized enzyme folds into its correct three-dimensional shape (tertiary structure)
- that is where an enzyme binds its substrate
193
Lock & key hypothesis
analogy worked well to explain how even similar substrates (the “keys”) were unable to bind to the same enzyme (the “lock”) and undergo catalysis.
- However, the more recent introduction of
the induced-fit hypothesis better explains the enzyme-substrate relationship.
194
induced-fit model
a model of enzyme activity that describes how an enzyme changes shape to better accommodate
a substrate
- enzymes are not rigid objects, like locks,
but are flexible.
- prior to substrate binding, enzyme changes its shape, aka its conformation, so that the active site becomes even more precise in its ability to bind to its substrate
195
The enzyme cycle
- An enzyme binds to one or more substrates, forming an enzyme-substrate complex. The enzyme then converts the substrate(s) into one or more products.
- Since enzymes remain unchanged after a reaction, enzyme molecules can rapidly bind to other substrate molecules, catalyzing the same reaction repeatedly = enzyme cycle
- typical rates vary between about 100 and
10 million substrate molecules per second!
196
A cofactor is
a non-protein group that binds to an enzyme and is essential for catalytic activity
- are often metals, such as iron, copper, zinc, and
manganese
- Many enzymes require a cofactor--> Ex, an essential enzyme for providing one of the key components of for mitochondria for the production of energy
requires a magnesium cofactor
197
Coenzymes
aka Organic cofactors
- an organic molecule that acts as a cofactor of an enzyme
- are often derived from water-soluble vitamins
- Many coenzymes shuttle molecules from one enzyme to another.
- Ex, NAD+, a derivative of vitamin B3 acts as an electron carrier during a number of biochemical pathways
198
Conditions & Factors That Affect Enzyme Activity: Enzyme & Substrate Concentration
- both affect rate of reaction
- With excess substrate, the reaction rate is proportional to enzyme concentration. --> essentially, as enzyme concentration increases, the rate of reaction increases
-As substrate concentration increases with constant enzyme levels, the reaction rate rises initially because more substrate binds to the enzyme. However, once all enzyme active sites are occupied (saturation point), the reaction reaches its maximum rate --> enzymes r saturated with substrate.
199
Conditions & Factors That Affect Enzyme Activity: Inhbitors
- lower the rate at which an enzyme catalyzes a reaction.
- Inhibitors= molecules that bind to an enzyme & decrease its activity. --> Some work by binding to the active site of an enzyme, while other inhibitors bind to critical sites located elsewhere in the structure of the enzyme
200
competitive & noncompetitive inhibitors
competitive inhibitors= a competitor substance that mimics the substrate binds to the enzyme active site to block enzyme activity
noncompetitive inhibitors= inhibitors that bind to an enzyme at a site that is not the active site, changing the shape of the enzyme, reducing the ability of the substrate to bind efficiently
201
Reversible & Irreversible Inhibition
reversible inhibition=binding of the inhibitor to the enzyme is weak and readily reversible. Enzyme activity
returns to normal following the release of the inhibitor
Irreversible inhibition= bind so strongly to the enzyme through the formation of covalent bonds that they
completely disable the enzyme.
-->,many irreversible inhibitors that act on critical enzymes are highly toxic to the cell. Ex, cyanide is a potent poison cuz it binds strongly to and inhibits cytochrome oxidase, the enzyme that catalyzes a key step in cellular respiration.
--> Many antibiotics are toxic to bacteria and work by inhibiting enzyme activity in the bacteria
- Irreversible inhibition can be overcome only by the cell synthesizing more of the enzyme
202
Penicillin & Irreversible Inhibition
The antibiotic penicillin acts by inhibiting the synthesis of peptidoglycan, component of bacterial cell wall
- The enzyme transpeptidase catalyzes the formation of a peptide bond between the two amino acids that are responsible for linking two parts of peptidoglycan.
