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MCAT > Molecules: Biochemistry > Flashcards

Molecules: Biochemistry Flashcards

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1
Q

Hydrogen bonding

A

intermolecular bonding between H and F, O, or N

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2
Q

Hydrophobic molecule

A

Nonpolar molecules aggregate together away from water due to the strong cohesive hydrogen bonding between water molecules

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3
Q

Hydrophilic molecule

A

Molecules or ionic compounds which dissolve easily in water because their negatively charged ends are attracted to the partial positive charge of water’s hydrogens while their positively charged ends are attracted to the partial negative charge of the oxygen

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4
Q

Hydrolysis

A

A macromolecule is broken into two smaller molecules through the addition of water

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5
Q

Dehydration

A

the reverse reaction of hydrolysis in which two molecules combine to form a larger molecule where water is formed as a byproduct

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6
Q

ATP hydrolysis reaction

A

Water serves as a nucleophile and attacks the electrophilic phosphoanhydride bond between the beta and gamma phosphates of the ATP molecule. The freed gamma phosphate can then be used by a kinase to phosphorylate target proteins

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7
Q

Fatty acids

A

building blocks for most complex lipids; composed of long chains of carbons (typically an even number) truncated at one end by a carboxylic acid which act as fuel for the body as they can serve as long term energy storage and their oxidation liberates large amounts of chemical energy

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8
Q

Saturated fatty acid

A

possess only single carbon-carbon bonds

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9
Q

Unsaturated fatty acid

A

posses one or more carbon-carbon double bonds

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10
Q

Triacylglycerols (triglycerides)

A

also known as fats or oils; constructed from a 3 C backbone called glycerol which is attached to 3 fatty acid chains; their function is to store metabolic energy and provide thermal insulation and padding

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11
Q

Adipocytes

A

fat cells whose cytoplasm contains almost nothing but triglycerides

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12
Q

Phospholipids

A

class of lipids built from a glycerol backbone but a polar phosphate group replaces one of the fatty acids; polar head, nonpolar tail which makes them well suited as the major strucutural component of cell membranes

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13
Q

Amphipathic

A

molecules that have a polar and nonpolar end ie. phopsholipid

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14
Q

Sphingolipids

A

class of lipids which contain a long chain fatty acid and a polar head group but the backbone molecule is an amino alcohol called shingosine

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15
Q

Phosphatids

A

class of lipids with a phosphatidic backbonde which is just another way of describing the glycerol backbone with a phosphate group attached

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16
Q

Steroids

A

four-ringed structures which include some hormones, vitamin D, and cholesterol which regulate metabolic activities

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17
Q

Terpenes

A

class of lipids that are often part of pigments in the body

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18
Q

Waxes

A

class of lipids formed by an ester linkage between a long-chain alcohol and a long-chain fatty acid

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19
Q

Vitamins

A

particular type of organic molecule that are essential, meaning they cannot be produced by the body

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20
Q

Fat-soluble vitamins

A

are transported in the body along with the fats obtained from the diet and also assist in the absorption of these fats; ie. Vitamin A and D

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21
Q

Eicosanoids

A

released from cell membranes as local hormones that regulate blood pressure, body temperature and smooth muscle contraction ie. prostaglandins

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22
Q

Lipoprotein

A

a class of proteins which contain a lipid core surrounded by phospholipids and apoproteins so that they can transport insoluble lipids in hydrophilic medium such as blood

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23
Q

Density of lipoproteins

A

when the ratio of protein to lipid is larger, the density of a lipoprotein is greater because proteins are more dense than lipids

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24
Q

Carbohydrates

A

the high concentration of C-H bonds allows for the storage of large amounts of energy (about half that of lipids) with alochols present along the carbon chain; structure of Cn(H20)n

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25
Q

Polysaccharides

A

long chains of monosaccharides formed by a dehydration reaction

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26
Q

Monosaccharides

A

single sugar molecules which the tissue can use for energy when the hydrolysis of polysaccharides occurs

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27
Q

Hexose

A

6 carbon carbohydrates ie. glucose and fructose

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28
Q

Glycogen

A

a branched glucose polymer with alpha linkages which is found in all animal cells but especially in muscle and liver cells

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29
Q

Glucose

A

hexose that can be oxidized to transfer its energy to ATP

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30
Q

Insulin

A

increases the rate of facilitated diffusion for glucose and other monosaccharides into cells

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31
Q

Starch

A

polsysaccharade made up of a large number of glucose molecules which plants use instead of glycogen for long-term energy storage

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32
Q

Cellulose

A

polysaccharide made up of glucose connected by beta linkages which is used as structural material for cell wall rather than for energy storage ie. amylose and amylopectin

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33
Q

Digestion of alpha and beta linkages

A

Humans have enzymes to digest the alpha linkages of starch and glycogen but do not have enzymes to digest the beta linkages of cellulose

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34
Q

Nucleotides

A

molecules made up of a five carbon (pentose) sugar, a nitrogenous base, and a phosphate group which are involved in comprising the building blocks of every organism’s genetic material and involved in the cell’s use of energy

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35
Q

Nucleosides

A

molecules consisting of a pentose sugar attached to a nitrogenous base

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36
Q

Nucleic acid

A

polymer of nucleotides ie. DNA, RNA

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37
Q

Phosphodiester bond

A

In DNA/RNA, it is the linkage between the 3’ C of one sugar molecule and the 5’ carbon of another (attached to phosphate group)

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38
Q

sugar phosphate backbone

A

backbone of DNA/RNA where glucose molecules are interconnected by phosphodiester bonds

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39
Q

DNA

A

deoxyribonucleic acid; contains the 4 bases adenine, guanine, thymine, and cytosine

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40
Q

Purines

A

two-ring nitrogenous bases ie. A and G

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41
Q

Pyrimidine

A

1 ring nitrogenous bases ie. C and T

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42
Q

Watson-Crick model

A

known as B form of DNA where the two strans lie antiparallel to each other bound together by hydrogen bonds between nitrogenous bases forming a double-stranded structure

