Biochemistry Flashcards
1
Q
Matter
A
anything that has mass and takes up space. Matter is made up of tiny particles called atoms.
2
Q
Atom vs Ion - similarities
A
Both have protons and neutrons in their nucleus and electrons orbiting the nucleus.
3
Q
Atom vs Ion - differences
A
Atoms are electrically neutral and have equal number of protons and electrons. Atoms have no overall charge.
Ions are electrically charged and have different numbers of protons and electrons. Ions have overall charges because they want to gain or lose electrons to achieve an octet configuration like the noble gases. Ions are negatively charged if they have more electrons than protons and are called anions. Ions are positively charged if they have more protons than electrons and are called cations.
4
Q
Intermolecular Bonds vs intramolecular bonds
A
Intramolecular forces are the forces that hold atoms together within a molecule. Intermolecular forces are forces that exist between molecules.
ionic bonds > Hydrogen bonding > Van der Waals dipole-dipole interactions > Van der Waals dispersion forces.
covalent, ionic, and metallic bonding
5
Q
molecule.
A
bonding between atoms results in a compound
6
Q
ionic bond
A
when one atom transfers electrons to another atom
form between metals and non-metals
write with square brackets with charge on outside
7
Q
covalent bond
A
two or more non-metals share one or more pairs of electrons
Covalent bonds form between atoms of non-metals.
Atoms can share up to three pairs of electrons to form single, double and triple bonds.
8
Q
polar covalent bond
A
unequal sharing of valence electrons between atoms in the pair
dipole, with one end being slightly positive and the other, slightly negative.
water is the most polar covalent
9
Q
Electronegativity
A
measure of an atom’s ability to attract electrons in a chemical bond
10
Q
London forces
A
Hold non-polar molecules together Very weak forces of attraction Momentary dipoles are created by the electrons contained within the compound, which are constantly in motion. weakest ch4
11
Q
Dipole-dipole forces
A
Hold polar molecules together
These forces are stronger than London forces
Medium
12
Q
Hydrogen bonding
A
is formed between the electropositive hydrogen dipole and an electronegative dipole of oxygen, chlorine, or fluorine
strongest
13
Q
hydrolysis
A
water to help break down molecules
Protein + water → amino acid + amino acid
14
Q
Condensation
A
two molecules combine to form one molecule
dehydration synthesis because water is removed (“dehydrated”)
Amino acid + amino acid → protein + water
15
Q
oxidation
A
process of losing electrons
16
Q
reduction
A
process of gaining electrons
One easy way to remember what happens in a redox reaction is to learn the expression: “OIL RIG,”
which stands for:
“Oxidiation is loss
Reduction is gain”
17
Q
Cellular respiration is an important example of a redox reaction
A
C6H12O6+6O2→6CO2+6H2O+ energy
18
Q
Neutralization
A
reaction of an acid and a base to produce water and a salt.
19
Q
Ionization
A
is the dissociation of a molecule into ions. H2O→OH–+H+
20
Q
Acids
A
dissolved in water, increase the concentration of the hydrogen ions
hydrogen ion (H+) gives rise to the following characteristics of an acidic solution:
It has a sour taste.
It conducts electricity.
It turns litmus paper red.
It has a pH below 7.
strong acids ionize completely with strong bases produce salt and water
weak acids ionize prtially
21
Q
Bases
A
when dissolved in water, increase the concentration of hydroxide ions. The hydroxide ion (OH–) gives rise to the following characteristics of a base:
It has a bitter taste.
It has a slippery feel.
It turns litmus paper blue.
It has a pH above 7.
22
Q
Pure water
A
neutral because it contains an equal number of hydroxide and hydrogen ions.
23
Q
carbonic acid-bicarbonate buffer
A
buffers in the body
Proteins
Amino acids
Carbonic acid
buffer contains both an acid and a base, so it can neutralize conditions that are either too acidic or too basic.
perfect body ph is 7.4
Water + carbon dioxide ↔ carbonic acid ↔ bicarbonate ion + hydrogen ion
H2O+CO2 ↔ H2CO3 ↔ HCO−3+H+
24
Q
Macromolecules
A
big” molecules classified as polymers made up of monomers
25
Building Macromolecules: Condensation Reactions
water must be removed in a condensation reaction. It is also sometimes called a dehydration synthesis reaction (because the molecule becomes “dehydrated”) and an anabolic (building-up)
26
Breaking down macromolecules
catabolic (breaking down) reaction called hydrolysis must occur. In this reaction,
27
four macromolecules
Carbohydrates
Lipids
Proteins
Nucleic acids
28
Carbohydrates
Building materials for energy
Cell identification and communication
Carbohydrates contain: Carbon, Hydrogen, and Oxygen in a 1:2:1 ratio.
simple: Monosaccharides, Disaccharides, Oligosaccharides
complex :Polysaccharides (Starch, Glycogen, Cellulose, Chitin)
29
Monosaccharides
ne sugar” (mono = one, saccharide = sugar).
