Flashcards

Biochem exam 2

izzy manche Inglês 131 flashcards

Know how to draw phosphodiester bond formation

Flashcards do conjunto (131)

1What is the primary and secondary structure of DNA?Primary = sequence of nucleotides
Secondary = base pairing between nitrogenous bases of the two different strands
2What are the primary and secondary structures of RNA?Primary = sequence of nucleotides
Secondary = base pairing WITH ITSELF (loops, not the same as the 2 different DNA strands)
3What are two methods to denature DNA and RNA structures?Put the peptide in extreme pH or very high temperatures
4How do extreme pH and high temps denature peptides?Break the hydrogen bonds
5What happens if you put the conditions back to normal and the parts of the structure are still near each other? (What is the special word for this?)The parts will anneal (rewind)
6What happens if you put conditions back to normal but the parts of the structure are NOT near each other?2 steps: 1) strands/parts will find each other
2) Base pairs will recognize and zipper
7How do strand of a structure "find" each other?random collisions and starting a short part of the complementary helix to kickstart the annealing process
8Why is RNA more stable in high temperatures than DNA?RNA has more opportunity for hydrogen bonding (hydroxyl group on C2)
9What happens to the UV light absorbance of a structure when the complementary strand is present? What is this effect called?Less absorption occurs. Hypochromic effect
10What happens to the UV light absorbance of a structure when the complementary strand is NOT present (denatured)? What is this effect called?More absorption occurs, especially at 260 nm (near aromatic rings). Hyperchromic effect.
11Where do you find the melting point on a heat of denaturation graph?The middle of the line (Tm)
12What are the "bubbles" in a structure and why are they there?Denatured sections. There because that region is probably high in A-T bonds, which do not bond as strongly as G-C (one less H bond)
13Why are structures with more G-C bonds stronger?G-C bonds make greater contributions to base stacking
14What is hydrophobic stacking?Nucleic bases are positioned in parallel planes to each other which minimizes their interactions with water.
15What bonds are involved in hydrophobic stacking?van der Waals and dipole-dipole
16Why is base stacking important?stabilizes 3-d structure of nucleic acids
17What is the technical definition of a mutation?spontaneous changes in covalent structure (nucleotide sequence)
18Why is Uracil not found in DNA?Cytosine can spontaneously denature into uracil, which is then recognized as a mutation. The main information storage system (DNA) cannot afford to let that happen
19What mutation does UV light exposure cause?Causes pyrimidine dimers which make kinks in DNA (tert structures)
20What does excessive oxidation do to DNA?Causes conformational change to DNA structure (ex. Guanine) and changes how the base pairs interact
21Which 2 bases are methylated more often?A and C
22Know how to draw phosphodiester bond formation
23What is the thermodynamic driving force of phosphodiester bond formation?pyrophosphate (2 phosphates linked) --H2O--> 2 PO4(3-)
24What do you need for DNA polymerase chain reaction (PCR)?-Taq polymerase (synthesizes new DNA)
- dNTPs (new bases)
- Mg 2+ buffer (helps pyrophosphate leave)
- Forward and reverse primers
-Template DNA
25Why is Taq used and not a human DNA polymerase?Taq can withstand the temperatures needed to initially denature the DNA (found in hotsprings)
26What do restriction enzymes do? How do they work?Catalyze hydrolysis of phosphodiester bonds. Recognize palindromic sequences.
27What are forward primers reading? How do we go about making them?Reading complimentary strand going to the right). Make the same sequence as the original strand but add some extra bases on either side primase has something to grab onto.
28What are reverse primers reading? How do we go about reading them?Reading coding strand going to the left. Write out the complimentary strand, WRITE FINAL PRIMER PRODUCT OUT IN THE 5'-3' direction, then add extra bases on either side
29What are "sticky ends"?unpaired nucleotides on either end of a strand. Happens after PCR
30How can DNA sequences be identified?Sanger sequencing method (using ddNTPs)
31How does sanger sequencing work?Add ddNTP; no 3' OH = no phospho chain extension. Results in gel with fragments that end with the ddNTP added
32What is the gel showing from a sanger sequence?4 columns to represent each of the ddNTP alterations. Top down is 3' to 5', largest to smallest. Showing the compliment to the original DNA sequence.
