BIOLOGY 2

Page 1

https://www.youtube.com/watch?v=8Kn6BVGqKd8 (Embed)

Krebs Cycle ( mitochondria )

Oxidation of Pyruvate:

1- Decarboxylation -- Carboxyl group is removed to form CO2

2- Reduction -- NAD+ is reduced to NADH , pyruvate loses an H

3- CoA (enzyme) binds to remaining group (Acetyl) = Acetyl CoA

(energy from reduction)

Result:

1 CO2, 1 NADH, 1 Acteyl CoA

(Doubled because glycolysis provides 2 pyruvate from 1 glucose)

Krebs Cycle ( 9 Steps )

Note: It is a cycle , loops as long as Acetyl-CoA is provided.

1-Condensation

Acetyl-CoA release CoA into oxaloacetate

2/3- Isomerization

Structure is transformed

4- First oxidation

molecule is oxidized with NAD+ = NADH / CO2 removed (using energy from redox reaction)

5- Second oxidation

molecule is oxidized with NAD+ = NADH / CO2 removed (using energy from redox reaction) + links back to CoA (enzyme) (using energy from redox reaction)

6- Substrate level phosporylation

Bond between molecule and CoA broken = GTP fromed

Side note = GTP transfers P to ADP = ATP formed

7- Third oxidation

molecule is oxidized by FAD = FADH2

8-Regeneration of oxaloacetate

Water molecule is added

9- Regeneration of oxaloacetate

molecule is oxidized with NAD+ = NADH

(Free to restart the cycle again)

Result:

1 ATP , 2 CO2, 3 NADH, 1 FADH2

(2x Because of 1 glucose)

NOTE: ALL of glucose has been transformed by now

TOTAL YIELD OF Glycolysis + Krebs Cycle:

2 FADH2

10 NADH

4 ATP

NADH= High energy electron carrier

FADH2= Medium energy electron carrier

Electron Transport Chain (cistrae)

1- NADH is oxidized = loss - H & 2x electron ( 2x electron = the pairs)

2- The pairs will then pass through several proteins ( Quinone, Cytochrome C, etc..) = lowers its energy state

3- Energy from that is used to pump out H+ into the cistrae

4- Because of CONCENTRATION GRADIENT -- H+ will go back in the matrix using ATP synthase ( protein ) = forms ATP (a lot)

NOTE: To maintain this gradient = the pairs will join together with Oxygen (we breath) to form = H20 -- known as (aerobic respiration)

RESULT :

for electron transport chain (chemiosis)

NET Yield of 1 glucose = 30 ATP ( 2 ATP are used for transport to mitochondrion )

Fermentation ( When oxygen is low )

Goal: keep glycolysis going & recycle NADH

NOTE: Instead of pyruvate to go to Kreb Cycle and Chemiosmosis.

2 types

Human (Lactic Acid)

Pyruvate -- Pyruvate reduced (NADH --- NAD+ ) -- Lactic Acid

Bacteria -- Pyruvate reduced (NADH --- NAD+ ) -- Ethanol

( CO2 is produced in the process)

Photosynthesis

general formula : 6 CO2 + 12 H20 --- C6H12O6 + CO2 + 6 H2O

Chloroplast = use the energy from light to form sugar and ATP

3 Main steps:

-Capture Light

-Use energy to create ATP + NADPH

-Use ATP + NADPH to form organic molecules

Pigments:

capture light

main one Chlorophyll

How they capture light:

Ring, when light hits it , displaces the double and single bonds

Energy is then transferred by electron moving.

Photosynthesis parts

Antenna Complex = Everything of Photosystem except reaction center

Role:

-Capture photon

-Orient pigment to capture light

-transfer electron to reaction center

Reaction center

NOTE:

-Photosytem 2 come before photosystem 1

- link by cytochrome/B6-f complex

PS2= 680nm

PS1 = 700nm

http://www.youtube.com/watch?v=sQK3Yr4Sc_k (Embed)

Light independent reactions

NOTE: energy acquire from dependent reactions goes to independent reactions

Calvin Cycle (Stroma of chloroplast)

3 Steps:

-Carbon fixation

-Reduction

-Regenereation of ribulose 1,5-biphosphate

RESULT:

-to form 1 glucose, cycle must do it 6 times

- key intermediate = G3P

- most transported out of chloroplast to form sugars

- rest of G3P used to regenerate ( cycle to begin)

