3 Flashcards
Why are there 2 phases of the Pentose Phosphate Pathway if the oxidative phase produces both NADPH and ribose 5-phosphate?
Some cells don’t need both of these products, only one
- ex. Liver cells and adipocytes need lots of NADPH but not ribose 5-phosphate, not constantly replicating their DNA
Oxidative phase produces a set ratio
Ribulose 5-phosphate gets shunted into non oxidative phase
Non-oxidative phase of the Pentose Phosphate Pathway
Recylces Ribulose 5-phosphate back to the oxidative phase (into G6P)
- Begins with 6 molecules of Ribose-5-phosphate
- Get converted into 5 molecules of Ribose 6-phosphate
- Easily converted to glucose 6-phosphate
Also produces glyceraldehyde 3-phosphate which can enter glycolysis
Diabetes Mellitus
Metabolic disorder marked by improper glucose uptake by cells and high blood glucose levels
- can lead to CVD, sudden weight loss, chronic kidney disease, impaired eyesight
- 30 million+ americans (10% of population)
Body fails to produce insulin (reuptake of blood glucose into cells)
Role of Insulin
What is insulin produced by and where?
What kind of hormone?
Peptide hormone that causes reuptake of glucose into cells from bloodstream
- Produced by Beta cells in the pancreas
- released into bloodstream when glucose levels are high, tells cells to absorb it
How does pancreatic insulin release work?
Where is insulin stored?
Glucose enters pancreatic beta cells through special transporter protein called GLUT2
- once inside, glucose proceeds through glycolysis and pyruvate products enter citric acid cycle
- causes ATP:ADP ratio to increase
High ATP levels cause an ATP-sensitive potassium channels to slam shut, building up potassium in cell
- reduces electric potential difference across cell membrane, causing voltage gated calcium channels to open allowing Ca in the cell
Causes Endoplasmic Reticulum to open its own calcium channels releasing more Ca ions into cytoplasm
- insulin is stored in vesicles in the plasma membrane
- Once cytoplasmic calcium reaches a certain level, vesicles fuse with plasma membrane and release
Insulin release from pancreatic B cell summary
Glucose is used to produce ATP
Causes a potassium buildup that triggers an influx of Calcium
Calcium is the stimulus for insulin release from secretory vesicles
What is calcium used for
Pancreatic insulin release, muscle contraction
Stimulants of insulin release
(Don’t need to know)
- High blood glucose levels
- Acetylcholine: main neurotransmitter of parasympathetic NS
- Arginine and Leucine amino acids
- Pancreatic beta cells stimulated by digestive enzyme cholecystokinin
Inhibition of Insulin release
Norepinephrine- stress hormone inhibits insulin, FIGHT OR FLIGHT
- increases blood glucose levels
Insulin responsive tissues
Do all cells need insulin to get glucose? which don’t?
Body cells that express receptors for insulin that insulin can interact with
- Skeletal, cardiac muscle and fat cells
Insulin binds to receptors, activating GLUT4 transporters which fuse with membrane allowing glucose to move into the cell
**NOT all cells depend on insulin to get glucose
- Liver and brain cells require so much that they get it themselves from the bloodstream
Different effects of insulin in the body
Glucose uptake
Glycogen metabolism
Lipid metabolism
Protein metabolism

Insulin affect on glycogen metabolism
- Upregulates glycogen synthesis in liver
- Inhibits glycogenolysis and gluconeogenesis
Insulin affect on lipid metabolism
- Promotes lipid storage by increasing triglyceride synthesis
- tells adipocytes to absorb more fatty acids from lipoproteins circulating in the blood
- links them with glycerol
- Opposes breakdown of triglycerides into fatty acid components by downregulating lipolysis
Insulin affect on protein metabolism
- Insulin prevents proteolysis
- Insulin absorbs amino acids to build new proteins
Stimulates protein synthesis
Type 1 Diabetes
How is it triggered?
What is the correction
Immune system destroys pancreatic Beta cells
- body can’t produce any insulin or to a lesser extent
Genetic risk factors, onset also triggered by environmental factors
**Require synthetic insulin to survive
Type 2 Diabetes
Body loses the ability to respond to insulin
-
insulin resistance
- Blood glucose levels too high
Brought on by lifestyle factors: obesity, stress, poor diet, lack of exercise
Can often recover in early stages with lifestyle changes, but may eventually need synthetic insulin as well
Role of Glucagon
Opposite of insulin
- Peptide hormone synthesized in pancreas by ALPHA CELLS
Secreted when too little glucose in blood –> actually respond to low insulin levels
- high insulin levels inhibit glucagon production + release
Binds to glucagon receptors; increases blood glucose conc
Affect of Glucagon on Glycogen metabolism
Promotes glycogenolysis and gluconeogenosis
Inhibits glycogenesis
Effect of Glucagon on lipid metabolism
Glucagon promotes lipolysis: triglyceride breakdown
- activates protein kinase A which activates hormone sensitive lipases in adipose tissue
Increases fatty acid conc in blood
- glycerol can also be used for energy in liver and kidneys
Effect of glucagon on protein metabolism
Inhibits protein synthesis and allows proteins to be broken down
- amino acids can be taken up by liver cells for new glucose molecules via gluconeogenesis
More stable nucleotide pairing? Why?
Cytosine and guanine, 3 H-bonds instead of 2
Nucleotides are joined by
Phosphodiester bonds
Sugar phosphate backbone
Is RNA or DNA more stable and why
RNA is less stable, only one strand and OH groups causes instability
- exception: RNA hairpin loops, double stranded RNA viruses
What is “Melting temp Tm” of DNA
Temp that 50% of strands are denatured, DNA with more G-C bonds have higher Tm
- use heat or chemical (like urea)
Annealing
Reverse of denaturing DNA where complementary bases bond again
DNA has grooves: major and minor
Binding sites for transcription factors

B-DNA
A-DNA
Z-DNA
B-DNA: most common conformation discovered by Watson and Crick; 10.5 base pairs per double helix turn
A-DNA: tighter, more condensed
Z-DNA: left handed, less condensed
Central Dogma
DNA ==> transcription ==> RNA ==> translation ==> protein
Alfred Hershey and Martha Chase
DNA is source of heritable info
- Viruses incubated with radioactive sulfur (protein) and phophorus (DNA)
- DNA was passed onto bacteria
Messenger RNA mRNA
Template to synthesize protein
Heterogenous Nuclear RNA (hnRNA)
Precursor to mRNA
Transfer RNA (tRNA)
Transfers amino acids to growing polypeptide chain
- unique clover leaf structure
- recognizes specific codons on mRNA to incorporate amino acids they code for into the protein
Ribosomal rRNA
Synthesized in nucleolus, essential role in translation
- some act as ribozymes (enzymes)
small interfering RNA (siRNA) and miRNA inhibit
Gene expression (production of proteins)
Reverse transcriptase enzyme
Transcribes RNA into DNA
- helps viruses propagate
20 amino acids created from 4 bases is possible due to
Reading aminos in groups of 3: codons
- 43 = 64 codons
Degenerate genetic code
More than 1 codon can encode 1 amino acid
Start codon
Stop codon
AUG (Met)
UAA, UAG, UGA
Wobble hypothesis
First two codons usually conserved, 3rd has wobble room
Conservative DNA replication (theory)
DNA molecule duplicated, orginal molecule conserved
Semiconservative DNA replication (true)
DNA strand separates and each strand serves as template for new
Dispersive DNA replication (theory)
DNA backbone broken and new molecule has sections of old and new (Double strand)
Meselson-Stahl Experiment (to discover how DNA is replicated)
- E. coli grown in media with 15N isotope
- DNA moved into media with 14N and allowed to replicate
- DNA extracted and centrifuged (15N heavier); new molecules had intermediate density
* could be dispersive or semiconservative - DNA extracted again after more replication, centrifuged and intermediate as well as 14N bands appeared
* rules out dispersive, = semiconservative
Prokaryote DNA replication
One origin of replication; sequence recognized by prereplication complex
- Replication proceed in both directions along chromosome
Steps of Eukaryote DNA replication
S PHASE OF CELL CYCLE
- Multiple origins of replication
- Replication produces identical sister chromatid connected to DNA molecule at centromere of chromosome
- Unwinding of double helix by helicase enzyme at replication fork
- single stranded DNA binding proteins prevent separated strands from rejoining
- Topoisomerase enzyme (DNA gyrase) relieves supercoiling caused by helicase by making incisions in one of the strands, uncoiling and rejoining
- Primase initiates DNA replication by synthesizing short RNA primer; RNA primer has free 3’ hydroxyl group used as starting point for synthesis of new strand
-
Okazaki fragments on lagging strand
- Ligase bridges gap between fragments
-
DNA polymerase: travels along separated strand and adds nucleotides in 5’ –> 3’ direction
* reads DNA 3’ to 5’
Prokaryotic DNA polymerase
DNA pol I: removes RNA primer, replaces primer with DNA, repairs DNA
DNA pol II: repairs DNA
DNA pol III: synthesizes new DNA and proofreads DNA via 3’ to 5’ exonuclease activity
Eukaryotic DNA polymerase
DNA pol α: initiates DNA synthesis
DNA pol δ: synthesizes new DNA and replaces RNA primer with DNA
DNA pol ε: extends leading strand and repairs DNA
DNA pol β: repairs DNA
DNA pol γ: replicates mitochondrial DNA
Telomerase
Extends telomeres; RNA dependent DNA polymerase
- repetitive sequences at ends of eukaryotic chromosomes
- otherwise ends would get shorter and shorter –> aging
Germ cells, stem cells, and cancer cells have telomerase
How many chromosomes?
Autosomes are?
23 linear pairs, 46 individual
22 autosomes: homologous pairs, 22 inherited maternally and matching 22 inherited paternally
23rd is XY sex chromosomes
How is DNA packaged?
Nucelosome: Basic subunit of DNA packaging; 200 bp wrapped around histone proteins
- histones further condensed into chromatin fiber
Chromatin further condensed into loop domains and then chromosomes
Chromsome structure
P arm (petite), Q arm and then centromere connecting sister chromatids
Heterochromatin vs Euchromatin
Heterochromatin: tightly coiled, dense form; hard to access DNA
Euchromatin: loose, spaghetti like configuration
- allows DNA to be readily replicated and transcribed
Chromatin configuration has to do with
Acetylation of chromatin (what enzyme?)
Chromatin configuration has to do with CHARGED attraction between DNA and histone proteins
- DNA phosphate groups negative, histone proteins positive at histone tails
Interaction is regulation by enzymes that add/remove acetyl groups from (+) charged lysine at the end of histone tailed
-
Acetylation: masks histone tails positive charge - promotes looser confirmation = euchromatin
- histone acetyltransferase
Histone deactelyase to go back to heterochromatin
98.8% of gene is noncoding
How do we produce 2 million unique proteins?
44% transposons, 24% introns and regulatory sequences, 15% noncoding DNA, 15% repetitive DNA
Alternative splicing, transcriptional and posttranscriptional modifications
Variable number tandem repeats (VNTRs) and short tandem repeats (STRs)
of repeats of sequences in DNA varies in people, used for DNA fingerprinting
Single nucleotide polymorphism
Differences in one nucleotide at a specific location between different people
Transposons
Class I and Class II
50% of genome; “jumping genes” sequences can jump to other parts of genome
-
Class I (copy and paste): DNA sequences transcribed to RNA then code reverse transcriptase enzyme
- uses RNA template to make DNA copy and inserts itself somewhere else in genome
- Class II (cut and paste): enzyme splices sequence from DNA and it moves elsewhere
Thought to increase genetic diversity and evolution
Centromeres
Contain blocks of repetitive DNA sequences rich in GC base pairs, tightly packed to maintain structural integrity
Cell Cycle
M phase
M/spindle checkpoint
Mitosis or meiosis, cell division
- spindle checkpoint: chromosomes attached to microtubule fibers
DNA is packaged as heterochromatin

