ap bio unit 6

DNA Replication

DNA- Deoxyribonucleic Acid - Made of a 5 carbon, deoxyribose sugar. Has directionality (5’ and 3’), Usually double stranded, strands run antiparallel, made of 4 bases (nucleotides)

• Guanine - Double ringed purine, always pairs with cytosine

• Cytosine- Single ringed pyrimidine, always pairs with guanine

• Adenine- Double ringed purine, pairs with thymine in DNA and Uracil in RNA

• Thymine- Single ringed pyrimidine, always pairs with adenine

RNA- Ribonucleic Acid - Made of 5 carbon ribose sugar. Has directionality (5’ and 3’), Usually single stranded, made of 4 bases (nucleotides)

• Guanine- Double ringed purine, always pairs with cytosine

• Cytosine- Single ringed pyrimidine, always pairs with guanine

• Adenine- Double ringed purine, pairs with thymine in DNA and Uracil in Rna

• Uracil- Single ringed pyrimidine, always pairs with adenine

DNA storage

• Eukaryotes store DNA in chromosomes that are extremely compact, linear chromosomes

  • DNA is compacted by wrapping around proteins called histones

• Prokaryotes store DNA in circular chromatids

DNA Replication- DNA making a copy of itself

• Happens during S-phase of Interphase

• Process is semiconservative

  • Each original piece of DNA is used as a template and complementary bases are added to complete the strand. 

  • This makes the new pieces half old- half new

• Overall Replication process has 3 parts

  • Untwist- DNA is untwisted to resemble a ladder

  • Unzip- the “ladder” is opened up to two halves at the replication fork (picture a zipper)

  • Fill in- DNA bases are added to the open DNA strand to close it up

  • Process ends with two identical pieces of DNA (4 strands total) and each piece of DNA is half old-half new

• Several Enzymes are involved in the process of replication

  • Topoisomerase- Untwists the DNA in front of the replication fork

  • Helicase- Unzips the DNA at the replication fork

  • Polymerase- Adds bases to the exposed DNA strands- ONLY ADDS BASES IN THE 5’ → 3’ DIRECTION!!!

  • Primase- Creates an RNA primer that tells DNA polymerase where to start on the lagging strand.

  • Ligase- Removes RNA primer and replaces it with DNA bases. 

• Leading vs. Lagging strand

  • Leading strand adds nucleotides as helicase exposes them

  • Lagging strand works AWAY from the replication fork and only in small sections (Okazaki fragments)

    • Works this way because polymerase only works 5’ → 3’

Gene Expression

Transcription- Process that copies DNA into mRNA to be sent to a ribosome

• Happens in nucleus of eukaryotes and the cytoplasm of prokaryotes

• Promoters are upstream of the transcription site and tell RNA polymerase where to begin transcription

• Uses complementary bases to make single stranded mRNA

  • Only one side of the DNA is used as a template strand

    • Also called the non-coding strand, minus strand, or antisense strand

    • Different genes use different template strands

  • Complementary strand is built by RNA polymerase

    • Reads DNA from 3’ → 5’ and builds RNA 5’ → 3’

    • GC AU

  • Post transcriptional processes:

    • Poly A tail- Added to 3’ end to protect from degradation in the cytoplasm

    • GTP Cap- Added to 5’ end to prevent degradation in cytoplasm

      • Caps are needed to protect from nucleases (enzymes that break down nucleic acids) found in the cytoplasm

    • Intron excision- large sections of mRNA are not needed for transcription and are removed (INtrons go IN the trash)

    • Exon splicing- exons are pushed together to have a functional mRNA ready to be read by the ribosomes (EXons are EXpressed)

    • Depending on the introns removed the same mRNA can code for different genes to be expressed (alternative splicing)

Translation

Translation- Process that happens in the ribosomes of ALL LIVING THINGS

• Prokaryotes perform translation WHILE transcription is happening

• Ribosomes are used to synthesize proteins. Rough E.R of eukaryotes is another site of translation (Rough because it's covered in Ribosomes)

  • Made of rRNA

  • 2 subunits (large and small)

  • Evidence of evolution since ALL living things use ribosomes and they work the exact same and make the same amino acids from the same codons. 

