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The “Central Dogma” Overview Of DNA How does DNA control the cell?. Transcription. Translation. DNA. mRNA. proteins. Enzymes Structure Movement Hormones Gas exchange Amino Acid Storage. Replication. So how does DNA “control” the cell?. Transcription. Translation. DNA. mRNA.

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The central dogma overview of dna how does dna control the cell
The “Central Dogma”Overview Of DNAHow does DNA control the cell?

Transcription

Translation

DNA

mRNA

proteins

Enzymes

Structure

Movement

Hormones

Gas exchange

Amino Acid Storage

Replication


So how does dna control the cell
So how does DNA “control” the cell?

Transcription

Translation

DNA

mRNA

proteins

Enzymes

Structure

Movement

Hormones

Gas exchange

Amino Acid Storage

Replication






Erwin chargaff
Erwin Chargaff

  • A = 30.9%

  • T = 29.4%

  • G = 19.9%

  • C = 19.8%




From dna to chromosome
From DNA to Chromosome

chromosome

nucleus

  • A strand of human DNA is about 3 m long…

  • How does it fit into all our cells??

  • Supercoiling

cell

Proteins that DNA wraps around

histones

Base pairs

DNA


Details of dna structure
Details of DNA Structure

  • Nucleotides are the monomers of nucleic acids

  • 5 carbon sugar

    • Ribose

    • Deoxyribose

  • Nitrogen Base

    • Adenine

    • Thymine

    • Cytosine

    • Guanine

    • Uracil

  • Phosphate

5’ Carbon

5’

4’

1’

2’

3’

3’ Hydroxyl


Details of dna structure1
Details of DNA Structure

5’ Carbon

3’ Hydroxyl

  • What do you notice about the 5’ and 3’ ends of the two strands?

  • They’re ANTIPARALLEL!!

  • Why? For the nucleotide bases to line up

3’ Hydroxyl

5’ Carbon


Details of dna structure2
Details of DNA Structure

5’ Carbon

3’ Hydroxyl

  • What holds the nucleotides together?

3’ Hydroxyl

5’ Carbon


Details of DNA Structure

  • Nucleotide Bases: Purines and Pyrimidines

    • PURINES

      • “Aggies are Pure” – A and G are Purines which have 2 rings

    • PYRIMIDINES

      • “TCU Cheerleaders build Pyramids” – T and C are Pyrimidines have one ring


Key questions
Key Questions

  • How do 3 m of DNA fit into each of our cells? (be specific!)

  • Why is a DNA molecule considered to have direction and to be “anti-parallel”?

  • What type of bonds form the sugar-phosphate backbone?

  • What type of bonds hold the nucleotide bases together?

  • From what you know about the bonding between base pairs, which pairs (A-T or G-C) do you think have more breaks and mistakes and why?


Question
Question:

  • How does the structure of DNA ensure the daughter strands will be identical to the parent strand?


Dna replication
DNA Replication

Parent strand

Origin of replication

Daughter strand

Bubble

Replication fork

2 new strands


Dna enzymes
DNA Enzymes

  • Helicase

    • Breaks hydrogen bonds to unwind DNA

  • DNA Polymerase III

    • Adds nucleotides ONLY to the 3’ end

    • Nucleoside PPP links to sugar-P backbone

    • Losing 2 Ps provides energy for bonding


  • Problem: Nucleotides can only be added to the 3’ end by DNA Polymerase…

  • Solution: Okazaki

  • Leading and Lagging Strands

    • Leading Strand

      • Continuous synthesis

    • Lagging Strand

      • Okazaki fragments

      • Joined by ligase


3’

Remember: DNA polymerase can only add nucleotides to the 3’ end, so DNA gets built in the 5’  3’ direction!

