MCAT misc

pKa < pH

deprotonated form

pKa = pH

50/50 depro/pro

pKa > pH

protonated

distal stimuli

These are the actual physical objects or events in the environment outside of your body. Think of them as things "at a distance" (distal). Examples include a campfire, a ringing telephone, or a fresh cup of coffee

proximal stimuli

These are the physical energies that actually reach, contact, and interact directly with your sensory receptors (proximal = close by). For example, the light photons hitting your retina from that campfire, the sound waves vibrating your eardrum from the telephone, or the volatile molecules binding to your nose from the coffee

sensory ganglia

These are clusters of nerve cell bodies located outside the central nervous system (in the peripheral nervous system). They act as regional relay stations where incoming sensory neurons assemble before sending their signals up into the spinal cord or brain

projection areas

These are specific, highly specialized regions located within the cerebral cortex of the brain. They are the final destination where raw sensory data is sorted, mapped, and analyzed (e.g., the primary visual cortex or the somatosensory cortex).

photoreceptors

@retina (rods and cones)

Function: Respond to electromagnetic radiation in the visible spectrum (light photons) to enable vision

rods

Highly sensitive to low levels of light; ideal for night vision and peripheral sight, but cannot distinguish colors.

cones

Require bright light to activate; responsible for high-acuity, fine-detail vision and color perception (split into red, green, and blue sensitive types)

hair cells

@inner ear, the organ of corti and vestibular system

Act as mechanoreceptors that detect physical movement and vibration

• In the Cochlea: Sound waves cause fluid movement that bends the microscopic bristles (stereocilia) on top of the hair cells, converting mechanical vibrations into electrical signals for hearing.

• In the Vestibular System: Fluid movement bends the hair cells during movement to track acceleration, head rotation, and linear balance

Nociceptors

@most commonly skin

Function: Detect noxious stimuli—meaning any physical or chemical threat that is intense enough to cause actual or potential tissue damage. They register this raw threat data and transmit it to the brain, which perceives it as pain. They can respond to extreme mechanical trauma (cutting/crushing), thermal extremes (burning), or chemical signals released by damaged cells (like histamines and prostaglandins)

thermoreceptors

@dermis, epidermis, hypothalamus

Function: Monitor changes in temperature.

• Skin Receptors: Monitor peripheral temperature changes to tell your brain if an object you touch is hot or cold. They are split into distinct "cold receptors" (activated below room temp) and "warm receptors" (activated above room temp).

• Hypothalamic Receptors: Monitor the core temperature of your actual blood to trigger metabolic defenses like shivering or sweating to maintain homeostasis

Osomoreceptors

@hypothalamus

Function: Measure the osmolarity of the blood

• essentially tracking how concentrated or diluted your blood plasma is. If you get dehydrated, the concentration of solutes in your blood rises, causing water to physically rush out of the osmoreceptor cells via osmosis, shrinking them. This mechanical shrinkage triggers an action potential that tells your brain to release Antidiuretic Hormone (ADH / Vasopressin) to make your kidneys conserve water, while simultaneously triggering the conscious sensation of thirst

Olfactory Receptors

@olfactory epithelium (ceiling of upper nasal cavity

Function: Are chemoreceptors that detect volatile, airborne chemical compounds (odorants)

(for smell)

taste (gustatory) receptors

@inside taste buds

Function: Act as chemoreceptors that detect soluble chemical compounds dissolved in saliva. These receptors are finely tuned to categorize molecules into five distinct primary taste profiles:

• Salty & Sour: Directly open ion channels when exposed to sodium ions Na+ or hydrogen ions H+

• Sweet, Bitter, & Umami: Use complex, specialized G-protein coupled receptors to bind sugars, toxic alkaloid compounds, or savory amino acids (like glutamate) respectively

absolute threshold

the minimum need to notice the stimulus from nothing (how heavy, loud, bright does it need to be for us to detect) - varies from person to person

threshold of conscious perception

when we actually notice it

difference threshold

must be enough for us to recognize that there is a difference between things, like something and nothing. the difference between an empty hand and pencil in hand

—> how much of a change is needed before we’re able to detect it?

