Biochemistry CH3 Flashcards
What do proteins do (generally)
Perform nearly all the work in cells and organisms
Name 5 things proteins do
Structure
Catalysis
Immunology
Transport
Storage
At least how many different proteins are found in human cells?
20000
Transport
Proteins help to move molecules around the cell and organism. Hemoglobin is a blood-based protein that carries oxygen from the lungs to tissue.
Hormones
These molecules communicate messages between cells. Relaxin is a protein hormone that helps women during childbirth by relaxing pelvic ligaments to make delivery easier.
Catalysis
Enzymes speed up, or catalyze, chemical reactions. Protease, an enzyme, breaks down proteins in cells to help organisms recycle unneeded proteins. This enzyme is also added to laundry detergent to degrade stains with protein (i.e. blood or food).
Structure
These proteins give strength to cells, organelles, and tissues. Collagen is the structural protein found in cartilage, skin, and tendons.
Protection
The human body protects itself from outside proteins and toxins by making proteins called antibodies to fight the foreign invaders.
All proteins are constructed from the same 20 standard _____ _____
amino acids
Which carbon are the functional (R) groups attached to?
Ca (alpha carbon)
What are the same groups that all amino acids have and what do they do?
NH3, CH, and COO-
It permits all amino acids to link together in a protein
Non-polar aliphatic amino acids
GAVPLIM - Great Adventures Very Predictably Lead Into Mountains
Glycine Alanine Valine Proline Leucine Isoleucine Methionine
Non Polar Aromatic amino acids
PWY - People Want Yachts
Phenylalanine Tryptophan Tyrosine
Polar neutral amino acids
STCNQ - Some Tiny Creatures Need Quests
Serine Threonine Cysteine Asparagine Glutamine
Acidic amino acids
Aspartic and glutamic acid (D and E)
Basic amino acids
RKH - Really Kind Hearts
Arginine Lysine Histidine
Disulfide bonds
Link amino acids together and form covalent bonds
When present, stabilize a proteins structure
Protein keratin
Protein component
Long chain of amino acids
polypeptide
Basic amino acids side chains are normally _______ charged.
positively
Condensation reaction
Formation of a peptide bond with the loss of water
Typically between one oxygen from the carboxylic acid group and two hydrogens from the amino group
Oligopeptide
Short chain of amino acids typically 2-20 amino acids
Peptide
amino acids linked together by peptide bonds
When the number of residues is 99 or less, we say its a
polypeptide
What makes a protein attain its status
After 100 residues have been added together.
When a protein has 100 amino acids, the protein has a mass of…
10,000 g/mol or 1 Da
__________ _______ is the term used to describe the chemistry of large compounds.
Supramolecular chemistry
Dipeptide
Amino functional group of one amino acid reacts with the carboxylic acid function group of a second, 2 monomers are joined together producing a dipeptide with the release of water.
Protein backbone
Connection of amino acids via peptide bonds, this is a protein backbone what links all amino acids together.
C terminal vs N terminal
Why are amino acids called residues?
To reflect the molecule remaining after the condensation reaction takes place.
Conformation
Proteins can have hundreds or thousands of amino acids joined together into a three dimensional structure.
Fibrous vs globular protein
Biologically active structures
Fibrous - Long extended structure of alpha helices
Globular - thick
Portions of proteins may exist in a random conformation, or, as they are often called…
intrinsically disordered
Four standard levels or protein structure…
Primary (1degree)
Secondary (2 degree)
Tertiary (3 degree)
Quaternary (4 degree)
Primary structure refers to…
The order of amino acids covalently bonded together including disulfide bonds, in a polypeptide chain.
N->C
Secondary Structure
Examine local three dimensional structure of amino acid residues close in linear sequence.
Alpha helices, beta sheets, and beta turns.
Alpha helices
Coiled structures of amino acids where backbone atoms form hydrogen bonds to stabilize this sequence.
A standard helix has ___ amino acids or residues per each turn while rising ___ angstroms per turn.
3.6
5.4
1 angstrom = 1E-10 m
The interior of a helix has no
space
Beta sheet is
Repetitive sheetlike structure. Zig zag orientation.
Beta sheets form when
Individual beta strands that interact by hydrogen bonding to one another.
Anti parallel beta sheets and parallel
Two versions
Anti-parallel beta-sheets form when one beta-strand ends and the amino acid sequence turns back around on itself. Then, an additional beta- strand can join other strands to form anti-parallel sheets.
anti parallel vs parallel sheets
H bonding partners are different and the distance of each repeat is unique.
Parallel repeats every 6.5 angstroms
Antiparallel repeats every 7.0 angstroms
What percent of amino acids are found in turns in a protein?
30%
Changes in the direction of the N à C direction of the primary sequence.
One type of common turn is the ____-____ , which is a four residue unit that turns 180 degrees.
beta turn
Beta turns are a different category than ____ _____
beta sheets
Beta turns can form with both
alpha helix and beta sheets.