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43
Q

Base pairing

A

hydrogen bonding between nitrogenous bases of DNA/RNA A-T/U and C-G

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44
Q

Antiparallel strands

A

one strand of DNA runds 5’ to 3’ while its complementary stran runs 3’ to 5’

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45
Q

Strandedness of DNA and RNA

A

DNA is double stranded while RNA is usually single stranded

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46
Q

base pairs (bp)

A

how the length of a DNA strand is measured

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47
Q

Complementary strands

A

two strands of DNA/RNA whose bases are able to hydrogen bond with each other

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48
Q

double helix

A

structure of DNA which contains two distinct grooves, the major and minor groove; each groove spirals once around the double helix every 10 base pairs

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49
Q

Number of hydrogen bonds between A-T/U

A

2

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50
Q

Number of hydrogen bonds between C/G

A

3 which means that more energy is required to separated GC bonds

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51
Q

RNA

A

ribonucleic acid is identical to DNA except that C number 2 on the pentose has a hydroxyl group attached, it is almost always single stranded and it contains the pyrimidine uracil instead of thymine and is not confined to the nucleus like DNA

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52
Q

ATP

A

adenosine triphosphate which is the main source of readily available energy for the cell

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53
Q

Amino acids

A

building blocks of proteins which contain side groups of varying physical and chemical properties

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54
Q

amide

A

an amine connected to a carbonyl carbon; creates a peptide bond which is formed via a dehydration reaction

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55
Q

side chain of amino acid

A

also called R group; each amino acid differs only in its R group which is attached to the alpha carbon

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56
Q

Categories of AA R groups

A

acidic, basic, polar, and nonpolar

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57
Q

Chirality of AA

A

alpha carbon has 4 chemically distinct groups (except for glycine) meaning that it will be chiral and will rotate plane polarized light

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58
Q

Glycine

A

Gly, G, nonpolar

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59
Q

Alanine

A

Ala, A, nonpolar

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60
Q

Valine

A

Val, V, nonpolar

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61
Q

Leucine

A

Leu, L, nonpolar

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62
Q

Isoleucine

A

Ile, I, nonpolar

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63
Q

Phenyalanine

A

Phe, F, nonpolar, aromatic

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64
Q

Tryptophan

A

Trp, W, nonpolar, aromatic

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65
Q

Methionine

A

Met, M, nonpolar

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66
Q

Proline

A

Pro, P, nonpolar

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67
Q

Serine

A

Ser, S, polar, hydroxyl group

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68
Q

Threonine

A

Thr, T, polar, hydroxyl group

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69
Q

Cysteine

A

Cys, C, polar, thiol group

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70
Q

Asparagine

A

Asn, N, polar, amine group

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71
Q

Tyrosine

A

Tyr, Y, polar, aromatic with hydroxyl group

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72
Q

Glutamine

A

Gln, Q, polar, amide group

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73
Q

Aspartic acid

A

Asp, D, acidic, carboxylic acid

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74
Q

Glutamic acid

A

Glu, E, acidic, carboxylic acid

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75
Q

Histidine

A

His, H, basic, aromatic

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76
Q

Lysine

A

Lys, K, basic, amine group

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77
Q

Arginine

A

Arg, R, basic, amine group

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78
Q

Primary structure

A

the number and sequence of amino acids in a polypeptide

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79
Q

Secondary structure

A

alpha helix or beta sheet which are reinforced by hydrogen bonds between the carbonyl oxygen of one amino acid and the hydrogen on the amino group of another

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80
Q

Conformation of protein

A

shape of protein which is determined by its primary structure

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81
Q

Tertiary Structure

A

the 3D shape formed by curls and folds of the peptide chain

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82
Q

Forces that contribute to Tertiary Structure

A
  1. Covalent disulfide bonds 2. electrostatic (ionic) interactions between acidic and basic side chains 3. hydrogen bonds 4. van der waals forces 5. hydrophobic bonding 6. kinks caused by proline
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83
Q

Cystine

A

a dimer that is formed by covalent disulfide bonds between two cysteine amino acids on different parts of the chain

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84
Q

Hydrophobic bonding

A

when side chains are pushed away from water toward the center of the protein

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85
Q

Quarternary structure

A

when 2 or more polypeptides bind together

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86
Q

Solvation layer

A

the solvent interface of any chemical compound or biomolecule that constitutes the solute; forces hydrophobic groups (if polar like water) into the inner area of the protein which is highly favorable because it allows a decrease in the size of the highly ordered solvation layer, increasing the entropy of the system

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87
Q

Denatured

A

when the native conformation is disrupted (losing most of its secondary, tertiary, and quaternary structure) so that it no longer functions

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88
Q

Denaturing agent: Urea

A

disrupts hydrogen bonds

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89
Q

Denaturing agent: Salt or change in pH

A

disrupts electrostatic bonds

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90
Q

Denaturing agent: mercaptoenthanol

A

disrupts disulfide bonds

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91
Q

Denaturing agent: organic solvents

A

disrupts hydrophobic bonds

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92
Q

Denaturing agent: heat

A

disrupts all bonds

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93
Q

Cytochromes

A

proteins which require a prosthetic heme group in order to function ie. hemoglobin and the cytochromes of the ETC in the inner membrane of the mitochondria

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94
Q

Glycoproteins

A

proteins with carbohydrate groups attached and are a component of the plasma membrane and are generally more than 50% protein ie. AB antigens on red blood cells that determine an individual’s blood type

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95
Q

Proteoglycans

A

mixture of proteins and carbohydrates and consist of more than 50% carbohydrate ; major component of the extracellular matrix

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96
Q

Two types of proteins

A

globular and structural

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97
Q

Minerals

A

dissolved inorganic ions inside and outside the cell; by creating electrochemical gradients across membranes, they assist in the transport of substances entering and exiting the cell; can combine and solidify to give strength to a matrix, and can act as cofactors assisting enzyme or protein function

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98
Q

Enzymes

A

typically globular proteins which function as catalysts lowering the energy of activation for a biological reaction, thus increasing the rate of that reaction without altering the equilibrium of the reaction

