BIS2A Section B Final Review

pKa=2pKa=9

At pH=1 At pH=7 At pH=10

-H+

protonated

deprotonated

protonated

deprotonated

H +

H+

-

H +

Hydrogen bonds and polarity

Answer: Fatty acidWhy don’t we observe hydrogen bonding with the carbon chains?

Hydrogen bonds and polarity

More hydrogen bonds help to stabilize interactions, allowing for stronger interactions. Ex: DNA molecules with a higher GC content require higher temperatures to denature.*What other macromolecules are affected by H-bonds?

How can more functional groups affect stability of binding? (Hint: interactions within DNA molecules)

What type of molecule is this?

Answer: Nucleic acid

Where can hydrogen bonding occur?

What type of molecule is this?Answer: Carbohydrate

Where can hydrogen bonding occur?

What type of molecule is this?

Answer: Fatty acid

Where can hydrogen bonding occur?

What structure can this molecule form?Answer: Phospholipid bilayer

Membranes are selective! Big things and small, charged things can’t get in without help.

What type of molecule is this?

Answer: Amino acid

Where can hydrogen bonding occur?

At the N and C terminus AND depends on the R group*Make sure you know how to recognize the different functional groups in a polypeptide

Be able to identify polar functional groups on the R group and understand how this will affect the amino acid’s polarity/ability to form hydrogen bonds

Which of these amino acids will most likely be found on the inside of a protein? What about the outside of a cytosolic protein? Nonpolar amino acids; polar amino acids

What type of bond is this?

Hydrogen bond

Are amino acids on the inside of the tertiary structure more likely to be polar or non polar?Non polar

What if I replaced a non polar amino acid with a charged amino acid on the interior of the tertiary structure?

Possible protein misfoldingand/or loss of protein function

DNA binding proteins

-Non-specific interactions with DNA backbone-Specific interactions by hydrogen bonding with nucleic acid sequence

What would happen if a mutation in the DNA binding portion of this protein changed an amino acid from aspartic acid (pKa=3.9) to arginine(pKa=12.5)? Assume physiological pH (7)

Negatively charged amino acidpositively charged amino acidBad for interacting with DNA

DNA binding proteins

-Non-specific interactions with DNA backbone-Specific interactions by hydrogen bonding with nucleic acid sequence

Which portions of this protein would more likely have polar R groups?

Non-polar R groups?

How does protein folding affect the entropy of a system?

Decrease entropy

Exergonicreaction

Endergonicreaction

Gibbs Free Energy

How might adding an enzyme affect the activation energy of the system? What about the potential energy of the products?

Decrease activation energy; no change in free energy of the system

Exergonicreaction

Endergonicreaction

Could an endergonic reaction with a ΔG = 7.0 kcal/mol be coupled to ATP hydrolysis?

Could an endergonic reaction with a ΔG = 8.3 kcal/mol be coupled to ATP hydrolysis?

Could an endergonic reaction with a ΔG = 1.5 kcal/mol be coupled to ATP hydrolysis?

Could an exergonic reaction with a ΔG = -12.6 kcal/mol be coupled to ATP hydrolysis?

Answer: No need, both are exergonic and will progress spontaneously

Answer: Yes

Answer: Yes

Answer: No

Let’s review redox

What do the negative values represent?

What do the positive values represent?

The molecule’s potential to donate an electron

The molecule’s potential to accept an electron

What is the terminal electron acceptor in respiration? For photosynthesis?

O2; NADP+

Is the external electron donor in photosynthesis higher or lower on the redox tower? What about in respiration?

Lower (more positive); higher (more negative)

What are plants synthesizing when they undergo photosynthesis?

What is their carbon source and where do they get it from?

CO2 from the atmosphere

What do photosynthesizers need to survive when placed in an inorganic aqueous environment?

CO2 gas and sunlight

Glycolysis and respiration

Where does respiration take place?

What are the different ways ATP can be produced during respiration?

ATP synthaseBy coupling ADPATP reactions to an exergonic reaction with a larger absolute value of free energy

Looks like there’s a lot of NAD+ being used up. Where do you get more?

