cell biology exam 3

density dependent communication between single celled bacteria, allowing them to coordinate their behaviors

quorum sensing

signaling molecules that can induce biofilm formation when bacterial population density is high.

autoinducers

a type of signal secreted by exocytosis from one cell and detected by a receptor on a target cell

extracellular signal (1st messenger)

type of protein that lies at the end of signaling pathways; bring about a change in cellular function/behavior

effector proteins

intracellular signaling molecules act as ______ ______ which relay the signal to the inside

second messenger

overall process by which an extracellular signal detected by a target cell is converted into an intracellular response that alters cellular behavior

signal transduction

signals remain bound to a “sending cell” and influence only target cells that the sending cell directly interacts with

contact dependent

signals are secrete to the extracellular fluid by the sending cell, but act as local mediators to influence only nearby target cells

paracrine

signals are secreted to the extracellular fluid by the sending cell, and travel long distances (i.g bloodstream) to target cells that are far away (i.g hormones)

endocrine

upon receipt of a signal, proteins can switch up from an inactive state to an active state, until another process turns them off

molecular switch

The addition of a phosphate group to a protein, which can change its activity.

phosphorylation

An enzyme that adds phosphate groups to proteins.

protein kinase

An enzyme that removes phosphate groups from proteins.

protein phosphatase

A protein that promotes the exchange of GDP for GTP, activating a GTP-binding protein.

GEF (guanine nucleotide exchange factor)

A protein that stimulates GTP hydrolysis to GDP, inactivating a GTP-binding protein.

GAP (GTPase-activating protein)

inhibition of an inhibitor activates a downstream protein

double - negative activation

bring together signaling molecules into complexes’ enhance efficiency by localizing signaling molecules in the same location of a cell, thus ensuring that proteins interact with each other and not with inappropriate partners

scaffold proteins

recognize a structural motif in another molecules (such as another domain or a covalent modification; these are modular and thus can connect multiple pathways

interaction domains

How do scaffold proteins increase signaling efficiency and specificity?

By localizing signaling proteins together so they interact with the correct partners.

post translational modification can alter protein interactions/functions in a matter of seconds, and thus result in a ___ response

fast

a signal that acts by changing gene expression (at the level of transcription and translation) results in a ___ response

slow

a switch like response, in which the cell abruptly changes between a high and low response (with no intermediate once the signal reaches a threshold concentration

all or none

a response that increases gradually with increasing signal concentrations, until saturation of the system (the response reaches a plateau at this point)

hyperbolic

a response that is reduced (but not absent) at low signal concentrations, but then increases steeply at an intermediate signal concentration; provides a “filter” against low level background signal

sigmoidal

the output stimulates its own production

positive feedback

the output inhibits its own production

negative feedback

prolonged exposure to a stimulus decreases a cells response to that level of stimulus

desensitization (adaptation); a type of negative feedback

3 mechanisms of receptor desensitization?

receptor sequestration, receptor down regulation, receptor inactivation

Cell-surface receptors that activate G proteins, which then regulate other cellular proteins, such as ion channels or enzymes.

G-protein-coupled receptors (GPCRs)

Cell-surface receptors that are enzymes themselves or interact directly with enzymes when activated by a signal.

enzyme-coupled receptors

notable features of GPCR

• single polypeptide with 7 transmembrane stretches

• deep ligand binding site at the center

• all use G proteins to relay signal to interior of the cell

g protiens are composed of 3 subunits

alpha, beta, gamma

What two changes occur when the trimeric G protein is activated

• The G protein is released from its coupled receptor.

• The α subunit separates from the βγ subunit pair.

How do activated G proteins relay signals?

Both the isolated α subunit and the βγ pair interact with target proteins, such as channels and enzymes, to relay signals toward effectors.

activated Gα subunit can activate this enzyme which synthesizes cyclic AMP from ATP

adenylyl cyclase

can act as a 2nd messenger by activating a kinase

cyclic AMP

A cyclic-AMP-dependent protein kinase that is activated by cAMP and phosphorylates target proteins.

PKA (cyclic AMP-dependent protein kinase)

What are the structural characteristics of enzyme-coupled receptors?

one transmembrane segment and can associate as dimers.

what is the most common type of enzyme-coupled receptor, enzyme-coupled receptors with kinase domains that phosphorylate tyrosine residues.

receptor tyrosine kinases (RTKs)

what are RTK families classified by and what two structural features do RTKs share?

receptors ligand (commonly hormones or growth factors)

1. single transmembrane pass

2. kinase domain

The process in which two receptor tyrosine kinases phosphorylate each other on tyrosine residues.

trans-phosphorylation

how are receptor tyrosine kinases (RTKs) activated

Ligand binding → RTK dimerization → trans-phosphorylation → recruitment of signaling proteins → downstream signaling.

A protein interaction domain that recognizes and binds phosphorylated tyrosine residues

SH2 domain

A GTP-binding protein (GTPase) that is activated by Ras-GEF and initiates the MAP kinase cascade

Ras

essential mechanism by which all living cells reproduce

cell cycle

what are the three major tasks of the cell cycle

replicate DNA (s phase DNA synthesis)

segregate chromosomes (M phase mitosis) = growth DOES NOT occur here

divide into two daughter cells (cytokinesis)

between M phase of previous cell cycle and S phase of the next cell cycle

G1

between the S and M phases of the same cell cycle

G2

G1, S, and G2 comprise

interphase

a critical “decision point” when a cell ensures that conditions are favorable and that all preparations have been completed before moving on to the next stage

cell cycle checkpoint

a cell commits to cell cycle entry and chromosome duplication if environmental conditions are favorable

late G1: Start (interphase checkpoint)

non-dividing state a cell enters when not satisfied

G0 (interphase checkpoint)

a cell commits to mitosis if all of its DNA has been successfully replicated

G2/M transition (interphase checkpoint)

a cell senses whether its chromosomes have been correctly bound by the spindle and, if so, triggers their segregation to opposite poles

metaphase-to-anaphase transition (mitotic checkpoint)

3 features of cell cycle control

1. switches are often binary

2. switches are irreversible

3. the entire system is robust and adaptable

What are the two major challenges of DNA replication?

