BICD 110-Midterm 1

What was the last eukaryote common ancestor?

LECA

Naked eye

~100um+

Light microscope

10nm to 1mm (higher resolution)

Electron microscope

0.1nm to 1mm (high resolution for smaller proteins)

atom

0.1nm

small molecule

1nm

globular protein

10nm

virus ribosome

100nm

bacterium

1um

animal cell

10 um

plant cell

100um

frog egg

1mm

Robert Hooke (1635-1703)

discovered (plant) cells, compound microscope (50x magnification), the cell is the most basic unit of life

Anthonie van Leeuwenhoek (1632-1723)

discovered microorganisms (protists, bacteria, sperm cells), red blood cells, cell theory, single lens microscope 200-300x magnification, observed that fertilization process requires sperm cell to enter oocyte, observed ‘lumen’ in the salmon red blood cells- the nucleus

Cork micrograph drawing (Hooke)

“honeycomb”; “pores”, “cells”

gum swabs (Leeuwenhoek):

'“animacules” (tiny animals): can grow=independent form of life

Rudolphi/Link (1804)

cells have independent cell walls (not shared)

Dutrochet (1824)

“the cell is the fundamental element of organization”

Schleiden (1839)

every part of a plant is made up of cells, cells made from ‘crystallization process’ stole crystallization process

Schwann (1839)

both plants and animals are composed of cells and their products

Virchow(1855)

all cells arise only from pre-existing cells

What is tenet 1 of cell theory?

all living organisms are composed of one or more cells

What is tenet 2 of cell theory?

the cell is the most basic unit of life

What is tenet 3 of cell theory?

all cells arise only from pre-existing cells

What did basic stains allow Brown and Flemming to discover?

the nucleus, chromosomes, and different stages of cell division due to positive and negative charge

What did a “black reaction” in neurons allow C.Golgi to discover?

identify the ‘internal reticular apparatus’ called the golgi apparatus

electrons have a smaller wavelength than photons

high-resolution images

transmission electron microscopy (TEM)

thin: stained/shadowed with heavy metals

thick samples: fixed, dehydrated, embedded in resin, sectioned, and stained with heavy metals

scanning electron microscopy (SEM)

surface of sample is metal-shadowed

cryogenic electron microscopy(cryo-EM)

hydrated, unfixed, unstained samples are plunge-frozen leading to the formation of vitreous ice

What did Porter, Claude, and Fullham obtain?

First electron micrograph of a cell

What did George Palade discover?

ribosomes of the endoplasmic reticulum, rough endoplasmic reticulum, lumen of rough endoplasmic reticulum, vesicles moving proteins from the rough endoplasmic reticulum to the gogli complex, lumen of golgi vesicle, golgi complex

increase absorption of photon

decrease emission of photon at longer wavelength

violet

400nm

indigo

445nm

blue

475nm

green

510nm

yellow

570nm

orange

590

red

650

some organisms produce flourescent protiens (FPs) which the genes can be

fused to a gene of interest to produce a recombinant fluorescent protein and express in an organism/cell line of interest

transfection/transduction of cells resulkts in the expression of an

ectopical protein

results in an overexpression of the protein

(endogenous+exogenous protein)

Roger Tsein GRP in all colors which allows for

identification and localization of proteins via fluorescence microscopy

Identification and localization of proteins via ‘immuno-labeling’

antigen A→ primary antibody (antibody directed against antigen A), secondary antibodies (marker-coupled antibodies directed against the first antibodies

antibody with a probe covalently attached

generating antibodies to the specific protein of interest, immune system generates proteins called antibodies to the antigens

antibodies by injecting a model animal

with the protein of interest

monoclonal antibodies

generate antibodies from a cell line which can be purified

cells/tissues fixed

with common fixative like formaldehyde or glutaraldehyde which cross-links amino groups on adjacent molecules, tissue embeded in paraffin for sectioning

Permeabilized

with non-ionic deterghent that makes plasma membrane permeable to reagents

stained

with a ‘marker’ that is covalently attached to specific antibodies with heavy metals that stain different biomolecules to gain contrast or with small flourescent dyes that bind to membranes, DNA, or other structures

What is the first key concept of chemistry of life?

Molecular Complementarity (to stabilize the complex with molecule compounds that complement each other)

What is the second key concept of chemistry of life?