Fermentation

What are these structures and what is the purpose of having so many membranes?

Mitochondria and chloroplast. More membranes = more room for ETCs!

Mitosis and Meiosis

1st step: Condensation of DNA into chromosomes.

Mitosis and Meiosis

What are these things?

DNA wrapped around histonesaka Nucleosomes

Mitosis and Meiosis

How many molecules of DNA are in this box?

2

Mitosis and MeiosisAside from generating diversity, how can crossing over increase the fitness of a species?

Removal of deleterious mutations during crossing over.

*However the converse can also occur where lethal mutations carried by the parent can end up in one offspring.

What is the ploidy of this cell?

Diploid

How are chromosomes sorted during cell division?

Microtubules

Central Dogma and Phenotype

Assume each coat color represents a different allele

How many alleles can each dog have? (Dogs are diploid)2

What does DNA look like?

Antiparallel

5’ phosphate; 3’OH*this gives the DNA its polarity; helps to identify one end from another

Base pairing:A—T C—G

Nucleic acid “language”

What are the enzymes involved in DNA replication?

What are the components of PCR?DNAPrimersPolymerasedNTPsThat’s all!

Is there lagging strand synthesis?No

Can you end up with PCR products of multiple sizes?

Generally no, but this can occur if you have non-specific primers.

What are the components of PCR?DNAPrimersPolymerasedNTPsThat’s all!

Can the polymerase become inactive if the reaction is heated to 95°C? No!

What DNA elements are needed for transcription?

Promoter, transcription start, transcription stop

What RNA elements are needed for translation?

Ribosome binding site, translation start, translation stop

Just to clear up some confusionProkaryotes can have genes organized in an operon (a cluster of genes under the control of a single promoter). Eukaryotes do not have this feature.

Translation

5’ 3’

In which direction does the ribosome read?

5’ 3’

5’3’

How many nucleotides are read at a time?

5’ 3’

3

Reading a codon table

Is a mutation in the third nucleotide in the codon more or less deleterious than a mutation in the second nucleotide?

Less

Neural cell

Epithelial cell

Do these two cells have the same genetic code? Yes

Neural cell

Epithelial cell

Then why do they look so different?

Different genes are expressed, giving rise to different proteins

Transcriptional Regulation

Label the polarity of this strand of DNA

5’ 3’Gene

Where is the promoter located?

Promoter

Where is the transcriptional start site?

Transcriptionstart site

Where is the translational start site?

Translationstart site

Where is the ribosome binding site?

Ribosomebinding site

Where is the transcriptional stop site?

Where is the translational stop site?

TranscriptionStop site

Translationstop site

Transcriptional Regulation5’ 3’

Gene

Promoter

Transcriptionstart site

Translationstart site

Ribosomebinding site

TranscriptionStop site

Translationstop site

Will the same gene still be expressed if we engineered a different promoter? A different RBS?

Yes

What if we kept the same promoter but put in a different gene?

The different gene would be expressed

How would transcription be affected?Change in polymerase binding will affect rate of transcription

Positive vs. Negative regulation

Both respond to environmental signalsExist in eukaryotes and prokaryotes

Work together for fine control over gene expression

G

What happens to lactose metabolism if we introduce a deleterious mutation into one or more of the lac operon genes?

Little to no metabolism

G

What happens to lac operon transcription if we mutate the operator for stronger repressor binding? For no repressor binding?

Regulation not affected regardless of lactose availability; transcription may occur even when lactose is unavailable

G

What happens to lac operon transcription if we mutate the CAP binding site so cAMP cannot bind?

Little transcription independent of lactose and glucose availability

Which proteins would you inhibit to reduce or stop heterocyst formation?

HetR, PatA, NrrA, NtcA

What happens to hetR regulation and HetR production in the presence of excess HetR?HetR will self regulate at the protein level to maintain a constant level of HetR protein activity

How else can HetR regulate itself?

HetR regulation of hetR expression: positive regulation in the presence of high HetR concentrations