5’

Parental DNA

5’

Okazaki fragments

3’

DNA polymerase

3’

Ligase

Leading and lagging have the same origin of replication, but since DNA polymerase can only add on the 3’ end, the lagging strand has to start backwards and make little pieces to link together

5’

Leading strand

One piece of 5’  3’

Many little pieces of 5’  3’ linked together later

Lagging strand


Test your understanding…On some paper, write A – H and decide whether each letter represents the 3’ or 5’ end of DNA. Then, label the sections (A-B, C-D, etc) as “leading” or “lagging”

A-B: Leading

C-D: Lagging

B

C

A

D

5’

3’

3’

5’

3’

5’

E

H

3’

5’

G

F

F-E: Leading

H-G: Lagging


Priming dna synthesis
Priming DNA Synthesis

  • DNA polymerase can only extend an existing DNA molecule; it cannot start a new one

    • Short RNA primer is built first on parent DNA by primase

    • RNA primer later removed by DNA polymerase I


Priming dna synthesis1
Priming DNA Synthesis

  • Closer look…

Primase builds the RNA primer

Replaces RNA nucleotides with DNA

Primase

DNA polymerase


Putting it all together
Putting it all together!

  • http://www.johnkyrk.com/DNAreplication.html


Editing and proofreading dna
Editing and Proofreading DNA

Why do we not always get cancer?

DNA can repair itself!!!

  • Since DNA polymerase III does 1,000 base pairs/second, it makes a lot of errors

  • DNA Polymerase I (only 20 bp/sec) excises mismatched bases, repairs the DNA, and removes the primer

  • DNA polymerase I reduces error from 1 in 10,000 bp to 1 in 100 million bp!!


Problems at the end
Problems at the end…

  • Ends of chromosomes are “eroded” with each replication (don’t get fully copied)

  • Telomeres are expendable, non-coding sequences at the ends of the DNA strand

    • short sequence of bases repeated 1000s of times

  • TTAGGG in humans


Telomeres and aging
Telomeres and Aging

telomere

  • In the absence of telomerase, the telomere will become shorter after each cell division.  When it reaches a certain length, the cell may cease to divide and die. 

telomerase

Extended telomere


Putting it all together1
Putting it ALL together

  • Summarize the roles of the key enzymes

  • Label the diagram showing the steps of DNA replication

  • DNA Structure – Questions and Practice


Summary of replication enzymes
Summary of Replication Enzymes

Unzips DNA (breaks H-bonds between nucleotides)

Builds RNA primer in leading strand and Okazaki fragments

Adds DNA nucleotides (20 bp/s); replaces RNA primer with DNA; repairs errors in DNA

Adds DNA nucleotides (1,000 bp/s)

Joins Okazaki fragments (using phosphate groups)



Protein synthesis
Protein Synthesis in DNA replication. Be sure to label 3’ and 5’ ends, too!

  • How does DNA control the structure and function of the cell?

    it makes proteins!

    • Structure: collagen, elastin, keratin

    • Enzymes: catalase, amylase, sucrase, etc

    • Hormones: insulin, glucagon, etc

    • Amino acid storage: albumin, ovalbumin, etc


The central dogma overview of dna
The “Central Dogma” in DNA replication. Be sure to label 3’ and 5’ ends, too!Overview Of DNA

Transcription

Translation

DNA

mRNA

proteins

Enzymes

Structure

Movement

Hormones

Gas exchange

Amino Acid Storage

Replication


The main things for dna transcription and translation
The “Main Things” for in DNA replication. Be sure to label 3’ and 5’ ends, too!DNA Transcription and Translation


Let s model it
Let’s model it… in DNA replication. Be sure to label 3’ and 5’ ends, too!


Protein synthesis1
Protein Synthesis! in DNA replication. Be sure to label 3’ and 5’ ends, too!

  • Transcription

  • http://www.johnkyrk.com/DNAtranscription.html

  • Translation

  • http://www.johnkyrk.com/DNAtranslation.html


Notas from gene to protein
Notas – From Gene to Protein in DNA replication. Be sure to label 3’ and 5’ ends, too!

Metabolism teaches us about genes

  • Metabolic defects caused by non-functional enzyme

  • Studying metabolic diseases suggested that genes specified proteins

    • PKY

    • Alkaptonuria (black urine)

  • Genes dictate the phenotype


1 gene – 1 enzyme hypothesis in DNA replication. Be sure to label 3’ and 5’ ends, too!

  • Beadle and Tatum – 1941


1 gene – 1 enzyme hypothesis in DNA replication. Be sure to label 3’ and 5’ ends, too!

