1

Overview of BCOR 11

(These are just some of themany themes we have talkedabout this semester)

Structure and Function

Water1.1. Cohesion/surface tensionCohesion/surface tension2.2. Temperature moderationTemperature moderation3.3. Solvent AbilitySolvent Ability

•• HydrophilicityHydrophilicity –– dissolves polar dissolves polarthings & ionsthings & ions

•• HydrophobicityHydrophobicity –– herds away herds awaynonpolar nonpolar thingsthings

4.4. Ionization abilityIonization ability (pH) (pH)

H

Hydroniumion (H3O+)

H

Hydroxideion (OH–)

H

H

H

H

H

H

+ –

+Figure on p. 53 of water dissociating

Incr

easi

ngly

Aci

dic

[H+ ]

> [O

H– ]

Incr

easi

ngly

Bas

ic[H

+ ] <

[OH

– ]

Neutral[H+] = [OH–]

Oven cleaner

0

1

2

3

4

5

6

7

8

9

10

11

12

13

14

pH Scale

Battery acid

Digestive (stomach) juice, lemon juiceVinegar, beer, wine,colaTomato juice

Black coffee RainwaterUrine

Pure waterHuman blood

Seawater

Milk of magnesia

Household ammonia

Household bleach

Figure 3.8

Various forms of Carbonmolecules and functional

groups

CC

C

C

CC

HCCCCC=OO

N H

HH

HHHHH

HH

=C

2

Amino Acids and Proteins LipidsCarbohydrates

monomers and polymers

Membrane Functions

3. transport

4. Signal detection

5. Cell-cellcommunication

2. Localize specific functions

1. boundaries6. Cell-celladhesion

A. Transport – channelsand pumps

B. Links to structuralproteins

C. Receptors - doorbellsD. Enzymes – localized

biochemical rxnsE. Energy Generation –

utilize gradient

Voltage Ligand Mechanosensitive

Proton pump

Sucrose-H+

cotransporter

Diffusionof H+

Sucrose

ATP H+H+

H+

H+

H+

H+

H+

++

+

+

++–

–

––

–

–

3

Rough ER Smooth ER

Centrosome

CYTOSKELETON

Microfilaments

Microtubules

Peroxisome

Lysosome

Golgi apparatus

Ribosomes

In animal cells but not plant cells:LysosomesCentriolesFlagella (in some plant sperm)

NUCLEUS

Intermediate filaments

ENDOPLASMIC RETICULUM (ER)

Mitochondrion

Plasma membrane

Figure 6.9

endoplasmic reticulumnucleus

mitochondrion lysosome

Golgi apparatus

cytosol

ribosomes

Animal CellAnimal Cell

Bacterial and Viruses

Storage and Transfer ofEnergy

ΔΔGG = = ΔΔHH - - TTΔΔSS

-

HOOH

HO

OH

+HO

OH

Enzymes bring substratestogether to lower the activationenergy of a reaction

Free

ene

rgy

Progress of the reaction

∆G < O

EA

Figure 8.14

A BC D

Reactants

AC D

B

Transition state

A BC D

Products

4

LIGHTREACTOR

NADP+

ADP

ATP

NADPH

CALVINCYCLE

[CH2O] (sugar)STROMA(Low H+ concentration) Photosystem II

LIGHTH2O CO2

Cytochromecomplex

O2

H2OO21

1⁄2

2

Photosystem ILight

THYLAKOID SPACE(High H+ concentration)

STROMA(Low H+ concentration)

Thylakoidmembrane

ATPsynthase

PqPc

Fd

NADP+

reductase

NADPH + H+

NADP+ + 2H+

ToCalvincycle

ADP

PATP

3

H+

2 H++2 H+

2 H+

Figure 10.17

Proton gradients powerreactions to create high

energy ATP

NADPHNADPH and ATPATPcan be used tocan be used totransfer energytransfer energy

Fatty Acid Oxidation (Fatty Acid Oxidation (ββ-oxidation) -oxidation)

Energy is capturedin many small stepsin this metabolicpathway

-captures Reducing potential NADH + H+

FADH2

Saturatedhydrocarbon

unsaturatedhydrocarbon

2e-2 H+removed

alcoholKetone2e-

2 H+removed

Ester(acid)

PrimingStep

Signaling, Informationtransfer, and feedback

loopsTRANSCRIPTION

RNA is transcribedfrom a DNA template.

DNA

RNApolymerase

RNAtranscript

RNA PROCESSING In eukaryotes, theRNA transcript (pre-mRNA) is spliced andmodified to producemRNA, which movesfrom the nucleus to thecytoplasm.