• As mRNA enters the ribosome the mRNA bases get read in sets of 3

  • Each set of 3 bases is a codon

  • Each codon codes for 1 amino acid. 

    • There may be more than one way to make an amino acid but each codon will only code for a single amino acid. 

  • Translation starts with the start codon AUG (initiation)

    • Codes for amino acid Met.

  • tRNA binds to each codon to add to the growing amino acid chain making a protein (elongation)

  • Continues adding amino acids until it reaches a STOP codon (UAG, UAA, UGA) (termination)

  • Amino acid chain is released and folds into protein

  • Must know how to read a codon chart

• Retroviruses work the opposite. Reverse transcriptase copies RNA INTO the DNA of the host. 

Gene Regulation

Regulatory sequence- a stretch of DNA that can affect the transcription of a gene

Epigenetic changes- Environmental changes that modify histones and/or DNA and may be reversible

Both Prokaryotes and Eukaryotes use gene regulation

1. Eukaryotes- Usually have genes grouped close together so complementary genes can be expressed at the same time. 

   1. Activated by same transcription factors

2. Prokaryotes- Genes are organized into transcriptional units called operons

   1. This allows prokaryotes to quickly turn genes on and off

Regulatory Sequences- DNA that interacts with regulatory proteins to control transcription

1. DO NOT CODE FOR PROTEINS!!!

2.  Allows for positive and negative control of transcription

3. DO NOT NEED TO BE CLOSE TO THE GENE IT REGULATES

Types of regulatory sequences:

1. Promoter- found upstream of transcription site and tell mRNA where to start transcription

2. Enhancer sequence

   1.  Can occur upstream or downstream of gene and increases the amount of transcription occurring (loops it or causes more mRNA to be transcribed)

   2. Positive regulatory sequence

3. Repressor proteins bind to promoter and stop transcription from happening (negative regulatory sequence)

   1. Silencer sequences can occur upstream or downstream from a gene and tell the repressor protein where to bind

   2. Blocks RNA polymerase from binding to the DNA

Importance of gene regulation

1. Allows organisms to maintain homeostasis by regulating protein production based on environment

2. Allows for organisms to differentiate cell types

   1. All your cells have ALL your DNA but only certain sections are expressed based on the type of cell

      1. Your skin does not grow a heart

3. Phenotype is dependent on the genes expressed and the amount of expression

Prokaryotic Gene Regulation

1. Prokaryotes perform transcription and translation at the same time

2. Operons are stretches of DNA that may code for several proteins but are produced at the same time

   1. Two types:

      1. Inductable- normally “off” but can be activated if conditions are right

      2. Repressible- normally “on” but can be turned off

Eukaryotic Gene Regulation

1. Eukaryotes can regulate genes at each step of the transcription translation process

   1. Epigenetics- control which genes are available to be read

   2. Pre Transcriptional Control- control whether or not transcription happens on part or all of a gene

   3. Post Transcriptional Control- Determines if mRNA even leaves the nucleus to get translated

   4. Pre Translational Control- Non-Coding RNA sequences (micro RNA) can destroy mRNA

   5. Post Translational Control- 

      1. Destruction of created protein

      2. Ubiquitin tags that signal for immune system to destroy the protein

      3. Modification after translation in the golgi

Methylation- silences genes when added to DNA or histones

Acetylation-  turns genes in an area “on”

Mutations

RANDOM changed to DNA sequence

Genes are read from “start” (MET) to a STOP codon

Can be positive, negative, or neutral (no effect)

• Most mutations are neutral

IN ORDER FOR A MUTATION TO AFFECT THE PHENOTYPE IT MUST CHANGE THE AMINO ACID!!!

