Biochemistry Flashcards

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Remember the basic structure and nomenclature of each amino acid, understand their chemical properties and classification,

Hello! This is an amino acid set by Fadil Nohur, aka fiddle_n. Here are a list of the 20 amino acids coded in the genome. Amino acids vary in their difficulty for learning. Some amino acids are easy to learn, whilst some defy memorisation (yes, tryptophan, I'm looking at you!). All amino acid pictures have been painstakingly edited and uploaded by none other than me, for your learning pleasure! Have fun learning, and maybe give me a high five if you feel like it ;)

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8721614164	alanine	Methyl R-group	0
8721614165	valine	2 Methyl R-group	1
8721614166	leucine	4 extra C	2
8721614167	isoleucine	Methyl moved to beta C	3
8721614168	glycine	H instead of R	4
8721614169	proline	Cyclic Shape	5
8721614170	cysteine	-SH R-group (thiol)	6
8721614171	methionine	Only one with -S	7
8721614172	phenylalanine	Benzene as R group	8
8721614173	tryptophan	Pentene-benzene R group	9
8721614174	tyrosine	phenol as R	10
8721614175	asparagine	Amide 1 C away	11
8721614176	glutamine	Amide 2 C away	12
8721614177	serine	Hydroxy as R	13
8721614178	threonine	Methyl and Hydroxy as R	14
8721614179	lysine	Amine 4 Cs away	15
8721614180	histidine	Imidazole (ring), under very acidic conditions both H get deprotonated	16
8721614181	arginine	4 N's, 3 Cs away	17
8721614182	aspartic acid	Carboxyl 1 C away, found deprotonated in cells	18
8721614183	glutamic acid	Carboxyl 2 C away, found deprotonated in cells	19
8721614184	S configuration	R/S configuration of Amino Acids	20
8721614185	L- enantiomer	The amino group is to the left	21
8721614186	R- enantiomer	The amino group is to the right	22
8721614187	Glycine	Only amino acid that is achiral	23
8721614188	Peptides	Covalent bond chain of amino acid residue. Requires condensation of two amino acids, forming H20	24
8721614189	Dipeptide	2 Amino Acids linked	25
8721614190	Oligopeptide	2-20 amino acid residue chain	26
8721614191	Polypeptides	Over 20 peptide chain, but less than 50	27
8721614192	Protein	Over 50 amino acids linked together	28
8721614193	The C=N bond has delocalization of electrons due to resonance, making it very stable.	The peptide bond is rigid because...	29
8721614194	Break a Polypeptide Bond	Requires 1 water molecule and hydrolytic enzymes to... (This process is commonly found in the digestive system)	30
8721614195	linear	The primary structure of a protein is...	31
8721614196	from amino to carboxy	In the primary structure of proteins the sequence is read...	32
8721614197	Hydrogen bonding between the oxygen of the carboxy and N of the amino group	In secondary structures the alpha-helix and beta-pleated sheets are stablilized by by...	33
8721614198	strengthen the helix shape because of the repulsive interactions with the surrounding environment	The R groups in the secondary structure alpha-helix...	34
8721614199	pointing up, while the other half point down	Half of the R groups in the beta-pleated sheets are..	35
8721614200	it contains kinks in its peptide	Proline affects tertiary structure of proteins because...	36
8721614201	Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline	Non Polar and Non Aromatic Side Chain	37
8721614202	Tryptophan, Phenylalanine, Tyrosine	Aromatic Side Chain	38
8721614203	Serine, Threonine, Asparagine, Glutamine, Cysteine	Polar Side Chain	39
8721614204	Aspartic Acid, Glutamic Acid	Negatively Charged Side Chain and Acidic	40
8721614205	Arginine, Lysine, Histidine	Positively Charged Side Chain and Basic	41
8721614206	Alanine, Leucine, Isoleucine, Valine, Phenylalanine	Hydrophobic and found inside of proteins	42
8721614207	Histidine, Lysine, Arginine, Glutamate, Aspartate	Hydrophilic and found on the surface of proteins because charge	43
8721614208	Zwitterion	Neutral Amino Acid because has negative and positive charges on it.	44
8721614209	Amphoteric	Can be protonated or deprotonated	45
