PCB 3023 Final Part I

Fall 2026. Dr Daughdrill

What are the three parts of the cytoskeleton

Intermediate filaments, Microtubules, and Actin filaments

Describe the size of Intermediate filaments, function, and where they are found'

10nm in diameter (larger than actin, smaller than myosin)

Function is to provide cell to withstand mechanical stress (have high tensile strength)

Found in the cytoplasm (anchored to plasma membrane at cell-cell junctions called desmosomes, found in nucleus (form the nuclear lamina)

Desrcibe the structure of one unit of the intermediate filament

8 tetramers

Tetramere: 2 staggered coiled-coil dimers

Dimer: 2 eclipsed alpha helical monomers

Describe the three types of cytoplasmic intermediate filaments

Ropelike

Keratin filaments: In epithelial cells

Vimentin filaments: In connective tissue, muscle cells, and glial (non-neuronal cells in the nervous system that do not conduct electrical impulses. They support the neurons ) cells

Neuro filaments: In nerve cells

Decribe the nuclear intermediate filaments

2D meshwork

Nuclear lamins: In all animal cells

What are nuclear lamins and what do they do?

Nuclear lamins are the proteins that create intermediate filaments that form the nuclear lamina. Those filaments stengthen the inner nuclear membrane

What happens to the nuclear lamina during cell division? How does it do this?

It disassembles and reassembles during cell divisoin

Phosphorylation of the lamins = weakens interactions between lamin tetramers, lamins disassemble

Dephosphorylation of the lamins = strengthens interactions between lamin tetramers, allows for lamins to reassemble

What are microtubules and what do they do?

Microtubules are formed from tubulin subunits that create tracks in the cell. These tracks can be used by motor proteins to transport organelles, vesicles, etc.

What is an example of stable and dynamic microtubules?

Stable: Cilia and flagella

Dynamic: Mitotic spindle during cell division

Describe the structure of one unit of a microtubule

13 parallel protofilaments forming a cylindrical structure

Protofilament: Multiple Dimers of alpha and beta tubulins

Dimer: (+) Beta tubulin and (-) Alpha tubulin

What leads to polymerization and depolymerization of a microtubule protofilament? Mention the GTP cap

Note that the Alpha and Beta tubulins are constantly hydrolyzing the GTP on Beta tubulin. The rate of the addition of a GTP bound Alpha-Beta tubulin dimer relative to the rate of the Alpha-Beta tubulin dimer getting its GTP hydrolyzed determines if the microtubule protofilament is growing or shrinking

Polymerization: GTP bound to Beta tubulin

Depolymerization: GDP bound to Beta tubulin

The GTP cap determines if the microtubule will grow or shrink. If there is no cap, that means the rate of GTP hydrolysis is faster than the rate of adding GTP bound Alpha-Beta tubulin dimers; the microtubule will rapidly shrink

What is the structure of a centrosome? What is the Alpha-Beta tubulin dimer and nucleation site complex called?

A centrosome is a centriole pair, surrounded by a gel-like protein matrix that has nucleation sites, with microtubules sprouting out from the nucleation sites

Alpha-Beta tubulin dimer and nucleation site complex is called the Gamma-tubulin ring complex. The Alpha-Beta tubulin’s negative (Alpha) end is embedded here with growth occurring at the postive (Beta) end

Do pen model for motor protein moving

Pen model for motor protein moving answer

Motor proteins do what to the Golgi and ER?

Contract Golgi and stretch ER

What is the basic strucutre of flagella/cilia? How does this make the flagella/cilia move?

They are made up of 9 pairs of microtubules plus associated dyneins surrounding 2 single microtubules

It makes the flagella/cilia move by one half of the ring structure using its dynein to pull its adjacent microtubule pair. The other half stays relaxed. This gies the oscillating movement of flagella and whiplike motion of cilia

Describe Actin filament structure, size, function, and where they are found

Actin filaments are made up of a twisted chain with a (+) and (-) end

Thin and flexible, 7nm in diameter

Function is to provide movement for cell. Play large role in muscle contractions

Found in the cytoplasm concentrated in a dense network just under the membrane called to cell cortex

How does polymerization of Actin filaments differ depending on the concentration of free actin in the cell?

High concentration of free actin: Actin filament can polymerize at both (-) and (+) end

Low concentration of free actin: Actin filament undergoes treadmilling

Describe treadmilling of Actin filaments. What is the result to the length of the actin filament

Actin monomers with ADP leaves from the (-) end, Actin monomers with ATP joing from the (+) end

This process keeps the Actin filment are about the same length

What proteins promote Actin polymerization? What protein prevents Actin polymerization?