Exon

Poly-A

RNA transcript(pre-mRNA)

Intron

NUCLEUSCap

FORMATION OFINITIATION COMPLEX

After leaving thenucleus, mRNA attachesto the ribosome.

CYTOPLASM

mRNA

Poly-A

Growingpolypeptide

Ribosomalsubunits

Cap

Aminoacyl-tRNAsynthetase

AminoacidtRNA

AMINO ACID ACTIVATION

Each amino acidattaches to its proper tRNAwith the help of a specificenzyme and ATP.

Activatedamino acid

TRANSLATION A succession of tRNAsadd their amino acids tothe polypeptide chainas the mRNA is movedthrough the ribosomeone codon at a time.(When completed, thepolypeptide is releasedfrom the ribosome.)

Anticodon

A CC

A A AUGGUU UA UG

UACE A

Ribosome

1

Poly-A

5′

5′

3′

Codon

2

3 4

5

Information stored in DNA isused to build proteins

DNA

mRNA

polypeptide

DNA -> mRNA -> Protein

5

DNA structureSugar-phosphate

backboneNitrogenous

bases

5′ endO–

O P O CH2

5′

4′O–

HH

OH

H

H3′

1′H O

CH3

N

O

NH

Thymine (T)

O

O P O

O–

CH2

HH

OH

HH

HN

N

N

H

NH

H

Adenine (A)

O

O P O

O–

CH2

HH

OH

HH

HH H

HN

NN

OCytosine (C)

O

O P O CH2

5′

4′O–

H

O

H

H3′

1′

OH2′

H

N

NN H

ON

N HH

H H

Sugar (deoxyribose)3′ end

Phosphate

Guanine (G)

DNA nucleotide

2′

NC

T

A

A

T

CG

GC

A

C G

AT

AT

A T

TA

C

TA0.34 nm

3.4 nm

G

1 nm

G

T

Amino end Growing polypeptide

tRNA

mRNA

Codons

3′

5′

Ribosomes translate the RNAmessage into a polypeptide

Second mRNA baseU C A G

U

C

A

G

UUUUUCUUAUUG

CUUCUCCUACUG

AUUAUCAUAAUG

GUUGUCGUAGUG

Met orstart

Phe

Leu

Leu

lle

Val

UCUUCCUCAUCG

CCUCCCCCACCG

ACUACCACAACG

GCUGCCGCAGCG

Ser

Pro

Thr

Ala

UAUUAC

UGUUGC

Tyr Cys

CAUCACCAACAG

CGUCGCCGACGG

AAUAACAAAAAG

AGUAGCAGAAGG

GAUGACGAAGAG

GGUGGCGGAGGG

UGGUAAUAGStop

Stop UGAStopTrp

His

Gln

Asn

Lys

Asp

Arg

Ser

Arg

Gly

UCAGUCAGUCAGUCAG

Firs

t mR

NA

bas

e (5′ e

nd)

Third

mR

NA

bas

e (3′ e

nd)

Glu

• Mitosis produces an exact copy of theparent cell.– Used for growth and asexual reproduction.

• Meiosis produces reduced (haploid)gametes, which are genetically unique.– Necessary for sexual reproduction.

Meiosis generates variation through:- independent assortment of chromosomes- crossing over

Mitosis vs Meiosis

Homologs pair inmeiosis 1

Sister chromatidsseparate in meiosis 2

haploid

Not paired diploid

6

Informationmust be copiedexactly eqchtime a celldivides

DNA replication machine

DNA sequences aredetermined by“poisoning” asynthesis reactionwith dideoxynuclotides

PCR is justrepeated cyclesof DNAsynthesis in atest tube

DNA is alwayssynthesized 5’ to 3’

Cellsdetectsignal &respond

Signal transduction pathwaysAMPLIFY the signal

1º messenger

2º messengers

EffectorEnzymes Target

Enzymes

7

Genes of operon

Protein

Operator

Polypeptides that make upenzymes for tryptophan synthesis

Regulatorygene

RNA polymerase

Promoter

trp operon

5′

3′mRNA

trpDtrpE trpC trpB trpAtrpRDNA

mRNA

E D C B A

The trp operon: regulated synthesisof repressible enzymes

Figure 18.21a

5′

Tryptophan absent -> repressor inactive -> operon “on”

Cell type–specific transcriptionEnhancer Promoter

Controlelements

Albumin gene

Crystallin gene

Liver cellnucleus

Lens cellnucleus

Albumin geneexpressed

Albumin genenot expressed

Crystallin genenot expressed

Crystallin geneexpressed

Liver cell Lens cell

Fig 19.7

All cells have thesame genes, butonly certaingenes areexpressed ineach tissue

Different set ofactivator proteinsin the two celltypes

Cell Cycle Regulators andCancer

Thank you!