EK Bio 1.1 Flashcards
1
Q
a-helix
A
Secondary Structure of Proteins and is a right handed helix.
2
Q
b-pleated sheet
A
Secondary Structure in Protein. Less common then a-Helix. Formed by hydrogen bonds (beta-stands) connecting latterly. 3-10 AA long in extended position.
3
Q
1/2 Vmax
A
The amount of substrate needed for the reaction to occur at 1/2 its max possible rate.
4
Q
Active Site
A
where substrate molecules bind and undergo a chemical reaction
5
Q
Adenine (A)
A
Bind with Thymine or Uracil (Double bond). Is a purine.
6
Q
Adipocytes
A
specialized in storing energy as fat.
7
Q
Allosteric Activator
A
attaches to a site on the enzyme other than the active site and increases the efficiency or the affinity of the enzyme for its substrate.
8
Q
Allosteric inhibitors
A
molecules that attach to a site on the enzyme other than the active site and inhibit the function of that enzyme.
9
Q
Allosteric interactions
A
.
10
Q
Allosteric regulation
A
the regulation of an enzyme or other protein by binding an effector molecule at the protein’s allosteric site. (Not enzyme active site)
11
Q
Amide
A
-CONH2 group
12
Q
Amino acids
A
composed of amine (-NH2) and carboxylic acid (-COOH) functional groups, along with a side-chain specific to each amino acid.
13
Q
Amphipathic
A
chemical compound possessing both hydrophilic (water-loving, polar) and lipophilic (fat-loving) properties
14
Q
Antiparallel
A
run parallel to each other but with opposite alignments
15
Q
ATP
A
coenzyme used as an energy carrier in the cells of all known organisms; the process in which energy is moved throughout the cell
16
Q
Base Pairs (bp)
A
form between specific nucleobases (also termed nitrogenous bases), are the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA.
17
Q
Carbohydrates
A
A carbohydrate is a biological molecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms, usually with a hydrogen:oxygen atom ratio of 2:1…. Cm(H2O)n
18
Q
Catalyst
A
Lowers Activation energy of a reaction to increase the rate of a chemical reaction
19
Q
Cellulose
A
an organic compound with the formula (C6,H10,O5)n, a polysaccharide consisting of a linear chain of several hundred to many thousands of β(1→4) linked D-glucose units.
20
Q
Coenzymes
A
A organic nonprotein component of enzymes. Many of the coenzymes are derived from vitamins. They make up a part of the active site, since without the coenzyme, the enzyme will not function. Example: NAD+ coenzyme is involved with many types of oxidation reactions where alcohols are converted to ketones or aldehydes.
21
Q
Cofactor
A
nonprotein component of enzymes
22
Q
Competitive Inhibitor
A
binding to the active site on the enzyme prevents binding of the substrate. They function by binding reversibly to the active site of the enzyme
23
Q
Complementary Strand
A
following the lock-and-key principle. either of the two chains that make up a double helix of DNA, with corresponding positions on the two chains being composed of a pair of complementary bases.
24
Q
Conformation
A
The precise shape of a protein or other macromolecule in three dimensions resulting from the spatial location of the atoms in the molecule. A small change in the conformations of some proteins affects their activity considerably.
25
Cystine
sulfur-containing amino acid that is formed from two molecules of the amino acid cysteine. Cystine is particularly abundant in skeletal and connective tissues and in hair, horn, and wool.
26
Cytosine (C)
Pyrimidine (Hexagon)
| Three hydrogen bonds with Guanine
27
Dehydration
involves the loss of a water molecule from the reacting molecule.
28
Denatured
a structural change in macromolecules caused by extreme conditions
29
Double Helix
arises as a consequence of its secondary structure, and is a fundamental component in determining its tertiary structure.
30
Double Stranded DNA
According to base pairing rules (A with T and C with G), hydrogen bonds bind the nitrogenous bases of the two separate polynucleotide strands to make double-stranded DNA.
31
Entropy
(usual symbol S) is a measure of the number of specific ways in which a thermodynamic system may be arranged, commonly understood as a measure of disorder.
32
Enzyme Specificity
comes from their unique three-dimensional structures. Example DNA Polymerase
33
*Enzyme-Substrate Complex
The intermediate formed when a substrate molecule interacts with the active site of an enzyme. Following the formation of an enzyme–substrate complex, the substrate molecule undergoes a chemical reaction and is converted into a new product. Various mechanisms for the formation of enzyme–substrate complexes have been suggested, including the induced-fit model and the lock-and-key mechanism.