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99
Q

Substrate

A

the reactant(s) upon which an enzyme works

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100
Q

Active site

A

the location on the enzyme where the substrate binds usually with numerous noncovalent bonds

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101
Q

Enzyme-substrate complex

A

the enzyme and substrate bound together

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102
Q

Enzyme specificity

A

enzymes are designed to work only on a specific substrate or group of closely related substrates

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103
Q

Lock and key model

A

the active site of the enzyme has a specific shape like a lock that only fits a specific substrate, the key

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104
Q

Induced fit model

A

the shapes of both the enzyme and the substrate are altered upon binding which increases specificity and helps the reaction to proceed by destabilizing the substrate

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105
Q

Saturation kinetics

A

as the relative concentration of substrate increases, the rate of the reaction also increases but to a lesser and lesser degree until Vmax has been achieved

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106
Q

Vmax

A

the point at which the rate of the reaction cannot proceed any faster as all the enzymes are saturated

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107
Q

Turnover number/kcat

A

number of substrate molecules one active site can convert to product in a given unit of time when an enzyme solution is saturated; kcat = Vmax/[E]

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108
Q

Michaelis consant, Km

A

the substrate concentration at which the reaction rate is equal to 1/2 Vmax and indicates how highly concentrated the substrate must be to speed up the reaction

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109
Q

Km trend

A

if a higher concentration of substrate is needed to achieve 1/2 Vmax (km) than it must have a lower affinity for the substrate (inversely proportional to intrinsic enzyme-substrate affinity)

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110
Q

Cofactor

A

a non-protein component (minerals or coenzymes) which an enzyme requires

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111
Q

Coenzymes

A

cofactors that are organic molecules (water soluble vitamins or their derivatives)

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112
Q

Water-soluble vitamins

A

many serve as coenzymes

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113
Q

Shape of reaction rate vs pH

A

bell curve

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114
Q

Shape of reaction rate vs. temperature

A

bell curve skewed left

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115
Q

Shape of reaction rate vs substrate concentration

A

gradually rises until it levels off at Vmax

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116
Q

4 Primary means of enzyme regulation

A
  1. proteolytic cleavage 2. reversible covalent modification 3. control proteins 4. allosteric interactions
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117
Q

Allosteric interactions

A

the modifiication of an enzyme’s configuration through the binding of an activator or inhibitor at a specific binding site on the enzyme

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118
Q

zymogen (proenzyme)

A

an inactive form of an enzyme which becomes irreversibly activated when specific peptide bonds on zymogens are cleaved; activation may also be instigated by other enzymes or a change in environment (ie. pH)

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119
Q

Feedback inhibition

A

negative feedback; one of the products downstream in a reaction series comes back and inhibits the enzymatic activity of an earlier reaction

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120
Q

Positive feedback

A

one of the products downstream in a reaction series comes back and activates the enzymatic activity of an earlier reaction

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121
Q

Allosteric regulation

A

regulation of enzymes caused by molecules that do not resemble the substrates of the enzymes that they inhibit and do not bind to the active site; instead, they bind to the enzyme and cause a conformational change

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122
Q

Positiive cooperativity

A

increases in substrate concentration increase enzyme efficiency as well as the reaction rate as the first substrate changes the shape of the enzyme, allowing other substrates to bind more easily ie. hemoglobin and oxygen

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123
Q

Negative cooperativity

A

Increases in substrate concentration decrease enzyme effeciency as well as the reaction rate as the first substrate changes the shape of the enzyme so that it is more difficult for other substrates to bind

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124
Q

Irreversible inhibitors

A

agents that bind irreversibly to enzymes and disrupt their function; typically via covalent bonds

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125
Q

Competitive inhibitors

A

compete with the substrate by binding reversibly with noncovalent bonds to the active site raising the apparent Km but not changing Vmax; can be overcome by increasing the concentration of substrate

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126
Q

Uncompetitive inhibitors

A

bind at a site other than the active site but do not bind to the enzyme until it has associated with the substrate to form the enzyme-substrate complex; apparent Km decreases but Vmax is lowered because the substrate stays bound to the enzyme for a longer period of time

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127
Q

Mixed inhibitors

A

bind at a site other than the active site and bind to either the enzyme alone or the enzyme-substrate complex; depending on type either increase or decrease Km; lowers Vmax

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128
Q

Noncompetitive inhibitors

A

a special type of mixed inhibitors; bind just as readily to enzymes with a substrate as to those without to a spot other than the active site; cannot be overcome by excess substrate so they lower Vm

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129
Q

Competitive inhibition: Km and Vmax

A

Km increases, Vmax constant

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130
Q

Noncompetitive inhibition: Km and Vmax

A

Vmax decreases, Km constant

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131
Q

Oxidoreducatase

A

catalyze the transfer of electrons or hydrogen ions ie. oxidation-reduction reactions

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132
Q

Transferase

A

catalyze reactions in which groups are transferred from one location to another

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133
Q

Lyases

A

catalyze reactions in which functional groups are added to double bonds or conversely, double bonds are formed via the removal of functional groups

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134
Q

Isomerase

A

catalyze the transfer of groups within a molecule, with the effect of producing isomers

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135
Q

Ligase

A

catalyze condensation reactions coupled with the hydrolysis of high energy molecules from ATP or some other nucleotide

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136
Q

Synthase

A

the particular type of lyase that catalyzes the addition of one substrate to the double bond of a second substrate; does not require ATP

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137
Q

Synthetase

A

another name for ligase that require energy input from ATP or some other nucleotide

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138
Q

Kinase

A

enzyme that phosphorlyates a molecule to activate or deactivate it

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139
Q

Phosphatase

A

enzyme that dephosphorylates a molecule to activate or deactivate it

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140
Q

Prostaglandin

A

lipids that act as hormones which bind with receptors intracellularly (since it is a hydrophobic hormone)

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141
Q

Gene

A

nucleotide sequence that can code for a certain product or set of products; a unit of heredity that codes for a trait

