MOLECULES to cells

what is the central dogma

DNA→RNA→Protein

what are the three things DNA must do

1. replicated faithfully

2. have the coding capacity to generate proteins for cellular functions

3. transmit from parent cell to daughter cell

4. orchestrate any organismal functions

where are genes located

on chromosomes in the nucleas

what is DNA made of

nucleaotides, phosphate+sugar+base

what are the purine versus pyrimidine bases

A and G=purine

C and T=pyrimidine

how are phosphodiester bonds formed

5’ phosphate to 3’ hydroxyl

how was DNA structure determined

x-ray crystallography→DNA precipated from a solution by adding ethanol providing the fibres for crystallography

what is Chargaffs rule

A=T and C=G

how are bases paired in DNA replication

hydrogen bonding; C and G have 3 compared to and A and T with 2

job of helicase

to unwind and open up DNA

job of topoisomerase

deals with overwinding with nucleases to snip DNA while ligase reconnects

what is the main enzyme in DNA replication

DNA polymerase III

what is required for DNA polymerase initiation

RNA primers→created by primase

what can DNA pol I do

removes RNA primers

what directino does DNA synthesis occur

5’ to 3’ direction

how is the lagging strand created

Okazaki fragments→multple primers involved so DNA synthesis can still move from 5’ to 3’ direction

what are the enzymatic activities of DNAP I

1. 5’ to 3’ dna polymerasation

2. 3’ to 5’ exonuclease activity; backwards correcting base errors

3. 5’ to 3’ exonucleasing removing RNA primers

whatis Rifamipicin

RNA polymerase inhibitor

what is the Nick translation

DNA polymerase I taking over from DNA polymerase III and removes the RNA primer replacing it with new DNA and then ligase seals the nicks between the DNA

what is the Haflick limit

telomere shortening→indicator of aging that cells can only divide a certain number of times

what is the role of transfer RNA

translocation protein synthesis

what is meant by +1 in transcription

intiaition site

what is upstream versus downstream

upstream=-5

downstream=+5

what is the purpose of sigma subunits

in prokaryotes they are required for specific promoter recognition

does RNAP bind specifically or nonspecifcally

nonspecifcally→binds then scans looking for promoter sequence

simple versus complex termination of transcription

simple means without a protein factor and a hairpin structure forms near mRNA end causing RNAP dissociation

complex is rho depednent so a helicase protein called rho is required to terminate transcription

how is RNAP acitivate

through phosphorylation of C-terminal tail domain

how is mature mRNA produced

1. splicesomes remove introns

2. 5’ cap and 3’polya tail are added

3. mature mRNA is transported from nucleas to cytoplasm via nuclear pores

what are the two components of a gene

1=coding sequence; what gets transcribed

2=DNA regulatory elements such as the promoter

are gene products always proteins

no they can function as RNA

what are the cell types that cannot still express all nessecary genes to build a new organims(Wilmut sheep)

cells that have lost there nucleai(erythrocytes)

senescent cells that lost telomeres such as skill cells and neurons

what are housekeeping genes

genes expressed in every cell type

job of small nuclear RNAS

splice mRNA to remove introns

what are mendelles principles

principle of dominance→allele can be cominant or recessive with dominant always being expressed when hetereozygous

principle of segregation→allelles of genes seperated during gametogensis

law of independant assortment→genes encoding different traits segregate indepednetly of one another

Huntingtons disease

autosomal dominant

what cells are assoicated with cancer and expressed in breast cells

BRCA

epidermolysis bullosa

mutation in keratin gene that is austosomal dominnant and causes blistering

describe DNA replication

always occurs 5’→3’

the origin of replication is thymine and adenine rich since they only have two hydrogen bonds

pre initiation complex binds to DNA and opens up creating replication bubble

helicase unwinds DNA and SS binding proteins prevents reannealing and protects nucleotides from nucleases which want to break phosphodiester bonds

as it super coils topoisomerase uses nuclease to snap and then ligase to repair dna to un super coil

then the elongation stage involes primase which is an enzyme that attaches RNA primers allowing DNAP III to create DNA

the lagging strand gets multiple primers

DNAP I removes the RNA primers

polio

FLU

Polio=+ssRNA acts as mRNA so it immedicatly translated in cytoplasm using host ribosomes

