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Biochemistry > module 3 amino acids > Flashcards

module 3 amino acids Flashcards

1
Q

what performs most of the work in cells

A

proteins

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2
Q

how many different proteins found in the human body

A

20,000

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3
Q

What are the 5 key functions of protein in the body

A

transport, hormones, catalysis, structure, protection

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4
Q

what role does protein play in transportation in the body

A

help move molecules around cells and organism;

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5
Q

which blood based molecule carries oxygen to lungs and tissue

A

hemoglobin

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6
Q

what role does protein play in hormones

A

messenger between cells

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7
Q

which protein based hormone during childbirth help women pelvic ligaments to relax

A

relaxin

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8
Q

what role does protein play in catalysis

A

in catalysis: enzymes speed up reactions

example: enzyme break down protein in cell to help organism recycle proteins

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9
Q

which enzyme is added to laundry detergent to remove stains with protein

A

protease

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10
Q

what role does structure play in proteins

A

gives strength to cells, organelles and tissues

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11
Q

what is found in cartilage, skin and tendon that helps maintain structure

A

collagen

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12
Q

what role does proteins play in providing protection

A

body protects from outside protein and toxins to fight pathogens and invaders

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13
Q

what are an example of proteins that provide protection

A

anti-bodies

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14
Q

how many different amino acids are there

A

20

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15
Q

How many amino acids are essential and non-essential

A

essential: 9

non-essential: 11

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16
Q

What are the essential amino acids

A

phenylalanine, valine, tryptophan, threonine, isoleucine, methionine, histidine, leucine, and lysine.

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17
Q

what are the 3 basic components of an amino acid

A

an amine group, carboxyl group, alpha carbon

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18
Q

what indicates the unique part of an amino acid

A

the “R” : side chain of the amino acid

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19
Q

how do we group side chains

A

by charge, size and polarity

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20
Q

what is physiological pH and how are amino acids shown

A

7.4

almost all amino acids have lost the carboxyl group(-COOH) and gained a proton in the amine group(-NHs)

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21
Q

what are the first set of amino acids call

A

non- polar aliphatic and are simple as they are straight chain

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22
Q

which amino acids are considered non-polar aliphatic

A

glycine, alanine, valine, leucine, isoleucine, proline, methionine

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23
Q

why do scientists have abbreviations

A

helpful to name a long string of amino acids connected to make a polymer structure

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24
Q

what is the size of aliphatic amino acids, where do they reside and are they water loving?

A

aliphatic amino acids are small( able to connect with other aliphatic amino acids), live inside the protein and go away from water( hydrophobic)

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25
Q

what is significant regarding the structure of proline

A

have a side chain that is backbone to nitrogen

unique structure: allows for increased stability and structure

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26
Q

what are non-aromatic amino acids

A

similar to aliphatic as they are non-polar and side chain is a ring- not as small as aliphatic but larger to maintain a rigid structure

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27
Q

what are the 3 amino acids considered non-aromatic

A

tyrosine; tryptophan, phenylalanine- abbreviation are found by phonetics; T, W , F

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28
Q

what are the characteristics of polar neutral amino acids

A

side chain has a dipole and most can hydrogen bond

can interact with water and found outside of protein and connecting with water

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29
Q

what are the amino acids considered polar and neutral

A

Serine, Threonine, Asparagine, Cysteine and Glutamine

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30
Q

what is unique about acid amino acids

A

their side chains have a pKa of less than 7 and losing proton in acidic environment and at physiological pH are negatively charged

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31
Q

what are the 2 acid amino acids and their abbreviations

A

aspartic acid Asp, D

Glutamic acid Glu, E

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32
Q

what are the characteristics of basic amino acids

A

side chains have pkA greater than 7 and are positively charged
found near water and polar charged because of hydrogen bond
in protein found near residue to interact with positive and negative charges

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33
Q

what are the basic amino acids and their abbreviations

A

Arginine: Arg, R
Lysine: Lis, K
Histidine: His, H

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34
Q

what is unique about histidine

A

does not have a charged group on its side chain

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35
Q

what happens with histidine at lower pH

A

pKa of side HN could be 6.00 and indicated by double dagger

at physiological pH= no charge

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36
Q

what is a unique property of cysteine and what can form?