Cell Cycle
Interphase (G1, S, G2)
90% of cycle, cell growth, organelle duplication, protein synthesis, DNA replication
DNA is packaged as euchromatin so proteins can be produced and allow transcription/translation
-
G1 phase: cell grows, protein synthesized
-
G1 checkpoint: Resting phase during G1 phase, can last indefinitely
- if not enough nutrients during G1 checkpoint
- Neurons, nonmitotic cells
-
G1 checkpoint: Resting phase during G1 phase, can last indefinitely
- S phase: DNA replication, # of chromosomes remains the same
-
G2 phase: more growth
- G2 checkpoint: DNA completely replicated/undamaged
Cyclins
Present at each stage of cell cycle (specialize), levels are cyclical and spike when its time to use them
- when at high levels, bind and activate cyclin dependent kinases which phosphorylate and activate proteins which promote activity of a certain phase
Mitosis
Cell division, makes two identical copies of a cell
- Occurs in somatic cells (all cells in body but germ cells)
- 4 phases: Prophase, Metaphase, Anaphase, and Telophase (PMAT)
Prophase
homologous chromosomes
- Nuclear envelope disintegrates
- Nucleoli disappear (dense regions that assemble ribosomes)
- DNA condenses into tightly packed chromatin
homologous chromosomes: pair of maternal and paternal copies of same chromosome
- not identical like sister chromatids
- diff alleles of same genes
kinetochore
Complex of proteins assembled on centromere - where spindle fibers attach during metaphase which forms mitotic spindle
- pull sister chromatids apart
Centrosomes
Centrosomes: 2 cylindrical centrioles which are made up of microtubule fibers, where spindle fibers come from
- 2 at each pole of cell
Mitosis
Metaphase
Chromsomes organized along metaphase plate
- cell must pass M checkpoint: chromosomes properly arranged and attached to mitotic spindle
Nondisjunction
Leads to:
Chromosomes fail to separate normally resulting in abnormal distribution in daughter cells
- leads to aneuploidy: having extra or missing chromosomes
Mitosis
Anaphase
Microtubule fibers pull apart sister chromatids
Telophase
Nuclear envelope and nucleoli reappaear for each daughter cell
Cytokinesis
Cytoplasmic division of a cell
- mediated by myosin and actin proteins
Create cleavage furrow
Meisosis
Sexual reproduction that generates gametes (egg and sperm cells)
- wants genetically variable daughter cells unlike mitosis
- produces 4 daughter cells with half the chromosomes of parents (haploid, 23 chromosomes)
Only occurs in germ cells
- produce ova and sperm via oogenesis and spematogenesis
2 rounds of division, PMAT
Meiosis I
Prophase I
Maternal and paternal copies of each chromosome (homologous chromosomes, 4 sister chromatids) = synapsis
- forms tetrads
- alleles differ
- chiasmata: points where homologs cross over genetic info
Meiosis I
Metaphase I
Random assortment
23 homolog pairs line up randomly
- daughter cells get some maternal and some paternal DNA
Random/independent assortment
Meiosis I
Anaphase I
2 chromosomes in pair are separated to opposite poles (become sister chromatid pairs)
- Daughter cells contain 23 chromosomes
Meiosis I
Telophase I
Cell splits into haploid daughter cells
- chromosomes still paired with identical copies

Meiosis II
Just like mitosis
1. Prophase II: nuclear envelope breaks down
2. Metaphase II: 23 chromosomes align along metaphase plate
3. Anaphase II: sister chromatids pulled apart
- Telophase II: nuclear envelope reforms and cytokinesis
Units to know:
kilo
milli
micro
nano
deci
centi
Base units
amps
Kelvin
seconds
meters
kilograms
moles
Derived units: combination of base units
ex. Hertz, Newton, Pascal
Hertz (Hz)
s-1
Frequency
Newton
kg x m/s2
Force
Pascal (Pa)
N/m2
Pressure
1 atm = 101,325 Pascal
Joule (J)
N x m
Energy, Work, Heat
Watt (W)
J/s
Power
Coulomb (C)
A x s or A = C/s
Electric charge
Volt (V)
J/C
Electric potential
Farad (F)
C/A
Capacitance
Ohm
Volts/Ampere
Resistance
Tesla
Newtons/ Amperes x meters
Magnetic field
Celsius
K-273
1 mile ~~ km
1 foot ~ cm
1 inch ~ cm
1 pound ~~ Newtons
1 gallon ~ L
1 Calorie ~ J ~ kcal
1.6 km
30 cm
- 5 cm
- 5 Newtons
4 L
4000 J ~ 1 kcal
Vectors
Magnitude and direction
- displacement
- velocity
- acceleration
- force
- magnetic/electrical fields
- bond dipoles
Subtracting vectors: reverse the vector being subtracted
Scalars
No direction, just magnitude
- temperature
- loudness
- distance
- speed
Velocity =
Displacement / time
m/s
Acceleration
Velocity / time
m/s2
Displacement vs. time graph
Slope = velocity
change in slope = ∆v = acceleration
Velocity vs. time
Slope = acceleration
Area under curve = displacement
Acceleration vs time graph
Area = velocity
Kinematics definition
Study of motion w/ reference to forces involved
Key kinematics eqns
d = vavg x time vavg = (vi + vf / 2)
a = ∆v / t
vf = vi + at
Kinematics eqn when don’t know final velocity
When you don’t know time
d = vit + .5 at2
vf2 = vi2 + 2ad
Free fall problems
vi = 0
a = g
d = y
d = vit + .5gt2 or vf = √2gy
Air resistance
Force due to air resistance eventually balances out due to gravity
terminal velocity: object no longer accelerating
Projectile Motion
Only force acting on object is gravity; no horizontal acceleration, force stopped acting on object when enters arc
- Movment in x and y direction function independently
- **Time is connector between x and y components
- Projectile has some initial vertical velocity
vx = vicosθ dx = vxt
vy = visinθ vy = 0 at top of curve
then use kinematic eqns vf2 = vi2 + 2ady
Force
Fundamental forces
Push or pull causes obj to accel
- 1 N = kg x m/s2
Fundamental forces: gravity, electromagnetic, strong nuclear, weak nuclear
Electromagnetic forces
Normal force:
force between two contacting surfaces
Electromagnetic forces:
Friction:
force of friction
force that resists movement
ffriction = u N
u = coeff or friction
N = normal force
Electromagnetic forces:
Tension:
pulling force exerted by a string or rope
Electromagnetic forces:
Centripetal force
Force that causes something to move in a circular path or elliptical path
- can be electromagnetic or gravitational
Electromagnetic forces:
Springs
Hooke’s law
Stretched or compressed
- elastic force
Fspring = kx
- k = spring constant (stiffness), x = distance
Newtons 1st Law
Law of Inertia
- in the absence of external force, a body will remain in motion or rest
Resistance to acceleration
More mass = more inertia
Newtons 2nd Law:
Acceleration is proportional to net force
Fnet = ma
connects energy and movement
Newtons 3rd Law
Every action has equal and opposite reaction
Conservative forces
Conserve energy, path-independent
- *only concern final and initial states
- energy not lost to environment
ex. Gravity, electrostatic, magnetic, spring, pushing/pulling
Non conservative forces
Dissipate energy, path dependent
- friction, air resistance, viscosity
F = mg
Gm1m2 / r2
Gravitational force between two masses
Electrostatic force
In a uniform electric field equation
Non uniform
Electromagnetic force between two charges not moving relative to each other
- In a uniform electric field: F = qE
- non uniform EF: F = k (Q1 q2) /r2
- Coulombs law
- k = constant
- Q1 and q2 are charges
Hookes Law
Spring forces
F = k∆x
k= stiffness of spring
Biological approach to human behavior is based off of
Genes, hormones, neurotransmitters
- Physical processes
Psychological approach
The brain working as a whole
- Emotions, attitudes, memories, cognition, personality
Ekman’s list of Universal emotions
- Happiness
- Surprise
- Sadness
- Fear
- Disgust
- Contempt
- Anger
Sociological approaches to behavior
Complicated systems - making sense of society
- lots of different perspectives
- Social constructionism
- Symbolic interactionism
- Functionalism
- Conflict theory
Difficulty using experiments - retrospective study designs, cross sectional designs; present moment relationships
- qualitative research, words not numbers
Social constuctionism
Notion placed on an object/event by society
Symbolic interactionism
Use of verbal, written, or physical communication and subjective understanding
Functionalism
All of society should serve a function for the society
Conflict Theory
Society is in perpetual conflict for limited resources
Cultural learning
behavior passed through culture
Adaptive traits
Trait which promotes reproductive success
Temperament
How an individual responds behaviorally and emotionally to stimuli from the world
Environmental factors for behavior
- Non-genetic influences
- ex. family wealth, stress, endocrine-disrupting compounds, complex family relationships
Genes expressed more or less with environmental stimuli
Experience shapes behavior
DNA promoters that initiate expression and regulatory genes for proteins could vary in people
- ex. allele in gene for promoting serotonin (5HT-T) makes people susceptible to depression
Nature vs. Nurture
heritability
Trying to characterize the heritability of a trait
heritability: degree of variation in a trait due to variation in the genotype
- (how much a trait is determined by genes alone
Twin studies monozygotic and dizygotic
Adopted children - genetics of real parent but environment of foster
Phenylketonuria (PKU)
Trouble metabolising phenylalanine
- Buildup causes cognitive impairment
- Low phenylalanine diet is best treatment
Epigenetics
Changes to genome that don’t involve changing actual nucleotide content
- ex. methylation of cytosine, silences specific genes
- stress, exercise, heritable
Pregnancy (lasts how long, divided into, prenatal development governed by)
Pregnancy lasts 37-41 weeks, 3 trimesters
- First trimester: major structures of fetus formed
- Second trimester: fetus grows
- Third trimester: getting swole
At 12 weeks, fetus organ architecture formed
Prenatal development:
- Umbilical cord connected to placenta: highly vascular bed of tissue, brinds fetal and maternal circulation in proximity to exchange nutrients, gases, waste
- Maternal malnutrition and smoking can harm fetal development
- Stress, anxiety, depression
Infancy to childhood
Reflexes for infants:
Palmar grasp reflex: baby grasps anything touching its palm
Rooting: infant searches for object touching mouth/cheek
Sucking: automatically sucks when something touches top of mouth
Moro reflex: in response to sudden movement/loud sounds; baby extends arms, throws back head and cries
Babinski reflex: toes stretch out when foot is tickled
Devlopmental Stages (3):
-
0-12 months
- Walking ~ 1 year
- Motor: standing w/ assistance, crawling, holding toys
- Social: primary caregiver, solitary, stranger anxiety, object permanence
- Linguistic: laughing, bubbling, simple words
-
12-24 months
- Physical independence: walking, climbing, drawing, throwing, stacking
- Social/linguistic: terrible twos, sense of self, boundaries (none)
-
3+ years
- More complex/mature behavior, toilet training, awareness of gender
- Further language development
Critical period of infancy
Time when experiences imprint life-long effects
- Language development is critical
Adolescence
12-19 years
- Cognitive, social , behavioral changes
Puberty
Puberty: biological changes
- earlier in females, menarche is landmark (first menstruation)
- development of secondary sex characteristics
- pubic hair, breasts and wider hips, facial hair and adams apple
- fat and muscle distribution different between sexes
- pubic hair, breasts and wider hips, facial hair and adams apple
All orchestrated by sex hormones- testosterone and estradiol
Obesity affects hormone exposure, earlier puberty
Adulthood
Prefrontal cortex develops until ~25
- Responsible for rational decision making
- Neuronal axons in prefrontal cortex covered in myelin sheaths, transmit signals faster
Aging
Degradation of telomeres
- limits cell division
- Gradual physical devline, more prone to disease
- mental processing slows and fluid intelligence
Crystallized intelligence
Knowledge accumulated over time
- Remains stable
- Elderly considered wise
Fluid intelligence
Fluid intelligence is the ability to think abstractly, reason quickly and problem solve independent of any previously acquired knowledge.
Endocrine system functions
Fluid regulation, metabolism, blood-glucose and calcium levels
- One of two physical systems that regulates BEHAVIOR
Network of organs that secrete signalling molecules into the bloodstream (hormones)
- some cause direct changes, some cause release of other hormones
- tropic hormones: target other endocrine glands, helps with control of systems
tropic hormones:
target other endocrine glands, helps with control of systems
Hormonal Axis: starts with
Endocrine system from brain southward; higher glands regulate lower ones
-
Hypothalamus: converts input from nervous system into endocrine signals
- hypo = low, below thalamus in forebrain, above pituitary gland
Hypothalamus releases high level hormones to the pituitary gland, where other tropic hormones released
- ex. GnRH (gonadotropic releasing hormone, triggers LH and FSH reproductive hormones)
- CRF- promotes ACTH which releases cortisol from adrenal glands