34
Enzymes
are biological molecules (proteins) that act as catalysts and help complex reactions occur everywhere in life
35
Fat-Soluble Vitamins
(DEKA) Body stores them in the liver and adipose (fat) tissue when not used.
36
*Fats
Fat molecules are made up of:
a molecule of glycerol (on the right) and
three molecules of fatty acids
Each fatty acid consists of a hydrocarbon chain with a carboxyl group at one end. The glycerol molecule has three hydroxyl groups, each able to interact with the carboxyl group of a fatty acid. Removal of a water molecule at each of the three positions forms a triglyceride
37
Fatty Acids
1) Any of the group of a long chain of hydrocarbon derived from the breakdown of fats (through a process called hydrolysis). It has a single carboxylic group and aliphatic tail.
2) sub-units of fats, oils and waxes
38
FeedBack Inhibition
occurs when the end product of a reaction interferes with the enzyme that helped produce it.
39
Glucose
molecular formula C6H12O6.
it is classed as a hexose, a sub-category of monosaccharides
Glucose is made during photosynthesis from water and carbon dioxide, using energy from sunlight.
Glucose may be stored in plants as the polymers starch and cellulose.
40
Glycerol
The glycerol backbone is central to all lipids known as triglycerides.
41
Glycogen
is a multibranched polysaccharide of glucose that serves as a form of energy storage in animals[2] and fungi. The polysaccharide structure represents the main storage form of glucose in the body.
In humans, glycogen is made and stored primarily in the cells of the liver and the muscles, and functions as the secondary long-term energy storage (with the primary energy stores being fats held in adipose tissue). Muscle glycogen is converted into glucose by muscle cells, and liver glycogen converts to glucose for use throughout the body including the central nervous system.
42
Guanine (G)
Trippe bond with C. Purine
43
Hexoses
is a monosaccharide with six carbon atoms, having the chemical formula C6H12O6.
44
Hydrogen Bonding
is the electrostatic attraction between polar molecules that occurs when a hydrogen (H) atom bound to a highly electronegative atom such as nitrogen (N), oxygen (O) or fluorine (F) experiences attraction to some other nearby highly electronegative atom
45
Hydrolysis
means the cleavage of chemical bonds by the addition of water.
46
Hydrolases
is an enzyme that catalyzes the hydrolysis of a chemical bond.
A–B + H2O → A–OH + B–H
47
Hydrophilic
is a molecule or other molecular entity that is attracted to, and tends to be dissolved by, water
48
Hydrophobic
is seemingly repelled from a mass of water.[1] (Strictly speaking, there is no repulsive force involved; it is an absence of attraction.)
49
Hydrophobic Bonding
interaction of nonpolar (un-ionizable) hydrocarbon molecules forced together because of stronger water-water interaction.
50
Induced fit model
This model proposes that the initial interaction between enzyme and substrate is relatively weak, but that these weak interactions rapidly induce conformational changes in the enzyme that strengthen binding.
51
irreversible inhibitors
usually covalently modify an enzyme, and inhibition can therefore not be reversed.
Irreversible inhibitors are generally specific for one class of enzyme and do not inactivate all proteins; they do not function by destroying protein structure but by specifically altering the active site of their target.
52
isomerases
a general class of enzymes which convert a molecule from one isomer to another. Isomerases can either facilitate intramolecular rearrangements in which bonds are broken and formed or they can catalyze conformational changes. The general form of such a reaction is as follows:
A–B → B–A
53
Km
substrate concentration that is required for the reaction to occur at 1/2 Vmax
54
Ligases
In biochemistry, ligase (from the Latin verb ligāre — "to bind" or "to glue together") is an enzyme that can catalyze the joining of two large molecules by forming a new chemical bond, usually with accompanying hydrolysis of a small chemical group dependent to one of the larger molecules or the enzyme catalyzing the linking together of two compounds, e.g., enzymes that catalyze joining of C-O, C-S, C-N, etc. In general, a ligase catalyzes the following reaction:
Ab + C → A–C + b
or sometimes
Ab + cD → A–D + b + c + d + e + f
where the lowercase letters signify the small, dependent groups.
Ligase can join two complementary fragments of nucleic acid and repair single stranded breaks that arise in double stranded DNA during replication.