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142
Q

Genome

A

the complete sequence of nucleotides of the genetic material

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143
Q

Central Dogma

A

DNA is transcribed to RNA which is translated to amino acids to form a protein

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144
Q

Epigenome

A

encompasses all of the epigenetic changes that affect gene expression

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145
Q

Histones

A

the sections of DNA that are not in use are wrapped tightly around globular proteins called histones; have basic functional groups that gives these proteins a net positive charge to attract negatively charged DNA strands and assist in wrapping porcess

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146
Q

Nucleosome

A

eight histones wrapped in DNA

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147
Q

Solenoid

A

nucleosomes wrapped into coils

148
Q

Supercoil

A

solenoids wrapped into coils f

149
Q

Chromatin

A

the entire DNA/protein complex; by mass about 1/3 DNA, 2/3 protien, and a small amount of RNA

150
Q

Euchromatin

A

uncoiled DNA which is accessible to be transcribed

151
Q

Heterochromatin

A

tightly condensed DNA which is not accessible to be transcribed

152
Q

Single copy DNA

A

nucleotide sequences represented by only one copy of a nucleotide sequence and are associated with regions of euchromatin that are being actively transcribed

153
Q

Repetitive DNA

A

present in non-coding regions of DNA which has multiple consecutive copies of the same nucleotide sequence and remains tightly coiled in regions of heterochromatin

154
Q

DNA methylation

A

example of epigenetic regulation which involves the addition of an extra methyl group to particular cytosine residues; causes DNA to be wound more tightly causing these sections to not be transcribed; can be inherited

155
Q

DNA acetylation

A

increases transcription

156
Q

non-coding RNA (ncRNA)

A

sections of RNA that do not code for protein products which contribute to the regulation of the chemical changes that affect chromatin structure

157
Q

Homologues

A

a chromosome and its partner chromosome which code for the same traits

158
Q

Diploid

A

any cell that contains homologous pairs of chromosomes

159
Q

Haploid

A

any cell that does not contain homologous pairs of chromosomes

160
Q

Polyploidy

A

when a a cell has more than 2 copies of homologous chromosomes

161
Q

Transcription

A

the process by which RNA is manufactured from a DNA template

162
Q

Translation

A

takes the nucleotide sequence of the RNA transcript and translates it into the language of amino acids, which are then strung together to form a functional protein

163
Q

Initiation (transcription)

A

a group of transcription factors identifies a promoter on the DNA strand, at the promoter the transcription factors assemble into a transcription initiation complex , RNA polymerase unzips the DNA double helix creating a transcription bubble

164
Q

Transcription factors

A

DNA binding proteins

165
Q

Promoter

A

a sequence of DNA nucleotides that designates a beginning point for transcription; help regulate where on the genome transcription can take place and how often certain sequences are transcribed

166
Q

Consensus sequence

A

the most commonly found promoter nucleotide sequence recognized by a given species of RNA polymerase; variation from this sequence causes RNA polymerase to bond less tightly which leads to the associated genes being transcribed less frequently

167
Q

Elongation (transcription)

A

RNA polymerase transcribes only 1 strand of the DNA nucleotide sequence into a complementary RNA nucleotide sequence; moves 3 to 5’ but transcribes 5’ to 3’

168
Q

Template/antisense strand

A

the transcribed strand of DNA

169
Q

Coding/sense strand

A

non-transcribed DNA strand that protects its partner against degradation; complementary to template strand

170
Q

Termination

A

the end of transcription which occurs when a specific sequence of nucleotides known as the termination sequence is reached

171
Q

Activators

A

bind to DNA close to the promoter to activate activity of RNA polymerase

172
Q

Repressor

A

bind to DNA cose to the promoter to repress activity of RNA polymerase

173
Q

Enhancer

A

short, non-coding regions of DNA found in eukaryotes; function similarly to activators but act at a much greater distance from the promoter

174
Q

Jacob-Monod model

A

model of prokaryotic genetic regulation; the genetic unit consists of the operator, promoter, and genes that contribute to a single prokaryotic mRNA (the operon)

175
Q

Lac operon

A

codes for enzymes that allow E.coli to import and metabolize lactose in the absence of glucose; activated when glucose is scarce and lactose is present; cAMP binds to and activates CAP which binds to a CAP site upstream of the lac promoter

176
Q

Catabolite activator protein (CAP

A

binds to a CAP site upstream of the promoter of the lac operon and activates it allowing for transcription and then translation of lac proteins ; example of positive control

177
Q

Lac operator

A

located downstream of the promoter; when lactose is not present, a lac repressor protein binds to the operator site and prevents transcription of lac genes; ex. of gene repression; when lactose is available it binds to lac repressor protein making it unable to bind to operator and transcription occurs

178
Q

Primary transcript

A

the initial RNA nucleotide sequence arrived at through transcription also called pre-mRNA or heterogeneous nuclear RNA, hnRNA

179
Q

5’ cap

A

post-transcription modification that serves as an attachment site in protein synthesis during translation and as a protection against degradation by exonucleases

180
Q

poly-A tail

A

post-transcription modification that has been added to the 3’end which aids in the export of mature RNA to cytoplasm after splicing and serves a role in helping to initiate translation, also protects from degradation

181
Q

Splicing

A

post-transcriptional modification where portions of the primary transcript are excised and discarded

182
Q

Introns

A

non-coding regions of DNA, often excised through splicing

183
Q

Exons

A

coding regions of DNA that often become part of the mature mRNA

184
Q

snRNPs

A

small nuclear ribonucleoproteins; contains an assortment of proteins and snRNA; during the splicing proces, they act as a ribozyme and splicing occurs when snRNPS recognize nucleotide sequences at the end of introns and pull the ends of the introns together forming a lariat

185
Q

Ribozyme

A

an RNA molecule capable of catalyzing specific chemical reactions

186
Q

Spliceosome

A

the complex formed from the association of the snRNPs and additional associate proteins; excises the introns and joins the ends of the exons together

187
Q

Alternative splicing

A

allows the cell to incorporate different variable coding sequences into the mature mRNA; different splicing patterns of the same gene can create different polypeptides