Monosaccharides are simple chains that can form rings when they dissolve in water.
All monosaccharides contain one subunit of carbohydrate.
There are two types of monosaccharide: aldoses and ketoses -C=O
Ribose, Glucose and Galactose are Aldose Monosaccharides
Ribulose and Fructose are Ketose Monosaccharides
30
ISOMERS
Glucose, Galactose and Fructose have the same chemical formula but different arrangement of atoms.
31
Disaccharides
formed when two monosaccharides combine by a covalent bond, called a glycosidic linkage, from a dehydration synthesis or condensation reaction.
Glucose + glucose → maltose + water
Glucose + fructose → sucrose + water
Glucose + galactose → lactose + water
32
polysaccharides:
```
Complex carbohydrates
pasta
Starch
Glycogen
Cellulose
Chitin
```
33
Alpha (α) 1-4 glycosidic bonds
Carbon-1 is below the glucose ring
34
Beta (β) 1-4 glycosidic bonds
Carbon-1 is above the glucose ring.
35
Amino acids:
Amino acids are the building blocks (or monomers) of proteins.
20 amino acids
8 essential form diet
Amino acids combine with other amino acids by dehydration synthesis to from peptide bonds
36
(1°) structure. protein
simple chain of amino acids joined together by peptide bonds, or a “polypeptide chain
37
secondary (2°) structure.
Secondary structures are formed by hydrogen bonds between the oxygen atoms of a carboxyl group and the hydrogen atoms of an amino group.
helix or beta pleated sheet
38
tertiary (3°) structure.
globular
| The most common are covalent bonds between sulphur atoms, called disulphide bridges.
39
quaternary (4°) structure
two or more polypeptides join together to make a functional protein
40
when are electrons stable
the closer they are to the nucleus when they are at a lower energy . thats why they take the lowest orbits first
41
group on periodic table tells you
valanence electrons
42
octect rule
eight electrons in the outer shell
| atoms bond in order to achieve the same electron configuration as a noble gas and become chemically stable
43
What does ‘polar’ mean for polar amino acids
The covalently bonded atoms in the ‘R’ side chain have some atoms that are more electronegative than others and this causes some areas of the ‘R’ chain to be more positive and some areas to be more negative, leading to a polar side chain.
44
Lipds
insoluble in water
dissolve in nonpolar liquids
energy storage yield 2x more energy than carbs or proteins
they provide physical and thermal insulation for the body, are key components in cell membranes, and act as raw materials for the synthesis of hormones.
mostly made up of hydrogen, carbon, and oxygen
45
There are four families of lipids
Fats
Phospholipids
Steroids
Waxes
46
fats
common form of energy storage and insulation in plants and animals.
composed of: one glycerol molecule
a maximum of three fatty-acid chains
Ester linkages
47
What type of chemical reaction do you think will take place when a fat molecule is formed
A condensation/dehydration synthesis, anabolic reaction
A dehydration synthesis (condensation) reaction occurs as a molecule of water is removed when the (-OH) group on the glycerol combines with the (-H) from the (-COOH) group in the fatty acid chain.
48
Saturated Fatty Acids
```
all single C–C bonds
saturated with hydrogen atoms
solids at room temperature
examples include lard and butter
has just c=o and H on end
```
49
Unsaturated Fatty Acids
one or many double bonds between carbons
at least one double C=C or triple C=C bond
not saturated with hydrogen
oils
50
Steroids
Sterols are compact hydrophobic molecules containing four fused hydrocarbon rings.
Types of sterols include cholesterol and many other important hormones.
51
Waxes
hydrophobic molecules that contain long-chain fatty acids linked to alcohols or carbon rings.
Waxes often form waterproof coatings, such as beeswax, paraffin, and the cuticle on plants’ leaves.
Waxes are used to manufacture items such as fuel, candles, and furniture polish
52
Nucleic acids
DNA (deoxyribonucleic acid)
RNA (ribonucleic acid)
ATP (adenosine triphosphate)
Nucleotide coenzymes (NAD+, NADP+, and FAD)
Nucleotides consist of a nitrogenous base, a five-carbon sugar, and a phosphate group.
joined together by a phosphodiester linkage
Adenine and guanine are called purines. They have a double-ring structure.
