Cell Molec - Exam 2 MOCK QUESTIONS

What are proteins?

Proteins do everything such as carry stuff, breaking things, holding them, sending messages and fighting infections. They’re built out of amino acids which are like lego blocks, and when linked together with peptide bonds, they create a long chain called a polypeptide.

Amino acids have central carbons, hydrogen, amino and carboxyl groups, and side chains. Side chains determines the amino acid’s behaviors as well.

Primary

straight chains of amino acids formed from peptide bonds. The order matters since it determines how proteins will fold. If one amino acid is wrong, chaos follows.

Secondary

chains folds into alpha helices or beta sheets which are stabilized by hydrogen bonds (like curls and waves).

Tertiary

when all those curls and sheets fold up into a complete 3D structure shape which creates a single polypeptide chain. It is held together by a mix of bonds and forces between side chains such as hydrophobic and hydrophilic interactions, hydrogen and ionic bonds, and disulfide bonds that act like super glue. This is how proteins decide their personality and shape.

Quaternary

when multiple folded polypeptides (the subunits again) join forces and form a functional protein complex. It provides stability, regulation, and cooperativity like a girl group where each member has their own talent which results in collaboration and coordination

How proteins fold

They’re guided by hydrophobic forces, hydrogen and ionic attractions, Van der Waals. All these together gives the protein their specific shapes which decides what their jobs are.

How proteins work

Once the proteins are folded and create their shapes, it create binding sites that helps them stick onto other molecules, a ligand. The enzymes, another type of protein, use the binding sites to grab substrates → turn to products → repeats process all over again

How proteins are controlled

proteins have rules they go by such as feedback inhibition where when the product is made, the end product turns off the pathway. Phosphorylation adds/removes phosphate which flips it on/off like a switch. GTP-binding proteins are like “mood rings” where GTP = active, GDP - shuts off (nap time).

Examples of proteins

Enzymes - speeds up reactions (DNA polymerase)

Structural - supports and shapes (collagen)

Transports - moves things (hemoglobin)

Gene regulation - turns genes on/off (transcription factors)

What happens when folding goes wrong

If the shape isn’t right then it can’t do its job or worse such as loss of function, clump up with other misfolded proteins which causes diseases like prions or Parkinson’s, or if the mess gets too big then the cell shuts down or dies.

What is DNA and its structure?

DNA is the blueprint like a recipe book that holds the code for making all the proteins in our body. DNA’s structure is like a twisted ladder = the double helix. Each side of the ladder is the sugar-phosphate backbone while the rung are the base pairs → A-T, G-C and are held together by hydrogen bonds.

Each DNA monomer = nucleotide and is made up by deoxyribose, phosphate group, nitrogenous base.

Complementary strand

5’-ATG CCA TTA G-3’ → 3’-TAC GGT AAT C-5’

Structure of a chromosome

A long thread of DNA wrapped around proteins called histones → forms nucleosomes (looks like beads on a string). Holds all or parts of our genetic information. Humans have 46 chromosomes (23 pairs) and each one contains thousands of genes → instructions for making proteins.

Beads coil tighter and forms chromatin fiber. Chromatin loops, folds and super coils → turns into a chromosome (most compact).

Chromosome parts 

centromere - attachment site for spindle fibers during mitosis

telomere - repetitive sequences at the end → protects DNA from being lost

histones - proteins DNA wraps around → helps compact and control access to genes

chromatin - complex of DNA + proteins

What is a nucleotide and its composition

Nucleotides are the basic units of DNA. Has three parts which are sugar, phosphate groups, nitrogenous base. 

Sugar - DNA uses deoxyribose, RNA uses ribose

Phosphate groups - attached to the sugar’s 5’carbon → what connects one nucleotide to the next in line

Nitrogenous base - gives the molecule its identity

How chromosome structure helps regulate DNA/gene expression

structure regulates DNA by deciding how tightly it’s packed. Loose packed = genes are readable and active, tightly packed = genes are silent and hidden. It’s also how genes are expressed.

How does DNA replication work?

unzips at origins of replication → helicase breaks H-bonds → each old strands act as temples → DNA polymerase builds new strands → primase starts process w/ short RNA primers → DNA polymerase proofreads → telomerase helps prevent DNA shortening at end

How does DNA repair work?

it fixes damage and keeps DNA accurate by cutting out damaged or incorrect bases → fills in gaps using correct complementary base → seals new piece into place and the strand is whole again. DNA polymerase double checks and if there’s a wrong base → enzymes remove and replace with correct one.

Enzymes and proteins necessary for DNA replication/repair mechanisms

DNA replication - helicase, primase, DNA polymerase, DNA ligase, telomerase

→ this is for making sure every new cells gets an identical copy of the genetic code = unzips the strands → builds new ones from OG templates → proofreads errors -? protects the ends to keep DNA complete and accurate

Repair - DNA polymerase, nuclease, DNA ligase, telomerase, mismatch repair enzymes

→ this is to help fix mistakes and protect the cell’s genetic code = cuts out the damage and replace it with right bases

How does translation work?

mRNA attaches to a ribosome, the site of protein synthesis → each tRNA carries one amino acid that have three-base anticodon which matches a codon on the mRNA → mRNA is read in sets of three bases → peptide bonds form → a release factors binds and the ribosomes released the completed protein

RNA → protein

How does transcription work?

RNA polymerase binds to specific DNA region → DNA unwinds → the RNA polymerase builds the RNA by using one DNA strand and adds complementary RNA nucleotides → reaches a stop signal, transcription ends and the RNA is released

For eukaryotes, RNA is edited and adds a 5’cap that protects RNA and helps ribosomes attach, a poly-A tail that protects from breaking down, and splice out introns which keeps useful parts and extracts junk

How to regulate genes after translation?

After translation, proteins must be folded into the correct shape, go through chemical modifications like phosphorylation, and targeted to specific areas of the cell.

How to regulate genes after transcription?

After transcription,cell can edit the mRNA by removing introns but keep exons. It adds a cap on one end and poly-A tail on the other to protect it. It controls how long the mRNA last before it breaks down and small RNAs can stick to mRNA = stop it from being used