188
Q

Degnerative genetic code

A

more than one series of 3 nucleotides may code for the same amino acid

189
Q

Codon

A

3 consecutive nucleotides on a strand of mRNA

190
Q

Stop/termination codons

A

UAA, UGA, UAG; signal an end to protein synthesis

191
Q

Initiation codon

A

AUG; indicates where translation will begin; codes for methionine

192
Q

Wobble pairing

A

flexibility in the bonding at the third base pair position in the codon and anticodon which explains why multiple codons can code for the same amino acid

193
Q

Ribosome

A

composed of a small subunit and large subunit both made up of rRNA where translation occurs

194
Q

Small/large subunits of ribosome

A

measured in terms of sedimentation coefficients in Svedberg units (S); 30S and 50S in prokaryotes (70S) and 40S and 60S in eukaryotes (80S)

195
Q

Nucleolus

A

manufactures ribosomes in eukaryotes

196
Q

Initiation (translation)

A

with the help of initiation factors the 5’ end of the mRNA attaches to the small subunit of a ribosome, a tRNA containg the 5’ CAU 3’ anticodon sequester the AA methionine and settles into the P site; this is the signal for the large subunit to join and form the initiation complex; most regulation of translation occurs during this step

197
Q

Elongation (translation)

A

the ribosome slides down the mRNA strand one codon at a time in the 5’ to 3’ direction, a new AA ataches to A site, the C terminus of methionine attaches to N terminus of amino acid at A site by peptidyl transferase , ribosome shifts, tRNA carrying methionine moves to E site and peptide is now in P site

198
Q

Termination (translation)

A

translation ends when the ribosome reaches a stop codon; when this happens, proteins known as release factors bind to the A site allowing a water molecule to add to the end of the polypeptide chain and the polypeptide is freed from the tRNA and ribosome , and the ribosome breaks up into its subunits to be reused later

199
Q

Chaperones

A

proteins that assist in the folding process of polypepyides

200
Q

Post-translational modification of proteins

A

these modifications are a mechanism for regulating gene expression by affecting which products ultimately become funciton; i/e adding sugar, lipid or phosphate groups , cleavage

201
Q

Signal peptide

A

20 amino acid sequence near front of polypeptide that is recognized by SRP that carries the entire ribosome complex to a receptor protein on the ER, mitochondria, nucleus or other organelles

202
Q

SRP

A

signal recognition particle

203
Q

Where does translation occur?

A

begins on free-floating ribosomes in cytosol and may be directed to other organelles if it ocntains a signal peptide

204
Q

Semiconservative replication

A

because each copy contains 1 strand from the original DNA and the one newly synthesized strand

205
Q

Origin of replication

A

replication does not begin at the end of the chromosome but toward the middle at a site called the origin of replication

206
Q

Replication unit/ replicon

A

each chromosome of eukaryotic DNA is replicated in many discrete segments called replicons

207
Q

DNA helicase

A

unwinds the double helix, separating the 2 strands

208
Q

DNA polymerase

A

synthesizes the new DNA strans by pairing complementary free-floating deoxynucleotides with the sequence of nucleotides on the exposed strands of DNA; cannot initiate replication without a primer

209
Q

Primase

A

an RNA polymerase that creates an RNA primer to initiate the strand

210
Q

Single strand binding (SSB) tetramer proteins

A

aka helix destabilizer proteins; prevents the single strand in the loop from folding back on itself

211
Q

Lagging strand

A

interrupted strand which is formed from a series of disconnected strands called Okazaki fragments

212
Q

5 main steps of DNA replication

A
  1. helicase unzips double helix 2. primase builds a primer 3. DNA polymerase assembles leading and lagging strands 4. RNAse H removes the primers 5. DNA ligase joins the Okazaki fragments together
213
Q

DNA ligase

A

joins together neighboring Okazaki fragments to form a completed copy of double-stranded DNA helix

214
Q

Telomere

A

repeated nucleotide units that the protect the ends of chromosomes; shortened by repeated rounds of replication , a condition that has been linked to aging and disease

215
Q

Telomerase

A

catalyzes the lengthening of telomeres in eukaryotic organisms

216
Q

Mitosis

A

a nuclear division without genetic change; it consists of a series of steps that organize and divide replicated chromosomes

217
Q

Prophase

A

condensation of chromatin into chromosomes, centrioles move to opposite poles of the cell, nucleolus and nucleus disappear as nuclear envelope breaks down , spindle apparatus begins to form

218
Q

Centromere

A

group of proteins that join together sister chromatids

219
Q

Centrioles

A

located in centrosomes

220
Q

Spindle apparatus

A

consists of astersm kinetochores, and spindle microtubules

221
Q

Asters

A

microtubules radiating from the centrioles

222
Q

Spindle microtubules

A

connect the 2 centrioles

223
Q

Kinetochore

A

a structure of protein and DNA located at the centromere of the joined chromatids of each chromosome; grows from centromere

224
Q

Metaphase

A

chromosomes align along the equator of the cell which ensures that they will be separated such that each daughter cell receives one of each chromosome

225
Q

Anaphase

A

sister chromatids split at their attaching centromeres and segregate to opposite sides of the cell; shortening of kinectochores pull the sister chromatids apart and moves them toward opposite poles; cytokinesis may begin to occur

226
Q

Disjunction

A

split of sister chromatids

227
Q

Cytokinesis

A

the actual separation of the cellular cytoplasm due to constriction of microfilament around the center of the cell

228
Q

Telophase

A

the nuclear membrane reforms, followed by the reformation of the nucleolus; chromosomes decondense ; cytokinesis continues

229
Q

Mutation

A

any alteration in the genome that is not due to genetic recombination

230
Q

Spontaneous mutation

A

occurring due to random errors in the natural process of replication and recombination

231
Q

Induced mutation

A

occur due to mutagens

232
Q

Mutagen

A

damage DNA and increase the frequency of mutation above the baseline frequency of spontaneous mutation