Endocrine system
Hormonal axis: hypothalamus signals ____ via the ____
What hormones?
Pituitary glands
-
Anterior pituitary: receives input from hypophyseal portal system (connecting blood vessels, hormones)
- Releases Luteinizing Hormone, (LH)
- Follicle Stimulating hormone, (FSH)
- thyroid stimulating hormone (TSH)
- Adrenocorticotropic hormone (ACTH)
- Prolactin (milk production)
- Endorphins (reduce perception of pain)
- Growth hormones
-
Posterior pituitary: controlled by hypothalamus via neuronal signals instead of hormonal
- Antidiuretic hormone (ADH) regulates fluid balance
- diabetes insipidus: inability to regulate fluid balance
- Oxytocin (labor)
- Antidiuretic hormone (ADH) regulates fluid balance

Endocrine system
Thyroid and Parathyroid
Hormone?
Located in the throat
- Releases thyroid hormone which affects metabolism and behavior

Endocrine system
Pancreas
Abdomen, less important behaviorally

Endocrine system
Adrenal glands
Above kidneys
2 distinct areas:
- Cortex: secretes cortisol and mediates chronic stress response
- Medulla: epinephrine and norepinephrine, and flight or fight response

Endocrine system
Ovaries and testies
Secrete estrogen and testosterone
Endocrine system hormonal axis from top to bottom:
Hypothalamus
Pituitary glands: antieror and posterior
Thyroid and parathyroid
Pancreas
Adrenal glands
Ovaries and testes
Estrogen and testosterone
Promote libido, interest in sexual behavior (sex drive)
- testosterone associated with aggression
- both sexes secrete some of both
Oxytocin
Labor contractions, latation, social bonding (affection, mood)
- primary examble of positive feedback, more oxytocin leads to more contractions which leads to more oxytocin
- antidepressant, orgasms
*Produced by hypothalamus, secreted by pituitary gland
Prolactin
Induces lactation
- Stress response, anxiety, depression, contributor to post-partum depression
Produced by anterior pituitary gland
Melatonin (secreted by? production suppressed by?)
Secreted by pineal gland in brain
- induces sleep
- blue light suppresses melatonin production
Hunger is regulated by (3 hypothalamic hormones)
Both produced in hypothalamus:
Leptin: reduces hunger, released by adipocytes (fat cells)
- also has roles in reproduction, immune system, obesity
Ghrelin: promotes hunger, released by cells in gastrointestinal tract when stomach is empty (stomach growl –> ghrelin)
- learning, mood, sleep, reproduction
Neuropeptide Y (NPY): stimulates appetite
Stress Hormones
ADRENAL GLANDS
epinephrine and norepinephrine: secreted by adrenal medulla
- acute stress response, fight or flight
- also secreted by neurotransmitters
cortisol: released by adrenal cortex, chronic stress response
- increases blood sugar
Thyroid hormone
Promotes metabolism
hypo/hyperthyroidism:
- hypo- fatigue and depression
- hyper - irritability
Mechanism of Nervous system
Stimuli –> perception –> response
Neurons components
Consists of dendrites: receive input from other nerves/organs
Soma
Axon: action potential travels down from dendrites
Axon terminal

At rest, electric potential difference of neuron membrane is
Does stimuli reduce or raise this potential?
-70 mV
Stimuli REDUCES electric potential difference, -55 mV causes action potential fire
Action potential
Synapse
Travels down axon to axon terminal
- releases neurotransmitters at the synapse
synapse: space between one neuron and another (or target cell)
Reflexes
neuromuscular junction
Automatic behaviors that occur in response to certain stimuli
Reflex arc: simple neural pathways that control reflexes
- ex. Patellar reflex, sensory neuron stretches from knee to spine
- motor neuron signals back down to quadricep muscle
Synapse between motor neuron and muscle is neuromuscular junction
- motor neuron releases neurotransmitter acetylcholine which causes muscle to contract
Sensory neurons are _____ neurons
Motor neurons are _____ neurons
AFFERENT neurons, carry info about stimuli to CNS
EFFERENT neurons, signal effect to target cells
SAME, sensory afferent motor efferent
Neurotransmitters
Excitatory vs. Inhibitory
Push the membrane potential difference in either direction
Neurons geneally receive multiple signals, the SUM of inputs decide whether it will fire action potential
excitatory: depolarizes membrane of target neuron, easier for signal to travel (higher mV, -70 to -55)
inhibitory: hyperpolarizes target neuron, less likely to send signal
How do neurotransmitters change electric potential?
Bind to receptors that open up ion channels
- High specificity to different signals –> receptor subtypes
- different receptors in diff neurons
ex. serotonin can have excitatory or inhibitory effect

Acetylcholine
Neurotransmitter, muscle contractions
- also communicates signals between central NS and autonomic NS
- sends signals from parasympathetic neurons to target
Glutamate
Neurotransmitter; excitatory, depolarizes neurons
- most common neurotransmitter, 90% of neuronal connections in brain
- learning and memory
Opposite of GABA
GABA (gamma-amino butyric acid)
Neurotransmitter, inhibitory
- Opposite of glutamate, hyperpolarizes neurons
- slow or block certain signals in the brain
Dopamine
Associated disease?
Neurotransmitter; reward pathways and addiction
- increased by psychoactive drugs, euphoria
- mediates motor functions
- loss of dopamine-secreting neurons in substantia nigra leads to Parkinsons disease
Serotonin
Antidepressants name
Regulates mood, appetite, sleep, intestinal movement
- current hypothesis is depression associated with low serotonin
Antidepressants: selective serotonin reuptake inhibitors (SSRIs)
- prevent serotonin from being taken up by neurons, stays in synapse longer
Endorphins
Neurotransmitter; suppress pain and produce euphoria
Agonist vs. Antagonists
Agonists: Compound that activates a certain receptor, causing a response
- partial agonists: not as strong
Antagonists: bind receptor but don’t cause a response, prevents neurotransmitter from being able to exercise its affects
Peripheral Nervous System
Extending nerves from brain and spinal cord to everywhere else
- somatic and autonomic

PNS
Somatic NS
Voluntary acitivities, efferent motor nerves and sensory afferent nerves
PNS
Autonomic Nervous System
Unconcious activities
- digestion, heart rate, breathing, pupil dilation, urination
- ddivided into sympathetic and parasympathetic
PNS
Autonomic NS
Sympathetic NS
Fight or flight response to acute stress
- mobilizes resources to deal with emergency now
- HR increases, epinephrine released, more resources to muscles
- Pupils dilate, start sweating
Also suppresses unnecessary functions like digestion, slows paralstalsis
- tunnel vision, less likely sexual arousal
PNS
Autonomic NS
Parasympathetic NS
Rest and digest response
- blood vessels restrict supply to muscles, dilate in digestive tract
- promotes digestion, salivation, urination, defecation, lacrimination (tear production), sexual arousal
PNS
Autonomic NS
Enteric NS
Regulates activity of the gut
Central Nervous System
Brain and spinal cord
Forebrain (2 subunits)
Advanced functions like reasoning
-
Diencephelon: contains thalamus, hypothalamus, and pituitary gland
-
thalamus: relays sensory and motor signals
- regulates sleep and alertness
- hypothalamus: bridge between NS and endocrine system
- Pituitary gland: releases hormones
-
thalamus: relays sensory and motor signals
-
Telencephalon:
-
cerebrum: cerebral cortex and subcortical structures
- cerebral cortex: right and left hemispheres
-
subcortical structures: LIMBIC SYSTEM
- olfactory bulbs: detecting odors
- hippocampus: consolidates short term memory into long term
- basal ganglia: eye movement, voluntary movement, habitual learning
-
cerebrum: cerebral cortex and subcortical structures

