module 3 amino acids Flashcards
what performs most of the work in cells
proteins
how many different proteins found in the human body
20,000
What are the 5 key functions of protein in the body
transport, hormones, catalysis, structure, protection
what role does protein play in transportation in the body
help move molecules around cells and organism;
which blood based molecule carries oxygen to lungs and tissue
hemoglobin
what role does protein play in hormones
messenger between cells
which protein based hormone during childbirth help women pelvic ligaments to relax
relaxin
what role does protein play in catalysis
in catalysis: enzymes speed up reactions
example: enzyme break down protein in cell to help organism recycle proteins
which enzyme is added to laundry detergent to remove stains with protein
protease
what role does structure play in proteins
gives strength to cells, organelles and tissues
what is found in cartilage, skin and tendon that helps maintain structure
collagen
what role does proteins play in providing protection
body protects from outside protein and toxins to fight pathogens and invaders
what are an example of proteins that provide protection
anti-bodies
how many different amino acids are there
20
How many amino acids are essential and non-essential
essential: 9
non-essential: 11
What are the essential amino acids
phenylalanine, valine, tryptophan, threonine, isoleucine, methionine, histidine, leucine, and lysine.
what are the 3 basic components of an amino acid
an amine group, carboxyl group, alpha carbon
what indicates the unique part of an amino acid
the “R” : side chain of the amino acid
how do we group side chains
by charge, size and polarity
what is physiological pH and how are amino acids shown
7.4
almost all amino acids have lost the carboxyl group(-COOH) and gained a proton in the amine group(-NHs)
what are the first set of amino acids call
non- polar aliphatic and are simple as they are straight chain
which amino acids are considered non-polar aliphatic
glycine, alanine, valine, leucine, isoleucine, proline, methionine
why do scientists have abbreviations
helpful to name a long string of amino acids connected to make a polymer structure
what is the size of aliphatic amino acids, where do they reside and are they water loving?
aliphatic amino acids are small( able to connect with other aliphatic amino acids), live inside the protein and go away from water( hydrophobic)
what is significant regarding the structure of proline
have a side chain that is backbone to nitrogen
unique structure: allows for increased stability and structure
what are non-aromatic amino acids
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
what are the 3 amino acids considered non-aromatic
tyrosine; tryptophan, phenylalanine- abbreviation are found by phonetics; T, W , F
what are the characteristics of polar neutral amino acids
side chain has a dipole and most can hydrogen bond
can interact with water and found outside of protein and connecting with water
what are the amino acids considered polar and neutral
Serine, Threonine, Asparagine, Cysteine and Glutamine
what is unique about acid amino acids
their side chains have a pKa of less than 7 and losing proton in acidic environment and at physiological pH are negatively charged
what are the 2 acid amino acids and their abbreviations
aspartic acid Asp, D
Glutamic acid Glu, E
what are the characteristics of basic amino acids
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
what are the basic amino acids and their abbreviations
Arginine: Arg, R
Lysine: Lis, K
Histidine: His, H
what is unique about histidine
does not have a charged group on its side chain
what happens with histidine at lower pH
pKa of side HN could be 6.00 and indicated by double dagger
at physiological pH= no charge
what is a unique property of cysteine and what can form?
side chain is un-charged, but 2 cysteine can react to form a disulfide bond- by sulfur atom which creates a covalent bond
what is the function of a disulfide bond
stabilize protein structure when present
common in amino acids that appear outside of the cell
which protein is made of disulfide bonds and is responsible for strength of hair and strong bonds maintain shape
keratin
what forms when amino acids are put together in a chain
polypeptide
proteins are considered?
synthesized from how many amino acids
large: macromolecule
100-300 amino acids
select proteins have 29,000
what dictates the sequence of the amino acids and where does synthesis happen
cells dna dictate sequence
synthesis at ribosome: amino acids are linked together in a chain covalently
how does a dipeptide form
amine group of one amino acid reacts with carboxyl group of the second and water is released
what is gained and lost in the formation of a dipeptide bond and what type of reaction is it
1 oxygen from carboxyl group and 2 H from amine group as water is released
condensation reaction
what is the definition of a peptide
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
define oligopeptide
short chain of amino acids: 2-20
could see the word peptide interchabaly used
what are N and C when discussing peptides
N-terminal: amine end
C-terminal: carboxyl end
How would you name a 4 amino acid bond( tetrapeptide) of alanine, glutamate, cysteine, serine
single letter and 3 letter
A-E-C-S
ala-glu-cys-ser
also named 4 residue
what is the protein backbone
formed from peptide bonds in the protein-all form this- links all amino acids together
side groups point away from protein backbone
what are amino acids referred to in peptide bonds
residue
reflect the molecule structure after condensation reaction
what is a polypeptide
molecule with 99 or less amino acid( residue)
when is protein status given to a peptide
when over 100 amino acid( residue) in the bond
what is the mass of proteins and how is it written
10,000 g/mol or 10kDa
k=kilo or 1,000
what is supramolecular chemistry
chemistry of large compounds
define conformation
thousands of amino acids joined together in a 3D structure- either fibrous or globular
define intrinsically disordered
what is the exception to the rule
random conformation
proteins that are intrinsically disordered and functional
what do proteins need to do be functional
adopt a structure as structure and function are vitally connected
what are the 4 standard levels of protein structure
primary, secondary, tertiary, quaternary
Describe primary structure for protein
order of amino acid covalently bonded in peptide chain-includes disulfide bonds
what do scientists use to describe primary structures
1- letter abbreviations and often fill 2 lines
what is the process for describing a primary structure
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
what is the secondary structure
used to examine local 3D structure of amino acid residue close in sequence
what are three parts of secondary structure
alpha-helice, beta-sheet and beta-turn
what are alpha-helices
coiled structures of amino acids that is stabilized by the backbones of hydrogen bonds
In the helix- how many amino acid residue per turn and how many as it rises
3.6 per turn while rising and 5.6 angstrom per turn.