233
Q

Gene mutation

A

alteration in the sequence of DNA nucleotides in a single gene

234
Q

Chromosomal mutation

A

occurs when the the structure of a chromosome is changed

235
Q

Somatic mutation

A

mutation in a somatic cell which is not passed to offspring

236
Q

Point mutation

A

if a mutation changes a single nucleotide in a double strand of DNA ie. base substitution, addition, deletion

237
Q

Transition mutation

A

a base substitution exchanging one purine for another purine and vice versa

238
Q

Transversion mutation

A

a base subsitution exhanging one pyrimidine for a purine or vice versa

239
Q

Base substitution mutation

A

results when one nucleotide is swapped for another during DNA replication

240
Q

Addition mutation

A

inserting a new nucleotide into the sequence

241
Q

Deletion mutation

A

deleting a nucleotide from the sequence

242
Q

Silent mutation

A

type of neutral mutation in which the amino acid sequence is unchanged

243
Q

Missense mutation

A

base substitution changes a codon, creating a missense codon which results in the translation of a different AA

244
Q

Nonsense mutation

A

change to the nucleotide sequence creates a stop codon where none previously existed

245
Q

Frameshift mutation

A

when the deletions or additions occur in multiples other than 3; changes the reading frame

246
Q

Chromosomal deletion

A

portion of the the chromosome breaks or is lost during homologous recombination and/or crossing over events

247
Q

Duplication

A

when a DNA fragment breaks free of one chromosome and incorporates into a homologous chromosome

248
Q

Gene duplication/amplification

A

increase the amount of a gene’s product

249
Q

Translocation

A

when a segment of DNA from one chromosome is exchanged for a segment of DNA on another chromosome

250
Q

Inversion

A

the orientation of a section of DNA is reversed on a chromosome

251
Q

Transposons/transposable elements

A

DNA segments that excise themselves from a chromosome and reinsert themselves at another location

252
Q

Proto-oncogenes

A

certain genes that stimulate normal growth in human cells

253
Q

Oncogenes

A

genes that cause cancer

254
Q

Carcinogens

A

mutagens that cause cancer

255
Q

Tumor suppressor genes

A

help regulate normal cell growth ie. retinoblastoma nd p53 proteins which act at checkpoints during the cell cycle

256
Q

Gametes

A

haploid reproductive cells

257
Q

Meiosis I

A

separates homologus chromosomes to produce 2 haploid cells m each with one copy of the 23 chromosomes

258
Q

Prophase I

A

homologous chromosomes line up alongside each other, matching their genes exactly and exchange DNA via crossing over leading to genetic recombination

259
Q

Importance of genetic recombination

A

provides variation in the genetic makeup of gametes and their offspring

260
Q

Tetrad

A

the side by side homologues exhibiting a total of 4 chromatids

261
Q

Synaptonemal complex

A

the complex of 2 homolgous chromosomes zipped along each other where nucleotides are exchanged during crossing over

262
Q

Chiasma

A

the point where 2 chromosomes are attached creating an X shape during crossing over

263
Q

Gene linkage

A

increases the likelihood that certain traits will be inherited together

264
Q

Gene mapping

A

determines the locations and relative distances of genes on chromosomes from the rates o single and double crossover events

265
Q

Metaphase I

A

2 homologues remain attached and move to the metaphase plate

266
Q

Anaphase I

A

homologous chromosomes each separate from their partner, independently assorting to create 2 haploid cells

267
Q

Telophase I

A

nuclear membrane may or may not reform and cytokinesis may or may not occur (although both do in humans)

268
Q

Meiosis II

A

appears much like mitosis

269
Q

Nondisjunction

A

if during anaphase I or II the centromere of any chromosome does not split

270
Q

Primary nondisjunction

A

nondisjunction in anaphase I, one cell will have an extra chromosome and the other will be missing a chromosome

271
Q

Secondary nondisjunction

A

nondisjunction in anaphase II, one cell having one extra chromatid and the one cell lacking one chromatid

272
Q

Gametogenesis

A

the production of gametes

273
Q

Spermatogonium

A

undergoes mitosis to produce 2 diploid copies known as primary spermatocytes

274
Q

Spermatocytes

A

each undergo meiosis I to each become 2 spermatids

275
Q

Spermatid

A

undergo maturation (loses cytoplasm and gains a tail) to become a sperm

276
Q

Oogonium

A

undergoes mitosis to produce 2 primary ooctyes but arrest at prophase I until puberty

277
Q

Primary oocyte

A

completes meiosis I producing a secondary oocyte (the other daughter cell receives no cytoplasm and is discarded which is called a polar body)

278
Q

Secondary oocyte

A

completes meiosis II only when penetrated by a sperm during the act of fertilization, during meiosis II another polar body will be discarded; arrest at metaphase II and released at ovulation

279
Q

Ovum

A

matures from ootid after meiosis II

280
Q

Zygote

A

results from the joining of the genetic material of the sperm and ovum

281
Q

Mendelian ratio

A

3:1 F2 generation of F1 x F1

282
Q

Locus

A

position on chromosome

283
Q

Allele

A

codes for a specific outcome in a particular trait

284
Q

Wild type

A

the most common allele type for a certain trait within a population

285
Q

Genotype

A

individual’s genetic makeup

286
Q

Phenotype

A

expression of trait

287
Q

Complete dominance

A

dominant allele masks expression of the recessive allele

288
Q

Law of Segregation

A

alleles segregate independently of each other when forming gametes during meiosis so that any gamete is equally likely to possess any allele

289
Q

Penetrance

A

the probability of a gene or allele being expressed if it is present ie. in complete dominance the penetrance of the dominant allele is 100%

290
Q

Expressivity

A

measure of how much the genotype is expressed as a phenotype; the degree of expression of a trait

291
Q

Incomplete dominance

A

when a heterozygous individual exhibits a phenotype that is intermediate between its homozygous counterparts

292
Q

Co-dominant

A

if the heterozygote expresses both phenotypes ie. blood type

293
Q

Law of Independent Assortment

A

genes located on separate chromosomes assort independently of each other, such that genes that code for distinct traits when located on separate chromosomes do not affect each other during gamete formation

