Exam # 2 - Lecture Notes 7-9 COPY Flashcards
T/F: Lipids are not polymers, nor macromolecules.
True
Lipids are rich in ________.
hydrocarbon
What is the defining characteristic of lipids?
They are hydrophobic
______ ______ are the simplest lipid.
Fatty acids
What is the makeup of a fatty acid?
A long hydrocarbon chain with a carboxyl group at one end, and a methyl group at the other end
If you have a carbon-carbon double bond or more than one, it makes you…..
unsaturated
Whenever you have a double-bond…you get ___ atoms locked in a plane.
six
Molecules with the same atoms arranged differently are called _______.
isomers
If the carbons are on the same side of the double bond, it’s called a ___ isomer.
cisc
If the carbons are on alternating sides of the double bond, it’s called a ___ isomer.
trans
Which fatty acid do we find in nature?
cis fatty acids are found in nature
Where do the trans fatty acids come from?
Human industry
What does the omega number tell you?
Tells the position of the first double bond in a fatty acid counting carbon’s from the methyl end
Unsaturated fats lack the ________. Double bonds mean less _______.
hydrogens, hydrogen
What is the makeup of a fat?
Three fatty acids + 1 glycerol
What is a glycerol?
Three carbons in a chain. Each carbon has a hydroxyl group attached (total of three hydroxyl groups)
The hydroxyl group on the glycerol reacts with the _______ group on the fatty acid. What results?
carboxyl group. DEHYDRATION and COVALENT BOND
What is the major function of fat?
To store energy
What are the three “energy nutrients” that you get in your diet?
Fat, carbs, protein
Fats store energy, they’re going to serve as a ______ or _______.
cushion or insulation
Most animal fats are _________ fats.
saturated
Most vegetables fats, fish fats…are _______ fats.
unsaturated
Your animals fats, which are SATURATED fats, are typically _____ at room temperature. Your plant and fish fats are UNSATURATED, typically ______ at room temperature.
solid, liquid
It’s easier to pack saturated fat because the tails are _______. It’s harder to pack unsaturated fat because that cis configuration double bond make a _____ in the tail.
straight, kink
What type of lipid surrounds of cells?
Phospholipid
What is the makeup of a phospholipid?
Two fatty acids + 1 glycerol + phosphate group + additional chemical group
The phospholipid is both hydrophobic and hydrophilic…so it’s called __________.
amphipathic
So the phospholipid in being _______ is the ideal barrier. Cell membrane.
amphipathic
A steroid contains…
four fused rings
________ is a steroid.
Cholesterol
Cholesterol is also a what, and why?
An alcohol because of the ol-
Which means it must have a what?
hydroxyl group
So cholesterol is a ______, among the ______’s it’s a _______, and this _______ also happens to be an _______.
lipid, lipid’s, steroid, steroid, alcohol
Cholesterol is an important _______ ______ for making other biological steroids.
starting point
_______, which is the stress hormone.
Cortisol
_________ is also an important component of the cell membrane of cells.
Cholesterol
Bile is _________ and helps to digest ____.
amphipathic, fat
Fat is digested in your _____ ________.
small intestine
Your _____ creates bile and cholesterol.
liver
What is bile made out of?
Cholesterol
What vitamins do is, again, provide a ______ material, a _______, to make some very special bio molecules.
starting, precursor
Protein is a polymer made from a monomer called an _____ ____.
amino acid
The polymer is called a _________, and each contains many different _____ _____.
polypeptide, amino acids
The covalent bond that joins the amino acids is called a ________ bond.
peptide
When we say protein…really what that means is one polypeptide _______ into a specific shape.
folded
Once again, ______ to build a bio molecule…and a covalent bond that results is called a ______ bond.
dehydration, peptide
A protein…which is a polypeptide….________.
FOLDED
It’s the polypeptide ______ into a particular conformation. That’s a protein.
FOLDED
Proteins are an ______ source
energy
Where do you store your protein?
In your muscles
It’s not really a store of protein…it has a function…that function is _______ _________.
muscle contraction
Your muscle contracts because it is full of ________ _______.
contractile proteins.
Mother’s milk has _____ in it…casein is a ______ protein.
casein, storage
Another function of proteins is structural support . What protein is common within your bones?
Collagen
The receptor that a hormone binds to is made out of what?
Protein
Proteins play a fundamental role in ____-____ _________ because all receptors are proteins.
cell to cell communication
Proteins are involved in ________. We just talked about muscle contraction…that is what enables movement.
movement
________ is a protein! It transports oxygen. So _______ is another function of proteins.
Hemoglobin, transport
Defense…._________. _______ is an example of an immune function that is provided with a protein.
antibody
_________! ________….the molecule on which our biochemistry most depends, also made from protein.
Enzymes
What two functional groups are found in every amino acid?
