BS 161 Final Study Guide

What is amino acids?

Macromolecules to Remember 

• Carbohydrates:

What are the types of RNA?

• Amino Acids:

- Protein backbone:

• Nucleic Acids:

• RNA: OH on 5-Carbon ring (sugar)

• DNA: H on 5-Carbon ring

What is a tryptophan synthesis?

Don't forget about the age old question of ● What is a function?

• Lipids: Don't forget about the age old question of what is augmented product?

• fatty acid:

• triglyceride: Don't forget about the age old question of How are president elected?

• phospholipid:

Transcription: 

Key Ideas:

• DNA—> RNA

• DNA is used as a template to make RNA

• Differences in Prokaryotes and Eukaryotes:

• bacteria lack nuclei, DNA is not in a separate compartment of cell, so transcription and  translation occur together is one compartment

• eukaryotes: have nuclei which contains the genetic info of a cell. machinery for replication  is found within the nuclei. Transcription and translation are separate. transcription happens  in the nucleus where the DNA is found, then the RNA is moved out of the nucleus for  translation to occur.  Don't forget about the age old question of What are Conversation without Technologies and its value?

- two types of chromatin: euchromatin (DNA that is expressed) and heterochromatin  (inactive DNA)

- only euchromatin is associated with transcription 

- in eukaryotes, transcription is activated by histone acetylation  

• 3 Types of RNA:

• mRNA: RNA that contains information for protein synthesis.

• tRNA: VERY IMPORTANT IN TRANSLATION. it transports the amino acids to the  ribosome, positions each amino acid at the correct place on the elongating polypeptide  chain. Involved in translating the nucleotide code into amino acids

• rRNA: major component of ribosomes. Ribosomes are made of mRNA and protein • Transcription Process:

• Need DNA template

• Need ATP, GTP, CTP, and UTP

• Need RNA polymerase

• DNA Template - Structure of a gene

• promotor: defines the start of transcription

• terminator: defines end of transcription

• Initiation: requires a promotor that recruits the RNA  

Polymerase and other transcription factors.  If you want to learn more check out What is the impact of political culture?

• General transcription factors: help RNA pol bind, need  

specific transcription factors to lead to high level of  

transcription, bind to TATA box 

• direction of transcription is “downstream” We also discuss several other topics like What are the 5 types of variables?

• RNA polymerase- can only add ribonucleotides to 3’ end  

(like DNA Polymerase), it can initiate strand synthesis  

(unlike DNA Polymerase) 

- moves along the template strand of DNA in the 3’ to 5’  

direction 

• Elongation: step where RNA Pol is moving along DNA  

template, assembling the RNA, adding nucleotides to the 3’  

end. As it moves along DNA, it continues to untwist the  

double helix (exposing 20 bases at a time), DNA double  

helix can reform behind it, displacing the new RNA molecule  

from its template

• Termination: RNA Pol encounters a terminator sequence  

that tells RNA Pol to stop.

• prokaryotes: once it reaches terminator sequence, it  

stops, releasing both RNA and DNA

• eukaryotes: end of gene is signaled by Polyadenylation Signal (AAUAAA) which tells RNA  to terminate.  

• RNA Processing: only in eukaryotes: transcription produces a primary transcript that is  processed to form a mature RNA

• 5’ end is “capped” (5’ cap is unique to mRNAs)

• 3’ end is polyadenylated

• RNA Splicing: Removal of introns

Translation: 

Key Ideas

• RNA—> protein

• requires a lot of energy! 

• mRNA is read as sequence of 3 bases called codons

• each codon specifies one amino acid

• there is redundancy (several codons may specify  

the same single amino acid, but no codon codes for  

more than one amino acid)

• tRNAs read the codon sequence to assemble the  

protein

• anticodon is unique to each tRNA, anticodon reads  

the mRNA by pairing with the mRNA codon

• 3’ end of tRNA is the amino acid attachment site

• Aminoacyl-tRNA Synthetases: enzyme that attaches a  

specific amino acid to a specific tRNA

• the carboxyl end of amino acid is linked to the tRNA

• result is aminoacyl-tRNA (charged amino acid):  

requires 1 ATP

• Ribosomes bring the mRNAs and tRNAs together for  

protein synthesis  

• each ribosome has binding site for mRNA and three  

binding sites for tRNA

• P site: holds the tRNA carrying the growing  

polypeptide chain

• A site: holds tRNA with next amino acid to be added to chain

• E site: (exit site) discharged tRNAs leave the ribosome at this site

• Translation Steps

• Initiation: bringing all parts together. large and small subunits of ribosome assemble with  mRNA and aminoacyl-tRNA, initiator tRNA

• Elongation: adding each amino acid to chain. tRNA comes into the A site. Amino acids  form new peptide bonds and the whole structure moves over. tRNA from A site goes to P  site. tRNA from P site goes to E site where it is released.

