Phys Exam 1 - Lectures 1-4

What are the 3 purines? What is their structure?

adenine, guanine, and hypoxanthine, large 2-ring base

What are the 3 pyrimidines? What is their structure?

cytosome, thymine, and uracil, smaller 1-ring base

What is the significance of the purine hypoxanthine?

found in tRNA → breakdown produces uric acid which can lead to conditions like gout

At what carbon do ribose and deoxyribose differ structurally? In what way?

C2, RNA has an OH while DNA has an H (DEoxy)

What step of the central dogma can be reversed? In what situation?

transcription can be reversed (mRNA to DNA) by retroviruses like HIV

The majority of cells lie in what checkpoint of the cell cycle? What is another word for this phase?

G0 (ex. Neurons, old cells, skeletal and cardiac muscle), senescence

What are the two phases of the cell cycle?

interphase (G1, G0, S, G2), and mitotic phase (mitosis + interphase)

What is the relevance of cell cycle checkpoints?

ensure that cell has all components to successfully continue through cycle, will undergo apoptosis if not

Of 3 billion base pairs, how many are genes?

10% (20-25,000)

Where do transcription factors bind in a gene? What sequence most commonly lies here (25% of genes)?

basal promoter region, TATA box

Where does RNA polymerase bind on a gene?

transcription start site

Regulatory regions are 1000s of base pairs away from the promoter but do what to reach it? What do they contain?

bend, enhancers + silencers

How far apart are the basal promoter region and transcription start site? Why is this relevant?

10-35 BP, RNA polymerase binds to transcription factors that are bound at the basal promoter region

What 3 steps are completed during mRNA processing?

splicing of introns, addition of 5’ guanine, addition of 3’ poly A tail

What is the function and orientation of the 5’ guanine cap?

not recognized by enzymes (protection for mRNA), tells ribosome where to start translation, extra methyl group + put on backwards

What is the function of the 3’ polyA tail and how many adenines does it contain?

protects 3’ end of the mRNA and prolongs ability to make polypeptides until tail is degraded, ~250 As

Where does translation always begin?

at the first AUG of the mRNA (start codon)

What are the large and small subunits of ribosomes in humans? What is their function?

large (60s) and small (40s), small small: binds to mRNA and reads codon to produce anticodon, large: stitches amino acids together to make polypeptide

Essential amino acids

acquired from diet

Non-essential amino acids

made from human body

Conditionally essential amino acids

a non-essential amino acid (made by body) that requires an essential amino acid to be produced

What is the significance of the urea cycle?

when proteins are broken down, they release ammonia which must be transformed into urea by the liver and excreted via the kidneys

Where are membrane and secretory proteins made and what are their 5 destinations?

the ER, can stay in the ER or go to the GA, lysosomes, plasma membrane, or be excreted

Phosphorylation (post-translational modification)

addition of a phosphate group to serine, threonine or tyrosine

Lipidation (post-translational modification)

attaches a lipid, such as a fatty acid, to a protein chain, embeds protein to membrane

Ubiquination (post-translational modification)

adds ubiquitin to a lysine residue of a target protein, marking it for destruction (usually after 4-7 Us)

Disulfide bond (post-translational modification)

covalently links the “S” atoms of two different cysteine residues

Acetylation (post-translational modification)

adds an acetyl group to the N-terminus of a protein to increase stability, addition of one C = methylation

Glycosylation (post-translational modification)

attaches a sugar, usually to an “N” or “O” atom in an amino acid side chain, protein becomes more soluble

Post-translational modifications are ___ and often change the proteins ___ and therefore ___

transient, shape, function

Function of monosaccharides

energy (ex. glucose)

Function of disaccharides

transport of monosaccharides

Function of oligosaccharides

3-14 units, used for glycosylation

Function of poly/complex saccharides

14+ units, used for storage (ex. starch or glycogen)

Why is ATP considered a high energy molecule?

the negative oxygens of the three phosphate groups repel each other

Oxidation is the __ of electrons while reduction is the ___ of electrons

loss, gain

What is the significance of the 3 NADH and 1 FADH2 made during one TCA cycle?

serve as electron carriers in the electron transport chain

How many ATP are made by NADH vs. FADH2 during the ETC? Why is there a difference?

2.5 vs. 1.5, FADH2 does not shuttle protons

NADH path during ETC

complex 1 → coenzyme Q → complex 3 → cytochrome C → complex 4 → final electron acceptor (O2)

FADH2 path during ETC

complex 2 → coenzyme Q → complex 3 → cytochrome C → complex 4 → final electron acceptor (O2)

How does cholesterol help control the fluidity of the plasma membrane?

structure is very rigid → restricts excess movement of membrane, prevents membrane from becoming too loose when it’s hot and too rigid when it is cold

What is the function of triglycerides?

fat storage and transport

Fats are broken down via beta oxidation into what molecule?

acetyl coA

Why do fats usually have an even # of carbon?

built from acetyl coA (2C) and 2C from malonyl coA

What are ketone bodies? What is the most prevalent one?

alternative energy molecules made from fat when glucose levels are low, beta-hydroxybutyrate

What is a clinical problem seen regarding ketone bodies?

DKA → body has severe lack of insulin and starts breaking down fat which floods the bloodstream with acidic ketone bodies

Fat digestion begins in the ___ where they are packaged into what type of molecule?

small intestine, chylomicrons

Chylomicrons enter the bloodstream to deliver triglycerides to what two places?

the muscle (fuel) and fat cells (storage)

The liver produces what two fat molecules? What are their functions?