An amino group, carboxyl group
What happens to the carboxyl group under cellular pH?
This weakly acidic carboxyl group, under cellular pH, will ionize and lose a proton. It will loose the hydrogen on the hydroxide. The carboxyl group (minus the H on the carboxyl) will become negatively charged, and the hydrogen that was lost will go to the amino group, giving it a positive charge
In every amino acid is a central ______ atom.
carbon
A central carbon atom that we donate as ______.
alpha…alpha carbon
Also…a ________ atom is bonded to every alpha carbon.
hydrogen
What is the final bond to the alpha carbon?
An R group, or side chain of the amino acid
Again, how do we get twenty?
The the R group that varies the twenty variations
If you have ______ or ______, it makes you polar.
oxygen or nitrogen
There are a total of ____ charged amino acids.
____ of them are acidic, therefore negatively charged.
____ of them are basic, therefore positively charged.
5, two, five
How is a polypeptide built from these amino acids?
Which functional groups are going to react?
The carboxyl group of one amino acid will react with the amino group of another amino acid
What kind of reaction is this, again?
DEHYDRATION
Amino reacts with carboxyl…dehydration…covalent bond…and that covalent bond is called a _______ bond.
peptide
We ALWAYS add onto the ________.
carboxyl
The backbone contains a repeating pattern of…which atoms?
N-C-C
For every peptide bond, there’s also a _______ group.
carbonyl
Likewise, for every peptide bond, what used to be an amino group is now just this ________ connected to this nitrogen.
hydrogen
When we say “polypeptide backbone”, what is everything that is included?
Repeating pattern of N-C-C, carbonyl oxygens and amino hydrogens
When dehydration occurs, you no longer have those ______ from the amino and carboxyl group.
charges
At one end…we will have a free amino group…it never reacted with anything.
At the other end…we will have a free carboxyl group…also never reacted with anything.
So amino and carboxyl are the two ends of a polypeptide.
We call this the __-_______ for nitrogen…
and the __-_______ for the carboxyl.
N-terminus, C-terminus
What is the enzyme that cuts the bacterial cell wall?
Lysozyme
What is the primary structure for a protein?
What is the chemistry that holds it together?
Which amino you have and in what order.
Covalent bonding holds the amino acids together
How does the cell do this? How do you build glycine and then proline and then glutamic acid, etc. How do you know how to do that if you’re the cell? What do you NEED to build something of such complexity?
YOU NEED INSTRUCTIONS. You need a CODE.
The order of amino acids in a protein is determined by the order of ________ in the _____ of that protein.
nucleotides, gene
In other words…the order of amino acids in a protein is determined by the sequence of the _____ for that protein.
GENE
What are genes for?
They encode the structure of our proteins, which in turn, run the cell
Genes specify the _______ ______ of the protein for the cell.
primary structure
It is the precise ________ _______ that causes the protein to fold in a particular way.
primary structure
Which structure causes the protein to fold in a particular way?
PRIMARY STRUCTURE
Secondary structure is characterized by _________ _______ of the polypeptide.
localized folding
What are the two types of localized folding?
1) Coils (alpha helices)
2) Sheets (beta pleated sheets)
So we have ______ ______ between backbone atoms.
hydrogen bonding
What is the chemistry of the secondary structure?
Hydrogen bonding
The overall three dimensional structure formed by the entire polypeptide is called _______ structure.
tertiary
Tertiary structure is going to involve the __ ______ interacting with each other to hold this chain together.
R groups
The ____ is where the non-polar amino acids are.
core
Non-polar amino acids cluster in the interior of proteins, and they interact wit each other by __________ ________.
hydrophobic interactions
What holds the tertiary structure together?
ALL FOUR WEAK INTERACTIONS COLLABORATE TO HOLD TOGETHER A TERTIARY STRUCTURE
In secondary structure, the hydrogen bonding is going to involve the _________ atoms.
backbone
The tertiary structure, recall, is the entire polypeptide ________.
folded
Proteins are said to be in one of two structures, which are….
Linear or fibrous structure
What is it that causes a chain to become a glob?
It’s hiding the non-polar amino acids. The non-polar side chain is trying to hide from the water
One amino acid…one in particular…will provide a covalent interaction…which amino acid is it?
Cystine
Which chemical group is only found in cystine?
Sulfhydryl group
Now full disclosure…you have to have ___ of them…not one, but ___
TWO
When the protein folds, if there are two cystine’s that effectively end up in each others faces…a chemical reaction can happen, known as an ________ reaction.
oxidation
All oxidations remove ________.
hydrogen
You remove hydrogen…and that is one product. Then you have those two sulfur atoms which are ________ bonded together, through _______!
covalently, oxidation
Two cystine’s in a protein can become covalently bonded…and this is referred to as a _______ ______
disulfide bond/disulfide bridge
Which proteins have this feature?