Midbrain
In between, vision and eye movement
- Inferior colliculus: auditory input (not the primary place)
- Superior colliculus: visual input (not the primary place)
- Substantia nigra: neurons communicate with dopamine for voluntary movements
Midbrain and medulla oblongata + pons form the Brainstem, physical support for the brain
Hindbrain
Basic functions like breathing
-
Cerebellum: forms distinct structure at the base of the brain
- coordinates movement, balance
- Medulla oblongata: autonomic functions like breathing, heart rate, blood pressure
-
Pons: relay station for signals between cerebellum, medulla, and rest of brain
- sleep, respiration, swallowing, taste

Brainstem
Midbrain and medulla oblongata + pons form the Brainstem, physical support for the brain
- contains reticular activating system (RAS) – modulates alertness and arousal
Diencephelon:
Forebrain
contains thalamus, hypothalamus, and pituitary gland
-
thalamus: relays sensory and motor signals
- regulates sleep and alertness
- hypothalamus: bridge between NS and endocrine system
- Pituitary gland: releases hormones
Telencephalon:
Forebrain
- cerebrum: cerebral cortex and subcortical structures
- cerebral cortex: right and left hemispheres
-
subcortical structures: LIMBIC SYSTEM
- olfactory bulbs: detecting odors
- hippocampus: consolidates short term memory into long term
- basal ganglia: eye movement, voluntary movement, habitual learning
Limbic system
Emotion, motivation, memory
subcortical structures: LIMBIC SYSTEM + hypothalamus, amygdala
- olfactory bulbs: detecting odors
- hippocampus: consolidates short term memory into long term
- basal ganglia: eye movement, voluntary movement, habitual learning
- amygdala: episodic memory, attention, emotion
- Nucleus accumbens: reward, motivation, learning; implicated in addiction
Cerebral cortex 4 lobes
-
Frontal lobe: voluntary movement, memory processing, planning, motivation, attention
* Broca’s area: language production - Parietal lobe: all sensory processing but vision
- Occipital lobe: vision, back of brain
-
Temporal lobe: meaning, visual memories, language
* Wernickes area: language comprehension
Brocas area
Located in frontal lobe of the cerebral cortex
Language production
Wernickes Area
Location
Located in temporal lobe of cerebral cortex
- language comprehension
Lateralization (brain)
Tendency of left and right hemispheres to specialize
- different neurons respond differently to neurotransmitters
Spinal cord
Link between central and peripheral NS
- both brain and spinal cord protected by cerebrospinal fluid (CSF)
Also protected by meninges (tough membranes) and by bones (skull and vertebrae
Vertebrae
Holes in middle for spinal cord;
cervical (C1-C7), thoracic (T1-T12), lumbar (L1-L5), sacrum (S1-S5)(fused together)
Ends with coccyx
- D.orsal
- A.fferent nerves
- V.entral
- E.fferent nerves

Dermatomes
Areas of skin with nerves that correspond to different vertebrae

Methods of studying the brain/other parts of body
Observing injury and stimulation to certain areas with electrodes or chemicals
Electroencephalograms (EEG): using electrodes on brain, identify function not structure
Computed Tomography (CT): 2D x-rays to make 3D image
Magnetic Resonance Imaging (MRI): magnetic fields, no radiation, better at imaging soft structures
Positron Emission Tomography (PET): radiolabels glucose with fludeoxyglucose, emits positrons as it decays
- more decay = more glucose metabolised = more neural activity
- can diagnose tumors, strokes, dementia
fMRI: now preferred over PET, relies on differences in magnetic properties b/w oxygenated hemoglobin (arterial blood) and deoxygenated hemoglobin (venous blood)
- visualize blood flow
Genes
DNA sequence that codes for a protein that produces a trait
- Genes found at specific locations are called locus
Variations in same gene are alleles - one on each homologous chromosome
- dominant or recessive
- hemizygous = one copy present
- homozygous = two
Wild type: most common variant (W+W+)
Mutant: mutated alleles
Loss of function mutations
Gain of function mutations
Tend to be recessive, can be covered
Gain of function usually dominant
Test cross
Backcrossing
Homozygous recesssive cross to determine genotype
Crossing offspring with parent genotype
Codominance
Two dominant alleles expressed
ex. ABO blood types, type AB
Incomplete dominance
Blended phenotype, heterozygote
Penetrance
Likelihood a genotype will manifest a phenotype
Expressivity
Severity of a phenotype
Inheritance Patterns
Pedigrees
Autosomal: non sex chromosomes, recessive can skip generations
de novo: spontaneous mutation
Sex-linked: usually X-linked, recessive or dominant
Mendel’s Laws
Segregation:
Independent assortment
Dominance:
Linkage:
Segregation: allele pairs segregate randomly from each other into gametes
Independent assortment: alleles for separate traits independently inherited; not always true due to linkage
- linkage: genes close to each other on same chromosome are usually inherited together unless genetically recombined (crossing over at chismata)
Dominance: recessive alleles mask to some degree
Centimorgans and linkage
Single vs. Double crossover b/w homologs
Distance associated with a 1% change in recombination frequency
- ex. 1 Cm = 1% chance of recombination
- 50 Cm = unlinked
Double crossover- genes so far apart 2 crossover events cause them to be on same chromosome
Evolutionary system:
- Variation
- Reproduction
- Differential reproduction due to selective pressure
Natural selection
Describes how favorable traits are favored over time
- underlying mechanism
Fitness is relative to environment
Altruism
Acting in a way that benefits others survivals
- I’d save 2 brothers or 8 cousins
Group selection
Natural selection applied to a group level
Inclusive fitness
Traits passed on that promote survival of the group
- altruism, empathy, sharing alleles
Hardy-Weinberg Equilibrium
Mathematical relationship between alelles and phenotype frequencies
Used to model stable gene pools
-
gene pool: evolutionary success indicated by popular alleles in gene pool
- stable:
- no mutation
- random mating
- large population size
- no natural selection
- stable:
A = p
a = q
allele frequency: p + q = 100%
phenotype frequency: p2 + 2pq + q2 = 1
Earth age
Life age
Human age
4.6 billion years
3-4 billion years
200,000 years
Natural Selection Types:
stabilizing
directional
Dispruptive
stabilizing: favors intermediate phenotypes
Directional: favors one extreme
Disruptive: both extremes favored
Ways gene pools may change:
Natural selection and chance
Genetic drift: change in gene pool due to random chance, usually in smaller populations
- Bottleneck effect: natural disaster artifically increases/decreases allele frequency
- Founder effect: reduction in genetic diversity due to small group founding a new colony
Random errors in the genome accumulate at a fixed rate; can be used to tell how long ago there was a shared ancestor
Gene flow: movement of alleles due to migration between populations
Factors influencing evolution:
Gene flow
Random Chance
Migration
Mutation
Selective pressure
Species
Group of organisms that can form fertile offspring and reproductively isolated from other groups
- contested, doesn’t apply to asexual organisms, like bacteria or hybridization
Reproductive Isolation
Prezygotic and Postzygotic barriers
Prezygotic: prevent zygote from forming
Postzygotic: prevent formed zygote from being visibile or fertile
- hybrids: two different species make viable offspring thats usually sterile
Inbreeding vs. Outbreeding
Inbreeding: Breeding between closely genetically related individuals
- deleterious recessive mutations
Outbreeding: breeding with and passing alleles between unrelated members of same species
- genetic diversity
Divergent vs. Convergent Evolution
Divergent: Common ancestor splits into two species due to different traits
Convergent: two species become more phenotypically similar, not as common
Parallel Evolution
Coevolution
Parallel Evolution: 2 closely related species share a common ancestor and evolve similar traits independently
Coevolution: evolution of two species in response to eachother, symbiotic relationships
Symbiosis and types
Relationship between two organisms that benefits, harms, or has no effect for one or both parties
- Mutualism: both organisms benefit
- Commensalism: one organism benefits, no effect on other
- Parasitism: parasite benefits from harming its host
Center of mass equation
Xcenter = m1x1 + m2x2… / (m1 + m2)
x = distance to masses from reference point
Static vs. Kinetic Friction
Static: opposes movement of an object not moving
- magnitude depends on force applied to object
Kinetic: opposes object in motion
- constant magnitude
Different materials have different coefficients
Fmax = us N
- Force required to move object depends on coeff of static friction and normal force on object
Fkinetic = uk N
Pulleys and inclined planes
Reference work
Gravitational and centripetal force equations
Fgrav = Gm1m2 / r2
- G = gravitational constant
- 6.67 x10-11 m3 /kg s2
Fcentripetal = mv2/r
- if caused by gravity, then g = v2/r
Torque
JOINTS, DIPOLES (rotate to align in electric field)
Force applied to rotate an object around a fixed axis
- rotational force applied to a lever arm at a distance from the fulcrum
T= Fdsinθ
Strongest torque = force at 90 degrees, greatest distance from fulcrum
- sin90 = 1
Clockwise = neg T
CCW = positive