Cytosine, thymine, and uracil are called pyrimidines and have a single-ring structure
53
Benedict’s reagent
simple sugars - carbs
light blue reagent
of The Iodine test (using Lugol’s solution) for polysaccharides, such as starch
light brown to a deep purple- black, if starch is present.
54
Lipid Testing
Sudan IV Lipid Test
Turns from a pink to a red colour, if lipids are present.
55
Biuret’s Protein Test
Biuret’s reagent changes from light blue to a deep purple.
56
What are enzymes composed of
Enzymes are proteins; they are composed of amino acids arranged in tertiary or quaternary structures, with complex conformations (shapes).
57
How do enzymes help reactions occur
In order for a reaction to occur, the reactions have to overcome the activation energy (Ea) barrier.
The activation energy is the amount of energy that must be available in order for a reaction to occur.
Enzymes work by lowering the activation energy.
58
How does the structure of enzymes allow them to lower the activation energy of reactions and increase the speed chemical reaction?
Enzymes lower the activation energy required for the reaction to occur by attaching to the reactants and positioning them so that they are in the optimal orientation to break or make chemical bonds between them.
When reactants begin to interact with enzymes, they are called substrates.
59
induced fit.
Once the substrate begins to attach, the active site changes shape slightly to hold on to the substrate and fine-tune its position. The process of induced fit for splitting apart a molecule into two parts is shown in the following image. The process works in a similar way to combine two molecules into one.
Then, the enzyme substrate complex combines with water (hydrolysis), which changes the shape of the enzyme slightly so that the substrate can break apart
60
Coenzymes
help by moving molecules from one enzyme to another. Many coenzymes are derived from vitamins. For example, the coenzyme NAD– is a derivative of vitamin B3
61
pepsin
his enzyme is secreted into the stomach, where it breaks down proteins into smaller fragments called peptides, so that they can be broken down further in the small intestine. If this enzyme’s levels are too low, or its action is blocked (or “inhibited”), then many proteins, like gluten (found in wheat and other grain products) and casein (found in dairy products), are not completely digested, resulting in many health problems.
62
enzyme in cellular respiration
cytochrome c oxidase
helps to combine the highly reactive waste oxygen molecules produced during this process with hydrogen, to create water. If this enzyme is absent, or its function is inhibited, then the process of cellular respiration stops within seconds and death is rapid. Carbon monoxide is a potent inhibitor of this enzyme.
63
Acetylcholine
acetylcholinesterase breaks down acetylcholine
helps signals to pass between nerve cells, but the system only works if the amount of acetylcholine is strictly regulated. If this enzyme is absent or inhibited, then excessive acetylcholine will accumulate in the nerve synapses. This will cause paralysis in the muscles, including those that control breathing, and lead to death. The venom of many poisonous snakes includes chemicals that block the activity of acetylcholinesterase.
64
enzymes in bread making
amylase- from braley seeds is used to break down flour (starch) into simple sugars, which are then converted by yeast into alcohol and carbon dioxide. The carbon dioxide produced makes the bread rise.
65
how is apple juice clear
pectinase,
66
Advantages of Cellulosic Ethanol:
Using agricultural waste or switchgrass to produce ethanol would not compete with food production. This means that the critical food supplies needed to feed people would not be used for producing fuel instead.
67
Disadvantages of Cellulosic Ethanol:
Currently, there is a problem with using agricultural waste and switchgrass for ethanol production because it does not ferment as easily as other agricultural products, like corn. Because of this, it does not yet produce ethanol abundantly or cheaply
68
What is the function of an enzyme?
Enzymes lower the activation energy required for the reaction to occur by attaching to the reactants and positioning them so that they are in the optimal orientation to break or make chemical bonds between them.
Increasing the amount or concentration of a substrate or enzyme will increase the number of successful enzyme-substrate collisions, thereby increasing the enzyme activity.
After that the rate of reaction declines as the temperature increases further.
69
How does an enzyme know when to be “on” or “off” and how is enzyme activity regulated?
Enzyme inhibition: Competitive and non-competitive
Feedback inhibition
allosteric site involved
70
The allosteric site is a place on an enzyme
that will not bind substrates that bind to the active site
that will bind to other specific molecules that will change the shape of the enzyme and influence its ability to be active or not
71
Competitive
If the enzyme activation or inhibition happens on an active site,
they can bind to the active site and block the normal substrate from binding.
poison cyanide blocks the active site on cytochrome c oxidase and so stops cellular respiration
ie poisons
72
Non-competitive
If the enzyme activation or inhibition happens as a result of changes on the allosteric site,
When these regulatory molecules bind to the allosteric or regulatory site on the enzyme, they force a change in the shape of the enzyme.
