BIOCHEMISTRY: PBL

What does DNA contain?

• Nitrogenous base

• Phosphate group

• 2-Deoxyribose

purines structure

Are double ringed bases, A and G
contain 9 atoms in their heterocyclic ring

Pyrimidine structure 

Are single ringed bases, C, T and U
contain 6 atoms in their heterocyclic ring

enzymes involved in replication 

• Helicase

• gyrase

• SSB protein

• primase

• DNA pol 3

• DNA pol 1

• DNA ligase

Difference between eukaryotic and prokaryotic replication 

• Eukaryotic rep uses way more enzymes, prokaryotes (13)

• there are multiple origins of replication in eukaryotes

RNA 

• Single stranded

• Used to transfer information and the synthesis of protein (translation)

• Has Uracil instead of Thymine

types of RNA 

• tRNA

• rRNA

• mRNA

• micro RNA

• small interfering RNA

difference of transcription in prokaryotic cells and eukaryotic cells (initiation)

Prokaryotic cells use one RNA polymerase made of the core enzyme and sigma subunit, only require one type of RNA polymerase to make all RNA's

In eukaryotic cells, transcription factors are required to recognise the promotor region. different RNA polymerases make different types of RNA.

What are enhancers

Sequence of DNA which increase transcription rate by binding to transcription factors

what are silencers 

specific DNA sequences that bind repressor proteins to reduce or stop the transcription of a gene

promotor sequence in prokaryotes 

-35 region: 35 spaces behind th eactual start of transcription
-10 region (pribnow box): 10 nucleotides before the start of transcription

promotor regions in eukaryotes

Have specific sequences within the promotor:
TATA box
CAAT box
GC box

Rho dependent termination

protein called rho which starts moving up the mRNA, once it reaches the RNA polymerase it detaches it from the DNA strand.  

Rho independent/intrinsic termination 

• RNA polymerase encounters a particular sequence of DNA called inverted repeats. 

• EG. CCGG....GGCC

• one the inverted repeats are tarnscribed, they tend to want to react via hydrogen bonds. 

• they interact and then form a hairpin loop which signals to RNA polymerase to detach. 

what happens after transcription

Poly a tail addition
splicing 
5' capping

poly a tail 

addition of many adenine bases
prevents degradation
initiates translation. 

exons and introns 

exons: code for amino acids
introns: do not code for amino acids. 

Splicing  

SNRP's onto the intron
very specific bases near the intron ends
branch point in the middle A, with an OH- group attached. 
SNRP's cleave at the 3' splice site

intron structure+splice sites

• Splice sites are the specific sequences for the process, with GU at the 5' end and AG at the 3' end of the introns.

• There is also a branch site, 18-40 bases upstream from the 3’ splice site, with a conserved sequence.

How does splicing work 

1.     G on the 5’ end of the splice site loops back close to the branch site (at the invariant A). 

2.     The 2’ hydroxyl of the A performs a nucleophilic attack on the phosphodiester backbone at the 5' splice site, forming a loop structure and releasing exon 1

3.     The AG at the 3' end of the exon then does the same to the G at the 3' splice site, fusing the two exons.

What are sugars

• carbs which serve as energy storage molecules

• Cell-cell recognition

monosaccharides 

sugars made of one unit
building blocks to bigger sugars

example monosaccharides (Draw)

Fructose
glucose

how are dissacharides formed 

Condensation reaction where theres a loss of a water molecule. 

alpha and beta orientation of monosacharides

• Alpha (α) Glucose: The hydroxyl group (-OH) on carbon number one (the anomeric carbon) points downward below the plane of the ring.

• Beta (β) Glucose: The hydroxyl group (-OH) on carbon number one points upward above the plane of the ring

what bonding is within maltose

alpha (1,4)

lactose bonding type 

beta (1,4) 

amylose bonding type 

alpha (1,4)

cellulose 

beta (1,4)

building blocks of lactose, maltose and sucrose

lactose: glucose+galactose
maltose:glucose+glucose
sucrose: glucose+fructose

amylopectin bonding type+building block

a 1,4 and a 1,6 glucose
branching occurs every 24-30 units

glycogen 

a 1,4 and a 1,6 glucose
Branching occurs around every 10 units

why is glycogen different to amylopectin 

Rapid energy mobilization

how does the structure of amylopectin and glycogen relate to function

both branched polymers of  a -glucose that function as energy storage molecules, but their structural differences reflect the distinct metabolic needs of plants and animals

• very compact molecules 

what are lipids

compounds that occur often in nature that are (mostly) not soluble in water, but soluble in organic solvents

• Provide energy storage, form cell membranes, and help produce hormones

what are the two main groups of fatty acids 

1. Open-chain compounds → Fatty acids, triacylglycerols, sphingolipids, phosphoacylglycerols, glycolipids

2. Fused-ring compounds → Steroids (cholesterol)

fatty acids are amphipathic

the carboxyl group is hydrophilic and the hydrocarbon tail is hydrophobic  

unsaturated fats characteristics

• healthy fats from plants 

• double bonds

• usually cis

• lower melting points

saturated fats characteristics

• animal based

• no double bonds

• higher melting points

Triacylglycerols

Can be found in fat cells (adipose tissue) and make storing of fatty acids possible. They are storage for metabolic energy

Lipase = enzyme used to hydrolyze the ester linkages of triacylglycerols

Glycerol = 3-carbon compound that contains 3 hydroxyl groups, one bound to each carbon. 

Phosphoacylglycerols+ the two types

building blocks of cell membranes 

Phosphatidic acid
Phosphatidyl ester

Waxes

mixtures of esters of long-chain carboxylic acids and long-chain alcohols 

Very hydrophobic and remain solid at room temperature. 

Protective coating for plants

Sphingolipids

structure based on sphingosine (18 carbon amino alcohol), does not contain glycerol. In a phospholipid the sphingosine replaces the glycerol. 

Abundent in the nervous system

steroids

fused-ring system with 6-membered rigs (A.B,C rings) and 5-member ring (D ring). 

EG. cholesterol, testosterone

Cholesterol

• highly hydrophobic

• found in cell membranes

• precursors to some hormones

• At high temperatures, cholesterol restricts movement to prevent the membrane from turning fluid. At low temperatures, it acts as a spacer that stops fatty acid tails from packing too closely together

how are the lipid bilayers connected

held together by noncovalent bonds (van der Waals/hydrophobic interaction).

membrane fluidity and fatty acid structure relation 

Unsaturated fatty acids with = bonds cause a kink → disorder in packing of the chains → greater fluidity