55
Lipids
Lipids are a group of naturally occurring molecules that include fats, waxes, sterols, fat-soluble vitamins, monoglycerides, diglycerides, triglycerides, phospholipids, and others. The main biological functions of lipids include storing energy, signaling, and acting as structural components of cell membranes
56
Lock and key model
A model for enzyme-substrate interaction suggesting that the enzyme and the substrate possess specific complementary geometric shapes that fit exactly into one another
57
Lyases
is an enzyme that catalyzes the breaking (an "elimination" reaction) of various chemical bonds by means other than hydrolysis (a "substitution" reaction) and oxidation, often forming a new double bond or a new ring structure.
58
Michaelis Constant
a constant that is a measure of the kinetics of an enzyme reaction and that is equivalent to the concentration of substrate at which the reaction takes place at one half its maximum rate
59
Minerals
naturally occurring substance that is solid and inorganic
60
Mixed Inhibitors
is a type of enzyme inhibition in which the inhibitor may bind to the enzyme whether or not the enzyme has already bound the substrate but has a greater affinity for one state or the other.[1] It is called "mixed" because it can be seen as a conceptual "mixture" of competitive inhibition, in which the inhibitor can only bind the enzyme if the substrate has not already bound, and uncompetitive inhibition, in which the inhibitor can only bind the enzyme if the substrate has already bound
61
Monosaccharides
also called Simple Sugar, any of the basic compounds that serve as the building blocks of carbohydrates. Monosaccharides are polyhydroxy aldehydes or ketones; that is, they are molecules with more than one hydroxyl group (−OH), and a carbonyl group (C=O) either at the terminal carbon atom (aldose) or at the second carbon atom (ketose). The carbonyl group combines in aqueous solution with one hydroxyl group to form a cyclic compound.
62
Negative Cooperativity
means as ligands bind to the protein, the protein's affinity for following ligands will decrease
63
Negative Feedback
the diminution or counteraction of an effect by its own influence on the process giving rise to it, as when a high level of a particular hormone in the blood may inhibit further secretion of that hormone, or where the result of a certain action may inhibit further performance of that action.
64
Noncompetitive inhibitors
A type of enzyme inhibition where the inhibitor reduces the activity of the enzyme and binds equally well to the enzyme whether or not it has already bound the substrate.
A type of enzyme inhibition where the inhibitor reduces the activity of the enzyme and binds equally well to the enzyme whether or not it has already bound the substrate.
65
Nucleic acids
are made from monomers known as nucleotides
66
Nucleoside
Nucleosides are glycosylamines that can be thought of as nucleotides without a phosphate group.
67
Nucleotides
has three components: a 5-carbon sugar, a phosphate group, and a nitrogenous base. If the sugar is deoxyribose, the polymer is DNA. If the sugar is ribose, the polymer is RNA.
68
Oxidoreductases
is an enzyme that catalyzes the transfer of electrons from one molecule, the reductant, also called the electron donor, to another, the oxidant, also called the electron acceptor. This group of enzymes usually utilizes NADP or NAD+ as cofactors.
For example, an enzyme that catalyzed this reaction would be an oxidoreductase:
A– + B → A + B–
In this example, A is the reductant (electron donor) and B is the oxidant (electron acceptor).
In biochemical reactions, the redox reactions are sometimes more difficult to see, such as this reaction from glycolysis:
Pi + glyceraldehyde-3-phosphate + NAD+ → NADH + H+ + 1,3-bisphosphoglycerate
In this reaction, NAD+ is the oxidant (electron acceptor), and glyceraldehyde-3-phosphate is the reductant (electron donor).
69
Phosphatids
.
70
Phosphodiester bonds
is the linkage between the 3' carbon atom of one sugar molecule and the 5' carbon atom of another, deoxyribose in DNA and ribose in RNA. Strong covalent bonds form between the phosphate group and two 5-carbon ring carbohydrates (pentoses) over two ester bonds.
71
Phospholipids
are a class of lipids that are a major component of all cell membranes as they can form lipid bilayers
72
Polypeptides
are chains of amino acids.
73
Polysaccharides
are polymeric carbohydrate molecules composed of long chains of monosaccharide units bound together by glycosidic linkages and on hydrolysis give the constituent monosaccharides or oligosaccharides. They range in structure from linear to highly branched. Examples include storage polysaccharides such as starch and glycogen, and structural polysaccharides such as cellulose and chitin.
