Exam 1 Flashcards
Name 2 metabolites that are also carbohydrates
Glucose and Glycerol
What are 3 species that have the same structure as the TATA box binding protein?
We are supposed to notice that the shapes of these proteins are visibly similar. That is because they are homologous, the structures are very similar.
When did oxygen come into the atmosphere?
Oygen came into the atmosphere about 2.25 BYA which, if you notice, is exactly halfway down the time line. You should be able to more or less reproduce this diagram, I want you to know the significant dates. Remember these are billions of years not millions.
What are the 3 domains of life?
Bacteria, Eukarya, and Archaea
Describe bacteria, eukarya, and archaea in detail
- Eukarya include all eukaryotes – organisms with nuclei. All animals and plants big enough to see are eukaryotes, but not all eukaryotes are multicellular. Amoebas, yeast, and parameciums are examples of single celled eukaryotes.
- Bacteria and Archaea have no nuclei and used to be lumped together as prokaryotes. In 1977 Carl Woese discovered that the Archaea are very different from the bacteria, and much closer to us, the Eukarya.
What are the 4 bases in DNA and draw them out
Describe the differences between major and minor grooves
Draw out Adenine paired with Thymine and Guanine paired with Cytosine
What happens during DNA replication?
The 2 maternal strands separate, and each of those strands specifies a newly constructed strand by Watson Crick base pairing.
How does Coulumbs Law relate to biochemistry?
Like charges repel, unlike charges attract, and the strength of the force varies with the distance between them “r”. It’s the Coulomb equation, basically q1xq2/r2
What is the difference between a hydrogen bond acceptor and donor?
A hydrogen bond needs a donor and an acceptor.
The donor can be NH or OH but never CH.
The acceptor is generally an unshared electron pair, it helps if you know what an sp3 molecule or sp2 molecule looks like. And the strongest H bonds are lined up exactly, not tilted off to the side.
Describe what the Van der Wal reaction looks like
Draw how electric dipoles work with water
How do phosphate groups affect DNA structure?
The phosphates in DNA all are negatively charged, and they repel each other. That force makes folding into a double helix less likely, but other forces allow the helix to form – mainly hydrophobic attraction between the stacked base pairs.
Describe the differences for primary, secondary, tertiary, and quanterany structures
- Primary structure = covalent bonds. Amino acids are held together by peptide bonds.
- Secondary structure = repetitive 3D structure, held together by hydrogen bonds between peptide bonds.
- Tertiary structure is non-repetitive larger scale 3D structure. Contributing factors, van der Waals, H bond, ionic forces – but mostly the hydrophobic effect.
- Quaternary structure = more than one chain. All weak forces contribute, but salt bridges are often important.
How can a protein act as a form determining function?
This protein (DNA Polymerase III) shown is a great example of form determining function. The beta subunit of DNA Polymerase III is a “sliding clamp” which makes the polymerase adhere to the DNA for millions of base pairs worth of replication. You can see that it is a dimer, and that the toroidal (bagel, doughnut) shape is perfect for trapping the long DNA double helix in its center.
Illustrate Koshland’s Induced fit
This illustrates Koshland’s Induced fit. A small molecule can cause a large change in the conformation of a large molecule (like a protein) and here the shape change is a signal that iron is bound to this enzyme (Lactoferrin).
What is the difference between L isomer and D isomer?
How does the Fisher reaction work in this picture?
In the original Emil Fischer projection, the MOST oxidized carbon is on top and is given the number “1” and the longest carbon chain is shown vertically. A substituent at “2” is called an alpha substituent.
When you focus on one carbon in the chain, the carbons above and below it are BEHIND the plane and the substituents left and right are IN FRONT OF the plane, so you see a sp3 tetrahedron. TILTING a Fischer drawing 90 degrees changes it from L to D or vice versa. SWAPPING any 2 groups also changes the designation.