33Q5: What is the general structure of Sugar?(CH2O)n (Carbo-hydrate)
34What are 3 things carbohydrates do?-Energy Storage
- Provide cellular structural support
- Cellular communication/ recognition
35What type of monosaccharide is glucose?aldohexose
36What are interchangeable words for sugars?saccharides, carbohydrates, glucose (sometimes)
37Which structure (D or L) are natural sugars found in?D (also the type we have to memorize)
38Draw D-Glucose
39How do you determine when a structure is D or L?If the priority group of the chiral carbon (in this case the OH) is on the right (D) or left (L)
40What is the reaction to make the ring structure of glucose?an alcohol and aldehyde reaction
41What is a pyranose?A saccharide structure with a 6-membered ring containing 5 carbons and an oxygen
42Draw Beta-D-glucopyranose
43How do you remember where to put the Hydrogen groups on the B-D-glucopyranose?Down Up Down Up (look at last card)
44Why is Beta the more stable conformation?Because all hydroxyl groups are equatorial --> gives more room for hydroxyl groups (minimizes repulsion)
45What is the anomeric carbon?The carbonyl carbon: connected to the OH and O in the ring (has to be in ring/ chair form)
46What is an epimer?Structures with different configurations at ONE chiral carbon
47How to tell the difference between beta and alpha bonds?Look for the hydrogens on the anomeric carbons to be facing different ways
48How do you tell if something is a reducing sugar?If the anomeric carbon can unfold to form an aldehyde (if the anomeric carbon is attached to a hydroxyl group)
49What does a reducing sugar do?Reduces stuff (adds a hydrogen to something else)
50What is the benefit of having a starch (polymer) present rather than loose glucose?reduces osmotic pressure by linking groups (bc osmolarity counts # of things)
51What are the benefits of having beta linkages in polymers?tensile strength
52What is the relationship between glucose and all other types of sugars?All other sugars are epimers of glucose
53What are proteoglycans?sugars branching off proteins
54what is a main function of proteoglycans?lubricant between joints (moves nutrients through bc no blood)
55What types of structures can proteases read?L only
56What is the less sweet form of fructose?Furanose
57Why is cellulose stronger than glycogen?Cellulose is Beta linked, so it will form sheets that will allow for H bonding and strengthen the structure. Glycogen is alpha bonded which will make a branched chain (not very strong)
58What is the difference between glycoproteins and proteoglycans? Where do they live? How do they function?Proteoglycan: 1 linear protein, many repeating sugar units
Glycoprotein: Globular protein, branched sugar attached
Where: P=connective tissue, G=cell surface
Function: P=cartilage and lubricant, G=signaling
59How do proteoglycans lubricate joints?The sulfate branches are negatively charged and repel each other as well as attract water molecule, making a gel
60What are some variations possible for polysaccharide linkages?- order of the polysaccharides, could be branched or not
- alpha vs. beta anomeric carbons
- different carbons linking (1->3, 1->4, etc.)
61Q6: What is the function of a lipid?structural support, forms cell membrane, store energy
62What is the general structure of a lipid?carboxylic acid + chain of fatty acid
63What does "18:4n-3" mean?In the structure, there are 18 carbons, 4 doubles bonds, and the first double bond begins on the 3rd carbon from the end
64Are lipids conjugated? Why or why not?Not conjugated; if they were conjugated the lipid could conduct electricity which is the opposite of what its supposed to do (meant to insulate)
65Which structure has the double bonds, saturated or unsaturated?unsaturated: with double bonds present, the structure is less saturated with hydrogens
66Why do unsaturated fats have a lower boiling point compared to saturated fats even though they have double bonds?The structure is more compact and less likely to get tangled up with other structures, more van der Waals interactions in saturated fats
67Which type of unsaturated fat is produced in nature, cis or trans?cis
68Why are trans fats bad for you?Since they make long, straight chains, they can stack on themselves and become very dense. The body is only meant to handle the more looser packed cis fats. Too much tans fats can lead to fatty liver disease,
69Which molecule holds more energy, fats or carbohydrates? Why?Fats: can have long chains, more C-H bonds (energy storers). Can also hold for long-term because they don't need water to store energy, making them more dense
70How does saponification work?Remove glycerol group to make fatty acid salt
71How does soap work?Grease will van der Waals interact with fatty acid chain of charged lipid. The polarity of the carboxylic acid will dissolve into water and the grease will wash away.