Lipids
2 layers = bilayer membrane, polar exterior and nonpolar interior
- small nonpolar molecules can diffuse easily, large polars can’t
Sterols
Glycolipids
Sterols
Lipids
Cholesterol, modulates fluidity of plasma membranes
- characteristic 4 ring structure
Steroid hormones
Glycolipids
Carbohydrate modifies the lipid instead of a phosphate group
Peptidoglycan, lipopolysaccharide
- cell signaling and cell adhesion
- amphipathic structure
- either glycerol or sphingosine backbone
Glyceroglycolipid
Sphingolipid: sphingomyelin clusters with cholesterol to form “lipid rafts”
- modulate fluidity and clusters for signaling
Proteins of cell membrane
Integral
Lipid-anchored
Peripheral
Glycoproteins
Integral: embedded in plasma membrane
- transmembrane proteins: completely cross cell membrane
- protein pumps, ion channels, G protein-coupled receptors
Lipid-anchored: bound to 1+ lipid molecules which anchor protein to membrane
- G-protein: intracellular, coordinate cascade initiated by G protein coupled receptors
Peripheral- found in cytoplasm, temporarily attached to integral proteins
- enzymes and hormones, only briefly interact with membrane
Glycoproteins: glycosylated proteins (addition of carbohydrate)
- Major Histocompatibility Complex (MHC)
- antigens of ABO blood type system
- cell recognition and communication processes
Liposomes
Lipid bilayers enclosing a spherical space
- lab derived, deliver material to target cells
- test cell membrane permeability
- can also embed proteins
Micelles
Structurally simpler liposome, only a single layer lipid membrane
- can reduced surface tension of a solution
- surfactants
- don’t contain membrane proteins
Fluid Mosaic Model
Cell membrane is constantly in motion; motion is constrained
- Forms coherent hole but pieces are visible
Phospholipids can move horizontally but not vertically
- need enzymes to catalyze movement
- Flippase: moves phospholipids from external side to internal side
- Floppase: opposite
- Scramblaser: bidirectional
Degree to which phospholipids can move laterally is membrane fluidity
- makes space for diffusion and imbedded proteins
- too much/too little fluidity would be an issue
Modulating fluidity of bilayer membrane
Cholesterol: regulates extremes
- at cold temperatures, cholesterols ring structure gives fatty acid tails a rigid shape; keeps space between them
- inhibits fluidity in heat
Phospholipid structure
Phosphate head, saturated and unsaturated fatty acid tails
-
saturated: no C=C double bonds; stackable, interact with each other easily, and higher melting pt
- interactions between tails which are closer together
- unsaturated: at least one C=C; lower melting points and more fluidity
Simple Diffusion (Passive Transport)
Down concentration gradient, high to low
- small molecules:
- gases (O2, CO2)
- essential for respiration
- small uncharged polar molecules
- H2O, ethanol, urea
- gases (O2, CO2)
Osmosis (simple diffusion)
Isotonic, Hypotonic, Hypertonic
Water diffuses to side with highest solute concentration
- semi-permeable membrane
Isotonic: equal conc of solutes
Hypotonic: more solute inside than outside, cell can burst or swell
- increases pressure, headaches and drowsiness
- IV hydration administers isotonic saline
Hypertonic: more solute outside cell, cell shrinks
- can be used to preserve food, kills bacteria (plasmolysis)
Osmotic Pressure
Van’t Hoff’s Law
Water exerts pressure on membrane and blocks any more from passive
Minimum pressure to prevent further osmosis
Van’t Hoff’s Law: π = MRT
- M = molarity (n/L) (moles / Liters solute)
- R = ideal gas constant
- T = temp in Kelvin
Molality
Moles solute / kg solvent
Osmolarity:
Molarity of all solute particles (1 mol NaCl would be 2 osm/L)
Van’t Hoff Factor
π = iMRT
i = # of particles per molecule
ex. NaCl i=2
Facilitated Diffusion (passive transport)
Molecules too big or polary undergo facilitated diffusion
- Transmembrane channels serve as transporter for molecules
- specific for solutes
- respond to stimuli to open
- flow is down concentration gradient, no ATP
Against osmotic gradient, thermodynamically favored (increases entropy)
Channels can bottleneck and rates of diffusion level off = saturation kinetics
Aquaporins
Transporter specific for water
- transmembrane proteins that selectively conduct water molecules
- highly polar
- rate of osmosis is limited
Ion Channels
Transport ions
- extremely specific
- selective for when they open up
- response to signals
- voltage: changes in electric membrane potential
- response to signals
Voltage gated ion channel: neuronal signaling and propagation of action potentials
Ligand-gated transporters: open in response to signal molecules
- neurotransmitters
Channels can respond to light, pressure, shearing (breaking off), stretching
Active Transport
Requires ATP to move solute AGAINST a concentration/electrochemical gradient
- Primary and secondary active transport
Primary Active Transport
Transmembrane proteins catalyze ATP hydrolysis –> releases energy –> moves solutes across membrane
- transmembrane ATPases catalyze hydrolysis of ATP
- can also be powered by redox reactions or energy from photons
redox example: Enzymes of electron transport train in mitochondria use energy released from redox rxns to translocate proteins across inner mito membrane against conc gradient
ex. Sodium Potassium pump
* Na+K+ ATPase
Sodium Potassium Pump
Body maintains difference in concentrations of Na and K ions inside and outside of cell
- Sodium has higher conc out of cell “blood is salty”
- Potassium has higher conc inside cell
3 sodium in for 2 K+ out for each ATP molecule
- Maintains a net charge imbalance of -1 inside cell
- ** contributes to membrane potential
Secondary Active Transport
Active and passive transport
- Active transport generates conc gradient which powers passive transport of something else
- spontaneous process powers a nonspontaneous one
- direction can be opposite or same
- symporter and antiporter
ex. Sodium-Glucose cotransporter: symporter moves sodium and glucose into cell via passive transport using NaK pump conc gradient
cyt =
cytosis=
endo =
exo=
phago =
pino=
cyt = cell
cytosis= cell absorption/ release
endo = inside
exo= outside
phago = eat
pino= drink
Endocytosis
Some substances too large to be transported by transmembrane proteins; endo/exocytosis used for uptake and release of growth factors, antibodies, and other proteins, low density lipoprotein (contains cholesterol)
Endocytosis: cells absorb molecules by engulfing them
- area of plasma membrane surrounds a material forming a vesicle
-
vesicle buds off from internal face of membrane
- pinocytosis: cell engulfs liquid
-
phagocytosis: cell engulfs a solid
- typically by phagocytes of immune system to ingest foreign particles/pathogens
-
vesicle buds off from internal face of membrane
- receptor-mediated endocytosis: cell is targeting specific molecules
Exocytosis
Membrane of intracellular vesicle fuses with plasma membrane
- lipids or proteins bound for plasma membrane or secreted proteins
- in some cases, release is controlled by calcium ion signaling
ex. influx of Ca2+ ions into neurons leads to release of neurotransmitters into synaptic cleft
- neurons release neurotransmitters via exocytosis
Once a cell ingests a substance (endocytosis)
Endosomes are membrane bound organelles that function as sorting compartments
- identify engulfed substances that should be reused in plasma membrane like receptor components vs those the cell needs internally or should be degraded
early endosomes: are located close to plasma membrane, do most of sorting
late endosomes: main role is delivering matrial to lysosomes: recycler of cell; highly acidic with special enzymes
- For phagocytosis, phagosomes deliver pathogens to lysosomes
Avogradros Number
6.022 x 1023
Number of units/atoms in one mole of a substance
Multiplying exponents (scientific notation)
Dividing in scientific notation
Adding and subtracting them
Multiply front number, add exponents
Divide front number, subtract exponents
Manipulate decimals so that terms are to the same exponent and then add
For triangles,
cosθ =
sinθ =
tanθ=
cosθ= adjacent over hypotenuse
sinθ = opposite over hypotenuse
tanθ = opposite over adjacent
Special Right Triangles
30-60-90
45-45
sin90 = 1
cos 90= 0
cos 0= 1
sin0 = 0

