Unit 1.5 Flashcards
- protein monomer
amino acids (20 different ones)
protein chemistry
- recognize them by carbon, hydrogen, oxygen and nitrogen and sulfur
- only biological molecule that has sulfur, this is a defining feature
- amino acid starts with a carbon, a carboxyl, an amino and they are acidic
protein naming
- _________ amino acid
o beginning is based on R group and has 4 possible names
• carbon and hydrogen R only: nonpolar
• R is polar: polar
• if there is a NH3+ or any plus: basic
• if there is a o- or anything negative: acidic
• Exception: cysteine has a sulfhydryl which would be non polar but it is actually polar. it will form a covalent bond called a disulfide bridge. This acts polar like so is classified as so
R groups differ in
- size
- shape
- polarity (interactions with water)
- ionization
o acidity, basicity - special additions
o functional groups
o sulfur - We can classify them as polar, non-polar, charged acidic or charged basic.
polymer formation
- condensation synthesis
- forms a peptide bond: c (with double bonded oxygen) with nitrogen (with a hydrogen attached)
- forms dipeptides then polypeptides
- protein name is used when a polypeptide has a job or a function to perform!
4 levels of structure of a protein
primary all to quaternary (only large proteins have this)
- primary
just order of amino acids in a polypeptide determined by the DNA
- secondary
a. 2 types of folding that occur due to R groups and some chemistry of carboxyl and amino functional groups which creates some attraction or repulsion based on the order of amino acids
i. alpha helix
ii. beta pleated sheet
* Kind of randomly mixed versions of both. Determined by the DNA but seems random to us (see ribbon model picture).
- tertiary
a. sometimes, there are positive and negatively charged functional groups in amino acids. This creates a bending and shifting in the molecule to create a 3d shape
b. a series of interactions between R groups (not functional groups!). Folds the polypeptide into a globular shape
tertiary interactions
hydrogen bonds, disulphide bridges, ionic bonds, van der waals, hydrophobic exclusion
hydrogen bonds (tertiary interactions)
(in water)
- found often in proteins
- weak intermolecular force\
disulfide bridge (tertiary interactions)
(in water)
- only in two copies of the same amino acids
- creates a strong covalent bond between sulfur and itself. sulfur can make two bonds
- only happens to cysteine
- intramolecular
ionic bond (tertiary interactions)
(in water)
- any basic functional groups and acidic functional group
- this will form an ionic bond due to their opposite charges
wan der waals force (tertiary interactions)
(in water)
- weak forces (London Dispersion)
- represented by a dotted line
hydrophobic exclusion (tertiary interactions)
- all nonpolar things kind of don’t have any charges for water to attach to
- this causes the things to be excluded
chaperone protein
- can help a polypeptide chain to come together in such a way that these above bonds form
- quaternary
o only some go through this stage
o chemical interactions (most common is hydrogen bond) hold together multiple polypeptide chains
• hemoglobin consists of 4 polypeptide chains that carry oxygen (2 alpha, 2 beta). you can carry more stuff per molecule
protein designation
only 3,4 has a protein designation. You can call a polypeptide chain in tertiary and quaternary a “protein” since it has a function.
proteins and R Groups
- Because the 3rd and 4th structures depend on interactions between R-groups, any change in the environment or any alteration of the R-group characteristics (e.g. by binding to another molecule) can result in a change in the shape of the protein.
- It is these changes in shape that allow proteins to do work = contracting muscles, facilitating chemical reactions, pumping nutrients, receiving chemical signals, etc.
why is A variety of functional groups in the R portion of amino acids important
Different chemical properties along the length that can contribute to the three dimensional folding of the protein
why is 20 different monomers that can polymerize important
A large variety of polymers can be formed, which accounts for the many functions of proteins
why is formation of large polymer chains that have four levels of structure important
One advantage of quaternary structure is that individual peptides can be used as modules in several different functional proteins, allowing more total proteins to be produced by a limited genome.
Another advantage is that a single protein may have multiple active sites, allowing it to catalyze several reactions at once, or to transport several cargo molecules.
active site
binding site for substrate
substrate
the thing that the enzyme breaks down
enzyme substrate complex
the substrate bound to the enzyme together
Describe the effects that enzymes can have on substrates.