FLU=-ssRNA so it gets transcribed in the nucleas by virion polymeriases and then translated

VSV chicken pox=dsDNA so it gets transcribed in the nuclease by host RNAP II

how do virusues move inside of cells

through microtubules and dyneines moving towards the nuclease

what info is versus is not contained in viral genomes

IS: virus genome replication, assembly and packing of genome, reuglating virus replication, modulation host defences, and spreading to other cells

NOT: genes for complete protein synthesis and those nessecary for energy production or membrane synthesis

inputs of photosynthesis

water, CO2, sunlight

relationship between stromata and thylakoids

stromata allow carbon dioxide in and out of cells and the thylakoids house chlorophyll which is a pigment in plants absorbing the suns photons

describe photosystem II→the first stage in light reactions

1. occurs in the thylakoid membrane that houses chloroplast

2. chlorophyll in PSII and electrons becomes excited

3. electrons flow into thylakoid membrane and it becomes negativly charged→beginning electron transport chain

4. as the electrons move thorugh thylakoid emebrane they operate on proton pumps which pulls hydrogen ions into the membrane

5. in this process water molecules are broken down to supply the electrons from hydrogen and oxygen is realased

6. PSI chlorophyll gets excited and move through the thylakoid membrane to ATP synthase

7. in this process NADPH is created through electrons bonding H+ and NADP

8. large amount of hydrogens in the thylakoid want to diffuse through ATP synthase and bond ADP to another phosphate creating ATP

9. ATP and NADPH are important creations

what light stimulates most photosynthesis

red and blue

definition of photosynthesis

process that converts sunlight into glucose

calvin cycle light independent reactions of photosynthesis

1. RuBP bonds with CO2

2. ATP and NADH break down the six carbon molecule into phosphoglycerate→ 2 PGA

3. some of these will bond to create glucose and some will be broken down further to keep cycle going and create RuBP

formula of photosynthesis

6CO2 + 6H2O → C6 H12 O6 + 6O2

what inhibits beta oxidation (fatty acid breakdown)

malonyl CoA which is formed during synthesis of fatty acids

difference between CAT 1 and CAT 2

carnitine acyl transferase-1 functions in the mitochondrial membrane adding an acyl carntine and taking a CoA

carnitine acyl transferase-1 functions in the mitochondria in adding a carntine to leave with fatty acid CoA

catalyst

substance speeding up a chemical reaction but is not consumed in the reaction

what are required for enzyme activity

cofactors→vitamins and metals

process of converting pyruvate into acetyl CoA

pyruvate dehydrogenase

B1= removes Co2

B3=NAD+

B5=CoA

what is the michaelis menten equation

what is the line weaver burk plot equatin

differences in beta oxidation and fatty acid synthesis

fatty acid breakdown: two carbons sequentially removed, oxidizing agents are FAD+and NAD+,occurs in mitochondira

fatty acid synthesis: carbon units are added via molonyl-ACP, reducing agent is NADPH, and it occurs in the cytoplasm

what connects carbohydrate and lipid metabolism and how

mitochondrial citrate carrier→citrate carried out of TCA if ATP is high for fatty acid synthesis which breaks down to acetyl CoA

what is the steady state assumption in enzyme kinteics

what happens in competitive inhibition versus uncompetitive inhibiton

competitive→increase in kM because more substrate is needed byt Vmax unaffacted

uncompetitive→decrease in KM and decrease in Vmax

what is the purpose of signal sequences on proteins

used to sort where protein goes

three types of transport

1. via nuclear pores→requires a nuclear locator sequences

2. transport across membranes→proteins get folded and unfolded and transported via portein translocaters