  • Beadle and Tatum – 1941

    • Compared different nutritional mutants of bread mold, Neurospora

    • Created mutations by X-ray treatments X-rays break DNA)

    • Wild type grows on “minimal” media (sugar)

    • Mutants require different amino acids because each mutant lacks a certain enzyme needed to produce a certain amino acid

    • Conclusion: Broken gene = non-functional enzyme

  • Problems with:

    • One gene – one enzyme

      • not all proteins are enzymes, and they’re coded by genes too

    • One gene – one protein

      • many proteins consist of several polypeptide, and each polypeptide has it’s own gene

  • One gene – one polypeptide?


Defining a gene
Defining a gene… in DNA replication. Be sure to label 3’ and 5’ ends, too!

  • “Defining a gene is problematic because small genes can be difficult to detect, one gene can code for several protein products, some genes code only for RNA, two genes can overlap, and there are many other complications.” – Elizabeth Pennisi, Science 2003

  • How would YOU define a gene in your own words?


The central dogma
The “Central Dogma” in DNA replication. Be sure to label 3’ and 5’ ends, too!

Transcription

Translation

DNA

mRNA

Protein

Reverse Transcription

Replication


From nucleus to cytoplasm
From nucleus to cytoplasm… in DNA replication. Be sure to label 3’ and 5’ ends, too!

  • Where are the genes?

    in DNA on chromosomes in the nucleus

  • Where are proteins synthesized?

    on ribosomes (free or on the ER) in the cytoplasm

  • How does the information get from the nucleus to the cytoplasm?

    mRNA is made in the nucleus and can travel into the cytoplasm to the ribosomes


deoxyribose in DNA replication. Be sure to label 3’ and 5’ ends, too!

ribose

A-T, C-G

T-A, A-U, C-G

Double

Single


Transcription basics
Transcription Basics in DNA replication. Be sure to label 3’ and 5’ ends, too!

  • Initiation

    • RNA polymerase binds to promoter sequence on DNA

      • where to start reading = Promoter (initiation site)

      • which strand to read = template strand

      • direction on DNA = reads 3’5  builds 5’  3’

  • Elongation

    • RNA polymerase unwinds DNA ~20 bp at a time

    • Reads DNA 3’  5’

    • Builds RNA 5’  3’

    • No proofreading, about 1 error/105 bases

    • Many copies, short life, no problem 

  • Termination

    • RNA polymerase stops at termination sequence

    • mRNA leaves nucleus through pores


  • Transcription
    Transcription in DNA replication. Be sure to label 3’ and 5’ ends, too!


    Rna processing or editing
    RNA Processing or Editing in DNA replication. Be sure to label 3’ and 5’ ends, too!

    • 5’ cap

      • protection

      • targets mRNA for ribosome

    • Poly-A tail

      • protection

      • leads mRNA out of nucleus

    • Spliceosome

      • composed of snRNPs (small nuclear ribonucleoproteins)

      • introns – intervening, interrupting = removed by spliceosome

      • exons – expressed


    Sliceosome
    Sliceosome in DNA replication. Be sure to label 3’ and 5’ ends, too!


    Putting it together transcription to translation
    Putting it Together – Transcription to Translation in DNA replication. Be sure to label 3’ and 5’ ends, too!

    • How does mRNA code for proteins?

    • How can you code for 20 aa with only 4 nucleotide bases (A, U, G, C)?

    • How can an alphabet of 4 letters (nucleotides) translate into an alphabet of 20 letters (aa)?!


    Breaking the code
    Breaking the code in DNA replication. Be sure to label 3’ and 5’ ends, too!

    • Nirenberg and Matthaei

    • Determined 1st codon – amino acid match

      • UUU coded for phenylalanine

    • Created artificial poly(U) mRNA

    • Added mRNA to test tube of ribosomes and nucleotides

      • mRNA synthesized a single amino acid polypeptide chain: phe-phe-phe-phe-phe-phe


    DNA in DNA replication. Be sure to label 3’ and 5’ ends, too!

    Gene 1

    3’

    5’

    DNA

    Transcription

    mRNA

    5’

    3’

    codon

    Translation

    Protein

    Amino acids


    The code
    The CODE!! in DNA replication. Be sure to label 3’ and 5’ ends, too!

