Bio Chem Chapters 1 & 2 & 3

Lipids b/c not covalently linked but rather have hydrophobic interactions

Yes, the same is glucose

A functional group containing -SH

Not as soluable although it has many rings

Monomers after being incorportated into polymer is a residue

1. Proteins---Peptide bonds

2. Nucleic Acids--Phophodiester bonds

3. Polysaccaride-- Glycosidic linkages

--Metabolic reactions

--Support cellular structures

*Sometimes store energy

--Store energy

--Support cellular structures

--Sometimes encode information

--Store information

--Sometimes carry out metabolic reactions

--Spontaneous

--Delta G is less than 0

--Looses energy/energy is not left over

When G is greater than 0

--Energy is gained

decrease in enthalpy, increase in entropy

G = change in enthalpy - temp*change in entropy

Happens w/ gain of H or loss of O

Happens w/ loss of H or gain of O

Yes, b/c we are highly organized

(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

All negatively charged thigns attracted to surface and polymerize

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

--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)

--2 base

--Adenine + guanine

--1 base

--Cytosine + guanine

--Ribose has two hydroxls at c#2 and c#3

--Deoxyribose has hydroxol at only c#3 and H at c#2

--Length 34 A (10 BPs)

--Width 11 A

--Diameter 20 A

--Right handed spiral

--Major and minor grooves

--Dimensions are above

--Antiparallel

--Bases in centre

--Phosphate backbone exposed in solvent

--Short, single stranded polymer of nucleotides

1. Exonuclease

---Cleave @ end of stand

2. Endonuclease

---Cleave @ some other point

--11 BP length (longer than 10 BP length)

--DNA helix has diameter of 26 A (larger diameter)

--Rather vertical interactions

--Strongest between C+Gs

--Is this temperature where half the DNA has been seperated into single strands

---Depicts melting point

--Seeing how much the nucleotides absorb

--Absorb more UV when unstacked vs. stacked

20-25C below melting

A + G = C + T

UAA = TAA

UGG = TGG

UGA =TGA

--Missing phenylalanine residue at 508th amino acid (doesn't affect 507th b/c redunancy)

--Extracellular low in Cl so transport of Cl into fluid happens

--Means water goes into the cells

--Short segments of DNA that are copied and inserted randomly

Mod--- (45%)

High---(3%)

3% of genome

2-10 BPs

Repeat thousands of times

Used for fingerprints

--Transfer from species to species rather than parent to offspring (virus + mammal)

1/1000 BP

3 mill sites

Where we differ in our genome

--Lowered temp to 55C so primers can hydrolyze

--Put to 75 C to add new DNA by extending

--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

--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)

--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

20^x

N-C partial dbl bond

--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

--Hydrogen bonds form between amide and carbonyl groups of adjacent strands

1. Parallel: neighbours run in same direction

2. Neighbours run in different direction

--Happens usually in teritarty structure when linking multiple secondary structures

X-ray crystallography

--Polypeptide segement with hydrophobic core

1. Hydrophilic: Where the loops are usually found

2. Hydrophobic: Usually secondary structures b/c hydrophilicity is limited, not much room for H20

--Largest force governing protein structure

--Makes hydrophobic parts aggravate to avoid water

--Molecules + ions that help keep poly peptides in place

examples: ion pairs (charged; positive + negative), Zn2+, disulphide bonds

--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.)

--Not for protein stability much

--When cys residues are blocked then proteins still form normally

--Through oxidation

----Cytoplasm is reducing environment which is why disulfide bonds are more suitable for extracellular environments

--Used in protein stability

--20-60 residues w/ 1 or 2 zinc ions

Asp, glu or cys, his

S, N, O

1 good b/c not readily oxidated

--Most stable teritary structure

--Could be multiple (depending on pH, binding partner etc.)

--Not random

Degarded

--Aggregated protei

Intra--tangles

extra--plaques

--Made of tau which is usually used in assembly of microtubules

--Made of amyloid-B

----Precursor of membrane protein

--A synuclin

----Accumulation = symptoms

--Increased expression of a synuclin

--Forms alpha helices upon binding to other molecules

Normal PrPc---Contains mostly alpha

PrPsc--Mostly beta, triggered PrPc to conform to its conformation