Enzymes will lower the activation energy, which is the energy to start a reaction. They will do this by stressing or distorting the bonds of the substrate (reactants) in order to speed up the formation of a product. They are biological catalysts, which means they can be used more than once and are unchanged in the reaction.
denature
prevent it from binding and acting on its substrate. unfolding enzyme. can be refolded but only when the structure is shifted slightly.
pH, temperature, salt can denature an envy,e
rate of reaction remains high
as long as tertiary structure remains
amino acids are replenished in body
through diet.
salty solutions`
- disrupt osmotic gradient
- mess up tertiary folding
- looks like the same graph as an ion
temperature vs rate of reaction
- graph looks a little sideways bell curve. top is “optimal temperature”
- only right side ends due to denatured enzyme
- at the cooler temperatures, the molecules move less so the enzyme would have very little chance of encountering the substrate and colliding with it.
- enzyme also becomes more flexible as solution temperature increases which aids in induced fit
- at super high temperatures, the molecules move too much. hydrogen bonds become weak because of heat. this causes the structure to unfold and even though the collision rate is higher, the structure doesn’t allow it to bond
enzyme concentration
- graph looks like a line more enzymes is more rate of reaction - more stuff so more collisions - it is a linear relationship - when and if a reaction plateau’s , that means that the substrate is all fully reacted
As the enzyme concentration increases, the rate of reaction will increase. This is due to a greater number of collisions
substrate concentration
- graph looks like a line then it reaches a point of saturation and plateaus
excess enzyme then you start increasing the substrate concentration - 100 substrates and 50 enzymes is still 50 enzymes!
- it plateaus at the point of saturation until the enzyme is saturated by the substrate and the rate will no longer increase despite further increase in substrate.
what affects the rate of reaction
substrate and enzyme concentration
pH vs enzyme activity
- There is a bell curve graph with the top being the “optimum pH”
Enzymes have an optimum pH
- Increase or decrease in pH changes ion concentration in solution
- Ions alter structure of the enzymes or substrate
- Additional hydrogen ions (positively charged, acidic) interact with negatively charged parts of enzymes
- Additional hydroxide ions (negatively charged, basic) interact with positively charged parts of enzyme
- Disrupt balance of forces that maintain specific shape
- If the active site is deformed then the substrate can’t bind to the enzyme
nucleic acid function
- making the proteins that are inside the cell
- make up the genes
- also work in transfers of energy. DP is when one phosphate is hydrolyzed. only adenine and guanine do this
directions to make proteins
DNA
making proteins
RNA
nucleic acid polymer
nucleic acid
nucleic acid monomer
nucleotide
nucleotide structure
CHONP
- phosphate group
- 5 carbon sugar (pentose. in RNA it is ribose sugar. DNA is deoxyribose sugar. It has the oxygen removed)
- nitrogenous base (called that because it has nitrogen. this is the one thing that varies in nucleotides)
DNA Nucleotides
- Adenine (2 rings therefore purine)
- cytosine (1 ring therefore pyramidine)
- guanine (2 rings therefore purine)
- thymine (1 ring therefore pyramidine)
RNA Nucleotides
- Adenine (2 rings therefore purine)
- cytosine (1 ring therefore pyramidine)
- guanine (2 rings therefore purine)
- uracil (1 ring therefore pyramidine)
RNA Bonding
o dehydration reaction
• phosphate group of one nucleotide binds to the hydroxyl group from the pentose sugar releasing water
• this is RNA
DNA bonding
o hydrogen bonding
• in between A and T, G and C. they are oriented upside down
• this is in DNA and creates the double helix
phosphodiester bond
O-phosphate – O
RNA vs DNA
- DNA is more stable
- RNA has a pyramidine base called uracil while DNA has a pyramidine base called thymine
o thymine has better hydrogen bond linkage to create a tighter double stranded structure - RNA is single strand, DNA is double helix
- RNA is found everywhere while DNA can be found only in nucleus
- sugar name: RNA ribose (C#2 OH), DNA deoxyribose (C#2 H)
DNA structure
o A and T form 2 hydrogen bonds
o G and C form 3 hydrogen bonds
- alternates phosphate and ribose. then the nitrogenous base sticks out
- condensation synthesis keep the molecules together so the bases stick out. this creates hydrogen bonding between the two chains which keeps them together
“acid” since the phosphate groups are oriented outwards while the basic parts form the rungs of the ladder. overall, molecule acts acidic.
