Bio 97 Midterm Review

Talar Tfnakjian

OH: T, TH 8-9 am

Natural Sci I room 2108

ttfnakji@uci.edu

Emily Ling

OH: Mon 9-10 AM SH 149

Wed 3-4 PM SH 149

linge@uci.edu

About this Review

• We are happy that you could make it and glad to see that your are utilizing your resources.

• This review is not meant to be a substitute to studying, but a guide to assess your knowledge for your midterm.

• We will do our best to cover the important aspects, but we cannot cover every single topic.

• Please feel free to stop us and ask questions, that way we can tailor the information to meet your needs.

• Complete the evaluation at the end of your packet and turn it in to us and help yourselves with candy on your way out :D

Lecture 1

The Words to Know

• Genetics is the study of inherited traits• Genes are the basic units of heredity• The Genome is the entire set of hereditary

instructions – (genes + instructions for gene regulation, etc.)

• Genotype the genes that comprise an individual.– Alleles (the different “flavors” of a gene)

• Phenotype the physical manifestation of the genes; observed traits

The Relationships Between Genotype, Phenotype, and

Environment

Genotype Phenotype

Environment

Ex of genotype as a factor: eye colorEx of environment + genotype as a factor: HeightEx of environment as a factor: HIV+

(IF your have CCR5+ wt)

Griffith ExperimentDiscovered: Bacterial Transformation

Point: There is SOMETHING, we don’t know what yet, that is being passed for the dead S strain cells to the R strain cells

This something is making the R strain turn into S strain cells

Avery (+2 other peoples’) ExperimentImplicated DNA as genetic material

Hershey & Chase ExperimentDetermined that it really is DNA!

QuickTime™ and a decompressor

are needed to see this picture.

Image from wikipedia

Summary of Lecture 1 Slide from Professor Yi

• Definitions– Gene, genome, genotype, phenotype,

environment, wild-type, mutant– Classical versus molecular genetics

• Experimental demonstrations that DNA is the genetic material– Make sure you understand the Griffiths,

Avery, and Hershey-Chase experiments

Lecture 2

What is DNA composed of?

• The basic building block of DNA is deoxyribonucleotide ( deoxyribose sugar, phosphate group, and a Nitrogenous base)

• Note that the difference between DNA and RNA is the sugar content ( Ribose in RNA).

The bases are categorized by number of rings into:

1-Purines (Adenine , Guanine)

• Have two rings

2- Pyrimidines ( Cytosin, Thymidine)

• Have one ring

The bases are complimentary: Purines pair up with pyrimidines

-Adenine pairs with Thymidine

Guanine always pairs with Cytosine

A T

G C

2 H-bonds

3 H-bonds

as a consequence the amount of A is equal to T, likewise amount of G is equal to C (Chargff’s rule)

Putting the Pieces Together

The building blocks of DNA polymer (WHAT ARE THEY CALLED AGAIN?) are linked together through phosphodiester bonds between the 5’ Phosphate and 3’ hydroxyl on the ribose sugar.

The Double Helix

• Two anti-parallel linear polymers of nucleotides form a right handed helix.

• The two chains are connected by hydrogen bonds between the complimentary base pairs and stabilized by base stacking.

DNA Replication• Replication happens in a semi-conservative manner; meaning each

parental strand serves as a template for new strands to be synthesized.

How exactly is DNA replicated?

• It all begins with the origin of replication

• Many enzymes are required for replication to happen

• Here’s what happens

DNA is always synthesized 5’ to 3’

Everything sounds great, polymerase continuously adds the nucleotides 5’ to 3’ , but wait…This works for one strand only

Lagging Strand is Synthesized discontinuously

• The same enzymes are still in action

Problem solved

Tip: a great way to get used to replication and familiarize yourself with the directions is to practice…

I will illustrate on the board..

Nothing is perfect…even Replication

• Every now and then, polymerase incorporates the wrong nucleotide

But luckily, it possesses a proof reading function, where faulty nucleotides are recognized and are replaced by the correct one.

Replication coming to an end...

• Finally the RNA Primer is removed by DNA polymerase and Ligase seals the nick by forming a phosphodiester bond.