The enzyme stays in the “on” or “off” position until the allosteric regulator is removed.
73
Allosteric activators
Activation of enzyme activity occurs when allosteric activators change the enzyme’s shape and stabilize it, which keeps all of the active sites available for substrates to bind to
74
Allosteric inhibitors
Inhibition of enzyme activity occurs when allosteric inhibitors bind to the allosteric site and change the enzyme’s shape and stabilize it to make all of the active sites unavailable
75
Feedback inhibition
occurs in metabolic pathways involving a series of sequential reactions in which each step is catalyzed by a specific enzyme
example of a negative feedback process because as the amount of product produced increases, the rate of the reaction decreases.
76
cell membrane
phospholipids. A phospholipid “head,” containing a phosphate group, and a long “tail,” made up of two fatty-acid chains.
The head region is classified as hydrophilic (meaning “water-loving”) because it is water-soluble.
The reason why the head end is hydrophilic is because it contains a polar phosphate (PO4) group
The tail portion of a phospholipid is hydrophobic (meaning “water-fearing”) and non-polar, because they are not water-soluble.
This means that the tail end wants to point away from water. The hydrophobic tail contains one glycerol molecule attached to two fatty-acid chains, which means that each part of the tail is attracted to fats or oils because it is made up of fatty acids.
77
whats in the phospholipid bilayer
fluid mosaic combo of lipid bilayer, the proteins, and the cholesterol
membrane are proteins and cholesterol. They can fit in because of the bends caused by the unsaturated lipid layer.
The cholesterol molecules are free to drift around within the lipid bilayer to fix any breaks in the membrane. Cholesterol also helps to maintain the fluid condition of the bilayer. At low temperatures, cholesterol keeps the phospholipids apart, and at higher temperatures, it attracts the phospholipids and stabilizes the membrane.
The proteins are called integral proteins, because they are embedded in the membrane and function as channels through which ions and other molecules can travel in and out of the cell.
One important type of protein embedded in the membrane is the glycoproteins, which are proteins with an attached carbohydrate. They act as receptor sites for hormones and aid in the cell’s adhesion to other cells.
78
Passive transport
The movement of materials across a cell membrane without using any of the cell’s energy is Passive Transport.
diffusion, osmosis, and facilitate diffusion
79
Diffusion
movement of molecules from an area of higher concentration to an area of lower concentration.
Diffusion occurs more rapidly in a gas than in a liquid and at higher temps
Large molecules cannot diffuse across cell membranes.
80
Osmosis
Water molecules move from a region of higher water (lower solute) concentration to a region of lower water (higher solute) concentration.
osmotic potential of solutions can be measured with a device called an osmometer,
osmotic potential of solutions can be measured with a device called an osmometer,
iso, hyper and hypo
81
Facilitated diffusion
```
when molecules enter cells with the aid of “helper molecules” known as transport proteins. Transport proteins move materials into or out of cells along the concentration gradient (from high concentration to low concentration), so no energy is required.
Since glucose (needs a transport proteins) is constantly being used inside cells for energy, the concentration of glucose inside the cell is lower than its concentration outside the cell.
```
82
Active transport
The movement of molecules, atoms, and ions against a concentration gradient across a cell membrane using the cell’s energy, in the form of ATP
store nutrients, waster removal, and homeostasis - low to high
An ion is drawn onto the transport protein.
ATP is used to move the ion through the membrane.
The ion is released inside, on the other side of the membrane, where its concentration is higher.
83
Endocytosis
A portion of the cell (plasma) membrane surrounds the material to be transported into the cell.
Phagocytosis is the process by which cells engulf large, solid particles. WBC
Pinocytosis is the process by which liquid droplets enter the cell, along with any small particles they may contain. This occurs in nearly all cell types, almost all of the time.
Receptor-mediated endocytosis (RME) enables the cell to acquire bulk quantities of specific substances. RME involves the use of receptors to recognize and bind molecules before they are engulfed. it is how cholesterol enters the cell. if there is too much cholesterol there are not enough receptors to bring it into the cells so it gets hard and sticks in arteries and veins forming plaque leading to CVD
84
Exocytosis
vesicles to export large molecules out of the cell. This is useful for removing large waste particles