It’s those proteins that leave the cell.
When a cell makes protein…it’s for one of two reasons. What are those two reasons?
1) Either the cell requires that protein for it’s own functioning…in which the proteins stays in the cell to do its job
2) The protein leaves the cell, to perform its function elsewhere
* Two possibilities, stays or leaves.**
It is those proteins that LEAVE the cell that often have this _______ _______.
disulfide bridge
What’s the logic? Why would proteins that have disulfide bridges leave the cell?
Extra stabilization. If for example, an enzyme, leaves their cell of origin, it’s a GOOD IDEA for those enzymes to have some additional…BONDING. Yeah, to hold their structure in an unforgiving environment.
So that’s the logic, extra stabilization for proteins that could need that.
If a protein has multiple polypeptides, we say that it has _______ structure.
quaternary
How is quaternary structure held together?
ALL FOUR WEAK INTERACTIONS, just like tertiary structure
Again, what is quaternary structure?
Two or more polypeptides coming together to form a final protein
One more interaction may stabilize quaternary structure, what might that be?
Disulfide bridge
The fourth level is also stabilized by ________ _______. Possibly…possibly…namely in proteins that what?
disulfide bridges. Proteins that leave the cell
_____-_____ have disulfide bridges stabilizing their tertiary structure, as well as their quaternary structure.
anti-bodies
Primary structure:
Secondary structure:
Tertiary structure:
Quaternary structure:
Primary structure: the order of the amino acids in the protein
Secondary structure: localized folding of the polypeptide…either into coils or into sheets
Tertiary structure: the entire polypeptide folded
Quaternary structure: perhaps…multiple polypeptides coming together
Folding happens SPONTANEOUSLY…based on the ______ _______ of that protein.
primary structure
Why is pH important to establish the shape of the protein?
It will dictate the charges. Some amino acids are acidic, some are basic…whether the amino acids lose protons or receive them depends upon the ambient pH
If you should boil a protein, what might happen?
The weak interactions will not resist the thermal energy of the environment
What’s it called when all the weak interactions break and the protein unfolds?
Denaturation
If the protein is in an environment where there’s other protein..also denatured…it will not _______ properly.
renature
When you boil an egg…you boil it…what happens to the protein? They denature…and proceed to do what?
Stick to other proteins. If you denature every protein by boiling…they will then stick to other protein.
It will be very difficult to uncoil an egg because there’s so many protein..so many proteins that they stick to one another
Which protein effectively “hugs” the other protein as it’s being made by the ribosome, allowing it to fold without interacting with other proteins within the cell.
chaperon proteins
What are the two types of nucleic acid?
DNA and RNA
Where do you find them?
In the nucleus
What are the monomers of nucleic acids?
Nucleotides
How many different nucleotides are there?
Four
You join nucleotides by dehydration…become covalently joined. The chain is called a ___________.
polynucleotide
The covalent bond that results from dehydration is called a _____________ ______.
phosphodiester bond
Two main functions of nucleic acids…
Polynucleotides…
Nucleotides…
Polynucleotides store information
Nucleotides store energy
What three parts makeup the nucleotide?
5 carbon sugar, phosphate group, nitrogenous base
Which sugar lacks the oxygen?
Deoxyribose
If you have one ring, six atoms, you are called a _________.
pyrimidine
If you have two rings, fused…one has six atoms, the other has five atoms…then you’re called a _______.
purine
What are the pyrimidines?
Thymine, cytosine, and uracil
What are the purines?
Adenine and guanine
The nitrogenous base is joined at carbon number…?
one
The phosphate of one nucleotide is joined to the _____ of the last nucleotide.
sugar
So this chemistry means we’re always going to have a ________ on one end and a ____ on the other.
phosphate, sugar
So the end with the phosphate is called the ____ prime end, because…
five prime end because there phosphate is joined to the carbon number five prime
The end with the sugar is called the ____ prime end, because…
out of respect to this three prime hydroxyl
What does the polynucleotide backbone consist of?
A repeating pattern of phosphate-sugar.
Two distinct ends…a five prime end and a three prime end. Held together covalently by phosphodiester bonds.
What are the three differences between DNA and RNA?
1) The sugar - DNA, deoxyribose. RNA, ribose
2) The bases - Thymine only found in DNA. Uracil only found in RNA
3) The chain - DNA, two chains (helix). RNA, one chain
Explain: DNA –> RNA –> Protein
This is simply saying that making a protein requires two steps.
The DNA or gene is first copied into the other type of nucleic acid called RNA. It’s the RNA that is decoded.
DNA copied into RNA.
THIS IS NOT A CHEMICAL REACTION. NOT CONVERTING DNA TO RNA. JUST COPIED
Likewise, the RNA remains in tact. It is NOT converted into protein. IT’S DECODED.