    • For ALL life!! (yes, even prokaryotes…)

      • Strongest support for common origin for all life

    • Code is redundant

      • Several codons for each amino acid

    • Start codon: AUG = methionine

    • Stop codons: UGA, UAA, UAG


    Translation
    Translation in DNA replication. Be sure to label 3’ and 5’ ends, too!

    • Ribosome reads mRNA in codons

    • tRNA brings in correct amino acid

    • tRNA matches codon of mRNA = anticodon

    • Amino acids assembled into polypeptide chain


    Trna structure
    tRNA Structure in DNA replication. Be sure to label 3’ and 5’ ends, too!

    • “clover leaf” structure

      • anticodon on “clover leaf” end

      • amino acid on 3’ end

      • anticodon written 3’  5’ to match codons which are 5’  3’


    Aminoacyl trna synthetase
    Aminoacyl in DNA replication. Be sure to label 3’ and 5’ ends, too!tRNAsynthetase

    • enzyme which bonds amino acid to tRNA

      • endergonic reaction (does it require energy?)

      • ATP  AMP (how many phosphates do we use?)

      • Energy stored in tRNA-aa bond

        • Unstable


    Ribosomes
    Ribosomes in DNA replication. Be sure to label 3’ and 5’ ends, too!

    • Facilitate coupling of tRNA anticodon to mRNA codon

      • Organelle or enzyme?

    • Structure

      • Ribosomal RNA and proteins

      • 2 subunits: large and small

      • A site (aminoacyl-tRNA site)

        • Holds tRNA carrying next amino acid to be added to chain

      • P site (peptidyl-tRNA site)

        • Holds tRNA carrying growing polypeptide chain

      • E site (exit site)

        • Discharged tRNA leaves ribosome from exit site


    Building a polypeptide
    Building a Polypeptide in DNA replication. Be sure to label 3’ and 5’ ends, too!

    • Initiation

      • Brings together mRNA, ribosome subunits, proteins and initiator tRNA

  • Elongation

  • Termination

    • Release polypeptide

    • “release protein” bonds to A site

    • Bonds water molecule to polypeptide chain


  • Polyribosomes
    Polyribosomes in DNA replication. Be sure to label 3’ and 5’ ends, too!

    • Many ribosomes read single mRNA simultaneously making many copies of a protein!


    Protein targeting
    Protein Targeting in DNA replication. Be sure to label 3’ and 5’ ends, too!

    Signal polypeptide

    • ~20 aa at the beginning of the polypeptide

    • Recognized by SRPs (signal recognition particles)

    • SRP brings polypeptide and ribosome to ER so that polypeptide is secreted into the ER as it’s built3.

  • Destinations – other signal polypeptides used to target

    • Secretion

    • Nucleus

    • Mitochondria

    • Chloroplasts

    • Cell membrane

    • Cytoplasm


  • Comparing! in DNA replication. Be sure to label 3’ and 5’ ends, too!


    Mutations
    Mutations in DNA replication. Be sure to label 3’ and 5’ ends, too!

    • Point Mutations

      • 1 base pair change

      • Base-pair substitution

        • Silent mutation: no amino acid change because of redundancy in code

        • Missense: change amino acid

    • Nonsense: change to stop


    Mutations1
    Mutations in DNA replication. Be sure to label 3’ and 5’ ends, too!

    • Insertions – adding base(s)

    • Deletions – losing base(s)

    • BOTH cause frameshift


    Gene regulation
    Gene Regulation in DNA replication. Be sure to label 3’ and 5’ ends, too!

    • In a nutshell…


    Prokaryotes regulate transcription through operons
    Prokaryotes regulate transcription through operons. in DNA replication. Be sure to label 3’ and 5’ ends, too!

    Area where RNA Polymerase binds

    Area where repressor can bind to stop binding of RNA polymerase

    Segment of DNA containing several genes, a promoter, and an operator

    Regulatory gene = codes for repressor; gene is upstream/downstream from operator


    2 kinds of feedback
    2 Kinds of Feedback in DNA replication. Be sure to label 3’ and 5’ ends, too!


    Prokaryotes regulate transcription through operons1
    Prokaryotes regulate transcription through operons. in DNA replication. Be sure to label 3’ and 5’ ends, too!