Polymerization, subunits need to come together

What is the third key concept of chemistry of life?

Chemical equilibrium( proteins can bind to each other at one dynamic rate, dissociate at another rate, reactants spatially controlled)

What is the fourth key concept of chemistry of life?

Energy-’high energy’ phosphoanhydride bonds supports unfavorable reactions (chemical energy)

Thermal energy

noncovalent interaction lowest bond strength

van der waals

noncovalent interactions second lowest bond strength

hydrogen bonds

noncovalent interactions third lowest bond strength

noncovalent interactions

molecules interact fall apart but environmental heart→ unstable→ don’t want K+ to interact

Hydrolysis of ATP phosphoanhydride bonds

covalent bond third strongest bond

c-c<c=c

covalent bond more bonds equal more bond strength

weak interactions

additive interactions contribute to protein complex ability, in an aqueous enviornment Kd is a measure of affinity for the enzyme, more stable less molecules, low Kd high affinity, high Kd low affinity more molecules less stable

conformational selectivity

conformational change is followed by ligand binding

induced fit

binding of one molecule changes the conformation of the other (increases molecular complementarity)

hydrophobic effect

nonpolar substance is surrounded by highly ordered water molecules low entropy with hydrophobic aggregation the water molecules are released into bulk solution are less ordered being higher entropy a thermodynamically favorable process

‘emergent properties’

a property that an individual subunit does not have, but which arises from the collective/complex system

What is the ‘RNA world’ Theory?

nucleotides→ random non-enzymatic polymerization→ short oligomer pool→ recombination→ long oligomer pool→ folding and emergence of ribozymes→ encapsulation→ emergence of first RNA replicase

Step 1 of building a cell

create a barrier which separates in from out, interior biochemical environment differs from the exterior, protection of endogenous macromolecules and processes

Amphiphatic phospholipids spontaneously assemble into a bilayer structure

bilayer advantages: self assembly (hydrophobic effect), fluidity, barrier

Fatty acid composition of the bilayer fluidity

cis c=c bond introduces a rigid kink which prevents tight packing in a membrane bilayer whereas the reduced form is straight without kinks and the oxidized form has rigid kinks

PC

methylation, phospholipid

PS

Serine, phospholipid

PE

ethanol, phospholipid

PI

oleoid- hydroxy groups to phosphate Ser knows where Golgi is, phospholipid

PG

phospholipid

SM

Sphingomyel cholestrol lover, phospholipid

cholesterol

phospholipid

Cerebroside

sphingolipids with carbohydrates

LPS

lipids have specific carbohydrates

Homeoviscous Adaptation

cells dynamically change their membrane lipid composition to control membrane fluidity

decrease transition temperature

unsaturated bonds, shorter acyl chains

increase transition temperature

saturated bonds, longer acyl chains

cholesterol fluidity impact

lowers membrane permeability, adjusts membrane fluidity: low temp increases fluidity high temp decreases fluidity

hydrophobic molecules

all pass through the bilayer

small uncharged polar molecules

some pass through

large uncharged polar molecules

slightly pass through

ions

do not pass through the bilayer

phosphorylation

kinases catalyze transfer of phosphoryl group to amino acid side chain from ATP, serine, theorenine, tyrosine

acetyl lysine

epigentic control, cytoskeleton dynamics

3-Hydroxyproline

crosslinking of collagens, requires ascorbic acid

3-methylhistidine

urinary excretion reliable index of muscle protein breakdown

y-carboxyglutamate

high affinity binding of calcium ions

O-glcNAc-threonine

sending out more hydrogen bonds causing it to be more sticky , placeholder for S/T phosphorylation sites

primary structure

linear sequence of amino acids linked by peptide bonds

secondary structure

local alpha helices or beta sheets, held together by hydrogen bonds, 3.6 amino acids per turn, R groups project outward, prolines don’t participate

tertiary structure

peptide three-dimensional shape

quaternary structure

association between multipeptide complexes

supramolecular complexes

can be very large, consisting of tens to hundreds of subunits

the more disordered the protein the more

exceptional conformational flexibilities that contribute to their multiple functions

coiled coiled motif

two alpha helices wound around each other, alpha helix heptad repeat sequence with a hydrophobic residue at positions 1 and 4