Weber’s Law and JND

“just noticeable difference”

depends on how much we’re already experiencing

ex: if we put a pencil in our hand vs. putting a pencil in our hand that’s already holding a book (we won’t notice the pencil really)

signal detection theory

our perception depends on the stimulus strenght AND the observer’s psychological and physical state

—> decision making process

gestalt principle(s)

rules of human perception that describe how our brains group similar elements, recognize patterns, and simplify complex images to understand the world. They propose that we perceive objects as complete "wholes" rather than a sum of their individual parts

• proximity

• similarity

• continuity

• subjective contours

• closure

the law of pragnanz

When confronted with a complex or ambiguous visual pattern, the human brain will organize it in the simplest, most stable, and most symmetrical way possible

monocular cues

For objects further away, one eye is plenty because the brain can look for environmental art tricks embedded in the scenery:

• Relative Size: If two objects are assumed to be the same size, the one that casts a smaller image on your retina is perceived as being further away.

• Interposition (Overlap): If one object physically blocks your view of another, your brain automatically organizes the blocking object as being closer.

• Linear Perspective: Parallel lines (like railroad tracks) appear to converge and meet at a single point in the distance. The tighter the lines pinch together, the further away they are.

binocular cues

When objects are close to you (within roughly 20 feet), your brain relies heavily on having two eyes positioned slightly apart:

• Retinal Disparity: Because your eyes are a few inches apart, each eye captures a slightly different image. Your brain compares these two flat images; the greater the difference between them, the closer the object must be.

• Convergence: When looking at something close to your face, your eye muscles must physically pull your eyes inward (cross-eyed). Your brain tracks this muscle tension to calculate exactly how close the object is.

amarcrine cell

Amacrine cells run sideways, but they are located further down the assembly line, right where the bipolar cells connect to the final ganglion cells.

• Direction of Data: Horizontal and Temporal. They connect adjacent bipolar cells and ganglion cells together sideways.

• Primary Function: They act as specialized filters that process complex, dynamic adjustments to your vision, particularly motion detection and changes in illumination.

• How They Work: While horizontal cells handle static contrast (edges), amacrine cells are fine-tuned to notice changes over time. They help your brain register when an object physically moves across your field of view, or adjust your eyes' sensitivity when you suddenly step out of a dark theater into bright sunlight.

bipolar cells

Bipolar cells are the main forward-transmission lines of the retina. They bridge the gap between the outer retina (where light is captured) and the inner retina (where data is sent to the brain).

• Direction of Data: Vertical. They take information directly forward from the photoreceptors (rods and cones) and hand it straight down to the ganglion cells.

• Primary Function: They act as the primary collectors of raw visual data. They are specialized to detect simple contrast and establish receptive fields.

• How They Work: They come in two major varieties to help you see boundaries:

  • On-center bipolar cells: Fire rapidly when light hits the exact center of their mini-receptive field.

  • Off-center bipolar cells: Fire rapidly when the center of their field becomes dark.

horizontal cells

Horizontal cells get their name because they run entirely sideways, perpendicular to the main flow of information. They are located at the border where photoreceptors meet bipolar cells.

• Direction of Data: Horizontal (Lateral). They connect adjacent photoreceptors together sideways.

• Primary Function: They are responsible for a critical phenomenon called lateral inhibition, which sharpens visual contrast and accentuates edges.

• How They Work: When a specific photoreceptor is highly stimulated by a bright patch of light, the horizontal cells will sweep sideways and aggressively suppress/inhibit all the surrounding, neighboring photoreceptors. By muting the neighbors, the bright spot looks much sharper and more distinct to your brain. This is exactly how your eyes can easily spot crisp borders, like a black letter typed onto a white page.

feature detection

look for the color, its form, and motion

parvocellular cells

parvo pathway has really high spatial resolution, but poor temporal resolution (motion). it figures out the boundaries and details of stationary objects and its color

magnocellular cells

allows us to encode motion: has high temporal resolution and poor spatial resolution

5 types of tactile receptors

Meissner’s Corpuscles, Pacinian Corpuscles, Merkel Cells, Ruffini Endings, Free Nerve endings

MPMRF (miss piggy makes real food)

messinner’s corpuscles

@shallow skin (dermal papillae)

Light touch, flutter, and low-frequency vibrations.

