sarcomere

A band = myosin length (so it doesn't change length!)

H zone = space between the actin (so it gets smaller)
I band = space between myosins in adjacent sarcomeres (so it gets smaller)

http://www.maxanim.com/physiology/Sarcomere/Sarcomere.htm

Mutation

mutation - change in genome that's not genetic recombination

either at the chromosome level or nucleotide level:
spotaneous/induced
mutagens


nucleotide level mutation:
point mutation- change 1 base pair
e.g., base-pair mutation - 1 bair pair swap (e.g., at to gc=transition, at to ta =transversion)
missense mutation occurs in aa coding region e.g., sickle cell anemia = 1aa change in hemoglobin
neutral = no change in aa function
silent = no change in aa (could change a promoter thought)
end of base-pair

point mutation type 2 = insertition/deletion of base-pair
frameshift mutation or nonframeshift
frameshift = deletions/insertions in non-multiples of 3 >usually bad prot
nonframeshift = deletion/insertions in multiples of 3 >partial/complete functional prot

nonsense mutation results either point or insertion/deletion > new stop codon



chromosomal level
deletion/duplication/translocation/inversion
deletion = break off or lost during homologous recombination/crosssing over
duplication = dna fragment break off and incorporates into homologous chromosome
aneuploidy = delete/dup of entire chromosome (e.g., down = 3 copies chrom21)
polyploidy = delete/dup of sets of chromosomes

translocation = dna from one chromosome inserted into another chromosome
inversion = orientation change on one chromosome
these are cause by transposition (eu and prokaryotes)-transposon excise from chrom & reinsert
transposon - can 1+ genes or control element
can copy before moving
allow cell to change genetics without meiosis

mutation
forward or back (change move or revert to original state)
wild type - original
e.g., his + (wt) and his- (forward) to revert (back) and to further change (forward)

Cellular metabolism

anabolic = energy stored
catabolic = energy release to ATP

Catabolic
1. nutrient > CO2, H20
2. ADP + P > ATP

Cellular Respiration
1. anaerobic metabolism
2. aerobic metabolism

Reactions

1. thermodynamically favorable (release free energy)
2. thermodynamically unfavorable (require free energy)

covalent bonds are stable so molecules don't react spontaneously at phys conditions
activation energy excites stable ground state > reactive transition states
activation energy (not thermodynamics) determine reaction rate
so exergonic reactions don't occur due to high activation energy without assistance

enzyme = act as catalysts, lower activation energy
unaltered at end of reaction
act only on substrates (unlike inorganic catalysts)
only speed up 1 reaction of substrate (of many potential ones)
specificty = 3D #3 and #4 structure
enzyme has active site where substrate binds (conformation change)

enzyme and substrate have weak ionic or H bond
break via thermal motion
enzyme active site = R groups (polar nonpolar electrically charged)
so nonpolar substrate can't bind to polar/charged active site
coenzymes may be required for binding (nonproteinaceous, unchanged)

enzyme stabilize transition state substrate molecule
(lowers activation energy)
don't change reaction equilibria
increase reaction rate by bonding multiple reactants simultaneoulsy

enzymes are controlled
temperature, pH, substrate [], and
chemical agents:
1.competitive inhibitor -compete for enzyme active site, overcome by [substrate]
2.noncompetitive inhibitors - change enzyme not at active site
3.irreversible inhibitors - bond enzyme active site permanently

allosteric enzymes have active/inactive states
negative modulators stabilize inactive state

cooperativity - enzyme with 2+ identical binding sites where one bind increases 2nd site bind affinity

Organic compound

organic compounds:
1. carb
2. lipid
3. protein
4. nucleic acids

Carbs:
monosaccharides
3-6 C
C=O group in straight chain form
polysaccharides
6C monosaccharid chains
6C = hexoses e.g., glucose
polysacc = glycogen = 100s glucose

condensation= mono > polysacc
1 h20 is remove per 2 monosacc joined

hydrolysis = polysacc breakdown
1 h20 per 1 bond between 2 monosacc split

Lipids:
CHO
(may have P and N)
fat molecule = gylcerol + 3 fatty acids
glycerol (3C each with OH hydroxyl)
fatty acids = 4-24C chain with COOH
so fat = 3 fatty acids + glycerol via condensation
3fatty acids from hydrolysis of fat

Protein:
CHON (sometimes S)
H
R-C-COOH
NH2
20 aa common in proteins
each aa has the above C with amino and carboxyl group and side chain R
R makes aa unique
aa joined via condensation > peptide bonds
peptide bonds between COOH and NH2 of successive aa

1 aa = polypeptide
protein = 1+ polypeptides (each polypeptide = subunit)
multimeric= structure composed of several identical or different subunits held together by weak bonds
proteins stabilized by H bonds and covalent disulfide bonds
disulfide bond (S of 2 cysteine)
#1 linear sequence of aa
#2 spatial arrangement of nearby aa and locations of disulfide between subunits
motif = a-helix, b-sheet
#3 spatial arrangement of aa residues in polypeptide
#4 multimeric prot only have interactions between polypeptides

Nucleic Acid
1. deoxyribonucleic
2. ribonucleic acid
each have nucleotides
PN covalent bond to 5C sugar
DNA has 4 nucleotides (different nitrogenous base)
purine = adenine and guanine (2 rings)
pYrimidine = cYtosine thYmine (1 ring)
nucleotides bond at the P group and the deoxyribose
sequence of nucleotides = genetic info
DNA 2 nucleotide chains (oriented in opposite directions)
H bonds hold the bases together
double helix means only TA and GC
4 rungs = AT, TA, GC, CG

RNA
mRNA = DNA instructions transferred to cytoplasm for protein synth
rRNA = ribosomes, structural component of protein synth
tRNA = carry aa to ribosome for prot synth (according to mRA)

RNA has ribose, uracil not thymine, single stranded

Enzyme Inhibitors

competitive = compete for active site (like musical chairs); overcome by increasing [substrate]

noncompetitive = changes enzyme shape so it can't interact with active site of enzyme

irreversible = binds enzyme active site and never dissociates

Water

Water is the solvent for most biological reactions
Hydrolysis = breakdown of macromolecules (nutrients)
examples: carbs ->glucose, nucleic acids->nucleotides, protein->amino acids, triglycerides->fatty acids
hydrogen bonds = strong intermolecular bonds of water
hydrophillic = polar portion of molecule will dissolve in water
antipathic = a molecule that is part polar and part nonpolar

Oxidation (lose) Reduction (gain)

Oxidation is losing electrons (oxidized form NAD+, donating molecule is oxidized)

Reduction is gaining electrons (reduced form NADH, accepting molecule is reduced)

coenzyme store/release energy in form of electrons via oxidation and reduction

Enzymes

Enzyme characteristics
1. lower activation energy
2. increase reaction rate
3. don't change free energy (G)
4. aren't changed/consumed

Induced Fit hypothesis
Active site of enzyme is flexible and changes when the correct substrate approaches

Cofactors-nonprotein molecules that aid in binding enzyme+substrate (ES)
apoenzyme = enzyme without cofactor
holoenzyme = enzyme with cofactor
prosthetic group = enzyme with tightly bound cofactor
coenzymes = organic cofactors that cannot be produced by the body (organic groups, biotin, vitamin derivatives)