Promotes: Actin-related proteins (ARP’s) and Formins

Prevents: Thymosin

Describe the structure of Myosin I. What direction does it move towards?

Myosin I has a general head domain and a varying tail domain. The tail binds to cargo and the head moves along the actin filament in the (+) direction

Note that Myosin I can also be anchored to the cell membrane and move actin filaments in the cell cortex. This is essential for reshaping the cell

Do hand model for Myosin I moving along actin

Hand model for Myosin I moving along actin

What is the structure of Myosin II? What is the structure of a Myosin II filament? What is the function of Myosin II?

Myosin II is a dimer with two heads and a coiled-coil tail. These tails interact with eachother to form the Myosin II filament with the heads protruding. The function of Myosin II is to slide oppositely oriented actin filaments passed each other. This is what causes a muscle contraction

What is the structure of a skeletal muscle fiber. Create a flow chart of descending complexity

Skeletal muscle fiber > Myofibrils > sarcomeres (contractile unit of a myofibril) > Myosin II and actin filament arranged in specific structure

How do you trigger a contraction?

An electrical signal from an action potential travels through the T tubules which triggers release of Ca2+ from the Sarcoplasmic reticulum. The Ca2+ is released into the cytoplasm surrounding the myofibrils. The Ca2+ binds to Troponin (associated with the end of Tropomyosin) which causes a conformation change in the Tropomyosin. This change causes the Tropomyosin to no longer inhibit the Myosin heads so that they can now slide the Actin filaments past eachother, causing a muscle contraction.

How does Tropomyosin inhibit Myosin?

It blocks the binding site of the Myosin head and Actin filament.

Briefly describe the experiment that was used to figure out that viruses inject DNA

Label DNA with 32P and Proteins with 35S to track which component was injected into the bacteria during infection.

Chop of viral heads with a blender, keeping the bactera in tact.

Analyze cells to see if they contained 32P or 35S.

Cells contained 32P

C and G forms how many Hydrogen bonds. What about A and T

3 for C and G

2 for A and T

What is the difference between the 5’ ane 3’ end?

5’ has a phosphate group attached

3’ has a hydroxyl group attached

What are the three components of the DNA sequence that is needed for cell division

Telomeres: Makrs the end of each chromosome

Replication origin: Where DNA starts to get duplicated

Centromere: Site of attachment for the mitotic spindle

Know the PS handout for chromatin fiber

PS handout for chromatin fiber answer

What do histones have that make them able to bind with any DNA

Histones have a lot of Lys and Arg which are (+) to bind to the (-) DNA

Function of Initiator proteins

Binds to specific DNA sequences to begin the replication origins by inducing local unwinding of DNA

Function of DNA polyermase

Catalyzes phosphodiester bond formation; also contains exonuclease domain which recognizes mismatched pairs and removes the mismatched nucleotide (proofreading)

Function of Sliding clamp

Keeps DNA polymerase attached to template strand so it can slide without falling off

Function of Clamp loader

Uses ATP hydrolysis to lock the sliding clamp onto DNA

Function of Topoisomerase

Relaxes the negative supercoiling created from unwinding DNA

Function of Telomerase

Elongates Telomeres by synthesizing reptitive sequences

Function of Primase

RNA polymerase that makes a primer

Function of RNA nuclease

Removes RNA primer

Function of Repair polymerase

Fills gap created by RNA nuclease

Function of DNA ligase

Conects Okazaki fragments

Function of Replication Protein A (RPA)

ssDNA binding protein that coats the exposed DNA segment of the lagging strand. This protects it from getting degraded by nucleases

What is the simplified process of Lagging strand synthesis

Primase makes RNA primer

DNA polymerase makes the Okazaki fragment

RNA nuclease removes the primer

Repair DNA polymerase closes gap

DNA ligase seals the nick, joining the two Okazaki fragments together

How does DNA topoisomerase relieve tension created by unzipping DNA

DNA topoisomerase makes a single strand cut in the DNA

Why does DNA telomerase replicate the ends of the DNA segment?

After the last RNA primer is removed, there would be no Hydroxyl end to signal DNA replication. As a result, the DNA strand would continually get shorter after each replication and valuble DNA would not get replicated

The ends are replicated so that the repeated ends are what gets “cut” off

Whatr is the general process of DNA repair

Damage occurs

Damaged segment is recognized and removed (excised)

Repair polyermase fills excised portion

DNA ligase seals nick

What does Mismatch repair do? How often does the Replication machine make a mistake? What about after Mismatch repair? When does it usually occur?