Nitrogenous Base
The nitrogenous bases form an alphabet for coding. Words in DNA language are all 3 letters long, this creates 64 possible combinations of nucleotides for 20 amino acids. 3 possible combinates that exist for one same protein. This helps to protect you if your DNA mutates since there is a chance that it makes the same code as was before.
hydrogen bonding and protein
involved in both secondary and tertiary levels of protein structure
the alpha helices and btal pleated sheets of secondary structure are stabilized by hydrogen bond formation between the amino and carbonyl groups of the amino acid backbone. hydrogen bond formation between r-groups helps stabilize the three dimensional folding of the protein at the tertiary level of structure
nucleic acid and hydrogen bonding
hydrogen bonds are important for complementary base-pairing between the two strands of nucleic acid that make up an molecule of DNA. complementary base-pairing can also occur within the single nucleic acid strand of an RNA molecule
induced fit
when a enzyme basically changes to “hug” the substrate
complementary base pairing
the A and T (or U), C and T. these bases are complementary in size and this configuration is the most stable hydrogen bonding configuration
thymine and adenine
have 2 hydrogen bonds
cytosine and guanine
have 3 hydrogen bonds
“Purines always glow”
purines are Adenine and Guanine
replication is for
DNA
transcription is for
mRNA
translation is for
mRNA
replication
- when you want to duplicate a cell
- splitting of DNA in half
- then you create another right hand side to match the original left hand split DNA and same thing for right side
- you know how two identical copies of the DNA
transcription
- how genes turn from just DNA instructions to actual proteins
- how DNA goes to mRNA (messenger RNA)
- first step is the same for replication. you first copy one half of the DNA
- insteaded of Adenine with Thymine, Adenine pairs with Uracil.
- this new mRNA can leave the nucleus, attach to a ribosome and code for a protein
translation
- how the mRNA turns into an amino acid sequence to turn into a protein
- this sequence from transcription is used. now every three bases codes for a specific amino acid. three bases together are called a codon
- you can have 1 of 4 bases in 3 different places which creates 64 different codons
o this allows you to account for the 20 different amino acids and reduces the danger of mutation - tRNA attaches to amino acids and then matches them to a mRNA to create a sequence of amino acids which create the right protein.
uracil vs thymine
Uracil is a little less stable than thymine and can make errors more easily. this means that the body would rather have errors in the protein that instructs rather than the instructions themselves because then only some proteins will be wrong, not the instructions itself. Also, mRNA should not be stable because then they would last forever and they are supposed to be messengers.
nucleoside
pentose sugar plus the nitrogenous base
peptide bond
a peptide bond: c (with double bonded oxygen) with nitrogen (with a hydrogen attached)
“purines
Always Glow”
- 2 rings
enzyme inhibition competitive
- inhibitor molecule has a similar shape to the substrate.`
enzyme inhibition noncompetitive
inhibitor binds to the allosteric site and induces a change in the active site.
enzyme inhibition competitive graph
- the reaction will reach the same rate, but it takes more substrate to get there. it will be a more linear looking curve
enzyme inhibition noncompetitive graph
will never reach the same level, because a proportion of enzymes is not functioning. it will be a more flat looking curve and will plateau at the same time but will be very not steep.
normal enzyme in a substrate concentration vs rate of reaction graph
looks like a steep line up to a saturation point and then it plateaus
enzymes act as catalysts by
- bending the shape of a molecule
- bringing a center of positive charge towards a negative charge to draw away a certain element to expose a certain bond
activation energy
enzymes lower the amount of energy it takes to start a reaction. (make a graph a smooth line instead of having a giant bump)
cofactor
- a molecule, ion or atom that is involved in allowing the enzyme to perform its function but it is not formally a part of the protein but it needs to be there (ex. magnesium ions which lure away electrons)
- vitamins and minerals!
coenzyme
o an organic cofactor is called a coenzyme
• these are complete molecules that are not formally part of the structure but like cofactors, it allows the enzyme to perform its job
catalysts
always return to their original shape allowing them to perform thousands of the same reaction
why are proteins important to life
- enzyme catalysis
- defence (antibodies)
- transport molecules around body
- support (fibres like hair, cartilage)
- motion (muscles)
- regulation (hormones)
- storage (calcium and iron)
alpha helix
the carbonyl (C=O) of one amino acid is hydrogen bonded to the amino H (N-H) of an amino acid that is four down the chain. The R groups of the amino acids stick outward from the α helix, where they are free to interact.
beta pleated sheet
- The hydrogen bonds form between carbonyl and amino groups of backbone, while the R groups extend above and below the plane of the sheet
- The strands of a β pleated sheet may be parallel, pointing in the same direction (meaning that their N- and C-termini match up), or antiparallel, pointing in opposite directions (meaning that the N-terminus of one strand is positioned next to the C-terminus of the other).