294
Q

Phenotypic ratio of dihybrid cross

A

9:3:3:1

295
Q

Sex-linked

A

genes located on the sex chromosomes

296
Q

Gene pool

A

total collection of all alleles in a population

297
Q

Glycolysis

A

the breakdown of glucose into pyruvate; can occur with or without oxygen; occurs in cytosol of all living cells; energy input/six-carbon phase and energy output/three-carbon phase; produces a net total of 2 ATP and 2 NADH; rate -limiting step: synthesis of fructose 1,6 bisphosphate

298
Q

Substrate-level phosphorylation

A

the phosphate group being donated to ADP is initially attached to another molecule and is transferred to DP by a kinase enzyme

299
Q

Fermentation

A

anaerobic respiration (metabolism in absence of oxygen); includes glycolysis as well as the reduction of pyruvate to ethanol or lactic acid and the oxidation of NADH back to NAD+ (which allows glycolysis to continue)

300
Q

Cori Cycle

A

lactic acid expelled from cells is transported through the blood to the liver, where it is oxidized back to pyruvate, this pyruvate is converted to glucose and can be sent back to other tissues to help produce ATP

301
Q

Pentose phosphate pathway (PPP)

A

begins with G6P creates NADPH (to be used for anabolic functions) and some five carbon sugars like ribose for nucleotides; oxidative branch (production of NADPH); non-oxidative branch (five carbon sugar)

302
Q

Glycogenesis

A

the storage of glycogen

303
Q

Gluconeogenesis

A

synthesis of glucose from non-carbohydrate products such as proteins and lactic acid; reverse of glycolysis; occurs in liver

304
Q

Beta-oxidation

A

factty acids oxidized to acetyl-CoA; occurs in mitochondrial matrix; first fatty acids are converted into acyl-CoA, at the expense of 1 ATP, along outer membrane of the mitochondrion, the acyl-CoA is then brought into the matrix where it is cleaved 2 carbons at a time to make acetyl-CoA; produces FADH2 and NADH for every 2 carbons taken from the original fatty acid

305
Q

Ketogenesis

A

in mitochondria of liver cells, fatty acids are converted into a ketone body which can be shared with other organs for energy; occurs during a prolonged fast when the body is no longer able to synthesize sufficient glucose

306
Q

Ketone bodies

A

acetone, acetoacetic acid and beta-hydroxybutyrate; spare glucose for the brain and RBCs by providing an alternative source of energy for other organs;

307
Q

Lipoprotein

A

complex of lipid and protein produced primarily in the liver, intestines and adipocytes and are expelled from these cells via exocytosis

308
Q

Chylomicrons

A

primary transport molecules that carry lipids from the intestines to the liver where they are repackaged into VLDLs or HDLs

309
Q

Very low density lipoproteins (VLDL)

A

transport lipids such as triglycerides, phospholipids, and cholesterol from the liver to other parts of the body such as muscle and adipocytes

310
Q

High density lipoproteins (HDL)

A

pick up stray fatty acids and trigylcerides from the periphery and bring them to the liver

311
Q

Lipase

A

hydrolyzes triglycerides and releases free fatty acids into the bloodstream

312
Q

Protein anabolism

A

occurs primarily during the fed state and should be associated with glycolysis, glycogenesis, and lipid storage

313
Q

Protein catabolism

A

occurs primarily during the fasting state and should be associated with gluconeogenesis, glycogenolysis, beta oxidation, and ketone body synthesis

314
Q

Insulin and glucose levels

A

insulin is released from the pancreas in response to increased blood glucose levels and promotes glycolysis in tissues, glycogenesis in liver and muscle, fatty acid synthesis in liver, and fatty acid storage in adipocytes; promotes ketogenesis in late starvation

315
Q

Glucagon

A

released from the pancreas in response to decreased blood glucose levels and promotes glycogenolysis in the liver and muscle, gluconeogenesis in liver, fatty acid release in adipocytes and beta oxidation in almost all tissues

316
Q

Epinephrine/cortisol and glucose levels

A

released in response to stress and promotes glycogenolysis, the removal of glucose from storage and gluconeogenesis

317
Q

Oxidative phosphorylation

A

occurs when oxidation reactions provide the energy for phosphorylation; requires the presence of oxygen as a final electron acceptor

318
Q

Citric acid cycle/TCA/Krebs Cycle

A

begins with acetyl CoA transferring 2 carbons to the 4 carbon oxaloacetate; 2 carbons are lost as CO2 and oxaloacetate is regenerated; each turn produces 1 ATP, 3 NADH and 1 FADH2 for a total of 2 ATP, 6 NADH, and 2 FADH2

319
Q

Electron transport chain (ETC)

A

series of proteins that carries electrons from NADH to O2 ie. ubiquinone and cytochrome c; Complex I receives 2e- from NADH and pumps 4H+ across membrane, Complex II receives e-s from FADH2 and transfers them to a quinone carrier, Q to make QH2; Complex III receives the electrons from QH2 and transfers them to cytochrome c, resulting in movement of 4 H+ across membrane; complex IV removes the electrons from cytochrome c and transfers them to oxygen moving 2 H+ across the membrane

320
Q

Proton-motive force

A

proton gradient from proteons being pumped into mitochondrial intermembrane space

321
Q

ATP synthase

A

the protons diffuse back into mitochondrial membrane through ATP synthase generating ATP (chemiosmotic coupling)

322
Q

NADH/ATP ratio

A

2 or 3 ATP per NADH molecule

323
Q

FADH2/ ATP ratio

A

2 ATP per FADH2 molecule

324
Q

Obesity

A

body index above 30

325
Q

Type I diabetes

A

autoimmune disease where the immune system attacks the beta cells of the pancreas and as a result insulin levels are almost nonexistent

326
Q

Type II diabetes

A

characterized by increasing resistance to action of insulin at the target cell

327
Q

Separations

A

variety of lab techniques that use intermolecular forces to separate a mixture into its component parts