8721614210	Isoelectric point (pI)	Average 2 pka values below/above neutral (if more than 2 pka values, the average the ones that are closest together until you have two). Half protonated and other half is deprotonated at this point.	46
8721614211	Tertiary Structures	3D shape of 1 polypeptide chain that is stabilizied by hydrophobic interactions (hydrophobic amino acids inside protein and hydrophilic amino acids on the surface), acid-base interactions (salt bridges), H-bonding within protein between amino and carboxyl end of proteins, Disulfide bonds (oxidation of cysteine to cystine)	47
8721614212	Quartenary Structures	Interactions between peptides in a protein that has many subunits	48
8721614213	Lyases, Isomerase, Ligase, Hydrolase, Oxidoreductase, Transferase	Lil Hot	49
8721614214	Lyases	They cleave molecules into two molecules without water	50
8721614215	Isomerase	They help change molecules from 1 isomer to another, such as a constitutional to stereoisomer	51
8721614216	Ligase	They help add molecules together, usually large biomolecules that are the same	52
8721614217	Hydrolase	They use water to break molecules apart	53
8721614218	Oxidoreductase	Aid in the facilitation of oxidation-reduction reactions	54
8721614219	Transferase	They aid in the movement of functional groups from one molecule to another	55
8721614220	Lock and Key	Substrate and enzyme are complimentary and fit with one another.	56
8721614221	Induced- Fit	The Active site of the enzyme changes to compliment the substrate	57
8721614222	Co-factors	Metal cations used to aid in enzyme activity	58
8721614223	Saturation Kinetics	As substrates increases so does the reaction rate, until it reaches a point where it no longer does	59
8721614224	Temperature, pH, Salinity	Factors affecting Enzyme Activity	60
8721614225	Competitive Inhibition	Inhibitor competes with substrate for the active site of the enzyme. Adding more substrate overcomes this type of inhibition.	61
8721614226	Non Competitive Inhibition	Inhibitor has same affinity for enzyme and enzyme-substrate complex. It binds to the allosteric site of the enzyme.	62
8721614227	Km increases, while the Vmax stays the same, adding more substrate	In Competitive inhibition the inhibitor causes the km to ________ and vmax_________. Can overcome effects by____________	63
8721614228	Stays the same, decreases	In Non Competitive inhibition the km _____, while the Vmax ________	64
8721614229	Mixed Inhibition	Inhibitor has unequal affinity for the enzyme and enyzyme-substrate complex.	65
8721614230	Uncompetitive Inhibition	Inhibitor only binds to enzyme-substrate complex. Works best when theres more ES and more enzyme.	66
8721614231	Deprotonation	pH > pka	67
8721614232	Protonation	pka > pH	68
8721614233	Alanine	A	69
8721614234	Asparagine or Aspartic Acid	B	70
8721614235	Alanine	Ala	71
8721614236	Cysteine	C	72
8721614237	Cysteine	Cys	73
8721614238	Aspartic Acid	D	74
8721614239	Aspartic Acid	Asp	75
8721614240	Glutamic Acid	E	76
8721614241	Glutamic Acid	Glu	77
8721614242	Phenylalanine	F	78
8721614243	Phenylalanine	Phe	79
8721614244	Glycine	Gly	80
8721614245	Glycine	G	81
8721614246	Histidine	His	82
8721614247	Histidine	H	83
8721614248	Isoleucine	I	84
8721614249	Isoleucine	Ile	85
8721614250	Lysine	Lys	86
8721614251	Lysine	K	87
8721614252	Leucine	Leu	88
8721614253	Leucine	L	89
8721614254	Methionine	Met	90
8721614255	Methionine	M	91
8721614256	Asparagine	Asn	92
8721614257	Asparagine	N	93
8721614258	Proline	P	94
8721614259	Proline	Pro	95
8721614260	Glutamine	Gln	96
8721614261	Glutamine	Q	97
8721614262	Arginine	Arg	98
8721614263	Arginine	R	99
8721614264	Serine	Ser	100
8721614265	Serine	S	101
8721614266	Threonine	Thr	102
8721614267	Threonine	T	103
8721614268	Valine	Val	104
8721614269	Valine	V	105
8721614270	Tryptophan	W	106
8721614271	Tryptophan	trp	107
8721614272	Tyrosine	Tyr	108
8721614273	Tyrosine	Y	109
8721614274	Glutamine or Glutamic Acid	Z	110
8721614275	Oxidation	More Oxygen bonds are added, and less Hydrogen bonds	111
8721614276	Reduction	Less Oxygen bonds, and more Hydrogen bonds	112
8721614277	Transition Metals	Metals that change colors when they are oxidized	113