Contain four nucleotides which differ by the nitrogen base that is attached
Variety in the molecule so that it can code for the amino acids in a polypeptide chain
Nucleotides can have phosphates condensed or hydrolyzed
Can be used in energy transfer reactions
DNA is double stranded
More efficient in copying because the molecule can be copied using complementary base pairing in one step, rather than two (if it was single stranded)
RNA bases are read in groups of three
64 possible combinations to cover the 20 different amino acids
What are the two functions of nucleic acids:
To be copied when cells divide (DNA replication)
To have the code translated into the sequence of amino acids in the primary structure of a polypeptide chain. (DNA - RNA - protein)
What are the differences between DNA and RNA? (there are three of them)
DNA has a different sugar than RNA (deoxyribose vs ribose - differ by the functional group at C2’ - H in DNA, -OH in RNA)
Found nitrogen bases - purines (adenine and guanine) and pyrimidines (cytosine and uracil in RNA, cytosine and thymine in DNA)
DNA is double stranded with each strand being hydrogen bonded to the other one via the bases. RNA is single stranded
What is complementary base pairing? What are the rules for this association?
It is the hydrogen bonding that occurs between the bases. Purines bond with pyrimidines and it is always Adenine with Thymine and Guanine with Cytosine. The strands of DNA must be oriented antiparallel for this to work.
Why can’t other bases pair?
Purines are both are too large and would cause the double helix to bend out of shape. Even if they tried to pair, the hydrogen bonds wouldn’t be strong enough to resist the mechanical stress caused by their size
pyrimidines can’t bond because the hydrogen bond structure isn’t stable enough.
protein monomer
amino acids (amine, carboxyl group)
protein polymers
polypeptides (or, when in quaternary structure, they are proteins)
protein bond
peptide bond (C double bonded O and NH)
nucleic acid monomer
nucleotide (pentose, phosphate, nitrogenous base)
nucleic acid polymers
nucleic acid
nucleic acid bond
phosphodiester bond (C-O-P-O-C)
nucleic acid naming
- nitrogenous base (pyramidine or purine)
- ATP (three phosphates, pentose and nitrogenous base. It is a modified nucleotide)
- nucleotide (pentose, phosphate, nitrogenous base) vs nucleoside (pentose and nitrogenous base
uracil vs thymine
- uracil can easily pair with other bases. thymine has a methyl group which is hydrophobic which stops wrong pairings from happening
- uracil is less energetically expensive to produce
- uracil is readily produced by chemical degradation of cytosine, so having thymine as the normal base makes detection and repair of such incipient mutations more efficient.
- RNA, you need quantity while DNA you need quality
why is DNA double stranded
- much more efficient for copying since all you have to do is split it in half and then match the other side to create two copies of DNA for cell mitosis
why is RNA single stranded
RNA is only needed to be a messenger, it should take very little energy
- it is single stranded since you only need to copy half of the DNA strand which saves energy
- RNA needs to be made quickly, doesn’t matter if it gets attacked or mutated
how to improve rate of reaction
increase the temperature and the enzyme concentrations
why is carbon ideal for life
- makes lots of bonds (4) which makes a greater variety of molecules
- relatively stable (more closer to top, less atomic radius)
- can form large, stable molecule chains (carbon can also attach to itself)
- forms moderate energy bonds that can be broken and reformed easily
polymer chemistry of proteins
proteins structure: super diverse combinations
function: can do many different functions
polymer chemistry of nucleic acids
- massive information storage
- has the instruction manual and the assembly instructions make the very proteins of our body
- help in energy transitions
functional groups in proteins
- tertiary folding
- some interactions in secondary folding due to hydrogen bonds
- very strongly impacts the shape of function which can drastically change the function of protein
functional groups in nucleic acids
- has to do with the nitrogenous bases (changes the DNA/RNA structure itself)
hydrogen bonding
- has to do with the hydrogen bonding of complementary base pairing
- has to do with binding of an enzyme to substrate
molecular shape and proteins and nucleic acids
proteins: affects function
enzymes: impacts the binding of substrate
nucleic acids: affects the copying of DNA and the longevity of RNA
enzymes are
polypeptides
Salt concentration
will also affect the enzyme action. As salt concentration increases the ions will disrupt ionic bonds that hold together the tertiary structure. This will decrease the rate of reaction and potentially denature the enzyme.
high concentration of ions = low pH = acidic
low concentration of H+ = high pH = basic, more negatively charged ions OH-