(Know the difference between D and L and look at handout)
(The one on the right is important)
Draw out the structures of these amino acids:
Glycine, Alalnine, Proline, Valine, Leucine, Lysine, Argenine, and Histidine
Glycine, Alalnine, Proline, Valine, Leucine
- H is______
- S is _____
- What is Gibb’s free energy equation?
- Enthalpy, heat contact, energy to put molecules together
- Entropy, +positive is messy, -negative is tidy
- G= H-TS
Name the 2 important functional groups
- Guanidine is found in Arginine
- Imidazole is found in Histidine.
Also the Indole nucleus is found in Tryptophan.
Draw out the structures of these amino acids:
Lysine, Arginine, and Histidine
(Refer to handout too)
Draw out phenalalanine, isoleucine, leucine, methionine, tyrosine, valine, and inpole
Give the examples of a H in HK RED POLAR
Histidine and lysine have the same amount of carbons which is…
6
Draw out E and D structures
Give the examples of ED in HK RED POLAR (Could not get everything!)
Draw two amino acid to amino acid residues
Represent a peptide bond in a beta formation
This is a peptide chain maximally stretched – notice that the NH and C=O bonds alternate up and down. This is called the “beta” conformation, or “beta sheet” This chain starts at left and goes to the right.
This is also a depiction of primary structure, everything is connected by covalent bonds.
Draw a disulfide bond with the protein cytosein
Disulfide bonds formed by cysteine are also covalent and are also considered to be part of the primary structure of a protein.
What does this structure represent?
This is the primary structure of the hormone protein INSULIN. Notice there are 2 chains held together by disulfide bridges
Describe what a peptide bond is
A peptide bond is planar because the C and the N are sp2. So a plane of six atoms is defined, C C N C plus O and H. Thus a peptide chain could be thought of as a series of playing cards, a series of planar rectangles connecting only at the corners. The corners that connect are the alpha carbons, and that is also where the R groups are attached – perpendicular to the planar portions.
Where is alpha?
Where is beta?
- Lower left corner
- Upper left corner
This is a Ramachandran plot. The right handed alpha helix is in the lower left quadrant, and the beta sheet (and collagen helix) are in the upper left quadrant. Dark green is where there are likely to be angles plotted from real life proteins. White is “forbidden” but you do see Glycine residues there.
What does this structure represent?
This is the “smoothed” version of the right handed alpha helix. Notice that the green R groups all stick out away from the central core.
What is the difference between a right handed and left handed helix? (and draw it out)
Which is longer: Aplha or Beta?
Beta
Describe the coiled structure of keratin
This coiled coil structure is characteristic of keratins. Your hair and fingernails are made of alpha keratin – there is a heptad repeat, a repeating pattern of 7 residues in keratins
Draw the structure of proline
How do you go from procollagen to collegen?
Drink vitimin C
What is special about this collogen structure?
This is collagen, a very different kind of coil. Every third residue is Glycine which allows the 3 strands to wrap tightly around each other and make a cable (stories – Vitamin C and Dinosaurs).
What is the importance of Myoglobin?
This is Myoglobin – we will have an entire chapter on Myoglobin later. The protein is mostly alpha helical, the E and the F helices make up the heme pocket. The heme group is the gray thing. The E helix is blue here.
What is this structure?
This is a transmembrane channel protein (Porin) which seems inside out. The hole in the middle is lined with hydrophilic residues.
How many beta sandwhiches are in this structure?
This protein has 4 obvious beta domains (sandwiches) – it is constructed like the heavy chain of IgG, an antibody but this is CD4 which the HIV virus attaches to when it attacks the immune system.
How is Urea 8 molar? What does that mean?
8 molar urea uses up the H bonding capacity of water so the hydrophobic effect is diminished and proteins can unfold. Guanidinium = same thing. BME, mercaptoethanol breaks disulfide bonds by reducing them to –SH
QUESTION: Where does the 8 come in? Does mean 8 total bonds in the molecule
(There are also 6 on the outside)
What does that mean??