Photorespiration

Rubisco = multienzyme complex -- catalyze fixation of CO2 to RuBP to form G3P

O2 will compete for the active site of rubisco against CO2

GOAL :

To protect plants from photo oxidative damage

Too much O2 = BAD

Too much light = BAD

Photorespiration uses both LIGHT + O2

NOTE: Rate of Calvin Cycle ( carbon fixation) / Rate of photorespiration

( 1 Photorespiration for 4 Calvin Cycles )

at High Temperatures

stomata close = prevents loss of water

accumulates O2 + decrease of CO2 ( O2 cant get out and Photorespiration keeps going)

Light dependent reactions

- pigments excite by photon

- electron travel chlorophyll

- electron transport chain ( form ATP + NADPH (instead of water) )

How does it work ?

i) Atnenna hit with photon

ii) Manganese lose 1 electron

iii) Oxidize water to replace electron -- Creates CO2

iiii) 2 electron makes water

PS2

quinone carriers to b6f complex

pumps out H+ into tylkaoid lumen (using energy from light )

carried by protein to PS1

PS1

incoming electron from PS1 replaces electron loss during PS1

Light hits PS1, electron moves

pumps out H+ into thylakoid lumen (using energy of light )

that electron is joined with NADP+ to form NADPH

NADPH = high energy electron carrier

carries energy from light to stroma to create sugars

THE H+ comes back in due to concentration gradient

creates ATP !!!

THE PLANTS

C3: does nothing to regulate

C4: CO2 fixation to PEP and Calvin Cycle occurs in 2 different cells (CON= ATP had to be used to regenerate it)

CAM: the PEP pathway and Calvin Cycle occur in same cell but alternate NIGHT/DAY

( C4 happens at night and Calvin happens during the day )= mesophyll cell

DNA

Deoxyribonucleic Acid / Ribonucleic Acid

Nucleotides = Phosphate group + Pentose sugar + Nitrogenous base

linked by phosphodiester bonds

Purines: ( 1 extra ring)

Adenine

Guanine

Pyrimidines:

Cytosine

Thymine / Uracil

5' end = Free Phosphate Group

3' end = Free OH

DNA

heredity + function of cell

Sugar : Deoxyribose Sugar

Strands : 2x + helix + antiparallel ( held by hydrogen bonds)

A-T/U = 2 Hydrogen Bonds

C-G = 3 Hydrogen Bonds

RNA

transfer information (mRNA) + carriers amino acids (tRNA)

Sugar: Ribose sugar

Strands: 1x + Can bind to itself

Experiments

Frederick Griffith

Since in trial 4, the killer strain is heated (protein denatured), and combining with live normal strain: something is transferring the information of killer gene . --- DNA

Colin Macleod & Oswald Avery & Maclyn Mccarthy

Does the same experiment with 99.98% of the protein gone.

Hershey and Chase

Erwin Chargaff

Proportion of A-T

Proportion of C-G

Watson & Crick & Franklin

Using x-ray diffraction

=

determined the structure of DNA = double-helix

Meselson & Stahl

Shows the nature of dan which is semi-conservative

DNA REPLICATION IN

HUMANS VS BACTERIA

DNA replication

Need 3 things: Template / Polymerease / Free nucleotides

Polymerase = Adds bases to DNA ( ALWAYS FROM 3')

Primers= small RNA that stick on DNA, where Polymerase can Bind to bind to DNA

(synthesize by RNA polymerase)

MADE by RNA primase

BACTERIA

3 DNA Polymerase ( 12 3)

Endonuclease Activity = CUT DNA

Exonuclease Activity = EAT DNA

Parts:

Helicase: opens the DNA

Single strand binding proteins: stabilize the strand so that it don't bind again

Gyrase: prevents super-coiling

Repliosomes:

don't worry about it

gives DNA some slack

HUMANS

TELOMERES =

Repetitive DNA sequences (JUNK)

Lagging strand can shorten the DNA (VERY BAD)

(last primer can't be replaced by bases) = (shortening)

Telomerase adds to DNA some Junk sequence

RNA primes put primer on DNA

Junk DNA is complemented by DNA polymerase

ERRORS

sometimes UV Light will make Thymine dimer = TT bonds together but side to side

Photorepair = Photolyase cleaves the TT bond by using light energy

Excision epair = Mismatched pairs can be removed and correct inserted by dan excision repair enzyme

CELLULAR RESPIRATION

PHOTOSYNTHESIS

dna

DNA REPLICATION