Mile Marker 1 Exam

cell signaling pathway

reception, transduction, response

cell cycle phases

• Gap 1 (G1)

• S-phase

• Gap 2 (G2)

• Mitosis (M)

G1 Phase of cell cycle

preparation for DNA synthesis

(first phase of cell cycle)

→ cell metabolically active; duplicates, organelles, and cytosolic components

→ starts replicating centrosomes

8-10 hours

S phase of cell cycle

DNA synthesis

→ DNA is replicated

6-8 hours

G2 phase of cell cycle

Preparation for mitosis

→ cell growth continues

→ enzymes and other proteins are synthesized and replication of centrosomes is completes

4-6 hours

Mitotic phase of cell cycle

CELL DIVISION

1. Prophase

2. Metaphase

3. Anaphase

4. Telophase

"PMAT"

mitogens are

chemical messengers that signal a cell to cycle

cyclin-dependent kinases (CDKs)

drivers of progression through the cell cycle

Paired with cyclins

→ paired to facilitate appropriate transit through eukaryotic cell division (quality control)

How do prokaryotic cells divide?

binary fission

Where are the checkpoints in the cell cycle?

G1, G2, M

kinases are enzymes that

phosphorylate proteins

what ends a cell signaling cascade?

- removal of mitogen (induces cell cycle or division)

- inactivation of a kinase

each strand of ds-DNA molecules are joined by

hydrogen bonds

Central dogma

DNA -> RNA -> Protein

where is DNA in viruses

genomic material is within the viral core

DNA in prokaryotes (bacteria) vs. eukaryotes is located

prokaryotes: not compartmentalized from the rest of the cells

eukaryotes: within nuclear membrane

nucleotides are composed of

phosphate, sugar, base

→ sugar is a deoxyribose in DNA vs ribose in RNA

purines

Adenine and Guanine

Pyridines

cytosine, thymine, uracil

→ Uracil (U) instead of thymine (T) in RNA

base pairing

base pairs stabilized by 2-3 H-bonds

→ A-T = 2 bonds

→ G-C = 3 bonds

- allows one strand to serve as the template for a complementary strand when copied

what is the most common configuration of DNA

right-handed helix in B form

RNA can exist as

- mRNA (codes for protein)

- tRNA (carries AA to ribosomes)

- rRNA (component of ribosome)

what viruses use RNA as genome

- HIV

- Poliovirus

- Rabies Virus

must invade cell in order to replicate genome

still flows from DNA → RNA → proteins

→ RNA of virus is reverse transcribed to DNA from which mRNA and proteins are made

OriC

origin of replication

A-T rich

DNA polymerase synthesizes from

5' to 3'

DNA gyrase

Topoisomerase II

→ relaxes supercoiling ahead of the replication fork

antibiotics can inhibit!

→ novobiocin blocks binding of ATP to gyrase

** EUKARYOTES DO NOT HAVE DNA GYRASE**

what is the major replicative enzyme

Pol III

(prokaryotic DNA polymerase)

steps of synthesis of new DNA strand

1. DNA polymerase find the RNA primer 3'OH

2. matches the incoming base pairs with complementary base

3. forms ester bond

4. Pyrophosphate (Pi-Pi) is released providing energy for polymerization

Where are Okazaki fragments found?

lagging strand

What are the ends of eukaryotic chromosomes called?

telomeres

telomerase

enzyme responsible for synthesis of DNA ends

→ ribonucleoprotein composed of 2 subunits

5-FU

utilized as anti-cancer agent

- pyrimidine base

- can be converted to 5F-dUMP upon entry into cell → inactivates thymidine synthetase (TS) → dTTP leading to inhibition of DNA synthesis

helicase

unwinds DNA

(melts hydrogen bonds)

what are the types of mutations that occur in DNA

- Substitution

- deletion

- insertion

substitution mutations

1. Transition - substitution of a purine for a purine or pyrimidine for pyrimidine

2. Transversion - replacement of purine by pyrimidine or vice versa

what are the 4 main DNA repair mechanisms

- Base excision repair

- nucleotide excision repair

- mismatch repair

- direct repair (during transcription - photochemical cleavage of pyrimidine dimers)

recombination is the process by which

alleles observed at a specific location (loci) in parental chromosomes are shuffled in the offspring

→ leads to genetic variation associated with a specific loci when the information found there is shuffled

the exchange of DNA segments in a single cell

what are the 2 types of recombination

1. non-homologous - transposons or translocations

2. crossing-over (homologous) - during meiosis and lymphocyte differentiation to produce single antibody

Transcription

copying RNA from DNA template

(synthesis of RNA)

what are the 3 steps of transcription

1. Initiation

2. Elongation

3. Termination

TATA box

promotor region in eukaryotes recognized by TBP

→ determines start point

transcription factors

proteins that facilitate binding of RNA polymerase II to begin synthesis of mRNA

mRNA is produced in

nucleus

proteins are synthesized from

mRNA in cytoplasm

rho-protein assists in

termination of RNA synthesis in prokaryotes

translation

synthesis of proteins

1. activation

2. initiation

3. elongation - binding of aminoacyl-tRNA to A site

4. termination

How many amino acids are there?

20

What is the 1 start codon?

AUG

What are the 3 termination codons?