8721614278	Hemoglobin	This protein can hold 4 Oxygen molecules in total, and after the first Oxygen molecule has binded its conformation shifts to increase the affinity for more Oxygens	114
8721614279	Protonated	Amino Acids in low pH are found _____	115
8721614280	deprotonated	Amino Acids in high pHs are found ________	116
8721614281	cDNA	DNA that only contains the exons of a strand and made from reverse transcription of RNA. Purpose is to sequence specific genes, identify disease causing mutations, produce recombinant proteins or produce transgenic animals.	117
8721614282	Hill Coefficient	Tells you if protein exhibits cooperativity. If it is greater than 1 yes, if at 1 no.	118
8721614283	Gel Electrophoresis	Uses to separate macromolecules, such as proteins (kDa) and DNA (#base pairs, kilobases), based on size and charge. For DNA, use agarose gels because it weeds out large molecules because larger pores. Negative ions to cathodes, while positive ions to anode. Shows bands with smaller sizes farther away and larger sizes closer.	119
8721614284	Michaelis Menten Experiment	Keep enzyme concentration level, manipulate substrate concentration (by adding usually) to get Km and Vmax in the presence or absence of inhibitor.	120
8721614285	Sense, coding, non-template strand	DNA strand that RNA polymerase II doesnt bind to during transcription. But is the same as the mRNA made	121
8721614286	Antisense, noncoding, template strand	DNA strand that RNA polymerase II binds to during transcription. Complements mRNA strand.	122
8721614287	km increases, and the vmax decreases	In Mixed inhibition if the inhibitor favors the Enzyme more than the enzyme substrate the km_________ and the vmax__________	123
8721614288	km decreases and the vmax decreases	In Mixed Inhibition if the inhibitor favors the enzyme substrate more than the enzyme the km_______ and the vmax ___________	124
8721614289	km decreases and the vmax decreases	In uncompetitive inhibition the km________ and the vmax_________	125
8721614290	Competitive inhibition	The lineweaver burke plot shows km gets larger (line shifts to right of non inhibitor), but crosses the same point on the y axis (vmax)	126
8721614291	Noncompetitive Inhibition	The lineweaver burke plot shows the inhibitor present and inhibitor not present lines intersect at x axis and for the inhibitor present line it is higher than the inhibitor not present line (vmax gets smaller)	127
8721614292	Mixed Inhibition	The lineweaver burke plot shows an intersection somewhere in the plot not on an axis	128
8721614293	Uncompetitive Inhibition	The lineweaver burke plot shows no intersection only parallel lines.	129
8721614294	Km	at 1/2vmax it is the substrate concentration at which half of the enzymes active sites are full. High km means that theres more substrate not bound to enzyme, so enzyme has low affinity for substrate. At low km means there is not a lot of substrate unbound to enzyme so the enzyme must really like the enzyme.	130
8721614295	Enzyme Saturation Kinetics	At substrate concentrations below km adding more substrate greatly increases the rate of the raction, but at concentration higher than km the reaction rate does not increase that much faster as it reaches vmax.	131
8721614296	SDS PAGE	It is a way of separating proteins due to only their mass. It uses SDS a detergent to denature the protein. It is best for determining small size differences in proteins. We expect smaller protein fragments to travel farther (might be considered more compact)	132
8721614297	Native PAGE	It is a protein isolation technique that analyzes proteins in their native states. Separation is based off of charge and mass. Smaller/more charged/more compact proteins are more mobile than larger/not charged/less compact proteins.	133
8721614298	mutarotation	It is the rapid conversion of different anomers of a sugar. So in glucose it goes from alpha to beta.	134
8721614299	Tollens Reagent	Uses Ag(NH3)2 to detect reducing sugars by using the aldehyde of the sugar to reduce Ag+ to a metallic silver	135
8721614300	Benedicts Reagent	used to detect reducing sugars by oxidizing the aldehyde, which is indicated by a red precipitate.	136
8721614301	Terpenes	Precursors to steroid hormones. (C5H8) are units of isopropene.	137