Archaea
Unicellular, many are extremophiles
- thrive in extreme tmp, pH, or salt conditions
Use whatever energy source they can get their flagella on
- organic compounds
- ammonia
- hydrogen gas
- metal ions
- photosynthesis
Types of bacteria
Much more common than archaea; most in humans are commensal
Categorized by shape:
- coccus: sphere shaped
- bacillus: rod shaped
- spirillum: spiral shapped
Pathogens:
Bacteria that are harmful to the body
- harm host through different mechanisms
- reproduce intracellularly or outside of host
- secrete damaging toxins
- Normally treated with antibiotics
-
antibiotic resistance:
- pump out drugs with efflux pumps
- inactivating antimicrobial enzymes
-
antibiotic resistance:
ex. E coli
Staphylococcus aureus - multidrug resistance responsible for MRSA
Types of Aerobes/Anaerobes
obligate aerobes: oxygen required for metabolism
anaerobes: oxygen not required
- obligate anaerobes: can’t survive in presence of oxygen
- aerotolerant: tolerate O2
- facultative: aerobic metabolism when available
Prokaryotic cell structure
lack of membrane bound nucleus and organelles
- bacterial DNA resides in nucleoid region of cytoplasm
- Genetic material is single circular chromosome of dsDNA
- *transcription and translation occur simultaneously
Plasmids
Cell wall: provides structural support and extra layer of defense
- rich in rigid polysaccharide called peptidoglycan
- can take up gram stain
Plasmids
Many bacteria cantain smaller circular DNA fragments
- non essential genes; an confer antibiotic resistance or code for virulence factors: enhance ability to spread/harm host
Gram staining
Technique used to separate bacteria into two categories based on structure of cell walls
Gram positive: thick, peptidoglycan rich cell wall traps stain
Gram negative: thin layer of peptidoglycan followed by LPS
- ex. E coli
Antibiotics like penicillin target peptidoglycan wall and have trouble penetrating gram-negative outer membrane, makes them more difficult to treat than gram-positive
- LPS is antigenic and capable of inducing a deadly innate immune response in humans
Bacterial Respiration
Aerobic respiration w/o mitochondria
- Electron transport chain is located on cell membrane
- endosymbiotic theory: mitochondria originated when cyanobacterium was englufed by Eukaryotic cell
Prokaryotic vs Eukaryotic ribosome structure
Prokaryotic: 30S and 50S -> 70S
Eukaryotic: 40S and 60S -> 80S
Svedberg units: describe sedimentation rate
Difference between ribosomes allow antibiotics to target bacterial ribosomes
Flagella in eukaryotes vs. prokaryotes
Eukaryotic: composed of microtubules and whips back and forth to propel cell
Prokaryotic flagella: rotate to propel cell forward
- comprised of filament, basal body (responsible for rotation), and hook connects the two
Bacterial reproduction
Binary Fission:
- Circular chromosome replicated
- Cell growth
- New cell wall grows and segregates
- Two chromosomes pulled towards either half of cell
- Cell splits
as quickly as 20 min, growth constrained by nutrient resources
Bacterial 4 phases of growth
- Lag phase- bacteria adapt to new environment
- Exponential
- Stationary- growth limited by nutrients
- Death phase
In some viruses, capsid is enclosed within a lipid envelope of phospholipids and proteins
Sensitive to light and heat
Must be transmitted via bodily fluid
ex. HIV
Viral genomes
ssDNA, dsDNA, ssRNA, ds RNA
ssRNA:
- positive sense if they contain mRNA that can be translated to protein
- negative sense if RNA is complementary to mRNA and must be copied into mRNA by viral enzyme RNA replicase prior to translation
Retroviruses
Contain reverse transcriptase to transcribe RNA to DNA and integrate into host
- used in PCR for amplification
ex. HIV, responsible for AIDS, hard to treat because genome integrated with hosts - treated successfully w/ antiretroviral drugs that target reverse transcriptase
Retrotransposons
Mobile elements that make up 40% of human genome
Viral DNA vs Viral RNA
DNA: translocates to nucleus, trascribed by hosts RNA polymerase
RNA: immediately translated to protein in cytoplasm or reverse transcribed to DNA
Extrusion
Release of virions from host cell, leaves host cell intact (not lytic)
Horizontal gene transfer in bacteria
Achieving genetic variability despite asexual reproduction
Conjugation (fertility factor F+)(sex pilus)(major cause of antibiotic resistance)
Transformation
Transduction (bacteriophages)
Bacteriophages
Infect bacteria, more complex structure
Lytic- release lyses cell
Lysogenic (integration into host genome)
- creates prophage/provirus lies dormant in host until triggered by environmental signal
- then switches to lytic cycle
Antiviral mechanisms
Some target reverse transcriptase
Target attachment to host cell
Block assembly of new virions
Viroids
Small simple RNA particles that infect plants
Lacks capsid/envelope
Binds complementary RNA sequence in plants to silence gene expression
Prions
Misfoled proteins that cause other proteins to misfold and aggregate together, harming cell function
- Responsible for Creutzfeld-Jakob disease
- fatal neurodegenerative disease transmitted by eating beef from cattle w/ mad cow disease
- Fatal familial insomnia and kuru
Mycobiome
Nonharmful fungi
Pathogenic fungi
yeast infections, ringworm
Parasitic organisms
Why are they difficult to treat?
Protozoa: single celled parasites (eukaryotes)
- carried by mosquitoes -> malaria
Helminths: multicellular worms
Ectoparasites: multicellular, live outside host
- fleas, lice
Immune system mediates infections by eusinophils and IgE antibodies
- parasites tricky to treat because eukaryotic, same machinary
Restriction enzymes/ restriction endonucleases
Cleave DNA at specific sequences, DNAses
Sequences that restriction enzymes look for have defining features: 4-8 bp long, symmetric/palindromic inverted repeats
- Prokaryotic DNAses can act as defense against viruses
- Some DNAses are nonspecific and cleave DNA wherever they can
DNAse cleavage creates:
Blunt ends: small restriction enzymes
Sticky ends: EcoR1 restriction enzyme
Sticky ends more desirable because they can be ligated back with DNA ligase
DNA recombination
Vectors
Insert target sequence into “vector” (small DNA molecule that can transfer DNA into target cells by hijacking replication machinary and integrating itself)
Vectors:
-
plasmids: derived from prokaryotes circular DNA that replicate independently
- spliced, recombined, and introduced into bacteria
- Gene sequence “insert” is synthesized with 2 restriction sites matching plasmid vector
- reporter gene: in plasmid elicits visible phenotype change
- bacteriophage: incorporate larger sequences
Same techniques used for RNA if reverse transcriptase used
DNA recombination steps
- Synthesize gene seq insert with restriction sites
- Digest insert and vector
- Ligation of insert and vector
- Treatment of bacteria w/ plasmid
- Plasmid replication
- Select for bacteria w/ plasmid
Genetic engineering goals
- Mass protein production: insulin, vaccine components, inteferons, tumor necrosis factor
- Alterations to genetic code
Transgenic organisms:
Knockout organisms
Genomes have been modified
Organisms with 1+ genes deleted, can see which genes are necessary
- ex. cystic fibrosis caused by single mutation that hinders CFTR gene
GMO: genetically modificed in agriculture
Independent vs. Dependent variables
Independent: what researcher manipulates (x)
Dependent: what changes in response to x (y)
- dependent cant occur before independent
Confounding, mediating, and moderating variables
Confounding: affects both indep and dep variables; potentially obscures relationship b/w them
- ex. cigarette smoking obscures relationship between coffee and cardiovascular disease
- coffee drinkers smoke more cigs
- cigs –> CVD
Mediating variable: explains counterintuitive relationships b/w indep and dep variables
- ex. median household income –> cancer mortality rate
- mediated by availability of healthcare
Moderating variable: modulates intensity of relationship
- ex. workplace stress –> anxiety/depression
- moderated by exercise
Operationalization
process of defining variables in measurable, practical ways
Types of Studies
Experimental: researchers manipulate the world in some way
Observational: researchers analyze pre-exisiting patterns of variation to determine relationships
Quantitative: numerical measurements of variables
Qualitative: verbal/open ended measurements of variables
Mixed Method
Experimental controls
Negative controls: don’t receive the treatment/intervention of interest
- placebo
- crucial to demonstrate intervention effect
Positive controls: receive a treatment known to induce outcome of interest
- confirm adequacy and competency of procedure
Experimental validity
Controls and experimental groups treating the same
randomization: samples randomly allocated to control or treatment groups
blindness: researchers don’t know which sample is control/experimental when doing maintenence
- double blind: neither participants nor researchers know who is in control group
randomized control trial: participants randomized to treatment or control
Observational design
cross sectional study:
limitations:
cross sectional study: measuring various stats among a set of people, looking for correlations
- large samples
-
study types
- opinion poll
- surveys
- correlational studies
limitations:
- provide a limited snapshot of a certain population at a certain time, can’t provide info on causality (correlation doesn’t mean causation)
- no info about how things change over time
Observational Design
Longitudinal designs
Multiple measurements over time
risk factors: independent variables associated with higher risk of negative outcome
protective factors: independent variables associated with lower risk of negative outcome
cohort studies: group of subjects assembled based on an organizing principle and followed up over time
prospective analysis: data gathered moving forward
restrospective studies: data from past
Observational design
Case control studies
Compare cases to controls
cases: individuals with an outcome of interest
- identifying any differences between the two groups might shed light
- used in epidemiology to investigate cause of disease
case study: report on a single case
case series: multiple cases reported
Observational designs strength of evidence
Strong: meta analyses: data from multiple studies combined, reanalyzed
systemic reviews: assess outcomes of various studies
randomized controlled trials: experimental
cohort studies
case control
Weakest: case studies/series
National Institute of Health 7 principles for Research Ethics
- Research has social/clincal value
- Research has scientific validity
- Principle of fair subject selection
* participants chosen based on relevance for study’s goals - Principle of favorable risk-benefit ratio
- Principle of independent review
- Principle of informed consent
- Respect for potential and enrolled participants
Genetic screening
used to identify genetic predictors of various health outcomes
Limits on genome-wide association studies
Statistical power is low due to all the potential relationships
Effect size not large enough to motivate public health efforts
Causality
Ultimate goal of research
- basic factors for causality:
- association (correlation) between variables
- Establish that variation in the indep variable precedes variation in dep
- Plausible mechanism through which possible cause could exert effect
- Rule out possible mediating outcomes
Social structure
Family, education, healthcare, economy, gov’t and religion
Sociological theories
micro vs. macrosociology
No right or wrong theory, theories not mutually exclusive
Micro is small scale, macro is large scale interactions
Macrosociology
Functionalism
Understanding structures and institutions based on their functions
manifest functions: intended functions for institution
latent functions: unintended functions that are positive
latent dysfunctions: reinforces patterns of social inequality
Could be a matter of opinion -> AUTHORS TONE
Macrosociology
Conflict theory
Thought to have originated with Karl Marx but not associated with Marxism/Socialism
Competition for resources between structures or groups
- leads to conflicts and power differentials
- doesn’t necessary require conflict
ex. resources –> college –> economic opportunity
Microsociology
Symbolic interactionism
How people interact with symbols
- requires an interaction
-
symbols: something we assign meaning to
- has a shared sense of meaning in society
Social constructionism
Meaning of social structures/ concepts emerges from how we think and communicate about them
ex. gender roles, love, patriotism
*Tends to be macrosociological when compared to symbolic interactionism
Focuses on constructing the symbols
Microsociology
Rational choice theory
Choose actions to maximize the likelihood of accomplishing certain goals
ex. wanting intoxication, taking drugs
How people make choices
Microsociology:
Social exchange theory
View social interactions as interchanges with costs and rewards
ex. friendships: invest time and energy and receive benefits like support
** actual interactions
Microsociology
Feminist Theory
Goal of understanding and remedying gender injustices
Through focus on lived experiences and objective data
unintended consequences of Education
hidden curriculum: things you learn in educational setting that aren’t part of official curriculum
- values, norms, ways of interacting
- positive or negative
segregation: putting different things in different places
- legal segregation of schools
- still present in education systems due to uneven distribution of students based on race, ethnicity, poverty
stratification: arranging things in layers
- levels of socioeconomic status
- people with higher status have more options for access to education system
teacher expectations: may be based on stereotypes and may impact student performance
Family
kinship
Family defines early lives
kinship of descent: shared ancestry
kinship of affinity: based off marriage and adoption
primary kin: related through very close bond: parent child, marriage, siblinghood
secondary kin: primary kin of your primary kin
tertiary kin: primary kin of your secondary or secondary of primary
Family structure
Vary across cultures. change over time
ex. divorce rates, same sex partners
Violence and abuse can occur: physical, psychological, sexual, neglect
Religion
Institution with strongest impact
- function to replicate themselves over time and structure peoples lives
Provide rituals, community, ethical frameworks, important life events
religiosity: how religious a person considers themselves to be
Generally focus on christianity as practiced in Europe
Max Weber’s Sociology of religion
Religios organizations exists on a spectrum
churches (stable organized, bureaucratic)
then
denominations (diff interpretations, but same religious context)
then
sects (smaller dissident split off
cults: small tightly controlled and isolated
Religious modernizations
Cumulative impact of technological advance from last century
- secularization: decreased religiosity
- fundamentalism: literal, uncomprimising approach to religion
Governement organizes society by power and authority
Power: literal ability to get things done and compel certain behaviors
Authority: legitimacy and right of gov’t to structure citizens lives
Monarchy
Rulership/sovereignty is passed down in defined succession
- constitutional monarchy - UK
- absolute monarchy
Authoritarianism
Citizens have little to no input into gov’t
-
soft authoritarianism: have elections, limited choice of candidates
- gov’t minimizes its intrusion into citizens lives, but represses outward forms of dissent
Totalitarianism
Gov’t regulates every aspect of life, including citizens communication
Democracy
gov’t controlled by voting citizens
- direct: citizens vote for laws themselves
- indirect (democratic republic): citizens vote for representatives who then make laws
Capitalism
Private ownership of property and companies
Socialism
Collective ownership and distribution
- relies on state regulation
- recognizes private property
Communism
More extreme version of socialism, no sectors of economy under private ownership
Gov’t/Economic trends
Communism tends to be implemented by authoritarian/totalitarian gov’ts
Western European countries have implemented democratic socialism, allows private enterprise and market activity
Capitalism
Usually democratic nations
- Some authoritarian/totalitarian (especially fascists) states
Fascism
form of far-right, authoritarian ultranationalism characterized by dictatorial power, forcible suppression of opposition, and strong regimentation of society and the economy that rose to prominence in early 20th-century Europe
Division of labor
Leads to specialization
- Not all skills equally useful or demanded
- High demand skills
- highly specialized, higher wages
- Low demand skills
Medicalization
Treating medical conditions as social and cultural constructs
- addiction: used to be thought as a personal problem, now a medical condition
-
modern pregnancy care
- cold, clinical, and alienating
- leads to much lower death rates
- erectile dysfunction: used to be seen as unfortunate part of aging, now a medical condition
The “Sick Role”
A role that carries the rights and responsibilites of sick individuals in society
- Reflects social consensus that being sick is not your fault
- Sick people exempt from normal responsibilites
Sick people should typically follow the instructions of their doctors to get better
- exceptions: sometimes societies blame people for their illnesses especially those from lifestyle factors
- diabetes, smokers, obesity
Sick role works better. for acute illnesses than chronic conditions
Sick role not consistent across cultures
Medical Institutions
Hospitals: treat spectrum of conditions, inpatients
Doctor’s offices: non-hospitalized patients, outpatients
Acute care clinics
Medical ethics
Paternalism: doctor wants to do whats best for patient without informing them
Current paradigm of medical ethics
- Beneficence: acting for patients benefit
- Nonmaleficence: do no harm
- Respect for pt’s autonomy: pt’s make decision even if contradcit medical advice
- Justice: doctors provide care equally and fairly
The Illness Experience
Aim to analyze illness as a social construct
- how people experience becoming ill
- the decision of whether to seek care
- the experience of recovery
ex. some people see illness as punishment, others as a challenge
Epidemiology
Study of who gets illnesses and distribution patterns (by age, sex, location, behaviors)
- first applied to infectious diseases
- now all diseases
Socioeconomic status
Influence on health outcomes
Low SES populations have life expectancy up to 10 years shorter
Status and roles
How we situate in groups
status: any social category to identify people - very broad
Achieved status, ascribed status, master status
achieved status: status one works to attain, subjective
ascribed status: status assigned involuntarily, not based on actions
master status: status so dominant in someones life it crowds out other statuses
Role strain
Role conflict
Role exit
Role engulfment
Role strain: strain brought on by multiple responsibilities from one role
Role conflict: difficulty balancing multiple different roles
Role exit: process of disengaging from a role
Role engulfment: expansion of a role to dominate ones life
- closely related to what one does with energy and time
Primary groups
Secondary groups
Peer groups
Family groups
In groups
Out groups
Reference groups
Primary groups: long lasting with deep bonds, not always positive
Secondary groups: short lasting and more superficial
Peer groups: people often similar in age, status, background, interests, usually self selected
Family groups: people defined by genetic relationships and/or marriage/adoption
In groups: categories someone identifies as a member of
Out groups: categories someone doesn’t identify as a member of
- stereotypes, prejudice, discrimination
Reference groups: groups we compare ourselves to (evaluate self w/ reference to that group)
Dyads (2 people) less stable than
Triads (3 people)
Networks
Relationships b/w people/groups
Organizations
Coercive, normative, utilitarian
Subset of groups
- Specific structure
- Defined rules for entering/exiting
- Organization will exist once members are gone
Coercive organizations: people don’t choose to be apart of
Normative organizations: people join out of some shared ideal/ethical goal
Utilitarian organization: people join to make money
Types of Organizations
Bureaucracies
Ideal bureaucracy?
Rational, well organized, impersonal and typically large administrative systems
ex. gov’t, hospital, schools, courts
Studied by Max Weber in late 19th century
Ideal:
- Heirarchical
- Well defined roles, chain of command
- Organized by specialization
- Run impersonally
- Recruitment is technical, merit based
- Predictable career paths
- Politically neutral
Structural Organizations
Anarchist Collective
Democratic governance
Iron law of oligarchy
Anarchist collective: group w/o bosses with group-based, consensus oriented decision making
Democratic governance: flat organizational structures that minimize heirarchies
Iron law of oligarchy: group starts with democratic decision making will ended up dominated by small group
McDonaldization
Organizational approach that focuses on efficiency, calculability, uniformity, technological control
Emotional signaling
How we interact with each other; learned in childhood via socialization
- subconcious level: words, tone, facial expression, body language, text
- Physical stimuli and body language that communicate emotions
Difficulty observung emotional signals is sign of autism spectrum disorder
Signaling varies in cultures and b/w different groups
emotional signaling experimental findings
Male faces more likely to be interpreted as anger, females as sadness
Womaen may be more sensitive to emotional signals
Self Presentation
Self disclosure
Managing appearances
Ingratiation
Aligning actions
Altercasting
Self disclosure: what you disclose to others about yourself
Managing appearances: groom, dress, and act
Ingratiation: attempt to influence another person by becoming more likeable
Aligning actions: presenting your actions in a light that makes them more appealing in a certain setting
Altercasting: project an identity onto someone and then create an expectation that they should act the way you want
- ex. you’re premed so you should …
Front stage self vs. back stage self
How we present ourselves in front of audience vs. more authentic self, no longer in front of audience
Social Behaviors
Attraction
Sexual and friendly attraction
- physical attractiveness: a social construct, also objectively measurable correlates like facial symmetry
- attractive traits indicate suitability as a mate
Proximity: more likley to be attracted to people we see daily, more exposure effect
Similarity: more likely to be attracted to similar people
Social Behavior
Aggression
Impulsive behaviors regulated and restrained by
Defending against threats and obtaining greater access to resources
- used to reinforce and maintain social heirarchies
- testosterone levels in both sexes
Impulsive behaviors regulated and restrained by prefrontal cortex
- stem from emotional arousal mediated by limbic system
Also shaped by ones personal experiences
Molded by society norms and expectations
Social Behavior
Attachment
Bonds that form b/w children and their caregivers
- consistent, responsive caregiver leads to secure attachment
ambivalent attachment: inconsistent caregiver, intense distress when they leave
avoidant attachment: neglectful relationship, child doesn’t care
disoriented attachment: abusive caregiver, hesistant contradictory and confused behavior
Social Behavior
Altruism
Helping others at some cost to yourself
- puzzling behavior, rational choice theory
- Structured gift giving
Social Behavior
Social Support
Emotional, informational, tangible/material support, companionship support
Positive health outcomes
Biological explanation for social behaviors in animals
Foraging: how animals search for food; behaviors often learned, economic models can help make sense
Mating: animals have wide range of ways in engaging in courtship, copulating, and raising offspring
- mate choice: can be random, some respond to phenotypic signals (for genetic fitness or seemingly random (Fisherian selection))
Game theory: math that deals with decision making in gamelike scenarios
- ex. prisoners dillema: whoever cooperates gets off, if both do they go to jail, if both don’t nothing happens
Altruism: evolution that focuses on the gene, not the individual
- share genotypes with relatives
- inclusive fitness: natural selection operates at the group level
Social facilitation
People perform tasks better in group setting when psychological arousal is higher
- when situation gets too stressful, performance breaks down
Social Loafing
People work less hard in a group setting
- others pick up slack
- often not deliberate conscious choice
Bystander effect
People tend not to offer help to someone if others present
- diffusion of responsibility in a crowd
- model our behavior based on those around us
- social etiquette
case study: Kitty Genovese murder 1964
Deindividualization
Less of sense of self awareness ina large group due to psychological arousal
- lower perceived responsibility - dance clubs, raves
- contributing factors
- anonymity
- diffused responsibility
Group polarization vs. groupthink
Groupthink- pyschologist, associated with what historic event
Group polarization: group of people will arrive at final opinions that are more extreme than the initial positions of the individual members
- initial opinions get amplified
- “echo chambers” effects social media, people interact with similar people
- politics
-
contributing factors:
- informational influence : people in a group are more likely to press points in line with dominant viewpoint
- normative influence: our desire to be socially accepted, affirmed or admired within a group
- **Doesn’t have to be irrational, doesn’t require decision-making
Groupthink: irrational decisions made in groups due to pressures towards harmony and individual conformity
- psychologist Irving Janis proposed groupthink to explain Nazi invasion
-
characteristics:
- illusion of invulnerability: no serious harm will come to group
- illusion of morality: unbending belief in the moral righteousness of the groups cause
- illusion of unanimity: group assumes the majority of opinions in the group are unanimous
- self censorship: members who disagree dont share opinions
- pressure of dissenters: pressre not to contradict the majority
- collective rationalization: group finds reasons to ignore warnings and avoid reconsidering actions
- excessive stereotyping: negative views of outside opinions
- mind guards: certain members filer info that could destabilize consensus
- always involve irrational decisions made by group
Conformity
Someones behavior, beliefs, or thinking changes to line up with perspectives of others
- someone simply behaving the same way as a a group is not necessarily conformity
- convergence
- Internalization or conversion: genuine change in someone’s beliefs
Two kinds of compliance
Identification, Asch experiment
Foot in the door, Door in the face, lowball
Compliance: person conforms but internally dissents
- not the same as compliance to requests
-
identification: persons belief change only only in presence of group
-
Asch experiment: each subject shown a card with a line and another w/ 3 lines
- which line is same length as first card
- subjects repeat incorrect answers
-
Asch experiment: each subject shown a card with a line and another w/ 3 lines
Compliance: responses to requests from someone with no power to enforce the request
- marketing and sales pitches are request related compliance
- tactics:
- foot in the door: making a small request followed by a large one
- door in the face: making a large request you know will be rejevted followed by a small more reasonable one
- lowball: offer low price and raise it at last minute
Obedience
Change in behavior in response to a direct request from someone with power to enforce it
Stanford Prison Experiment (1971)
Students either guards or prisoners
- prisoners treated harshly by guards
- prisoners showed real suffering and guards showed sadistic tendencies
- showed how people readily conform to social roles
Social Norms
Formal
Informal
Taboos
Rules, spoken or unspoken, that regulate behavior, beliefs, attitudes, and values of members of society
- Formal: encoded somewhere, penalties for violation
-
Informal: not written, expectations with no penalties
- Folkways: insignificant informal norms that involve small details
- Mores: informal norms, incur severe disapproval when violated
-
Taboos: even more restrictive norms that generate extreme disapproval
- ex. incest
- blur line between formal and informal
Social control
Sanctions
Peer pressure
The way norms are taught, enforced, and perpetuated
- More general phenomenon
- sanctions: punishment/negative consequences for violating a social norm or reqards for following one
- peer pressure: desire for approval or fear of disapproval
Deviance
When someone doesn’t conform to the norms
Anomie
lack of the usual social or ethical standards in an individual or group.
Types of deviance: (not mutually exclusive)
Differential Association Theory
Labeling Approach
Primary deviance
Secondary Deviance
Strain Theory
Differential Association Theory: views deviance as behavior that is learned socially
- draws from symbolic interactionism
Labeling Approach: behavior affected by being labeled a deviant
Primary deviance: deviant acts committed before being labeled
Secondary Deviance: deviant acts committed after being labeled
Strain Theory: social and economic pressures towards deviance
Socialization
Agents of socialization
How we learn informal and formal norms by interacting with other people/institutions
- agents:
- family
- educational system
- mass media
- peers
- workplace
Fads
New behavior becomes extremely popular, then fades
Mass hysteria
Irrational fear of a perceived threat, verging on the point of a collective delusion
Riots
Spontaneous episodes of civil disorder
- classic example of deindividuation
Percent Yield
Percent Error
Actual/theoretical x 100
Actual -Theoretical /Theoretical x 100
ATP
Adenosine Triphosphate - cellular energy
- Protein synthesis, glucose metabolism, intracellular transport
- nucletotide adenine and ribose sugar
- form nucleoside adenosine
- 3 phosphate groups
- alpha, beta, gamma
- gamma is unstable, ATP hydrolysis
- alpha, beta, gamma