A

side chain is un-charged, but 2 cysteine can react to form a disulfide bond- by sulfur atom which creates a covalent bond

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37
Q

what is the function of a disulfide bond

A

stabilize protein structure when present

common in amino acids that appear outside of the cell

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38
Q

which protein is made of disulfide bonds and is responsible for strength of hair and strong bonds maintain shape

A

keratin

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39
Q

what forms when amino acids are put together in a chain

A

polypeptide

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40
Q

proteins are considered?

synthesized from how many amino acids

A

large: macromolecule
100-300 amino acids
select proteins have 29,000

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41
Q

what dictates the sequence of the amino acids and where does synthesis happen

A

cells dna dictate sequence

synthesis at ribosome: amino acids are linked together in a chain covalently

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42
Q

how does a dipeptide form

A

amine group of one amino acid reacts with carboxyl group of the second and water is released

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43
Q

what is gained and lost in the formation of a dipeptide bond and what type of reaction is it

A

1 oxygen from carboxyl group and 2 H from amine group as water is released
condensation reaction

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44
Q

what is the definition of a peptide

A

rigid amine bond formed from 2 proteins bonding together- have reactive amine and carboxyl groups on the end allowing for bonding with other amino acids

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45
Q

define oligopeptide

A

short chain of amino acids: 2-20

could see the word peptide interchabaly used

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46
Q

what are N and C when discussing peptides

A

N-terminal: amine end

C-terminal: carboxyl end

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47
Q

How would you name a 4 amino acid bond( tetrapeptide) of alanine, glutamate, cysteine, serine
single letter and 3 letter

A

A-E-C-S
ala-glu-cys-ser
also named 4 residue

48
Q

what is the protein backbone

A

formed from peptide bonds in the protein-all form this- links all amino acids together
side groups point away from protein backbone

49
Q

what are amino acids referred to in peptide bonds

A

residue

reflect the molecule structure after condensation reaction

50
Q

what is a polypeptide

A

molecule with 99 or less amino acid( residue)

51
Q

when is protein status given to a peptide

A

when over 100 amino acid( residue) in the bond

52
Q

what is the mass of proteins and how is it written

A

10,000 g/mol or 10kDa

k=kilo or 1,000

53
Q

what is supramolecular chemistry

A

chemistry of large compounds

54
Q

define conformation

A

thousands of amino acids joined together in a 3D structure- either fibrous or globular

55
Q

define intrinsically disordered

what is the exception to the rule

A

random conformation

proteins that are intrinsically disordered and functional

56
Q

what do proteins need to do be functional

A

adopt a structure as structure and function are vitally connected

57
Q

what are the 4 standard levels of protein structure

A

primary, secondary, tertiary, quaternary

58
Q

Describe primary structure for protein

A

order of amino acid covalently bonded in peptide chain-includes disulfide bonds

59
Q

what do scientists use to describe primary structures

A

1- letter abbreviations and often fill 2 lines

60
Q

what is the process for describing a primary structure

A

start with the N-terminal and work the sequence until the end C-terminal
this is useful for describing polar and non-polar stretches in the protein-
allows proteins to be studied and compared to others- usually by computer software

61
Q

what is the secondary structure

A

used to examine local 3D structure of amino acid residue close in sequence

62
Q

what are three parts of secondary structure

A

alpha-helice, beta-sheet and beta-turn

63
Q

what are alpha-helices

A

coiled structures of amino acids that is stabilized by the backbones of hydrogen bonds

64
Q

In the helix- how many amino acid residue per turn and how many as it rises

A

3.6 per turn while rising and 5.6 angstrom per turn.