• Maintaining extreme accuracy to minimize mutations.

• Ensuring every nucleotide is copied only once to prevent unwanted DNA additions or gene amplifications.

a permanent change to the DNA sequence caused by a failure in the DNA replication machinery

mutation

no change in the coded amino acid

silent mutation

produces an early stop codon

nonsense mutation

codes for a different amino acid

missense mutation

What is semiconservative DNA replication?

DNA replication in which each daughter DNA double helix contains one original strand and one newly synthesized strand.

catalyzes the stepwise addition of complementary bases to the 3’ -OH end of a polynucleotide chain - the newDNA stand will grow in 5’ → 3’ direction (requires a primer)

DNA polymerase

What provides the energy for DNA polymerization?

The release of pyrophosphate from an incoming deoxyribonucleoside triphosphate, followed by its hydrolysis into inorganic phosphates.

The growing DNA strand that provides a 3′-OH end for DNA polymerase to add new nucleotides.

primer strand

What happens to the incoming deoxyribonucleoside triphosphate during DNA polymerization?

Pyrophosphate is released, while the deoxyribose and one phosphate are incorporated into the sugar-phosphate backbone of the new DNA strand.

localized region of unpairing between parental strands which allows for replication to move progressively along the double helix

replication fork

at the replication fork, how will the new strands be synthesized?

• synthesis of one strand is continuous

• synthesis of other strand is non-continuous

• both are synthesized in the 5’ → 3’ direction

daughter strand that is synthesized continuously in the 5’ → 3’ direction. Slightly precedes synthesis of the lagging strand

leading strand

daughter strand that is synthesized discontinuously in the 5’ → 3’ direction. Direction of nucleotide polymerization is opposite to the overall direction of DNA chain growth

Lagging strand

transient pieces of DNA must be “backstitched” to produce a lagging strand with no gaps

Okazaki fragments

enzyme that produces a base-paired RNA primer (~10 nucleotides), which DNA polymerase will use to polymerize strands

DNA primase

How are Okazaki fragments synthesized and joined together?

DNA primase makes an RNA primer → DNA polymerase extends the fragment → the RNA primer is removed and replaced with DNA → DNA ligase seals the fragments together.

joins the 3’ end of the new fragment to the 5’ end of the previous one

DNA ligase

ATP hydrolysis to power mechanical work (moving in a cyclical manner to pry apart the helix). unwinds the dna double helix

dna helicase

cannot unwind the helix (like helicase) but bind single-stranded DNA to prevent hairpin structures (would be common in the lagging strand)

Single-strand binding proteins

protein that holds DNA polymerase onto DNA, increasing its processivity (ability to synthesize long stretches of DNA without detaching)

sliding clamp

A protein complex that uses ATP binding to engage and open the sliding clamp, locates the 3′ end of a primer strand, then hydrolyzes ATP to close the clamp around DNA.

clamp loader

position where the DNA helix is first opened for replication and high in A-T content

replication origin

structure formed when replication is actively taking place on both strands of the parental DNA double helix

replication bubble

Proteins that initiate DNA replication at the replication origin, acting before helicase unwinds the DNA.

initiator proteins

Initiator proteins bind to the replication origin and destabilize DNA. Two inactive helicases and their loading proteins are then recruited, forming the pre-replicative complex.

pre-replicative complex (preRC)

displaced dimers ahead of the fork

H2A-H2B

tetramers remain loosely bound, and distributed at random to daughters

H3-H4

protective dna protein complexes at the end of our chromosomes

telomeres

repeated sequences allow for easy addition of sequence to the ends by an enzyme

telomerase

What are cyclin-dependent kinases (CDKs), and how do cyclins regulate them?

CDKs are enzymes that phosphorylate target proteins to regulate cell-cycle events. Cyclins bind to CDKs and activate them by displacing an inhibitory T-loop from the active site.

What are the three main cell-cycle CDKs, and what do they regulate?

• G1/S-CDK: Required to pass the Start checkpoint.

• S-CDK: Required for chromosome duplication.

• M-CDK: Required for M phase and the metaphase-to-anaphase transition.

What are the two steps that regulate DNA replication initiation?

1. Licensing: Occurs during G1, when inactive helicases are loaded onto DNA, preparing the origin for replication.

2. Activation: S-CDKs phosphorylate initiator proteins, activating helicases and triggering DNA unwinding.

two identical copies of each chromosome

sister chromatids

ing-like structures that hold sister chromatids together, allowing proper spindle attachment and eventually cleaved so sister chromatids can separate during mitosis

cohesin

sister chromatids condense, and the spindle begins to form on the outside of the nucleus

prophase

the nuclear envelope breaks down, and sister chromatids begin to attach to the spindle

prometaphase

sister chromatids align at the equator of the mitotic spindle

metaphase

sister chromatids separate to opposite poles of the cell

anaphase

chromatids arrive at the poles and begin to decondense. The spindle disassembles, and the nuclear envelope starts to reform.

telophase

the cytoplasm is divided in two by a contractile actomyosin ring

cytokinesis

putative tyrosine kinase that was known to inhibit Cdc2

Wee1

the CDK found in fission yeast

Cdc2

use an antibody to isolate a protein of interest

immunoprecipitation

pause at one stage of the cell cycle (at high temp), then release to other stages (by shift down to lower temp)

block and release