Types of mutations:

1. Point mutations- A single base is CHANGED (not added or deleted)

   1. Silent mutations- the base is changed but the same amino acid is still the same so the protein is unchanged

   2. Missense mutation- ONE amino acid changes. Can have varying effect on protein depending on where the change occurs and what it was for (active site mutation could have a large impact on protein)

      1. Sometimes mutations lead to improvement of protein

   3. Nonsense mutation- Premature STOP occurs.

      1. Leads to an incomplete protein

2. Frameshift Mutations- Affects EVERY amino acid AFTER the mutation

   1. Insertion- a base is added to a sequence (AGG becomes ACG-G)

   2. Deletion- a base is removed from a sequence (AGG-CTA becomes AGC-TA)

Sickle Cell is a common example used for understanding the impact of mutations

Mutations in introns WILL NOT affect the protein

MUTATIONS ARE THE MAJOR DRIVING FORCE OF EVOLUTION AND NATURAL SELECTION

Viruses

Obligate parasites- must infect a host to reproduce

Not considered alive

1. Don’t grow or develop

2. Don’t metabolize energy

3. Cannot function or reproduce without host cells

Structures (from inside out)

1. Genetic information

   1. Either DNA or RNA

   2. Carries information on how to copy itself that it will insert into host cell

2. Capsid- Protein structure that protects the genetic information

3. Envelope- membrane like structure made of lipids

4. Protein Spike- Helps virus attach to and infect host

Extremely host specific!

1. Plant viruses only infect plants

2. Animal viruses only infect a particular animal (and only sometimes related species)

3. Bacteriophages only infect bacteria

Eukaryotic viruses are very diverse with unique genetic types (single stranded DNA or double stranded RNA)

Prokaryotic viruses are much less diverse

Retroviruses

1. HIV is a prime example

2. Store information as 3’ → 5’ single stranded RNA

3. Prevents info from being read by ribosomes (only read from 5’ →3’)

4. RNA has to be reverse transcribed into DNA to be expressed correctly by host

5. Unique because ALL other life goes from DNA→RNA→Amino Acids

6. Retroviruses go RNA→DNA→RNA→Amino Acids

Mutations in spike proteins lead to new strains of a virus

Infection with two different strains of the same virus can cause strains to combine

• Process is called Antigenic Shift or Viral Recombination

• Leads to infection between species (bird flu or swine flu)

• Reason why no one is permanently immune to the flu

Viruses reproduce in one of two ways

1. Lytic Cycle

   1. Uses host organelles to replicate self

   2. Happens very fast and causes cell to explode releasing more virus to surrounding cells

2. Lysogenic Cycle

   1. Virus adds its DNA to the host DNA

   2. Virus is copied every time the host cell replicates

Virus fluctuates between both cycles depending on cellular conditions

Bacteria have found ways to combat viral infection

• Have a set of enzymes that target specific DNA sequences found in the viruses

• Scientists have isolated these enzymes and can use them to isolate genes in other organisms

  • Allows them to target specific genes to replicate, turn on, or turn off

Biotechnology

Using biological process to create technology to manipulate or study life

1. Restriction Enzyme Digest

   1. Uses the enzymes from bacteria to cut DNA into segments that can be copied or measured

2. Bacterial Transformation

   1. Create a plasmid to give to bacteria

      1. Bacteria are heat treated to open pores

      2. Plasmid has info for protein scientists want made and an antibiotic

   2. After treating, expose bacteria to antibiotic and only those that received the plasmid survive

   3. Bacteria then make the protein found on the plasmid

      1. This is how me make insulin

3. Gel electrophoresis

   1. Each organism has unique DNA

   2. Restriction enzymes are added to DNA to separate specific genes

   3. Genes are then replicated and added to a gel with a current

      1. DNA is negatively charged so it will move to the positive end of a current

   4. Large sections of DNA travel slower through gel than small section so they get bunched at the top

   5. Unknown sample is compared to known samples to find a match