Mismatch repair fixes mismatched nucleotides. the Replication machine makes a mistake once evsery 10^7 nucleotides. After Mismatch repair, once every 10^9 nucleotides

Usually occurs during DNA replication

Nonhomologous end joining is used when? It results in what?

Nonhomologous end joining is used in Double strand breaks. Rejoins the two broken ends of DNA; results in loss of info at the site of repair

Homologous repair is used when? It results in what? When does it usually occur

Homologous repair is used in Double strand breaks. Results in a flawlessly repaired DNA strand with no loss of information

Usually occurs after DNA is replicated. Two homologous chromosomes must by physically close to one another

mRNA function

Codes for proteins

rRNA function

Forms the core of the ribosomes structure and catalyzes protein synthesis

miRNA function

Regulate gene experession

tRNA function

Matches the mRNA code to an amino acid

Describe the basic process of Transcription in prokaryotes

RNA polymerase is bound to the promotor and sigma factor

Transcription of DNA strand begins and the sigma factor releases

Transcription continues until terminator is reached where RNA polymerase and RNA transcript are released

What nucleotides are present in promotors and terminators?

Promotors: Lots of A and T

Terminators: Lots of C and G

What are general transcription factors? What part do they have an analogous role to in prokaryotic transcription?

Proteins that assemble on the promoters of eukaruyotic genes to load the RNA polymerase in the correct position. They have an analogous role to sigma factor in prokaryotes

List the general transcription factors and their function in eukaryotes

TFIID: Creates a distorsion in DNA which recruits other general transcription factors

TFIIB: Function is to form a bridge between TFIID and the RNA polymerase

TFIIF: Acts as an escort for RNA polymerase to find the promotor

TFIIE: Serves as a docking site for TFIIH

TFIIH: Phosphorylates the RNA polymerase to begin Transcription

Describe where Transcription takes place for Prokaryotes and Eukaryotes

Prokaryotes: Transcription happens in the cytoplasm where ribosomes immediately start translation

Eukaryotes: Transcription happens in the nucleus where it must get processed before it gets sent out to the cytoplasm for translation

Describe the three types of modifications that RNA undergoes in eukaryotes

RNA capping: Addition of an atypical nucleotide (Guanine with extra Methyl group attached) to the 5’ end

Polyadenylation: Addition of multiple adenine nucleotides to the 3’ end

Splicing: Removes Introns and stitches extrons together to form a mature RNA

What is the purpose of the three modifications of RNA?

RNA capping and Polyadenylation: Increase the stability of the mRNA, Facilitate transport from nucelus to cytoplasm, and Generally mark the RNA molecule as mRNA

RNA splicing: Last step so that the mature mRNA is able to move to the cytoplasm to get translated

What is alternative splicing? What is the function of it

Alternative splicing is when the RNA transcript gets spliced in multiple differenet ways

Allows for a single gene to code for multiple proteins by combining the exons in different combinations

Increases the coding potential of a genome

Function of aminoacyl-synthetases

They covalently couple each amino acid with the appropriate tRNA molecule

20 different amino acids, 20 different aminoacyl-synthetases

On the ribosome what are the three sites that are used to make the polypeptide chain during translation?

A site: Place where the new tRNA with amino acid attaches to

P site: Positions the growing chain so it can transfer its amino acids to the new aminoacyl-tRNA sitting in the adjacent A site

Large subunit translocates

E site: Ejection of the old tRNA

Small subunit translocates

How does the start/stop work in translation?

Start: Initiator tRNA carrying a Met amino acid is bound to a small ribosomal subunit and searches for a AUG coding sequence

Stop: Stop sequence codes for a special release factor which binds to the A site. During transfer of growing polypeptide chain to new tRNA and amino acid, OH group gets added to the end of the growing polypeptide chain instead of another amino acid. Large subunit translocates causes the release factor to enter the P site which causes the ribosome to release

Describe the chaperone proteins HSP70 and HSP 60

HSP70: Binds to the hydrophobic segments on misfolded proteins to protect from aggregation

HSP60: Chamber lined with hydrophobic residues that will hold a misfolded protein. These hydrophobic residues cause the undolding of the misfolded protein. The now unfolded protein will have a space to try and refold properly

Function of proteasomes

Break down misfolded proteins