65
Q

what does 1 angstom=

A

1.0x10-10

66
Q

which amino acids are found in the helix and which are less likely

A

likely to be found: alanine, arginine, leucine

less likely: proline and glycine

67
Q

Is there a space in the helix

A

no: it is solid though it looks like its hollow from diagrams

68
Q

In the helix where do the R groups point

A

away from the helix so that they can interact with with other chains, water or chemicals

69
Q

what is a beta-sheet

A

repetitive sheet like structure that is extended in zig zag fashion that put adjacent side groups as far apart as possible

70
Q

what forms a beta-sheet

A

individual beta strands that interact by creating hydrogen bonds with other beta strands

71
Q

what are the 2 forms of beta-sheet

A

parallel and anti-parallel

72
Q

How do anti-parallel beta sheets form

A

from single beta sheets that when the sheet ends it turns back on itself allowing a second single beta sheet to join and creates the anti-parallel sheet
Turn around is named anti-parallel because N->C direction is opposite of the arrow

73
Q

How does a parallel beta sheet form

A

2 single beta sheets are lined parallel to each other

74
Q

How do anti-parallel and parallel beta sheets differ

A

The hydrogen bonding is different and the distance of the repeat is unique to each one
parallel repeats every 6.5 angstrom and anti-parallel every 7 angstrom

75
Q

what percent of amino acids are found in the turn?

A

30%

76
Q

what do turns allow and what is the name of a common one

A

allow for proteins to make secondary structures next to each other
beta-turn

77
Q

Describe a beta-turn

A

4 residue unit that can turn 180 degrees
looks like a rope
can form with both alpha helix and beta-sheet

78
Q

what is a motif

A

collection of stable group of secondary structures

79
Q

what is an example of a motif

A

helix-turn-helix or

alpha helix followed by beta-turn followed by alpha helix

80
Q

what is the tertiary structure

A

OVERALL 3D structure of folded polypeptide

includes all the secondary structure and unstructured region of protein as a whole

81
Q

what maintains the tertiary structure that is necessary to function

A

disulfide bonds and non-covalent forces

82
Q

which protein is critical in muscle cells for binding and storing oxygen

A

myoglobin

83
Q

describe the myoglobin tertiary structure

A

8 alpha helices connected by turns and unstructured regions

84
Q

what is in the center of the protein myoglobin

A

a heme ring holds onto oxygen

85
Q

what is the heme ring called and what is the function

A

prosthetic group- non- amino acid necessary to maintain structure and function of the protein

86
Q

what is the stability range for proteins

A

20-65 kj/mol

87
Q

what is a protease inhibitor

A

tertiary structure that inhibits protease: globular shape

88
Q

which proteins fit into a fibrous class

A

keratin, collagen

fibrous proteins are long extended structure of alph-helices

89
Q

what does the quantnary structure describe

A

describes macromolecules that have 2 or more polypeptide chains that associate with one another

90
Q

what constitutes the quantary structure

A

the number and orientation of the independent chains

91
Q

what is the name of the protein that has 2 identical polypeptide chains and how is it described

A

staphlokinase: each polypeptide is positioned over the other
dimer: called a dimer as it has two polypeptides and so 2 subunits

92
Q

what is the name of a quanternary structure that has 4 subunits
what are the names of the subunits

A

hemoglobin and tetramer
2 alpha
2 beta

93
Q

differentiate between “in” endings and “ase” endings

A

“in” endings describe proteins that are not enzymes

“ase” endings denote enzymes that catalyze a reaction

94
Q

Describe an enzyme

A

proteins that catalyze a reaction-increase speeds
highly specific and needed
binding helps keep the reaction moving by decreasing the energy needed to get reaction started
more successful than inorganic molecule due to the complementary structure
results in reaction speeds 1000x more than uncatalyzed