• Termination: ribosome encounters a stop codon, which causes the ribosome to  disassemble. polypeptide is released from tRNA and tRNA is released from ribosome • Translation begins in cytoplasm, but for proteins that need to go somewhere else will have a  signal peptide region. (Ribosomes are directed to ER by a signal recognition particle that  brings ribosomes to a receptor protein in ER membrane)

Gene Expression in Prokaryotes: 

• Genes are organized into operons: transcriptional unit under the control of a single promotor  and operator

- promotor: nucleotide sequence that enables the gene to be transcribed - operator: segment of DNA that a repressor binds to

• the operon is transcribed as a polycistronic transcript  

• coordinate control of gene expression

Tryptophan Synthesis

• trp operon: consists of the operator, the promotor, and the genes they control • it can be switched on and off by trp repressor (repressor binds to operator, blocking RNA  Pol from attaching to promotor which prevents transcription of the operon’s genes. This is  reversible)

• repressor proteins are allosteric, change shape depending of binding of other molecules.  (trp repressor has two shapes: active and inactive)

• trp repressor is synthesized as INACTIVE. to activate, it must bind to tryptophan  • when concentrations of tryptophan are high, some of these molecules bind to the  repressor protein the activate it. Then the repressor binds to operator to turn the operon  off. 

Lac Operon

• When lactose is present in the cell, allolactose (an inducer) binds to the repressor, which  inactivates the repressor so the lac operon can be transcribed 

• When glucose and lactose are both present, and glucose levels are low, cAMP accumulates  in the cell. when cAMP is abundant, it binds to CAP (an activator of transcription), which  activates it so it attaches to the promotor and INCREASES its affinity for RNA Pol which  increases the rate of transcription.

• The lac operon is under dual control: negative control by lac repressor, positive control by  CAP

• repressor turns it on/off

• CAP speeds it up or slows it down (if the repressor is inactive)

• Two Types of Operons:

• Repressible operon: (trp operon) one that is inhibited when a specific small molecule binds  allosterically to a regulatory protein  

• Inducible operons: (lac operon) regulatory protein is synthesized as active (inhibotory), so  the operon is off. Allosteric binding by an inducer molecule makes the regulatory protein  inactive and the operon is turned on

Gene Expression in Eukaryotes 

• Gene expression is coordinated by similar control elements promoting simultaneous  transcription of related genes 

• Differs from bacterial because gene expression can be regulated at any stage: DNA  Packaging, Transcription, RNA Processing, RNA transport out of nucleus, Translation, and  Protein Activation

A. DNA Packaging

1. Level one packaging: Nucleosome  

a) DNA double helix wrapped around histone core

2. Level Two Packaging: Solenoid

• The way that DNA is packaged affects the gene expression. Chromatin structure  must be relaxed/de-condensed in order to replicate (and therefor be expressed) • DNAase cannot cut condensed chromatin

B. Transcription-Stage Regulation  

1. Histone Acetylation

• Two balancing enzymes:  

a) Histone Acetyltransferases (HATs): activate transcription  

b) Histone Deacetylases (HDACs): inhibitors, repressors of transcription, remove  acetyl groups

2. DNA Methylation: reduces gene expression

a) Methyltransferases: enzyme that add methyl groups to DNA bases, which inhibits  transcription  

• Methylated DNA turns off transcription

C. Fine-Tuning Transcription Initiation Mechanism for Gene Expression

• General and specific transcription factors are essential for high levels of transcription  • Enhancers are distal control elements.

• An activator is a protein that binds to an enhancer to stimulate transcription of a gene • Also have repressors to inhibit the expression of a specific gene by blocking the  binding of activators

D. Post-Transcriptional Regulation

• Cells can fine-tune gene expression in response to environmental changes without  altering transcriptional patterns

1. Alternative RNA splicing: specific regulatory proteins control intron-exon choices by  binding to regulatory sequences within the primary transcript

E. Translation Regulation of Gene Expression

1. Initiation of translation can be blocked by regulatory proteins that bind to specific  sequences/structures within untranslated RNA to prevent ribosome attachment  F. Post-Translational Regulation

• Many proteins must undergo chemical modification before they are functional • To mark a protein for destruction, cell attaches ubiquitin to it. Proteasome's recognize  and degrade the tagged protein. Mutations making cell cycle proteins impervious to  proteasome degradation can lead to cancer. 

Cell Signaling 

• Direct Communication

• Gap junction: animal cells

• Plasmodesmata: plant cells

• Direct contact: adjacent plasma membrane

• Paracrine Signaling

• signal released from cell has effect of neighboring cell

• important in development

• Endocrine Signaling

- hormones released and travel through circulatory to  

affect other places in the body

• Synaptic Signaling

- how our nerves work (animal cells only)

• 3 Steps:

1. Reception

• Signal —> binds —> activates receptor

2. Transduction

• receptor passes signal into a pathway

3. Cellular Response

• signal tells cell to do something

• Molecular Switches (on/off)

• 3 Main Ones:

1. Ligand Binding (noncovalent):

- protein binds a small molecule, changes shape of protein

- “allostery”

- ex) Tryptophan Repressor, Lac Enzyme

2. Protein Phosphorylation (covalent):

- covalent addition of a phosphate group to an amino acid

- proteins that can phosphorylate a substrate: Kinases

3. GTP Binding and Hydrolysis:

- functions similar to phosphorylation. GTP highly charged, binds, can change  shapeChemical Signals:

- hydrophobic: molecules can easily cross membrane

- hydrophilic: molecules need help crossing membrane

• Receptors in Plasma Membranes:

- Most hydrophilic signal molecules bind to specific sites on receptor proteins in membrane - 3 Main Types:

1. Ion Channel Receptors

2. G-Protein Receptors

3. Enzymatic Receptors

• G Protein-Coupled Receptor

- vision

- odor

transduced  

signal

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