72What is the main general rule of phospholipid structures?Middle carbon is always unsaturated
73___ catalyzes the hydrolysis of __ proteases endonucleases amylases phospholipasesamide linkages (peptide bonds)
phosphodiester bonds
glycosidic bonds
phospholipids
74How does snake venom work?Has phospholipases present that can dissolve cell membrane of prey
75What are myelin sheaths made of?sphingolipids (has charge)
76What is phosphatidylcholine?One of the 3 essential phospholipids: important for structural support of membrane and cellular signaling
77Draw Phosphatidylcholine
78Whats a saying to remember the structure of steroids?3 rooms and a bath (OH on ring, hydrocarbon chain on pent)
79What structure in vitamins ADEK make them only fat soluble?Isoprene
80What does amphipathic mean?Being both hydrophilic and hydrophobic (lipids)
81How does cholesterol affect a membrane?Low temp = makes a little less rigid (membrane might break without)
High temp = makes a little more rigid (membrane could fall apart without)
82PROTEIN FOLDING: What does a Ramchandran plot tell us about a protein's structure?shows where psi and phi bonds are allowed in a protein's structure
83What are psi and phi bonds? How to remember?Psi: angle of right-hand rotation around c-c bonds (PoPSiden is god of the c's)
Phi: angle of right hand rotation around n-c bonds
84Why do the psi and phi bonds determine a protein's secondary structure?Knowing the backbone rotation helps to know where the hydrogens will line up, determines if alpha helix of beta sheets
85Why do proteins have a dipole moment?The n-terminuses face upwards, the c-terminuses face downwards
86Why can't you have two oppositely charged amino acids next to each other in a primary protein structure?They will try to bond with each other and mess up the secondary structure -> messes up function of protein
87What happens to the specific rotation of a protein when the pH nears the charged amino acids pka?specific rotation increases
88Which amino acids destabilize alpha helices and why?Proline: R group connected to amino group, sterically hinders structure
Glycine: Having H as R group makes structure too flexible (not stable enough)
89What do Proline and Glycine cause in Beta structures?Beta turns (connects antiparallel Beta sheets, also found in hairpins)
90What are the differences between a fibrous and globular protein?Globular = functional
Fibrous = structural
91Give an example of a fibrous and globular proteinGlobular: hemoglobin
Fibrous: keratin
92What is the most abundant protein in vertebrates?Collagen (tendons, skin, bone, and teeth)
93What is unique about collagen's structure?triple helix with interchain H bonding
94What about alpha keratin's structure makes it function well?very strong protein found in mammal's hair and skin -> needs to be tough
- high number of cysteines = disulfide bonds = very stable tertiary structure
- more disulfide bonds means regular proteases like pepsin cannot break keratin down
- full of hydrophobic aa = water insoluble, waterproofs skin and hair
95Why do connected alpha helixes and beta sheets have to be on different planes?Beta sheets need hydrogens to be right next to each other to bond, so aloha helix needs to "sit up" to get out of the way
96What is the difference between a domain and a subunit?Domain = folds, has specific structure
Subunit = domain that can interact with other structures to make quaternary structure
97What are the three methods to determine 3d protein structure?X-ray crystallography
NMR
Cryo-EM
98X-ray crystallography:Finds protein structure based off electron density mapping
You need a LOT of 1 type of protein to get results
*small, see structure of protein and it's ligand*
99NMR spectroscopy:Applying magnetic field and radio pulses to find resonant structures in protein. Can also correlate what structures are near each other, further helps specificity of structure.
Needs proteins that are highly soluble (to separate structures) and need small proteins because of complex data
*can determine pKa*
100Cryo-EM:Protein is flash-frozen then imaged using electron microscope.