Pacinian corpuscles

@deep skin (deep dermis)

Deep pressure and fast, high-frequency vibrations

Merkel cells (discs)

@Shallow skin (epidermal/dermal border)

Continuous, deep static pressure and fine texture discrimination

Ruffini endings

@Deep skin (dermis)

Skin stretch and continuous sustained pressure

free nerve endings

@Throughout epidermis and tissues

Direct chemical, thermal, or mechanical damage (pain/temperature)

two point threshold

The minimum physical distance required between two separate points touching the skin for a person to perceive them as two distinct inputs rather than a single touch.

• This threshold is microscopic on highly sensitive areas like your fingertips (around 2mm) but massive on less sensitive areas like your upper back (around 40mm)

physiological zero

The baseline temperature of the human skin (normally around $33^\circ\text{C}$ or $91^\circ\text{F}$). Objects that match this temperature feel neither hot nor cold. An object feels "cold" only because it steals heat to drop your skin below physiological zero, and feels "hot" because it forces your skin temperature above it

gate theory of pain

A neurological model stating that non-painful sensory inputs (like deep pressure or vibration) can physically close a neural "gate" in the spinal cord, blocking real pain signals from traveling up to the brain

kinesthetic sense / propreception

sensory input that occurs within the body

the “sixth” sense, because the receptors unconsciously tell your brain where your body parts are

• constant sensory feedback

• @joints, tendons, and muscles

collagen

Extracellular, connective tissues: tendons, ligaments, cartilage, bones, skin, teeth

High tensile strength; resists pulling forces. Fibrous - L handed helix (no H bonds in it) → triple “super” helix (Gly) which has H bonds between helices

elastin

Extracellular; lungs, skin, blood vessels

High elasticity; allows stretching and recoiling.

keratins

Intracellular / Epithelial; epidermal tissue - hair, wool, skin, horns, nails

Mechanical armor; protects cells from mechanical tearing.  Fiborous: Alpha helix has H bonds, 2 combine → “coiled” coil with disulfide bonds due to Cys content

actin

Intracellular. Cytokinesis, inside muscle tissues to form thin filaments of the sarcomere

Dynamic movement; muscle contraction and cell pinching.  Globular; double R-helical linear chains (microfilaments)

tubulin

Intracellular; cytoplasm (builds spindle apparatus during mitosis)

Cellular highways; vesicle transport and chromosome splitting. Maintains cell shape Alpha + beta tubulin linked as a dimer → microtubule: hollow cylinder

myosin

walks on Actin (Microfilaments)

Plus (+) End

Sarcomere contraction, power stroke, ATP-driven pulling

kinesins

Tubulin (Microtubules)

Plus (+) End

Anterograde transport, secretory vesicles, moving away from MTOC

dyneins

Tubulin (Microtubules)

Minus (-) End

Retrograde transport, recycling waste, powering cilia and flagella motility

cadherins

Cell-to-Cell

Identical proteins on adjacent cells (Homophilic)

Yes, Ca2+ dependent

Holding epithelial sheets together; structural junctions (desmosomes).

integrins

Cell-to-Matrix

ECM proteins (Collagen, Fibronectin)

Not calcium dep

Cellular signaling, cell survival, cell crawling, and matrix anchoring.

selectins

Cell-to-Carbohydrate

Sugars / Glycoproteins on other cells

Yes is calcium dep

Inflammatory response; slowing down leukocytes via white blood cell rolling.

apoenzyme

The naked, purely protein portion of the enzyme. An apoenzyme is completely inactive because it lacks its necessary helper component

holoenzyme

The fully assembled, biologically active enzyme system. It is the complete unit consisting of the apoenzyme joined together with its required cofactor or coenzyme (Apoenzyme + Helper = Holoenzyme)

prosthetic group

A specific subcategory of helper. This is a cofactor or coenzyme that is bound extremely tightly or covalently to the enzyme's structure. Unlike other helpers that drift in and out, a prosthetic group never leaves; it is a permanent structural fixture of that enzyme.