3. transport through vesicles where the membrane fusion allows entry

what binds to protein when entering nucleas

nuclear transport receptor(NTR) which directs the protein to the nucleus and through RAN GTP is causes release itno the nucleus where ran GTP is hydrolyzed into RAN GDP

describe transport across membranes

transporter outer membrane complex(TOM) recoginzes protein destination and mitochondira via signal sequence→bound receptor complex then diffuses along the membrane to a contact site on the inner membrane(TIM) This then translocates across the outer and inner membranes throough chaperone proteins assisiting in translocation and refolding of proteins inside the organlle

purpose of the rough ER

it is the entry point for proteins destine for golgi, endosomes, lysosome, cell surface, ER itself;

once inside ER proteins will not re enter the cytosol and are transported by vesicle to other organelles

signal receptor particle and its receptor bind to the ER signal sequence in new protein as it emerges from the cytolsic ribsome and connect the ribsome to the ER for translational translocation

describe vesicle transport

vesicles bud from one membrane and fuse to another transporting protein and membrane compenents to various cell compartments and extracellulary

protein coat shapes the membrane into a bud and captures molecules for transport

composed of Clathrins or coat protein complex proteins

Clathrins

protein coat shapes the membrane into a bud and captures molecules for transport

describe microfilaments(actin)

smallest and most flexible and are 7 nm helical

g-actin is the monomer and F-actin is the polymer with two polymers forming double helix

whats actin purpose

involved in cell migration and the cytokinesis portion in seperating 2 cells during divison

types of actin

alpha is in muslce cells and beta and gamma or in non-muscle

structure of actin

barbed end is positive and pointed end has polarity

they assemble to the plus end more readily than the - end

thymyosin

actin monomer binding protein→about fifty percent is in filament form and the rest is bound to allow for rapid actin polymerization

what does actin polymerisation do and give an example

pushes out sudopods false feet for movement for example with human fibroblasts moving forward through malipodia and lamilpoding which attach to cell surface and the rest move backawards causing ruffling

stages of actin polyemerization

there is nucleation, alongation, and steady with nucealtion being the rate limiting phase requiring the binding of three actin monomers for intniation

what is critical concentration

number of free actin monomers to polymerize and is influences through actin binding proteins such as thyomyosin

describe treadmilling with acitin

with monomer concetration beyween the 2 critical concentrations of the barbed and pointed end

monomers added to the plus end at the same rate they are lost from the minus end

ATP actin added and ADP actin lost is equal

regulated by prolifin andcollifin

nucealting proteins in actin

ARP nucleaor complex is attached to the sides of preexisiting actin filaments

spire=binds four actin monomoers to act as nucleating seed for new filaments

formins serve to help with progressive elongation assocated with the barbed end to generate longer filaments

myosin

actin filaments moto protein which hydrolizes ATP into ADP and pi

when stimulated and uses hdyrolysis to move along the filament

shorters in actin bringing them closer together during muscle contraction

describe muslce

huge multinucleated cellls with majoirty of cytoplasm consisting of myofibrils which are the contractile units of muscle fibres and are made up of sacromeres which are the contractile unit of muscle

how are actin and myosin arranged

geomtrically with the sliding theory of muscle

whats an actin mutation

actin myopahty→ACTA1 gene mutations→mild to sever generalized muscle weakness and familial hypertrophic cardiomyopahty is cardiac mysoin mutations

describe microtubules

the longest filaments and are 25 nm and rigid

made of tubulin and the alpha is the negative end and the beta is the + end

13 stack around each other to form long hollow cylinders

microtubules nucleation occurs via gamma tubulin rig complex at the end of the microtubules organizing center with the + end growing

MTOC is at the centrosome and microtubules extend out from here

dynamic instability with micro tubules

rapid growth with GTP capped end followed by catastrophe phase due to accidental loss of GTP cap end with rapid shrinkage

gtp hydrolysis controls growth of microtubules

kinesins and dyinen’s

kinesisn function towards the plus and aid in forming mitotic spindle during mitosis whereas dyneisns are associated with flagella and cilia

describe intermediate filaments

rope like structures made up of 70 different protein types about 10 nm in diameter→provide rope like structure to combat mechanical stress→nuclear lamens

monomer→dimer→tetramere→protofilament

describe desmosomes

connect two cells and are a king of intermediate filament