95
Q

define substrate

A

chemical species that bind to the enzyme and are converted to another compound

96
Q

what is the generalized equation for a reaction catalyzed by an enzyme

A

E+S->ES->E+P

97
Q

what is the ES complex

A

Substrate bound to enzyme but not converted to product

98
Q

What are the 6 categories of enzymes

A

oxidoreductase: catalyze oxidation and reduction reaction
Transferals: catalyze transfer of a group from 1 molecule to the 2nd
Hydrolases: catalyze the breaking, hydrolysis, of bonds
Lyases: catalyze the form or break of double bond
Isomerase: catalyze rearrangement within single molecule
Ligase: catalyze joining of 2 molecules- or 2 parts of the molecule

99
Q

what is a co-factor

A

non-protein component critical for activity
examples: metal ion- have + charge not found in amino acid
iron, zinc, calcium bind tightly to enzyme
fumerase requires mg

100
Q

what is a coenzyme

A

an organic compound such as vitamin C and niacin aids enzymes by assisting in transfer of chemical groups from 1 compound to a second
w/o coenzyme: enzyme is not functional

101
Q

what is an apoenzyme

A

enzyme that lacks cofactor: ion or coenzyme

102
Q

What is a holoenzyme

A

cofactor added to apoenzyme to produce functional enzyme

scientist compare apoenzyme with holoenzyme to determine the roles of co-factors

103
Q

define enzyme activity and activation

A

ability to turn reactants into products
activation: enzyme is initiated to act or when it has increased ability to create products- occur when cofactor added or other factor that increases activity

104
Q

what is the active site of an enzyme

A

specific site where catalysis takes place in a structure
small in comparison to overall molecule
normally has 10 amino acids

105
Q

what happens at the active site

A

amino acids form non-covalent bonds with the substrate which creates a favorable interaction that propels the reaction forward
these interactions give enzyme great specificity for one molecule and provide the energy to move the reaction forward

106
Q

what is induced fit and give example

A

energy from interactions change conformation of enzyme to accommodate the substrate- the movements of the amino acids are small
example: glove change shape( enzyme) to fit hand( substrate)

107
Q

define transition strate

A

structure of molecule as its in transition to new molecule

high in potential energy and most unstable part of the reaction

108
Q

describe the analogy of used to show assisting a molecule through the transition state as shown in the module

A

student breaking a pencil
enzyme: students hand, substrate is the pencil
student pick up pencil= enzyme bind to substrate
change in structure occur when student bends pencil
enzyme is student hand help pencil to move through transition state as it bends before it breaks
students hands change shape( induced fit) of pencil
transition state of pencil is the point when the pencil is just starting to break
students hands help pencil get through the transition state which it would not be able to do without help

109
Q

what happens with increases in substrate concentratoin

A

increases the rate of a particular concentration range- stops as active sites fill up

110
Q

How does pH influence the rate of a reaction

A

has range that is active for the enzyme and has complementary shape and differs among enzymes and their environments

111
Q

How does temperature factor into rate of reactions

A

increased temperature increases the rate of the reactions
rule of thumb: for each increase of 10 degree celcius equals a double rate of the reaction speed
elevated temperature gives molecules more room to create more interactions within the environment through collisions

112
Q

define enzymatic inhibitors

A

slow down or stop enzymatic reactions

113
Q

What are reverse inhibitors and name all 3

A

there are 3 and they occur when binding happens during non-covalent interactions
competitive, uncompetitive, mixed

114
Q

what are competitive inhibitors

A

compete with natural substrate for active sites; when it binds it takes the place of where the natural substrate would bind
substrate is not being acted on so it slows down and less reactant becomes product
best competitive inhibitors bind to active site strongly so that substrate cannot bind

115
Q

what are uncompetitive inhibitors

A

bind at a spot distinct from active site and prevent catalysis
only binds to enzyme-substrate complex

116
Q

what are mixed inhibitors

A

bind to either the lone enzyme or the enzyme-substrate complex
bind at site distinct from active site so does not compete with the substrate

Biochemistry (9 decks)

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