ATP Hydrolysis
ADP phosphorylation
ATP loses phosphate group and is hydrolyzed to ADP
- Addition of a water molecule
- Releases large amount of energy, highly favorable and spontaneous
ADP phosphorylation unfavorable, nonspontaneous
ATP formation
Substrate level phosphorylation
Oxidative phosphorylation
Substrate level phosphorylation
Occurs during glycolysis and TCA, involves transfer of phosphate group from a glycolytic intermediate to ADP
- Enzyme catalyzed and coupled with favorable spontaneous reaction to help drive forward the nonspontaneous phosphorylation
- ex.
-
***final step of glycolysis, ADP phosphorylation paired with exergonic cleavage of phosphoenol pyruvate by pyruvate kinase yields pyruvate and ATP
- ***also occurs in citric acid cycle, except forms guanisine triphosphate GTP
-
***final step of glycolysis, ADP phosphorylation paired with exergonic cleavage of phosphoenol pyruvate by pyruvate kinase yields pyruvate and ATP
Oxidative Phosphorylation
Vast majority of ATP in eukaryotes
- Redox reactions involving NADH and FADH2 electron carriers that feed electrons taken from glycolytic substrates and citric acid intermediates into ETC
- As electrons passed through transport chain, protons pumped from mito matrix into intermembrane space
- electrochemical proton gradient
- Protons return to matrix by diffusing through ATP synthase, forms ATP
**Can only occur in presence of oxygen, terminal electron accptor of transport chain
- Substrate level phosphorylation doesn’t req oxygen
Guanosine triphosphate
Produced in citric acid cycle
- Powers biological reactions involved in signaling cascades and protein synthesis
High energy bonds in molecules besides ATP and GTP
Thioester bond of Acetyl CoA
Bonds in NADH and FADH2
Electrochemical cells are batteries
Involve
Redox reactions
Redox reactions are the
transfer of electrons (OIL RIG)
Reduction: gain of electrons, more bonds to hydrogen
Oxidation: loss of electrons, fewer bonds to hydrogen, more to oxygen
When an atom (usually carbon) gains a bond to oxygen, oxidation has occured
Alkynes most oxidated, alkanes most reduced
NAD+ and NADH
When NAD+ is converted to NADH, it gains two things: First, a charged hydrogen molecule (H+) and next, two electrons. As electrons are negatively charged, the combination of the positively charged NAD+ and H+, coupled with two electrons, effectively cancel each other out and neutralize the resulting NADH molecule. This is why NADH does not have a “+” sign next to it.
Electron Carriers
NADH and FADH2
- Reduced versions
- Transfer electrons to protein complexes of ETC
- When reduced, coupled with an oxidation of a different molecule
FADH is semi reduced form
Electron carriers are formed in glycolysis, citric acid cycle, and beta-oxidation
Electron transport chain
Electron carriers are formed in glycolysis, citric acid cycle, and beta-oxidation
- Then they’re oxidized by protein complexes in inner mitochondrial membrane
- Pass their electrons to protein complexes which act as pumps, use energy gained from electron transfers to drive hydrogen ions (protons) against their conc gradient
Proton gradient powers oxidative phosphorylation via ATP synthase
Final electron accpetor in ETC is a diatomic oxygen which is reduced to water