Motif
Collections of particularly stable groups of secondary structures are often referred to as a motif.
For example, one motif is a helix-turn-helix motif composed of an alpha helix, followed by a turn, and then another alpha helix.
Motifs occupy a position between secondary and tertiary structures but are not one of the…
four levels specified by scientists
Tertiary Structure
Overall three-dimensional structure of a folded polypeptide
Prosthetic group
Help with some function of a protein
In myoglobin it helps bind the oxygen that it stores.
Myoglobin
Critical in our muscle cells for binding and storing oxygen.
Prosthetic helps bind oxygen that it stores.
A heme ring is a ________ _____, which is a non-amino acid portion of the molecule necessary for the structure and function of a protein.
prosthetic group
Myoglobin and protease inhibitor fits in what class of protein structure
globular
Strength of covalent bond compared to protein stability range
400 kJ/mol (covalent bond)
20-65 kJ/mol (protein)
Protease
Protein enzyme that degrades other proteins, so a protease inhibitor regulates the activity of a protease.
What type of protein is this?
beta barrel protein
Quaternary Structure
Macromolecules that have two or more independent polypeptide chains that associate with one another. The number and orientation of these chains constitute the quaternary structure.
Example of quaternary structure
Staphylokinase - has two identical polypeptide chains
Dimer
Two polypeptides protein structure, two subunits.
Hemoglobin is another example of a…
protein quaternary structure
it is a tetramer
Tetramer
Four subunits
two subunits are the same called alpha subunits while the other two are beta subunits. (uncommon)
Ex: hemoglobin
Protein complex lumbricus erythrocruorin from an earthworm has ___ subunits as part of its quaternary structure
180
The “-in” ending is used for proteins that are not ______.
ex: hemoglobin, myoglobin, etc.
enzymes
Enzymes typically have the “___” ending.
ase
Ex: protease, staphylokinase, etc.
Enzymes
proteins that accelerate speeds of chemical reactions
lower activation energy
The result of a enzymes speeds up the reaction _____ times or even more compared to the rate of the uncatalyzed reaection.
1000
Enzymes work better in organic or inorganic catalysts
inorganic - due to their complementary structure
Hydration reaction adds
water across a double bond
Generalized reaction equation to illustrate an enzyme catalyzed reaction:
E + S —> ES —> E + P
P - product
ES - enzyme substrate complex
lyase
class of enzymes that creates double bonds or adds molecules to double bonds
Cofactor
Non protein component that are critical for activity, metal ions can be cofactors
Organic compounds function as cofactors as well and when they do they are called
coenzymes
lack of a coenzyme generally makes an enzyme non functional
examples of coenzymes
Vitamin C and Niacin
Apoenzyme
An enzyme without the cofactor (either ion or coenzyme)
Active site
Specific spot in their structure where catalysis takes place.
When the cofactor is added to the apoenzyme to produce a functional enzyme, this is called the
holoenzyme
Most active sites have about __ amino acid residues defining the space.
10
fraction of 100+ amino acids in a typical protein
Non covalent interactions between the active site and the amino acids do…
interact with the substrate which helps to generate a favorable energy change to enhance the reaction
Gives enzymes great specificity for one molecule and also provides energy to initiate the reaction
These interactions provide energy to change the conformation of the enzyme to accommodate this substrate, this is called an _____ ___
induced fit
Transition State
The structure of the molecule in its transition into a new molecule
high in potential energy and that it is the most unstable part of the reaction.
Increasing the concentrration of enzyme generally increases the ____
rate
Increasing the substrate concentration increases the rate up to a certain point?
yes, because the active sites fill up
The ph of the solution influences the rate?
yes, most enzymes have a particular pH range that is most active and hence has the most complementary shape for activity.
Temperature related to rate.
Critical factor for both the reaction conditions and for enzyme conformation.
Reaction rates for uncatalyzed reactions increase with increasting temperature (10 degrees C increase doubles the reaction) (more temperature more collisions)
Unfolding
renders enzyme inactive, too much increase in temperature can cause this.
Inhibitors
Slow down or stop enzyme reactions. Bind to the enzyme and prevent the reaction from taking place.
When the binding occurs through non covalent interactions we say these are
reversible inhibitors
Reversible inhibitors have three types:
competitive
uncompetitive
mixed
Competitive inhibitors
Compete with the natural substrate for the active site. When a competitive inhibitor binds, it takes the place that a natural substrate would occupy. Since the substrate is not being acted upon, it slows down the reaction rate and less reactant is turned into product.
Uncompetitive inhibitors
Bind at a spot distinct from the active site and prevent catalysis from taking place. Interestingly, the inhibitor only binds to the enzyme- substrate complex.
Mixed inhibitors
Can bind either to the lone enzyme or the enzyme-substrate complex. Like the uncompetitive inhibitor, the mixed inhibitor binds at a site distinct from the active site, so it does not compete with the substrate.
What type of inhibitor are found when an enzyme has two or more substrates
Uncompetitive or mixed