328
Q

Extraction

A

separation technique based on solubility; inovles 2 immiscible layers, commonly an aqueous layer and a less dense organic layer; substance of interest is drained

329
Q

Distillation

A

technique used to separate compounds that have significantly different boiling points; compound with lower boiling point will boil off first

330
Q

Fractional distillation

A

more precise method of distillation that can be used to separate liquids whose boiling points are fairly close together; vapor is run through glass beads, allowing the compound with the higher boiling point to repeatedly condense and fall back into solution

331
Q

Crystallization

A

pure substances form crystals more easily than impure substances; used to purify solid compounds; difficult to arrive at pure substance

332
Q

Chromatography

A

separation of a mixture by passing it over or through a matrix that adsorbs different compounds more or less strongly according to their properties, ultimately altering the rate at which they lose contact with the matrix

333
Q

Column chromatography

A

solution containing the mixture is dripped down a column containing the solid phase (polar); the more polar compounds in the mixture travel more slowly down the column, creating separate layers for each compound; compounds collected as elutes

334
Q

High pressure liquid chromatography (HPLC)

A

column and solution use an appratus that puts the system under high pressure

335
Q

Paper chromatography

A

a small portion of the sample to be separated is spotted onto paper; one end of the paper is then placed into a nonpolar solvent; the solvent moves up the paper via capillary action and dissolves the sample as it passes up; the polar components move more slowly because they are attracted to the polar paper

336
Q

Rf factor

A

distance of component/distance of solvent line; nonpolar substances have Rf closer to 1

337
Q

Thin-layer chromatography

A

similar to paper chromatography except that a coated glass or plastic plate is used instead of paper and the results are visualized via an iodine vapor chamber

338
Q

Size-exclusion chromatography

A

molecules are separated by their size through gel filtration; larger molecules elute first as smaller molecules must navigate through pores on gel

339
Q

Ion-exchange chromatograpy

A

molecules are separated based on their net surface charge; utlizies cationic or anionic exchangers that slow down the movement off charged molecules

340
Q

Affinity chromatography

A

uses highly specfic interactions to slow down select molecules; receptor-ligand, enzyme-substrate, antigen-antibody

341
Q

Gel electrophoresis

A

molecular mixture is placed in a gel and an electric field is applied; larger particles move more slowly in the agarose gel; because nucleic acids are negatively charged they migrate through the gel in response to the electric field

342
Q

Southern blotting

A

tecnique used to identify target fragments of a known DNA sequence in a large population of DNA; 1. chop up DNA 2. use gel electrophoresis to spread out pieces 3. southern blot into a membrane 4. add a radioactive probe made from DNA/RNA 5. visualize

343
Q

Northern blot

A

just like southern blot but identifies RNA fragments not DNA fragments

344
Q

Western blot

A

used to detect a particular protein in a mixture of proteins; similar to Southern blot with regards to overall technique

345
Q

Separation of enantiomers

A

use differences in crystallization or add stereospecefic enzyme that will react with only one enantiomer

346
Q

Nuclear magnetic resonance spectroscopy

A

study of the interaction between atomic nuclei and radio waves; aldehyde: 9.5 ppm; carboxylic acid: 10-12 ppm; benzene: 8 ppm; alcohol: 1-5 ppm; methyl: <1 ppm

347
Q

Splitting

A

caused by neighboring hydrogens that are not chemically equivalent; number of peaks = n +1 where n is the number of neighboring hydrogens that are not chemically equivalent

348
Q

Chemical shift

A

the difference between the resonance frequency of the chemically shifted hydrogens and the resonance frequency of hydrogens on a reference compound

349
Q

Integral trace

A

a line drawn above the peaks that rises each time it goes over a peak; the rise of the integral trace is proportional to the number of chemically equivalent hydrogens in peak beneath it

350
Q

IR spectroscopy

A

reveals functional groups due to intramolecular vibrations and rotations; bond must have a ipole moment or no energy will be absorbed; carbonyl: 1700 cm-1; OH: broad dip 3200-3600; aldehyde: twin peaks 2800-3000; N-H: 3300 (small with no carbonyl and bumpy and large for amide)

351
Q

Fingerprint region

A

complex vibrations that distinguish one compound from a similar compound are found in the 600 to 1400 cm-1 region

352
Q

UV spectroscopy

A

detects conjugated systems

353
Q

Mass spectometry

A

used to determine a compound’s molecular weight

354
Q

Molecular ion

A

the original molecule with one less electron created from mass spectrometry

355
Q

Parent peak

A

peak made by the molecular ion

356
Q

Base peak

A

peak with the most abundance

357
Q

Nucleic acid hybridization

A

allow scientists to identify nucleotide sequences by binding a known sequence with an unknown sequence (DNA-DNA, DNA-RNA, RNA-RNA); can be used to find a particular gene in a gene library

358
Q

Restriction enzymes

A

digest/cut nucelic acids only at certain nucleotide sequences along the chain (such sequences are called restriction sites or restriction sequences)

359
Q

Gene cloning

A

accomplished either through bacteria and a cDNA library or through PCR

360
Q

Vector

A

typically a plasmid or sometimes an infective virus with the gene of interest

361
Q

cDNA

A

DNA produced from mRNA using reverse transcriptase

362
Q

PCR

A

need primers, nucleotides, polymerase; 1. denature (heat) 2. anneal primers (cool) 3. polymerization repeat (heat)

363
Q

Microarray/gene chip

A

compares the levels of mRNA between 2 cells and/or conditions `

364
Q

Restriction fragment length polymorphism (RFLP)

A

human population is polymorphic at restriction sites thus it can be used to identify individuals

365
Q

Single nucleotide polymorphisms (SNPs)

A

the genome of one human differs from the genome of another at about one nucleotide in every 1000; can identify individuals

366
Q

Human gene therapy

A

involves genetic manipulation of an affected individual’s DNA in which the defective allele is replaced by the wild type

367
Q

Biometry

A

the use of statistical methods to understand biological data

MCAT (5 decks)

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