VLDL delivers triglycerides to the body tissues, HDL scavenges excess cholesterol and returns it to the liver

How does VLDL become LDL?

as it floats through the capillaries, it loses triglycerides via enzymes and becomes heavier/more densely packed

What is the rate-limiting step of cholesterol synthesis that statins target?

HMG-coA reductase

What two things does cholesterol produce?

steroid hormones and vitamin D

When is arachidonic acid released in the body?

in times of stress/injury, phospholipase cuts it out of the cell membrane

What blocks phospholipase and therefore blocks arachidonic acid from being released?

steroids

The COX pathway produces ___ and is inhibited by ___, therefore decrease what type of response in the body

prostaglandins, NSAIDs, inflammatory

The 5-LOX pathway produces ___ and ___ which serve what two functions?

leukotrienes, inflammatory response and lipoxins which inhibit inflammation (anti-inflammatory)

Respiration (cell function)

converting glucose and oxygen into energy (ATP) to fuel cellular activities

Metabolism (cell function)

breaking down nutrients, synthesizing proteins, and maintaining cellular structures

Reproduction (cell function)

create new cells through processes such as mitosis or meiosis

Membrane transport (cell function)

control the movement of substances in and out of the cell and intracellularly through processes like diffusion, osmosis, and active transport

Protein synthesis (cell function)

use genetic information to produce proteins through transcription and translation, crucial for various cellular functions

DNA and RNA function (cell function)

store and utilize genetic information encoded in DNA and RNA to maintain their structure and carry out cellular processes

Communication (cell function)

through chemical signals, allowing coordination and integration of different functions within the body

Waste removal (cell function)

eliminate waste products and toxins

Response to stimuli (cell function)

respond to external and internal stimuli, adjusting behavior and activities as needed

Specialized cells express higher levels of what that allows them to carry out common tasks with extraordinary precision, efficiency or scale?

enzymes, proteins, or organelles (to what degree is this function developed?)

The intracellular fluid makes up what percentage of body water? What is located inside it? What does it do?

28L (66%), high in K+, Mg2+, and phosphate, site of metabolic activity and ion regulation

The extracellular fluid makes up what percentage of body water? What is located inside it? What is it split into?

14L (28%), high in Na+, Cl-, HCO3- and Ca2+, split into IF and plasma

What is the function of interstitial fluid and what is its makeup?

surrounds cells, low in proteins, stable environment (pH, temp, ions)

What is the function of plasma and what is its makeup?

high in proteins, circulates in blood vessels, transporting nutrients, gases, and wastes

Water molecules form __ bonds with each other to create ___

hydrogen, surface tension

How does surface tension relate to cellular organization?

mimics the behavior of hydrophilic and hydrophobic interactions, supporting the formation of micelles, lipid bilayers, and organelle membranes

How does surface tension relate to respiratory function?

contributes to the alveolar surface tension, which must be overcome during inhalation

How does surface tension relate to ocular health?

maintains a smooth, continuous tear film over the cornea, essential for clear vision and optical surface integrity

Why does molarity vary with temperature but molality does not?

molarity is based on solvent volume, which can change depending on temperature, while molality is based on solvent weight in kg

What are electrolytes?

molecules that dissociate in H2O into their cation (Na+) and anion (Cl-) equivalents

Acids are proton __ while bases are proton ___

donor, acceptors

Buffers are usually composed of what two things?

a weak acid and its conjugate base

What is the henderson-haselbach equation?

pH = pKa + log[A-]/[HA]

When is buffering capacity best, according to the henderson-hasselbach equation?

when [A-] = [HA], pH = pKa

What happens to the bicarbonate buffer if [H+] increases?

it binds to HCO3- to form CO2

What happens to the bicarbonate buffer if [OH-] increases?

it binds to H+ to form H2O

At what temperature does random thermal motion cease?

absolute zero (-272 C or -460 F)

What is Fick’s Law of diffusion? What factors increase diffusion and what decreases it?

increase in concentration gradient of the substance, increase in SA of the membrane and increase in lipid solubility all increase net diffusion, increase in molecular weight of substance and membrane thickness both decrease net diffusion

Adding a solute to water always ___ the water concentration, so water always diffuses in the direction of the __ solute concentration

decreases, higher

Hydrostatic pressure

the force exerted by fluid at rest or by expanding fluid volume

Osmotic pressure and concentration of a non-penetrating solute are related in what way?

directly proportional to each other

If osmotic (diffusive) force = hydrostatic (pressure) force, how does water move?

no net diffusion

Iso-osmotic

same osmolarity of body and intracellular fluids or the same number of particles dissolved in saline as in the intracellular (interstitial fluid) and inside cells

Electrogenic

a net loss of positive change from the cell interior due to ATPase transporting 3 Na+ out and 2K+ in to cells

The cytoplasm is composed of ___ and houses ___

water, salts, and proteins, all organelles

The number of mitochondria present in a cell depends on what?

the metabolic requirements of the cell

Proteins involved in ___ are embedded within the mitochondrial inner membrane

respiration

Function of the GA

processes membrane-packaged proteins synthesized in the RER, recycles and redistributes membranes (packaging plant)

What do lysosomes contain and what is their function?

hydrolytic enzymes, destroy and breakdown proteins into material that can be re-processed

What is made in the nucleolus?

ribosomal subunits

Chromatin is made of __ + ___ and is condensed to form what?

DNA + histones, chromosomes

The plasma membrane is predominantly comprised of __ and __ and a small amount of __

proteins, lipids, carbohydrates

3 functions of the phospholipid bilayer

1. Forms basic structure of membrane, 2. Controls what enters and exits the cell via hydrophobic interior, 3. Responsible for the fluidity of the membrane

Why is the mosaic model of the plasma membrane important?

allows membrane proteins to float freely