UGA

UAG

UAA

point mutations

silent, missense, nonsense

only one base is altered

types of mutations in translation

- point mutations

- frameshift mutations

wobble hypothesis

variation can occur at the third base of codon

- 5' base of anticodon is often modified in tRNA-hypoxantine (I)

amino acids form

proteins

nucleosides form

nucleic acids

fatty acids and sterols form

lipids

saccharides form

carbohydrates

what are the most common secondary structures

alpha helix and beta sheet

protein folding depends on

1. primary sequence

2. Chaperonins (heat shock proteins)

3. environment

catalytic mechanisms of enzymes

1. acid-base catalysis

2. covalent catalysis

3. metal ion catalysis

4. proximity and orientation effects

pH < pKa

protonated form

pH > pKa

deprotonated

electron donating groups direct

ortho/para

electron withdrawing groups direct

meta

what type of bond is strongest in drug-target interactions

ionic bond

auxacophore

non-essential portion of a drug molecule that supports the pharmacophore and so modulates the pharmacokinetics and selectivity of a drug

what is the major route of transport across membranes utilized by drug molecules

passive diffusion

CYP enzymes require what type of cofactor

heme

amino acids consists of what 5 components

1. Central Carbon atom

2. Hydrogen

3. Carboxylic acid group (COOH) - weak acid

4. Amino group (NH2) - weak base

5. Side chain (R) - side chain differs between the AA's

what conformation of AA are used to make proteins

only L-amino acids are used to make proteins

non-polar (hydrophobic) AA's have a

carbon side chain

glycine, alanine, proline, valine, leucine, isoleucine

polar (hydrophilic) AA have a

polar, uncharged side chain (OH or NH2)

asparagine, glutamine, serine, threonine

aromatic AA have a

carbon ring with double bonds

phenylalanine, tyrosine, tryptophan

acidic amino acids (negative)

aspartate, glutamate

often involve pi-pi stacking

- primarily hydrophobic interactions

basic amino acids (positive)

arginine, lysine, histidine

what forces stabilize protein structure? (essential for driving high order structures)

- hydrogen bonding

- hydrophobic effects

- electrostatic interactions

- disulfide bonds (covalent)

- van der Waals forces

enzymes

catalysts, thus increasing rate of reactions, but do NOT affect the equilibrium of a reaction

not permanently modified - return to same state as before the reaction

hydrophobic environment effect on acid and base pKa

acids - INCREASE pKa

bases - DECREASES pKa

Km

subtract concentration at which the reaction velocity is half maximal

- a measure of dissociation constant for substrate

Kcat

Turnover number

(Vmax)/[Et]

Kcat/Km

measure of catalytic efficiency, the second order rate constant

the most efficient enzymes have rates limited by diffusion

reversible inhibitors

non covalent binding to enzyme and dissociation occurs at a significant rate

- does NOT react - only decreases enzyme activity

3 types:

1. competitive inhibition

2. non-competitive inhibition

3. uncompetitive inhibition

competitive inhibitors

bind to the substrate recognition site (active site) thus preventing substrate binding

- usually structural analogs of substrate

- raise the concentration of substrate necessary to reach saturation

non competitive inhibition

binding of a substrate of interstate's is not affected by inhibitor - a remote binding site

- inhibitor lowers the concentration of active enzyme (lowers apparent Vmax)

drugs that act on endogenous ligands affect

synthesis, storage, release, transport, degradation, or metabolism

includes Neurotransmitters, hormones, cytokines, and other intercellular mediators

drugs that act on extracellular process can cause

coagulation, thrombosis, inflammation, and immune responses

GPCR second messenger systems

→ cAMP-dependent protein kinase A (PKA)

→ Exchange protein activated by cAMP (EPAC)

→ cGMP-dependent PKG: activated by intracellular cGMP

→ phosphodiesterase: hydrolyze cAMP and cGMP

→ PLC-DAG/IP3-Ca2+ pathways: activates PKC and releases stored calcium

tyrosine kinase receptors

receptors for hormones (insulin) and growth factors

- binding of ligand induces receptor dimerization and cross-phosphorylation

Toll-like receptors (TLRs) initiate signaling of the

innate immune system

→ activation produces inflammatory responses to the pathogenic microorganisms

SNS activation

prepares the body for an integrated response to a disruption in homeostasis ("fight or flight")

PNS activation

conservation of energy and maintenance of organ function during times of minimal activity ("rest and digest")

sympathomimetic drugs

- block NE reuptake transporters

- increase presynaptic release of NE

- decrease the rate of catabolism of NE

catabolism

breaking down

- degradation of nutrients and cell constituents

anabolism

building up

- biosynthesis of biomolecules from simpler compounds

what is the body greatest energy reservoir

adipose tissue

85% of triglycerides stored here

(protein in muscles; glycogen in liver and muscles)

what makes a molecule more caloric (more energy)

- more carbons, less oxygens

- more reduced (more hydrogens)

what makes a molecules less caloric (less energy)

less carbons, more oxygen

dietary fuels (carbohydrates, lipids, proteins) are all broken down into

acetyl CoA → source of the TCA cycle (catabolic cycle of our metabolism)

the energy of ATP is stored in

terminal phosphate bonds

TCA cycle (citric acid cycle/Krebs cycle)

consists of 8 reactions: 5 of them are energy-providing key reaction, the others support these reactions

takes place in mitochondria (does not require O2 directly)

provides 12 ATP-equivalents of energy per acetyl-CoA

3 NADH/H+ = 9 ATP

1 FADH2 = 2 ATP

1 GTP = 1 ATP

what are the inhibitors of TCA cycle

NADH, acetyl Co-A, citrate, ATP, and succinyl-CoA