glycosylation

The covalent attachment of carbohydrate chains (oligosaccharides or sugars) to specific amino acid side chains on a protein

• It ensures proper protein folding, prevents the enzyme from being prematurely digested by proteases, and serves as an address tag targeting the enzyme to its proper home (like the lysosome or cell membrane).

heterochromatin

tightly wound, packed nucleosomes

—> less accessible to polymerases

euchromatin

unwound nucleosomes —> can be transcribed and replicated

DNA replisome

• topoisomerase

• DNA helicase

• SSB proteins (single-stranded DNA binding)

• DNA primase

• DNA polymerase III

• the sliding clamp and clamp loader

• DNA polymerase I

• DNA ligase

mismatch repair

a specialized post-replication repair system that scans the newly synthesized genome to detect and correct single base-base mismatches (like an accidental G-T pairing) and small insertion/deletion loops that managed to slip past the real-time proofreading "backspace" activity of DNA polymerase

—> S phase of cell cycle (might extend to G2)

nucleotide excision repair (NER)

used to fix bulky, helix-distorting lesions

endonucleases

a cutting enzyme that breaks internal phosphodiester bonds within a continuous DNA strand

*This sets them apart from exonucleases, which can only chew away nucleotides one by one starting from an exposed outer edge or end ($3'$ or $5'$) of a strand

nucleotide excision repair steps

• Damage Recognition: Specific surveillance proteins (like XPC or UV-DDB in eukaryotes) constantly patrol the genome, recognizing the physical structural bulge or distortion caused by the bulky lesion.

• Dual Incision: An endonuclease complex tracks to the site and makes two distinct cuts on the damaged strand—one upstream and one downstream of the mutation.

• Excision (Removal): The damaged single-stranded oligonucleotide fragment (typically 24 to 32 nucleotides long in humans) is peeled away and discarded.

• Resynthesis: DNA polymerase docks into the freshly cleared gap and uses the intact, opposite strand as a template to rewrite the missing sequence.

• Ligation: DNA ligase seals the final nick in the sugar-phosphate backbone, completing the repair.

base excision repair and steps

to fix small, non-bulky lesions that do not distort the shape of the DNA helix. These are single-base alterations usually caused by routine cellular metabolism, oxidation, or aging

Shine-Dalgarno Sequence

A specific, purine-rich RNA sequence (typically reading 5'-AGGAGGU-3') found exclusively on prokaryotic mRNA strands. It sits about 8 nucleotides upstream (just before) the code's starting line

4 major types of postranslational modifications

phosphorylation, glycosylation, ubiquitination, proteolytic cleavage

glycosylation

This modification involves the covalent addition of complex carbohydrate chains (oligosaccharides) to the protein. This typically occurs in the endoplasmic reticulum and Golgi apparatus, attaching sugars to either nitrogen atoms (N-linked) or oxygen atoms (O-linked) on the amino acids. Glycosylation significantly affects the protein's stability, solubility, and how it physically interacts with cell-surface receptors.

ubiquitination

This process involves the covalent addition of a small, 76-amino-acid regulatory protein called ubiquitin to a target protein's lysine residues. Attaching a single ubiquitin can alter the protein's cellular location or function. However, when a chain of multiple ubiquitin molecules is linked together (polyubiquitination), it acts as a molecular "death tag," marking the protein for destruction by the cell's disposal unit, the proteasome.

proteolytic cleavage

it involves the deliberate cleavage of peptide bonds to cut pieces away from the protein. Many proteins are originally synthesized in an inactive, elongated form (known as a zymogen or proprotein). Specific enzymes must perform a precise cleavage to cut away an inhibitory segment of the chain, allowing the remaining pieces to snap into the correct, biologically active protein structure (a classic example is the cleavage of proinsulin to form active insulin).

point mutation

result from 1 or small number of base changes

silent mutations

don’t change the amino acid seq, just have redunancy in code

—> no change in phenotype, neutral effect on fitness

missense mutations

change an amino acid in the protein [specifies a completely diff AA] which changes the primary structure of the protein which could be beneficial, neutral or deleterious

nonsense mutations

changes a codon that specifices an amino acid into a stop codon

—> leads to non fxning mRNA or protein (makes useless and short stretch of protein)

usually deleterious

frameshift mutations

shift the reading frame which alters the meaning of all subsequent codons

transcription factors

specialized proteins that control gene expression

Zone of Proximal Development (ZPD)

• The ZPD is the cognitive sweet spot of learning. It represents the range of tasks that are too difficult for a child to master alone, but can be accomplished with the guidance and encouragement of a More Knowledgeable Other (MKO), such as a teacher, parent, or more advanced peer.