*Need large proteins, low resolution results*
101Which method produces dynamic data? What does dynamic data mean?NMR spec. Dynamic = seeing how protein changes over time
102What does van der Waal interactions between misfolded proteins cause? What diseases is associated with this?amyloid fibrils; Alzheimer's
103How do we know protein binding is not random?Anfinsen experiment with RNase A
104Describe the Anfinsen experimentUrea (override hydrophobic effect) and mercaptoethanol (reduce disulfides to thiols) added to protein = unfolded, inactive state. Take away urea and mercaptoethanol -> disulfide bridges reform in the same spots
There is a 1% chance of this happening, meaning protein folding cannot be random
105What part of a protein's structure dictates folding pattern?amino acid sequence
106What does a sigmoidal curve represent? What does this mean in a system?cooperativity. If one factor fails, the whole system fails
107Which folds quicker: alpha helices or beta sheets? Why?alpha helices; hydrogen bonds are closer
108What factor "tips the scale" to make folding spontneous?the hydrophobic effect: less hydrophobic surfaces for water to have to cover increases entropy
109Do proteins have many or few intermediates when folding to it's native state?Many
110What drives conformational changes in proteins?ATP hydrolysis (protein folds after heat is produced)
111What is the GroELs complex? How do they work?Purpose is to fold proteins. Water pushes unfolded protein into complex (hydrophobic surfaces are exposed so hydrophobic effect and bonding with hydrophobic inside of complex make this happen). ATP hydrolysis causes barrel structure to rotate and stretch protein, making it fold correctly.
112What is a protoporphyrin? What is it's structure?Cofactor of globins that bind O2. Flat planar rings that coordinate metals (iron) which grab onto the O2
113Which amino acid residue coordinates the iron that binds oxygen?Histidine 8
114Why is CO binding to polyporphyrin a problem?CO has it's electrons stacked linearly, making it bind way stronger -> won't unbind, can't carry oxygen in that heme now
115How does His E7 help the CO problem?stabilizes O2 by hydrogen bonding, steric hindrance to keep CO away
116How does O2 binding cause structural changes to heme?Goes from T-state to R-state: plane flattens and octahedral state forms once oxygen arrives. Makes blood turn red
117How do you tell if something is a beta or alpha bond?Alpha is on the same plane, beta is on two different
118What's the difference between beta and alpha glucose?Alpha: has C1 AXIAL hydroxyl
Beta: has C1 EQUITORIAL hyrdoxyl
119What are similarities between amylose and cellulose? Differences?Both made up of D-glucose 1->4 but cellulose is beta. Cellulose is also longer.
120What are similarities between amylopectin and glycogen? Differences?Both made up of alpha1->4 bonds, both have branches alpha1->6. Glycogen branches more often but amylopectin is bigger.
121Class of lipids called tocopherols, membrane associated antioxidantsvitamin E
122Involved in oxidation-reduction cycle, important for blood Klottingvitamin K
123Visual pigment of rhodopsinvitamin A
124lack of this causes scurvyvitamin C
125Why do alpha helices form before beta sheets?hydrogen bonds form closer in alpha helix compared to beta sheets
126What does this graph tell us?Represents how proteins go through many intermediates before reaching their native state
Horizontal = structural changes
vertical = energy changes
127What are 2 reasons chaperone proteins exist?- reduces chance of denatured proteins aggregating (takes them in with hydrophobic area exposed)
- helps intermediates get over activation energy needed to continue reaction
128Why is ATP hydrolysis needed for the function of the GroEL/ES complexThermodynamics: heat produced from ATP hydrolysis helps structure transition from energy minimum
Structure: ATP hydrolysis drives the moving of the barrels to change intermediate structure
129Who do transmembrane proteins have to have a specific secondary structure (alpha helices, beta sheets)?protein backbone is polar and can't be in the membrane by themselves, need something to interact with -> fold on themselves
130What is glycosylation?adding a carbohydrate to a protein (enzyme-controlled)
131What role does glycosylation play?-specificity in binding
-very hydrophilic, so increases solubility
- sugars protect protein from hydrolysis (proteases won't be able to read)