Biochemistry Review

Cell Biology & Biochemistry, Cell Signaling

100

What is an amphipathic molecule? 

molecule with polar head groups and hydrophobic tail 

200

What are the 2 components of electrochemical gradient 

the concentration gradient and the charge on the membrane 

300

what is facilitated diffusion, and what how is it transported?  

facilitated diffusion-moves from high concentration to low concentration

the molecules binds to transporter but is passive and it has no energy is required 

400

What is the pH lysosomes are maintained at and how is it maintained? 

pH-5.5 

pH is maintained by enzymes that use energy to pump H+ into the lysosome

500

Where does DNA replication and transcription? 

nucleus 

Nuclei Acids

100

What are Plasmids and why are they important

• These are circular DNA molecules that can enter bacterial cells and replicate independently of the genomic DNA
• they are important since they can confer antibiotic resistance to the bacteria they enter 

200

What is the number of hydrogen bonds between A and T, G and C

A and T-  2 hydrogen bonds 

G and C- 3 hydrogen bonds 

300

Why is it important to known that the DNA strands run in opposite directions? 

• a pyrimidine is always H-bonded to the same purine (complementarity), each strand is the same but in the opposite direction
• This means that each strand can serve as a template for the other strand

400

When does polymorphisms occur 

occur when there is a difference in the bases that make up a gene between different individuals

500

What are the different types of RNA and what do they do? 

• mRNA that provides instruction for protein synthesis
• rRNA combines with proteins to form the ribosomes on which the proteins are synthesized
• tRNAs are the molecules that carry the individual amino acids to the ribosomes, according to the instructions on the mRNA, to be incorporated into the growing protein

DNA Synthesis

100

What are the differences between bacterial and eukaryotic replication 

Bacterial Replication

• Bacterial cells have circular DNA, with an origin
• The origin is the place that DNA replication begins in both directions
• The circular nature of bacterial DNA and its single origin are a couple of the differences between prokaryotic and eukaryotic DNA replication

Eukaryotic Replication

• There are multiple origins of replication in DNA in eukaryotes
• These replication “bubbles” arise at points along the DNA and synthesis proceeds along a fork in each direction from these points
• As in prokaryotic DNA replication, the new strand is formed from the template of the old on each strand – semi-conservative replication

200

What is topoisomerase? 

an enzyme that can break and rejoin the strands to relieve tension from twisting

300

What are RNA Primers? 

• Since DNA polymerase cannot add bases without a free 3’ OH group, RNA primers are synthesized to start replication
• Primase is the enzyme that adds the RNA bases in a 5’3’ direction, copying from the template strand
• The DNA polymerase then starts the DNA synthesis using the free 3’ OH on the last RNA base

400

What is a leading strand and lagging strand? 

leading strand- Replication proceeds on both sides of the fork but DNA polymerase can only synthesize in the 5’ to 3’ direction

lagging strand-The other strand is made in a stepwise fashion using “Okazaki fragments”, also made in the 5’ to 3’ direction

500

What are the repair steps? 

• Damaged DNA is recognized
• Enzymes able to break the phosphodiester bond remove the damaged area
• A DNA polymerase designed to repair, rebuilds the damaged area
• DNA ligase is needed to seal the nicks

Transcription

100

What is the big difference between RNA and DNA polymerases? 

is the ability of RNA polymerase to initiate synthesis

200

What are promoters for and where are they located? 

• Promoters are the site of attachment for the RNA polymerases and identify the start point for transcription

300

Gene is made up of what? 

a promoter and transcribed region

400

What is Poly (A) tail? 

is a protein binding site that protects the mRNA transcript from being degraded in the cytosol

500

What does the spliceosome do? 

attaches to the intron and cuts the intron out between these borders,

Translation

100

Frameshifting can also result is what? 

in a premature stop codon, producing a non-functional truncated protein

200

Name the steps of translation and describe them? 

Initiation 

• involves formation of a complex between the methionyl-tRNAiMet, initiation factors, the mRNA, and the small ribosomal subunit (40S)
• The large (60S) subunit binds to complete the ribosome which has 2 binding sites for tRNAs, the peptidyl (P) and aminoacyl (A) sites

Elongation 

• Peptidyl transferase, the rRNA of the large ribosomal subunit (not a protein), catalyzes the formation of the peptide bond

Termination 

• The elongation steps continue until a stop codon is reached (UGA, UAG or UAA)
• There are no tRNAs that match these codons so release factors bind to the ribosome, allowing the last peptide bond to form before releasing the new polypeptide (protein)
• The whole process of translation requires the expenditure of a lot of energy by the cell

300

What is a common posttranslational modification and when is it especially used for? 

Glycosylation is a common posttranslational modification, especially for secreted or integral membrane proteins

400

What is Polysomes? 

Multiple ribosomes can attach to an mRNA, each producing the same protein

500

Name the 5 different mutation and describe them? 

Point- a single base change 

silent-a change that specifies the same amino acid 

missense- a change that specifies a different amino acid 

nonsense- a change that produces a stop codon 

insertion- an addition of one or more bases 

deletion- a loss of one or more bases