Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
75 Cards in this Set
- Front
- Back
Which of the four biochemical molecules doesn't form polymers and why? |
Lipids b/c not covalently linked but rather have hydrophobic interactions |
|
What are the monomers in starch and cellulose? Are they the same? |
Yes, the same is glucose |
|
Thiol |
A functional group containing -SH |
|
Is cholestral soluable? |
Not as soluable although it has many rings |
|
Residue |
Monomers after being incorportated into polymer is a residue |
|
What are the three types of polymers? What are they linked by? |
1. Proteins---Peptide bonds 2. Nucleic Acids--Phophodiester bonds 3. Polysaccaride-- Glycosidic linkages |
|
Functions of proteins |
--Metabolic reactions --Support cellular structures *Sometimes store energy |
|
Functions of polysaccarides |
--Store energy --Support cellular structures --Sometimes encode information |
|
Functions of nucleic acids |
--Store information --Sometimes carry out metabolic reactions |
|
Exergonic |
--Spontaneous --Delta G is less than 0 --Looses energy/energy is not left over |
|
Endergonic |
When G is greater than 0 --Energy is gained |
|
When are all reactions spontaneous? |
decrease in enthalpy, increase in entropy |
|
What is the free energy equation? |
G = change in enthalpy - temp*change in entropy |
|
Reduction |
Happens w/ gain of H or loss of O |
|
Oxidation |
Happens w/ loss of H or gain of O |
|
Low entropy in organisms? |
Yes, b/c we are highly organized |
|
Prebiotic world theories (4) |
(1) H2, h20, hCN, NMH3 have all been present and sparked w/ lightning (2) HCN, HCOH + phosphate could have converted to nucleotides w/ energy (3) Monomers turning into polymers after water is evaporated (4) Hydrothermal vents and high heat |
|
Clay polymerization |
All negatively charged thigns attracted to surface and polymerize |
|
In order to be selected w/ natural selection then molecules need to be |
Stable and lots of monomers available to polymerize, needed to be able to fix CO2 b/c fixing CO2 allows for oxygen to form making aerobic organisms flourish |
|
Miescher---WBC experiment |
--Put WBC on bandages and dismissed that NUCLEIC acids could be genetic carriers b/c proteins have more variation/combinations to make (turned out to be wrong obvi lol) |
|
Two types of purines & made of |
--2 base --Adenine + guanine |
|
Two types of pyrimidines and made of |
--1 base --Cytosine + guanine |
|
Ribose sugar vs. deoxyribose sugar |
--Ribose has two hydroxls at c#2 and c#3 --Deoxyribose has hydroxol at only c#3 and H at c#2 |
|
Dimensions of DNA helix |
--Length 34 A (10 BPs) --Width 11 A --Diameter 20 A |
|
Feautures of DNA helix |
--Right handed spiral --Major and minor grooves --Dimensions are above --Antiparallel --Bases in centre --Phosphate backbone exposed in solvent |
|
Oligonucleotide |
--Short, single stranded polymer of nucleotides |
|
Two types of nucleases |
1. Exonuclease ---Cleave @ end of stand 2. Endonuclease ---Cleave @ some other point |
|
RNA + DNA diameter |
--11 BP length (longer than 10 BP length) --DNA helix has diameter of 26 A (larger diameter) |
|
Stacking interctions |
--Rather vertical interactions --Strongest between C+Gs |
|
Tm (Temp) |
--Is this temperature where half the DNA has been seperated into single strands ---Depicts melting point |
|
How do researchers test for denaturation in DNA? |
--Seeing how much the nucleotides absorb --Absorb more UV when unstacked vs. stacked |
|
What temp is the max renaturation rate |
20-25C below melting |
|
Chargoffs rule |
A + G = C + T |
|
Stop codons (in mRNA and DNA form) |
UAA = TAA UGG = TGG UGA =TGA |
|
Mutation in CF |
--Missing phenylalanine residue at 508th amino acid (doesn't affect 507th b/c redunancy) |
|
What does a CF lung look like w/ ions |
--Extracellular low in Cl so transport of Cl into fluid happens --Means water goes into the cells |
|
Transposable elements |
--Short segments of DNA that are copied and inserted randomly |
|
Moderately repeative vs. highly repeatative percentages |
Mod--- (45%) High---(3%) |
|
Dynamics of highly repeatitive |
3% of genome 2-10 BPs Repeat thousands of times Used for fingerprints |
|