- The structure of penicillin mimics the structure of the two amino acids that are normally brought together by the active site. --> Penicillin binds irreversibly to the active site of transpeptidase, effectively destroying the molecule
203
Conditions & Factors That Affect Enzyme Activity: Allosteric Control of Enzyme Activity
- Regulatory molecules often act like noncompetitive reversible inhibitors.
- These molecules bind to the enzyme at an allosteric site (not the active site), altering the enzyme's shape and affecting the active site.
- This process is known as allosteric regulation, which can either inhibit or stimulate enzyme activity.
- Allosteric activators= stabilize the enzyme's shape, increasing its affinity for the substrate.
- Allosteric inhibitors= stabilize an inactive form of the enzyme, causing the enzyme to release the substrate.
204
Conditions & Factors That Affect Enzyme Activity: Feedback Inhibition
- Allosteric regulators control chemical activity in cells, often by acting as inhibitors.
- An allosteric inhibitor is often a product of the pathway it regulates. When the product accumulates, it inhibits the enzyme that produces it.
- This mechanism is known as feedback inhibition, which prevents unnecessary synthesis of molecules.
- Ex, in the pathway producing amino acid isoleucine from threonine, isoleucine acts as an allosteric inhibitor of threonine deaminase --> High isoleucine levels inhibit threonine deaminase by converting it to a low-affinity state, slowing down the pathway.
-- >Low isoleucine levels reduce inhibition, allowing threonine deaminase to return to a high-affinity state, increasing isoleucine production.
205
pH Effects on Enzyme Activity
- Each enzyme has an optimal pH where it operates most efficiently.
- Deviations from the optimal pH decrease the reaction rate, with extreme deviations leading to a complete halt.
- Most enzymes have an optimal pH around 7, matching typical cellular environments.
- Enzymes secreted outside cells can have more variable pH optima. --> Ex, pepsin (stomach enzyme) has an optimal pH of 1.5, while trypsin (intestinal enzyme) has an optimal pH of 8, allowing them to function in their respective environments.
206
Temperature affects enzyme activity
- Temperature affects enzyme activity in two ways:1)it increases the rate of chemical reactions due to increased and stronger molecular collisions and 2) affects the structure of proteins, including enzymes. --> As temp rises, the kinetic motions of the amino acid chains in enzyme increase. At same time, the strength & frequency of the collisions between the enzyme molecules and any surrounding molecules increases
- Between 0°C and 40°C, the reaction rate doubles with every 10°C increase due to enhanced kinetic motion.
- Above 40°C, enzymes begin to denature as their three-dimensional structure unravels, reducing their function. --> hydrogen bonds & other forces start to break
- Enzyme activity peaks for most enzymes between 40°C and 50°C, with a steep decline after 55°C, reaching zero by 60°C.
Some enzymes have different temperature optima:
- Corn pollen enzymes work best near 30°C, with reduced activity above 32°C.
- Antarctic fish enzymes are most active around 0°C & can remain active at 85°C or higher, resistant to denaturation.
207
Lactose Intolerance
Lactose intolerance = the inability to properly digest lactose, the main sugar in milk.
- Lactose requires the enzyme lactase for breakdown into glucose and galactose in the small intestine.
- People with lactose intolerance do not produce enough lactase, leading to improper lactose digestion.
- Undigested lactose is consumed by gut bacteria, causing symptoms like nausea, cramps, and bloating.
- Many people manage lactose intolerance by taking commercial lactase enzymes when consuming dairy products.
208
Chymosin
- Chymosin is an enzyme used in cheese production, originally sourced from calves but now genetically engineered.
- In cheese-making, bacteria are added to milk to produce lactic acid, lowering the pH and denaturing milk proteins.
- Chymosin hydrolyzes casein, the main milk protein, causing coagulation into cheese curds.
- Different types of cheese result from processing curds, with fat-hydrolyzing enzymes contributing to stronger flavors (e.g., Romano cheese).