    Area where RNA Polymerase binds

    Area where repressor can bind to stop binding of RNA polymerase

    Segment of DNA containing several genes, promoter, and operator

    Regulatory gene = codes for repressor; gene is upstream/downstream from operator

    Too much product, stop; not enough, keep going!!

    Break it down if you’ve got it!


    2 examples of negative feedback
    2 Examples of Negative Feedback in DNA replication. Be sure to label 3’ and 5’ ends, too!


    Prokaryotes regulate transcription through operons2

    Area where RNA Polymerase binds in DNA replication. Be sure to label 3’ and 5’ ends, too!

    Area where repressor can bind to stop binding of RNA polymerase

    Prokaryotes regulate transcription through operons.

    Segment of DNA containing several genes, promoter, and operator

    Regulatory gene = codes for repressor; gene is upstream/downstream from operator

    Too much product, stop; not enough, keep going!!

    Break it down if you’ve got it!

    • Default “on” because repressor not bound

    • Product binds to repressor to “activate” and turn “off” transcription

    • Usually anabolic pathways (ex: trp)


    Prokaryotes regulate transcription through operons3

    Area where RNA Polymerase binds in DNA replication. Be sure to label 3’ and 5’ ends, too!

    Area where repressor can bind to stop binding of RNA polymerase

    Prokaryotes regulate transcription through operons.

    Segment of DNA containing several genes, promoter, and operator

    Regulatory gene = codes for repressor; gene is upstream/downstream from operator

    Too much product, stop; not enough, keep going!!

    Break it down if you’ve got it!

    • Default “on” because repressor not bound

    • Product binds to repressor to “activate” and turn “off” transcription

    • Usually anabolic pathways (ex: trp)

    • Default “off” because repressor bound

    • Product binds to repressor to “inactivate” and release the repressor and turn “on” transcription

    • Usually catabolic pathways (ex: lac)


    Prokaryotes regulate transcription through operons4

    Area where RNA Polymerase binds in DNA replication. Be sure to label 3’ and 5’ ends, too!

    Area where repressor can bind to stop binding of RNA polymerase

    Prokaryotes regulate transcription through operons.

    Segment of DNA containing several genes, promoter, and operator

    Regulatory gene = codes for repressor; gene is upstream/downstream from operator

    Too much product, stop; not enough, keep going!!

    Break it down if you’ve got it!

    • Presence of activator turns “on”

    • Ex: lac with lactose and no glucose

    • Default “on” because repressor not bound

    • Product binds to repressor to “activate” and turn “off” transcription

    • Usually anabolic pathways (ex: trp)

    • Default “off” because repressor bound

    • Product binds to repressor to “inactivate” and release the repressor and turn “on” transcription

    • Usually catabolic pathways (ex: lac)


    Eukaryotes regulate gene expression pre transcription during transcription and post transcription
    Eukaryotes regulate gene expression pre-transcription, during transcription, and post-transcription.

    • Histone acetylation

    • Acetylated = less bound = easier access

    • DNA methylation

    • methylated = more bound = less access

    • Controls access of RNA polymerase to promoter


    Eukaryotes regulate gene expression pre transcription during transcription and post transcription1
    Eukaryotes regulate gene expression pre-transcription, during transcription, and post-transcription.

    • Histone acetylation

    • Acetylated = less bound = easier access

    • DNA methylation

    • methylated = more bound = less access

    • Controls access of RNA polymerase to promoter

    • Transcription Factors = proteins that help RNA poly binding at promoter

    • Activation sites and enhancer proteins = also aid in RNA poly binding; 1000s of bp away

    • Aids in RNA polymerase binding


    Eukaryotes regulate gene expression pre transcription during transcription and post transcription2
    Eukaryotes regulate gene expression pre-transcription, during transcription, and post-transcription.

    • Histone acetylation

    • Acetylated = less bound = easier access

    • DNA methylation

    • methylated = more bound = less access

    • Controls access of RNA polymerase to promoter

    • Transcription Factors = proteins that help RNA poly binding at promoter

    • Activation sites and enhancer proteins = also aid in RNA poly binding; 1000s of bp away

    • Aids in RNA polymerase binding

    • Poly-A tail

    • 5’ cap

    • Alternate splicing = different combos of exons are expressed (some can be removed)

    • Essential in making antibodies

    • Alters mRNA transcript


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