what does 1 angstom=
1.0x10-10
which amino acids are found in the helix and which are less likely
likely to be found: alanine, arginine, leucine
less likely: proline and glycine
Is there a space in the helix
no: it is solid though it looks like its hollow from diagrams
In the helix where do the R groups point
away from the helix so that they can interact with with other chains, water or chemicals
what is a beta-sheet
repetitive sheet like structure that is extended in zig zag fashion that put adjacent side groups as far apart as possible
what forms a beta-sheet
individual beta strands that interact by creating hydrogen bonds with other beta strands
what are the 2 forms of beta-sheet
parallel and anti-parallel
How do anti-parallel beta sheets form
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
How does a parallel beta sheet form
2 single beta sheets are lined parallel to each other
How do anti-parallel and parallel beta sheets differ
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
what percent of amino acids are found in the turn?
30%
what do turns allow and what is the name of a common one
allow for proteins to make secondary structures next to each other
beta-turn
Describe a beta-turn
4 residue unit that can turn 180 degrees
looks like a rope
can form with both alpha helix and beta-sheet
what is a motif
collection of stable group of secondary structures
what is an example of a motif
helix-turn-helix or
alpha helix followed by beta-turn followed by alpha helix
what is the tertiary structure
OVERALL 3D structure of folded polypeptide
includes all the secondary structure and unstructured region of protein as a whole
what maintains the tertiary structure that is necessary to function
disulfide bonds and non-covalent forces
which protein is critical in muscle cells for binding and storing oxygen
myoglobin
describe the myoglobin tertiary structure
8 alpha helices connected by turns and unstructured regions
what is in the center of the protein myoglobin
a heme ring holds onto oxygen
what is the heme ring called and what is the function
prosthetic group- non- amino acid necessary to maintain structure and function of the protein
what is the stability range for proteins
20-65 kj/mol
what is a protease inhibitor
tertiary structure that inhibits protease: globular shape
which proteins fit into a fibrous class
keratin, collagen
fibrous proteins are long extended structure of alph-helices
what does the quantnary structure describe
describes macromolecules that have 2 or more polypeptide chains that associate with one another
what constitutes the quantary structure
the number and orientation of the independent chains
what is the name of the protein that has 2 identical polypeptide chains and how is it described
staphlokinase: each polypeptide is positioned over the other
dimer: called a dimer as it has two polypeptides and so 2 subunits
what is the name of a quanternary structure that has 4 subunits
what are the names of the subunits
hemoglobin and tetramer
2 alpha
2 beta
differentiate between “in” endings and “ase” endings
“in” endings describe proteins that are not enzymes
“ase” endings denote enzymes that catalyze a reaction
Describe an enzyme
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
define substrate
chemical species that bind to the enzyme and are converted to another compound
what is the generalized equation for a reaction catalyzed by an enzyme
E+S->ES->E+P
what is the ES complex
Substrate bound to enzyme but not converted to product
What are the 6 categories of enzymes
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
what is a co-factor
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
what is a coenzyme
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
what is an apoenzyme
enzyme that lacks cofactor: ion or coenzyme
What is a holoenzyme
cofactor added to apoenzyme to produce functional enzyme
scientist compare apoenzyme with holoenzyme to determine the roles of co-factors
define enzyme activity and activation
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
what is the active site of an enzyme
specific site where catalysis takes place in a structure
small in comparison to overall molecule
normally has 10 amino acids
what happens at the active site
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
what is induced fit and give example
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)
define transition strate
structure of molecule as its in transition to new molecule
high in potential energy and most unstable part of the reaction
describe the analogy of used to show assisting a molecule through the transition state as shown in the module
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
what happens with increases in substrate concentratoin
increases the rate of a particular concentration range- stops as active sites fill up
How does pH influence the rate of a reaction
has range that is active for the enzyme and has complementary shape and differs among enzymes and their environments
How does temperature factor into rate of reactions
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
define enzymatic inhibitors
slow down or stop enzymatic reactions
What are reverse inhibitors and name all 3
there are 3 and they occur when binding happens during non-covalent interactions
competitive, uncompetitive, mixed
what are competitive inhibitors
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
what are uncompetitive inhibitors
bind at a spot distinct from active site and prevent catalysis
only binds to enzyme-substrate complex
what are mixed inhibitors
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
