MCAT Biology

Polymers are made from?

Monomers

Enzyme that make polymers

Polymerases

Reaction of polymers

Polymerization

Nucleotides consist of

Sugar, Base & Phosphates

Nucleoside consist of

Sugar & Base

DNA is synthesized how?

5’ to 3’

Antiparallel/Complementary Sequence of DNA

5’ to 3’ then 3’ to 5’

What are the Pyrimidine bases

Cytosine, Thymine, Uracil

What are the Purine bases

Adenine & Guanine

What is a Genome

All the DNA in an organism

Genome of Prokaryotes

Single circular DNA

Restriction Enzyme

Enzyme that will cut up DNA & restrict the growth of viruses

Methylation

The adding of Methyl groups

Supercoiling

Twisting up the genome

DNA Gyrase

Enzyme that runs supercoiling

Genome of Eukaryotes

Several Linear Chromosomes

Histones

DNA wraps twice around

Nucleosomes

Set of histones with DNA wrapped around itself

Chromatin

Coils of nucleosomes

Centromere

Center region on the Chromosome

Sister chromatids attach where?

The Centromere

Spindle fibers attach where?

The Centromere

Where are telomeres located?

At the end of linear chromosomes

Telomeres are made of what

Both single and double stranded DNA

What is Transcription

DNA to RNA

What is Translation

RNA to Proteins

Genetic Code

What nucleotide will translate to amino acid

Codon

3 nucleotides to one amino acid

What is the Start Codon

AUG

What are the stop Codons

UAA, UGA, UAG

What are mutations caused by?

Polymerase errors

Point Mutations

Single base pair changes caused by polymerase making a mistake

Small Repeats

3 to 4 bases get replicated twice, end up with a small sequence repeat

Insertions/Deletions (small frameshift)

Puts a base in randomly, not putting all bases in

Missense Mutation

Codon for a specific amino acid, becomes a new codon for a new amino acid. Changed amino acid

Nonsene Mutation

Codon for specific amino acid becomes a STOP codon. Shortened protein

Silent Mutation

Codon for specific amino acid become a new codon for the same amino acid. No effect

Frameshift Mutation

Caused by insertions and deletions that changes the reading frame of the mRNA sequence

Endogenous Damage

Damage from inside the cell

Endogenous Damage: Oxidized DNA

Bases no longer able to base pair w/ one another; strands separate

Endogenous Damage: Crosslinked based

Bases physically linked together instead of hydrogen bonded

Endogenous Damage: Physical Damage

DNA is broken or missing bases; can’t replicate properly

Exogenous Damage

Damage to DNA from outside cell

Exogenous Damage: UV Radiation

Lead to pyrimidine dimers

Pyrimidine dimers

Base pairs with each other; not opposite strand causes deletions

Exogenous Damage: X-Ray

Double stranded breaks and translocations

Exogenous Damage: Chemicals

Can lead to physical damage or to intercalation and cause polymerase errors

Transposons:

Jumping gene; causes insertions/deletions(large), inversions and duplication

Mismatch Repair Pathway

Repairs bases due to DNA polymerase errors. Deleted after replication is complete

Base/Nucleotide Excisions Repair

Occurs prior to replication because defective bases will lead to polymerase errors. Removal of bad base, replaced with correct ones

Homologous End Joining

Repairs end joining, happens after replication (requires sister chromatid)

Non-Homologous End Joining

Repairs double stranded DNA breaks, essentially sticks two pieces of DNA together

Direct Reversal

No extensive complicated pathway, visible light reverses dimerization

4 General requirements for carrying out DNA replication

Semiconservative, 5’ to 3’ direction, Primer and template required

Helicase

Unwinds DNA

Topoisomerase

Cuts DNA, relaxes supercoiling

Primase

Puts down the RNA primer

DNA Polymerase

Replicates DNA, proofreads, remover primer

Ligase

Links Okazaki Fragments

Okazaki Fragments

Pieces of synthesized DNA

DNA Polymerase III

Main polymerase, processes replication fast, adds nucleotides 400 base pairs down

DNA Polymerase I

Adds nucleotide to RNA primer, proceeds replication slow, DNA excision repair

DNA Polymerase II

Backup for DNA Polymerase III

DNA Polymerase IV & V

Error prone 5’ to 3’ polymerase activity, DNA repair

Prokaryotic Replication

1 Origin of replication, 5 DNA polymerases and Replication starts at the origin, processes away from origin in both directions

Eukaryotic Replication

Multiple origins of DNA replication, several polymerases, complex multisubunit enzymes, replication proceeds away from origins

Characteristics of Eukaryotic Replication

Built in RNA primer, reverse transcriptase activity (RNA to DNA)

rRNA

Ribosomal RNA, catalytic part of functional ribose

mRNA

Messenger RNA, sequence of codons determines amino acid sequence of protein

tRNA

Transfer RNA, carries amino acids and ribosomes

hnRNA

Heterogenous nuclear RNA, initial unprocessed transcript, found in eukaryotes

miRNA & siRNA

Micro RNA and small interfering RNA, help regulate gene expression

Promoter

Binding site for RNA polymerase

Repressors

Bind to DNA to prevent transcription

Enhancers

Bind to activators, when close to promoter and other transcription factors, increase transcription

Polyadenylase

Stop site in eukaryotes signal

Prokaryotic Transcription

Transcription and translocation happen in cytosol, no mRNA processing, polycistronic and one RNA polymerase

Eukaryotic Transcription

Transcription and translation happen in nucleus & cytosol, mRNA processing, monocistronic, 3 RNA polymerases

RNA Polymerase I

Transcribes rRNA

RNA Polymerase II

Transcribes mRNA

RNA Polymerase III

Transcribes tRNA

Amino acyl tRNA synthase

enzyme that leads amino acid onto tRNA, cost 2 ATP equivalents to activate

P-Site

Growing protein held here

A-Site

New amino acid added here

Stop codon in A site

no tRNA that recognizes a stop codon, release factor, break bond between tRNA and final amino acid to release completed protein

Energy count for Translation Equation

Number of Amino Acids x 4

Post-Translational Modification

Protein folding > Covalent Modification > Processing

What is C-Peptide?

Helps to determine if someone can make insulin properly

Viruses

Obligate Intracellular Parasites, consist of protein and nucleic acid

Genome in bacteriophages are made of?

DNA or RNA

Lytic Cycle Steps

Attachment, Transcribe, Replicate and Lyse host cell

Hydrolase in Virus

Destroys the host cell genome

Lysozyme in Virus

Creates holes in bacteria cell

Lysogenic Cycle Steps

Attachment, Integration, Replicate, Excision and Lytic Cycle (under stress)

Repressor in Virus

Suppresses synthesis of viral genes

Stress triggers what in the Lysogenic

Excision & Lytic Cycle

Transduction in Virus

Piece if hist genome accidentally grabbed during excision, can be transferred to next host, how diversity is acquired for bacteria

Advantages of Productive Cycle

More viruses and an envelope

Unique characteristic of productive cycle?

Budding and Envelope

Envelope in Viruses

Easier infection of next host, they essentially blend in with host to gain access and infect host