Nucleic acids.ppt

Nucleic acids

Recall condensation reactions

• amino acid + amino acid (+ enzyme)→ dipeptide protein + H₂O

 2 nucleotides (+ enzyme)→ nucleic acid + H₂O

Recall hydrolysis reactions

 DNA + H₂O (+ DNAase)→ nucleotides (shown in pairs here)

• Lipids + H₂O (+ lipase)→ fatty acid chains + glycerol

4. Nucleic acids: C,H,O,N,P

– controls heredity, protein

synthesis, cell differentiation, information storage unit

– 5 nucleotides create the code for every living organism

(A,T,G,C,U)

– nucleotide has 3 parts

• 5 carbon sugar

• nitrogenous base

• phosphate group

– deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)

DNA nucleotides

(= amine base + sugar + PO₃)

Purines

• 2 rings

• building block for many organic molecules

• Adenine, Guanine

Pyrimidines

• single ring

– purine catabolism

– digested nucleosides

Cytosine Thymine Uracil

(Source=http://en.wikipedia.org/wiki/Image:Purines.gif |Date=19:06, 13 March 2007 |Author=Andervik)

ATP

= adenosine triphosphate

• Supplies energy to cells as enzymes remove a phosphate group

• ~ nucleotide

• Adenosine = nucleoside

– base molecule = adenine + ribose

• Molecule is recycled as PO₃ groups are added,

taken away

• ATPase removes 1PO₃ group at a time

General structure of a nucleotide

* Chemistry: labeling hydrocarbons

(molecule made of carbon and hydrogen)

– 1’ carbon = first carbon in a chain (most electroneutral)

– note 3’ and 5’ carbons in ribose…

1’

3’ 2’ 5’

4’

•Phosphate and ribose structure is consistent (2’ –OH group) •Each nitrogen base has a unique structure (diff # of C,H,O,N)

•All nitrogenous bases have rings

Structure of DNA

• 2 strands are antiparallel

• Phosphate-sugar ‘backbone’ • nitrogen base ‘rungs’ held

together by H bonds

• Base pair rule = Chargaff’s

rules

– purine + pyrimidine

• A – T • G - C

• Protective endcaps =

telomeres

– Repeating sequences, shorten as organism ages (why?)

5’

3’

3’

History…

• Chargoff published his A-T/G-C discoveries in 1950

• double helix structure was a semi-collaborative effort from two labs

– Rosalind Franklin: ‘new’ x-ray technology

• female scientists were not being recognized, so she didn’t like to share results

– James Watson and Francis Crick: tactile models

• played with all

Is every nucleotide base pair

essential?

• Repeating sequences: evolutionary relationships?

• End caps, telomeres: some control decoding ‘start’ and ‘stop’, other

functions?

• Exon – “expressed region” - DNA that codes for proteins

• Intron – “intragenic region” - DNA sequence that doesn’t code for an

amino acid

1) Cells determine a need for a protein

2) RNA processing: enzymes cut introns from mRNA 3) fuse together the necessary exons

4) edited sequence is ready for protein synthesis

• Some genes can translocate (jump) to create new varieties of protein expression = Transposons and Barbara McClintock’s Indian corn

(Red = Exon)

Cells have a life cycle

=

cell cycle

1. Interphase = about 80% of the life of a cell – proteins synthesized now

– G1: first growth stage

• Cell fills out – gets full set of organelles and cytoplasm

– S: synthesis

• DNA is duplicated, and synthesized into sister chromatids

• Proteins are manufactured to ready cell for future division

– G2: second growth stage

2.