• As the child gains proficiency with the help of structural support (scaffolding), the MKO gradually fades into the background, leaving the child with an expanded zone of independent ability.

stages of sleep and waves

alert: beta waves (high freq, low amp)

relaxed wakefulness: alpha

stage N1: theta

stage N2: theta waves + sleep spindles & K-complexes

stage N3: delta waves (low freq, high amp)

REM: rapid/irregular waves resembling awake beta/theta waves

SupraChiasmatic Nucleus (SCN)

Located within the hypothalamus, the SCN acts as the master pacemaker of the body

pineal gland

Receives inhibitory signals from the SCN when light is present and stimulatory signals when light fades —> melatonin

adrenal cortex

Releases steroid hormones that fluctuate throughout the day to modulate systemic alertness —> cortisol

dyssomnia

Disorders that make it difficult to fall asleep, stay asleep, or maintain normal sleep timing (issues with the quantity, quality, or timing of sleep)

• insomnia

• sleep apnea

• narcolepsy

parasomnia

Disorders characterized by abnormal, disruptive behaviors, movements, or perceptions that occur during sleep or during transitions between sleep stages.

• Sleep Stage Vulnerability: Most parasomnias (like night terrors and sleepwalking) occur during Stage N3 (Slow-Wave Sleep), whereas dreaming-related disorders occur in REM

piaget’s stages of cognitive development

1. sensorimotor stage

2. preoperational stage

3. concrete operational stage

4. formal operational stage

Fluid Intelligence

The raw capacity to reason quickly, think abstractly, and solve novel problems independent of acquired knowledge. This naturally declines steadily throughout late adulthood.

crystallized intelligence

The accumulation of knowledge, vocabulary, facts, and verbal skills gathered over a lifetime. This remains stable or increases with age

heuristics

mental shortcuts ("rules of thumb") used to make quick choices. They are efficient but prone to errors.

Availability Heuristic

Estimating the likelihood or frequency of an event based entirely on how easily examples of it can be recalled from memory.

• Example: Fearing a shark attack more than a car accident because shark attacks dominate dramatic news headlines.

representative heuristic

Categorizing or estimating the likelihood of something based on how closely it matches a pre-existing internal prototype or stereotype.

Base Rate Fallacy

The error made when an individual ignores statistical, numerical baseline data ("base rates") in favor of descriptive, stereotypic anecdotal details.

Disconfirmation Principle

The scientific standard stating that when potential evidence fails to support a hypothesis, that hypothesis should be discarded or revised. Human biases frequently violate this principle.

Belief Perseverance

The psychological phenomenon where an individual stubbornly maintains their core belief even after receiving direct, undeniable empirical proof that completely refutes it.

phonology

The actual sounds of language (speech sounds called phonemes). Learning to isolate these from ambient environmental noise is categorical perception.

morphology

The structural composition of words. Words are built from structural units of meaning called morphemes (e.g., "redesigned" contains three morphemes: re-, design, and -ed).

semantics

The literal meaning associated with words or sentences.

syntax

The grammatical structural rules governing how words are sequenced to construct meaningful, valid sentences.

pragmatics

The functional, contextual application of language. Adjusting delivery style, tone, and vocabulary based on social context and audience (e.g., speaking formally to a professor vs. casually to a friend).

Whorfian (Linguistic Relativity) Hypothesis

language shapes and dictates the boundaries of human cognition. Rather than language simply labeling pre-existing thoughts, the specific grammatical structure and vocabulary of an individual’s native language directly determine how they perceive, categorize, and think about reality.