How do you denature ribonuclease?
8M Urea
- Represent a titration of Alanine
- What does a mean when the acid has a ph= 2
- What does it mean when the base has a ph of 12?
Draw a titration curve of 1 mole of Alanine
If you start in the middle of the titration point, and add the lowest acid and highest base, what is the pI?
(2.3+9.9)/2= 6.1pI
What happens when a biochemist want to study a specific protein in an organ?
When a biochemist wants to study a protein
– he is faced with the fact that a tissue or organ might contain hundreds or thousands of different proteins and you have to get rid of all the ones you don’t want so you can focus on the single protein that you do want.
- Milk has a mixture of proteins, less than most tissues would.
What do you need to tell whether or not a protein is becoming purer and more concentrated?
- You need an assay to tell whether the protein is becoming purer and more concentrated. If you’re lucky you might be looking for an enzyme like Lactate DH.
- When NADH is produced it is visible to a UV spectrophotometer so you can look at how rapidly NADH is produced by the enzyme reaction.
How does dyalysis work?
Proteins are big, many reagents are small, and small molecules can escape from a dialysis bag whereas proteins can not.
How do you purify a protein?
By performing affinity chromatography is a way to purify a target protein, if you can find something that protein binds to avidly.
What is HPLC?
HPLC used to mean High Pressure Liquid Chromatography, but the name was changed to High Performance Liquid Chromatography. It is easy to get a crisp separation either between large molecules (proteins) or small molecules. And the results are highly reproducible.
(Need to Know!)
Describe what SDS electrophoresis is and how it works
SDS (Means 12) PAGE = Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis
The SDS detergent denatures the proteins – unfolds them. So the native charge is irrelevant, each protein is an unfolded “snake” with a coat of SDS “hairs” each with a negative charge. So there is no point in putting the sample in the middle of the gel, all samples will travel towards the (+) Anode. The speed depends on the size – smallest proteins move fastest in this system.
- Small goes the farthest distance
- Big goes the shortest distance
What is SDS?
- Denatures proteins with negative charges so theres no folding
- Is a detergent
What is isoelectric focusing?
Isoelectric focusing
A mixture of proteins is separated by electrophoresis in a pH gradient. Note that these proteins are in their native conformation and they are migrating because of their own native charge.
When they migrate to the pH that corresponds to their isoelectric point, they stop moving. Hence “Isoelectric Focusing.” 2-D electrophoresis means that after you do step one, you fuse the gel onto the top of an SDS PAGE gel.
When you turn on the perpendicular current the proteins are denatured by SDS and moved downward toward the anode (+) which will be at the bottom. Smallest move fastest. So you can separate very many proteins and get a clean separation.
(First separated by charge THEN by size)
Why is affinity chromatography the best?
It has a huge purifciation value
What does a gradient make do?
Measures density
Think of iced tea with sugar in the bottom – concentration increases as you go down the glass, and therefore density increases. Centrifuging in a density gradient can give separation of proteins by buoyancy.
Whats the difference in the spinning of small and big proteins?
What is the importance of immunoglobin?
Immunoglobin G showing the four chains – two light and two heavy, held together by disulfide bonds.
What is Sandwhich Elisa?
- Used in pregnancy tests to detect HCG
What are homologous proteins? Give an example.
What does orthologous mean? Give an example.
What does paralogous mean? Give an example.
- Proteins that are very similar to eachother. Humans and chimps.
- Same job in 2 related species. Cows and people are related, we are both vertebrates, we are both mammals. And RNAse does the same job in both.
- Different job, gene duplication. Angiogenin promotes the growth of new blood vessels. Two homologous proteins with DIFFERENT jobs are called PARALOGS and they arise from gene duplication.
Explain what is happening in the following picture.
Orthologs arise from speciation
Paralogs arise from gene duplication