Horizontal gene transfer |
--Transfer from species to species rather than parent to offspring (virus + mammal) |
|
What are SNPs and how often |
1/1000 BP 3 mill sites Where we differ in our genome |
|
PCR 3 steps |
--Heat up to 90-95 to seperate DNA
--Lowered temp to 55C so primers can hydrolyze --Put to 75 C to add new DNA by extending |
|
Pyrosequencing |
--A flash of light happens b/c of ATP --ATP is a result of pyrophophate degration --Pyrophosphate occurs when cleaves from dNTP aka the nuleotide is added in the DNA sequence |
|
Site-directed mutagenesis |
--Mimics natural selection by creating mutations --Creates mimics by creating variatons where oligonuclotides are identical to portion of gene except for a couple bases (corresponds to only some of codons) |
|
General rules for all peptides |
--Increased molecular mass for increased # of amino acids --Increased polypeptide chains for increased # of amino acids --Most polypeptides contain 100 and 1000 amino acid residues |
|
Possible # of amino acid sequences |
20^x |
|
What bond in secondary structure limits strain, rotation but satifies requirements |
N-C partial dbl bond |
|
Alpha helix structure |
--Twists in right handed helix --3.6 residues per turn, 12 residues long --Side chains outward --Does this conformation so it can form bonds between CdblbondO and N-H |
|
Beta-pleated sheed |
--Hydrogen bonds form between amide and carbonyl groups of adjacent strands |
|
Two types of sheets |
1. Parallel: neighbours run in same direction 2. Neighbours run in different direction |
|
Irregular structure |
--Happens usually in teritarty structure when linking multiple secondary structures |
|
What first imaged the irregular* structure of hemoglobin? |
X-ray crystallography |
|
Domain |
--Polypeptide segement with hydrophobic core |
|
What is usually found in the hydrophilic parts of the domain? What about the hydrophobic parts? |
1. Hydrophilic: Where the loops are usually found 2. Hydrophobic: Usually secondary structures b/c hydrophilicity is limited, not much room for H20 |
|
Hydrophobic effect |
--Largest force governing protein structure --Makes hydrophobic parts aggravate to avoid water |
|
Hydrogen bonding; does it help w/ protein stability? |
--Not really, just helps proteins already stabilized by the hydrophobic effect
|
|
Cross links |
--Molecules + ions that help keep poly peptides in place examples: ion pairs (charged; positive + negative), Zn2+, disulphide bonds |
|
Explain ion pairs |
--Electrostatis bonds are strong but doesn't help much w/ protein stability b/c it has costs to forming the pairs (burying the ions, loss of entropy etc.) |
|
Disulfide bonds |
--Not for protein stability much |
|
Evidence that disulfide bonds aren't for protein stability |
--When cys residues are blocked then proteins still form normally |
|
How do disulfide bonds form? |
--Through oxidation ----Cytoplasm is reducing environment which is why disulfide bonds are more suitable for extracellular environments |
|
Zinc fingers |
--Used in protein stability --20-60 residues w/ 1 or 2 zinc ions |
|
What do zinc ions bind to? |
Asp, glu or cys, his |
|
What ligands can Zn interact w/ |
S, N, O |
|
How many oxidation states for Zn ions? |
1 good b/c not readily oxidated |
|
Native structure |
--Most stable teritary structure --Could be multiple (depending on pH, binding partner etc.) --Not random |
|
What happens to proteins that usualyl cannot be folded properly? |
Degarded |
|
Amyloid deposits |
--Aggregated protei |
|
Alzheimer's disease consists of excess proteins of which intracellular and extracellular |
Intra--tangles extra--plaques |
|
Intracellular |
--Made of tau which is usually used in assembly of microtubules |
|
Extracellular |
--Made of amyloid-B ----Precursor of membrane protein |
|
Parkinson's accumulation of what protein |
--A synuclin ----Accumulation = symptoms |
|
Genetic component of parkinsons |
--Increased expression of a synuclin |
|
Goal of a-synuclein |
--Forms alpha helices upon binding to other molecules |
|
Difference between normal TSEs and abnormal in Mad Cow Disease |
Normal PrPc---Contains mostly alpha PrPsc--Mostly beta, triggered PrPc to conform to its conformation |