8721614302	Triterpenes	Precursors to cholesterol	138
8721614303	Steroids	3 cyclohexanes and 1 cyclopentane	139
8721614304	2	pka of carboxylic group on amino acid	140
8721614305	9	pka of amino group on amino acid	141
8721614306	10	pka of side chain of lysine	142
8721614307	12	pka of side chain of arginine	143
8721614308	6	pka side chain of histidine	144
8721614309	4	pka of glutamic and acidic acid	145
8721614310	Triglyceride	Storage form of fatty acid	146
8721614311	Fatty Acid	Fuel source for the body that consist of carboxylic head and hydrocarbon tail. Synthesis (from Acetyl CoA) occurs in the liver and in the cytoplasm of those liver cells. They are oxidized in the mitochondria to provide energy.	147
8721614312	Beta oxidation	Is the reverse of fatty acid synthesis. Occurs in the liver in the mitochondria of cells. Purpose is to make Acetyl coA that will drive gluconeogenesis.	148
8721614313	Chromatography	Used to separate proteins and other macromolecules, like nucleic acids. Forms bands of different compounds in column	149
8721614314	High Performance Liquids Chromatography (HPLC)	used to separate proteins based on polarity for small amounts. Stationary phase is silica beads and mobile phase is organic solvent. Compound will stick to silica/aluminum if polar, will move quickly down if nonpolar with organic solvent.	150
8721614315	Size Exclusion	Chromatography where proteins are separated based on size. The beads (stationary phase) have pores in them to let small proteins go through, so less retention rate, while larger proteins get stuck higher up the stationary phase.	151
8721614316	Ion exclusion	Chromatography where proteins are separated based on charge. Beads are charged, and so compounds with opposite charge are attracted to them, while those with the same charge are repelled and move down column quickly	152
8721614317	Affinity	Chromatography where beads are coated with antibody or enzyme that has high affinity for a protein, so compound gets lodged in the stationary phase and the rest of the mixture goes down the column.	153
8721614318	Peptide Hormones	Type of hormone that does not require transport proteins to remain soluble in the blood stream because they are hydrophilic and soluble in blood.	154
8721614319	Positive control	Controls where a phenomenon is expected.	155
8721614320	Lactose	Hemiacetal that can be further reduced. in Beta position. Galactose + glucose	156
8721614321	epimer	diastereoisomer that is different at one chiral center	157
8721614322	Maltose	2 glucose. Hemiacetal. Alpha position. Hemiacetal	158
8721614323	Sucrose	Glucose + furctose. Acetal. Alpha position.	159
8721614324	D-Fructose	Ketohexose	160
8721614325	D-mannose	Aldohexose. Man with gun	161
8721614326	D-galactose	Aldohexose	162
8721614327	D-ribose	Aldopentose. Everythings All Right	163
8721614328	Denaturing Gel	For mRNA and DNA that are large and single stranded, this type of gel causes them to move like long rods (like double stranded DNA) instead of their clumped 3D structures.	164
8721614329	melting temperature	temperature at which a protein is 50% denatured or unfolded	165
8721614330	Nuclear Localization	Signaling that tells proteins (such as nuclear factors) that they can enter the nucleus of the cell	166
8721614331	Transcription Factors	Also known as nuclear factors that have a DNA-binding site, so bind to response elements or specific nucleotide sequences. Also have activation domain, which is also known as the protein binding domain because they bind to other transcription factors.	167
8721614332	DNA Binding Site	Site in transcription factors that bind to response elements	168
8721614333	Activation Domain	Site that allows transcription factors to bind to other proteins or transcription factors	169
8721614334	Signal sequence domain	Its the sequence that tells the cell that a protein will be secreted out of the cell. This sequence makes ribosomes translating in the cytoplasm to move to the Rough Endoplasmic Reticulum.	170
8721614335	Hydrophobic	Types of amino acids that are best for protein-protein interactions, such as dimerization.	171