Lecture 3

Central Dogma Part I

• DNA must first be transcribed into a single stranded (ss) messenger RNA

DNA

RNA

Transcription (Lecture 3)

DNA vs. RNA

RNA

• RNA uses Uracil instead of Thymine to pair with Adenine: A = U

• 2’C has an -OH group (DNA doesn’t)

• In our case; RNA is ss – Chargaff’s rules don’t apply

Transcription

• Occurs 5’->’3– Template is READ 3’->5’

• RNA Initiation uses:– TATA box – Promoter-proximal elements

• Enhancers and silencers

• RNA Polymerase II– Bacteria only have 1 type of RNA polymerase– Eukaryotes have 3; I (rRNA), II (mRNA, snRNA),

III (tRNA, 50S of ribosome)

Sense vs. Antisense

• Sense/ coding strand has the exact same 5’->3’ sequence of nt’s as the pre-mRNA

• Antisense is the TEMPLATE strand.

Initiation is pretty complicated in Eukaryotes

• Prokaryotes have the Pribnow Box and a promoter region upstream from start site

• Eukaryotes can use enhancers or silencers to regulate rate of transcription

Initiation cont…

Enhancers and silencers upstream from the promoter-proximal region

Transcription factors (TFs) bind the promoter-proximal elements

the can also bind to the enhancers and silencers

Elongation and Termination

• Prokaryotes: Hairpin

• Eukaryotes: Region of AAUAA or AUUAAA

Splicing

Spliceosome recognizes 5’ GU, 3’ AG, and branch point A

EXONS: Desired portion of RNAIs part of the final mRNA

INTRONS: “In the way”

Alternative Splicing• 1 Gene can encode many different proteins (depending

on cell type as well)

Summary Slide from Lecture 3

• Central Dogma

• RNA and types of RNA

• Transcription

• Splicing

• Gene expression

Lecture 4

Central Dogma: We’re almost at phenotypic level!

• Basic idea of Central dogma is to illustrate how genotype is observable at the phenotype level

We went over how DNA is transcribed into RNA, now we will go over how RNA is translated into proteins.

The Key players of Translation

• Ribosomes

• Transfer RNA

• Aminoacyl-tRNA synthetase

AMIO ACID

Translation Steps

1- Initiation-ProkaryotesRecognitions of Shine Dalgarno sequence on mRNA

-EukaryotesThe small ribosomal subunit binds to 5’ cap and starts scanning until it reaches

the start codon.

Initiator tRNA binds start codon, initiation factors (IFs), and small ribosomal subunit (30S or 40S) this is called the initiation complex

The IFs leave and the large ribosomal subunit Is recruited.

2- Elongation• Ribosome moves one codon down on mRNA

• New tRNA enters the A (acceptor) site

• Peptide bond is formed

• Ribosome shift ( The new tRNA which was in A site is now in P, and the one is P site is in E site .

3-Termineation• The ribosome encounter a stop codon

• Release factors are bound to the A site

• The polypeptide bond is cleaved and the complex is dissociated.

• During elongation the polypeptide chain grows in N to C direction

41

Degeneracy of The Genetic Code

• All amino acids except Trp and Met are specified by multiple codons

• Synonomous codons (specifying same amino acid) generally differ only in the third base

• Much of the redundancy comes from the “wobble” in the codon-anticodon pairing at this third position in the codon

• The same anticodon can bind more than one codon

– A single tRNA can translate more than one codon

The anticodon G can bind C OR U

Crick-Brenner Experiment showed that the codon was a triplet

Lecture 5

Does Everyone Understand Crick-Brenner Experiment?

• Two types of mutations: (+) and (-)• Single mutants do not grow, but double (+)(-) mutant can grow• Assumed that each mutation was a single base pair frameshift: (+) is a

single bp insertion and (-) is a single bp deletion• The fact that the triple mutant (+)(+)(+) or (-)(-)(-) could grow (phenotype is

normal) argues for a triplet code Phenotype

+-+++----+

(phagegrowth)

PCR as in vitro DNA Replication

-DNA primers-DNA Template of interest-Heat stable polymerase (Taq)-dNTPs-PCR buffer

1) Denature the template95C

2) Anneal the primers50-65C

3) Proceed with elongation72C

Phenylketonuria (PKU)

• Another example of how genotype and environment can play a big role in phenotype

Summary Slice from Lecture 5

• PCR – How does it work?– Compare to in vivo DNA replication in Lecture 2

• Human genome– Most of genome does not encode for protein

• Molecular Genotype– The genotype is completely specified by the DNA

sequence– Connection between genotype and phenotype

Mitosis

Meiosis

Thank you for your time

• We hope this information helped you

• Good luck on your midterm…. remember to walk in with confidence