Mitosis

=nuclear division

(PMAT)

• Prophase:

chromosomes tighten up,

nuclear envelope dissolves, spindle microtubules form

– In animals, centrosomes are visible

• Metaphase:

centrosomes = opposite poles of cell, chromosomes lined up

along the middle by spindle

microtubules-kinetochore complex

• Anaphase:

sister chromatids split at

their centromere, new chromosomes

are pulled along spindle fibers to opposite centromeres

• Telophase:

cell membrane begins to pinch cells apart, chromosomes group together

– In plants, cell plate is formed

3. Cytokinesis = cell division

• 2 cell are separated by cell membrane

(and cell wall in plants)

• Nuclear membrane reforms

Telophase Cytokinesis

DNA resting state

(AKA interphase)

1) Coiled into chromosomes

 Genes = various lengths of DNA

 _{DNA is coiled onto histone proteins}

 8 histones + DNA = 1 nucleosome

 Supercoiled DNA = chromatin

 All the chromatin on one length of DNA = chromatid

 2 sister chromatids are held together with a centromere

protein

DNA replication…

• is required because all living things

– are made of somatic (=body) cells with a complete set of DNA, and

– new cells are needed when organisms:

• reproduce

• create new connections between new cells and old • grow

• heal

– Constant cellular damage from » Radiation

» Bad habits

» Other organisms’ bad habits that affect you » Illnesses

DNA replication

• Prokaryotes have circular DNA or RNA • Very short, so only 1

start point, few introns • membrane-bound

enzyme attaches to DNA, begins

replication process

• Eukaryotes have straight helix DNA

• very long, so multiple start points

• Occurs in nucleus

(soup of nucleotides, enzymes, proteins, etc)

• Meselsohn-Stahl found

that DNA replication is

semi-conservative

– 1 side of new helix is

original (= purple template

strand), the other is newly

made (red)

– one (of 2) template strand is “conserved” in every

replication sequence

The process…

1. Topoisomerase enzymes attach to supercoiled chromosomes to loosen coils so that…

2. Helicase attaches to DNA, unwinds and digests hydrogen bonds between nucleotide base pairs

− Replication fork = point on DNA that helicase attaches

− Can be at the middle of DNA strand (to create replication bubbles)

3. Single strand binding (SSB) proteins attach to strands to protect, keep separate

4. Primase begins new DNA sequence with RNA nucleotides (= RNA primer): provides protective caps to the new strand

5. As DNA unwinds, multiple DNA polymerase III (Pol III) attach to each strand to pair new nucleoside triphosphates (in 5’→3’ direction) to

existing template strands

6. Hydrolysis of highly reactive nucleoside 3P into appropriate

nucleotide(1P) helps to power helicase forward

7. Pol III slides along, making new pairs until DNA strands are complete

8. Pol III also proofreads new helix and repairs mismatched base pairs

9. DNA polymerase I (Pol I) replaces RNA primer with DNA nucleotides

10. DNA ligase joins all loose ends in the newly synthesized strands

11. Produces 2 semiconservative daughter DNA strands from 1 original helix

Making base pairs in antiparallel

strands…

• if DNA Pol III adds nucleotides in only one

direction (5’→3’), how do both sides of

helix get replicated?

From <http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookDNAMOLGEN.html>

Leading vs. Lagging strands

• Leading strand = new DNA strand being formed in a straight, continuous chain

• Lagging strand = new DNA strand being formed in short segments called

Okazaki fragments

– fragments attached together by ligase

One Pol III can work on both parent

strands…

• Pol III is a very large enzyme

with 2 active sites

• The enzyme loops DNA so that

DNA polymerase III can add

pairs to both sides at the same

time

• Saves space, time, energy

• Pol I and DNA ligase have

Final step in replication

1) Recoil into chromosomes

 Genes = ?

 DNA is coiled onto ? proteins

 8 histones + DNA = 1 ?

 Supercoiled DNA = ?

 All the chromatin on one length of DNA = ?

 2 sister chromatids are held together with a ? protein

Today,

• Find an animation for DNA replication

• Record the name of the site and publisher,

and give a brief summary of its value as a

study tool (no “yes/no” answers!)

– Did the creators do a decent job of providing the info you needed?

– Was the animation easy to follow?

– Would you recommend this animation to your peers?