74
Positive cooperativity
change in shape of the first subunit makes easier the binding of substrate to the second subunit,
75
Primary Structure
The primary structure of a peptide or protein is the linear sequence of its amino acid structural units, and partly comprises its overall biomolecular structure
76
Proline
When proline is in a peptide bond, it does not have a hydrogen on the α amino group, so it cannot donate a hydrogen bond to stabilize an α helix or a β sheet. It is often said, inaccurately, that proline cannot exist in an α helix. When proline is found in an α helix, the helix will have a slight bend due to the lack of the hydrogen bond.
Proline is often found at the end of α helix or in turns or loops. Unlike other amino acids which exist almost exclusively in the trans- form in polypeptides, proline can exist in the cis-configuration in peptides. The cis and trans forms are nearly isoenergetic. The cis/trans isomerization can play an important role in the folding of proteins and will be discussed more in that context.
77
Prostaglandins
Prostaglandins, are like hormones in that they act as chemical messengers, but do not move to other sites, but work right within the cells where they are synthesized.
78
Purines
G A
79
Pyrimidines
C T
80
Saturated fatty acids
have no double bonds between the individual carbon atoms of the fatty acid chain.
81
Saturation Kinetics
.an enzyme reaction in which there is enough enzymes to constantly have a substrate bound them and therefore the reaction is occurring at Vmax. This velocity is only limited by the concentration of substrates, not the enzyme
82
Side Chain
the functional group(s) attached to the constant or regularly repeating backbone
83
Solvation Layer
."From my understanding, Solvation layer "entropy" is in context of protein folding in aquaeous solution. Think "surface area". Protein unfolding= more surface area = more disorder = increase entropy for protein. Protein folding = less surface area = more order = decrease entropy of protein. In term of aquaeous solution (surrounding) , it's opposite. Protein unfolding = increase entropy for protein = decrease water entropy = not favorable for water. Protein folding = decrease entropy for protein = increase water entropy = more favorable.
Labrat07 SDN
84
Sphingolipids
.has three parts, a three carbon chain with two alcohols and amine attached and a long hydrocarbon chain. In sphingomyelin, the base sphingosine has several other groups attached as shown in the graphic on the left. A fatty acid is attached to the amine through amide bond. Phosphate is attached through a phosphate ester bond, and again through a phosphate ester bond to choline. The human brain and spinal cord is made up of gray and white regions. The white region is made of nerve axons wrapped in a white lipid coating, the myelin sheath, which provides insulation to allow rapid conduction of electrical signals. Multiple sclerosis caused by a gradual degradation of the myelin sheath.
85
Starch
is a carbohydrate consisting of a large number of glucose units joined by glycosidic bonds.
86
Substrates
is a molecule upon which an enzyme acts.
87
Sugar-Phosphate Backbones
The sugar phosphate backbone is an important stuctural component of DNA. It consists of 5-carbon deoxyribose sugars and phosphate groups. These sugars are linked together by a phosphodiester bond, between carbon 4 of their chain, and a CH2 group that is attached to a phosphate ion.
88
Transferases
class of enzymes that enact the transfer of specific functional groups (e.g. a methyl or glycosyl group) from one molecule (called the donor) to another (called the acceptor).
89
Triacylglycerols
is an ester derived from glycerol and three fatty acids..
90
Uncompetitive Inhibitors
.also known as anti-competitive inhibition, takes place when an enzyme inhibitor binds only to the complex formed between the enzyme and the substrate (the E-S complex).
91
Unsaturated fatty acids
At least one double bond
92
Vitamins
.
93
Water-soluble Vitamins
dissolve in water and are not stored by the body. Since they are eliminated in urine, we require a continuous daily supply in our diet. The water-soluble vitamins include the vitamin B-complex group and vitamin C.
94
Vmax
rate of reaction when the enzyme is saturated with substrate is the maximum rate of reaction,
95
Zymogen
.(or proenzyme) is an inactive enzyme precursor. A zymogen requires a biochemical change (such as a hydrolysis reaction revealing the active site, or changing the configuration to reveal the active site) for it to become an active enzyme.
96
Cysteine
Sulfur-containing nonessential amino acid. When two Cysteine AA bond a disulfide bridge is formed, a principal factor in the shape and function of skeletal and connective tissue proteins and in the great stability of structural proteins such as keratin.