Reduction potential E°
Some atoms/molecules want to gain electrons (be reduced) and some want to be oxidized
E°: how bad an atom/molecule wants to be reduced
** the more positive the reduction potential, the more a substance likes to be reduced
- tells us electric potential difference that results from the substance being reduced
- electric potential difference: not the same thing as energy; how energetically favorable reduction is
Reduction potential and redox in ETC
When each protein complex in sequence is reduced, it oxidizes the complex that comes before it
- each successive complex has more positive reduction potential, energy is released
-
wants to be reduced miore
- energy used to pump protons
-
wants to be reduced miore
3 biomolecules in human body that can be broken down for energy
Carbohydrates
Lipids
Proteins (to a lesser extent)
Glucose monomer is cells predominant source of fuel because
Can be easily stored as glycogen and its catabolism liberates lots of ATP via aerobic respiration
- under anaerobic conditions, glyolysis produces way less ATP
Glucose transport
Hydrophilic -> readily diffuse in bloodstream
- too large and polar to diffuse across plasma membrane
- special transmembrane transporters needed
- different types for diff purposes
GLUT1 transporter
Nearly all tissues, especially fetal, erthyroctyes, and cancer cells
Baseline cellular uptake, expression increases when glucose is low
GLUT2 transporter
Liver, kidney, and pancreatic cells
Bidirectional transport for glycolysis, glycogenesis, gluconeogenesis uptake and export
GLUT 3 transporter
Neurons, placenta
High glucose affinity, transports glucose into cell when when extracellular conc is low
GLUT4 transporter
Skeletal and cardiac muscle, adipose tissue
Storage as glycogen or triglycerides, upregulated by glucose and insulin
Insulin sensitive
Type 2 diabetes- GLUT4 becomes insensitive to insulin, stops being expressed at normal insulin levels
- difficult to correct blood sugar spikes
Resonance in peptide bonds causes:
Planar geometry
Restricted rotation of peptide bonds
Exceptional stability of amides

Conjugation (pi systems)
3+ pi orbitals align with each other, electrons delocalize throughout
Absorbs UV light, easily detected by UV sprectroscopy
Aromaticity
Electron delocalization
Huckels rule: 4n +2π electrons
- pyridine, pyrimidine, purine all aromatic
- imidazole
- pyrrole
Work
Something accomplished using energy
- measured in Joules
- 1 J = 1 N x m
W = F d or W = Fdcosθ
W = P ∆V
Mechanical advantage
Using a mechanical apparatus to perform work using less force
- inclined plane, pulley, seesaw
- for ramps, incline length /incline height gives the amount of force increased by just going vertically
Winput = Woutput
Increasing distance decreases force put in, increases force put out
Power
W/t (J/s) Watts
- the faster a system can do more work, the more powerful it is
Energy
Capacity of an object to do work
E = KE + PE
- all obj in motion have kinetic energy
-
KE = 1/2mv2 Joules
- mass in kg
Potential energy is stored in an object, comes in many forms
PEgrav= mgh
PEelastic= energy stored in obj due to compression
- 1/2kx2
Conservation of Energy
Energy can be neither created nor destroyed, only changed
- all energy creation is conversion from another form
closed system: no energy transfer (as heat)
Nonconservative force
Any force that causes energy to be lost from a system to the environment
- Friction and air resistance
PEi + KEi = PEf + KEf
ghi + 1/2vi2 = ghf + 1.2vf2 (mass cancels)
Work Energy Theorem
W = ∆E
Positive work= work done on an object by its environment, increases objects energy
Negative work= work done by an object on environment, decreases objects energy
Consciousness
Awareness that we have of our surroundings, internal states and ourselves
Medical: humans aren’t always conscious
- can vary in terms of degree and quality
- impaired by head trauma, sleeplessness, and substance abuse
Levels of awareness
Alertness (what brain structures), tiredness and fatigue
Alertness: increased awareness
- important brain structures: reticular formation and reticular activating system
- reticular formation: complex network of neuron clusters
Tiredness and fatigue: decreased awareness
sleep: temporarily and easily reversed loss of consciousness
Deeper unconscious is not easily reversed
Coma: lost consciousness, doesn’t react normally to stimuli, doesn’t move voluntarily, is not in normal sleep/wake cycle
Sleep
Crucial to our ability to live
Chronic low-level sleep deprivation is associated with a range of bad outcomes, poor cognitive perormance, increased risk of obesity, heart disease, diabetes
Measuring sleep
Electroencaphelogram (EEG): brain activity
EMG: muscle activity
EVG: eye activity
Polysomnography: sleep study measuring multiple physiological parameters
Sleep
Alpha vs Beta waves
Fully awake: beta waves, low frequency, high amplitude
Alpha waves: relaxed, calm, meditation, lower frequency
REM sleep (rapid eye movement)
- Quick bursts of eye movement
- Similar brain waves to beta/alpha
atonia: little muscle movement
- irregular breathing, heart rate (interupted homeostasis)
- Majority of dreaming
REM stages get longer as night progresses
Greater total REM sleep = more restful
REM rebound: catch up on REM after missing sleep
Non- REM sleep
3 stages
Stage 1:
-
theta waves: low frequency and low amplitudes
- slow eye movement, light sleep
Stage 2:
- theta waves with K-complexes: high amplitude bursts
-
sleep spindles: occ high freq bursts
- eye motion stops, heart rate and breathing slows
Stage 3
-
delta waves: high amplitude
- deep sleep (slow wave)
- memory processing and rest
- deep sleep (slow wave)
Sleep cycle times for adults and children
Adults have 90 minute cycles, children have 50 minute cycles

Regulating sleep
Circadian rhythm
Drowsiness and wakefullness come from?
Circadian rhythm: 24 hr sleep/wake cycles
Pineal gland -> melatonin -> drowsiness
Adrenal cortex -> cortisol -> wakefulness
Insomnia
Difficulty falling asleep
Narcolepsy
Excessive daytime sleepiness
- abnormal REM sleep
- cataplexy: loss of muscle control, sleep paralysis
- hypnagogic hallucinations
Sleep apnea
Airway obstruction during sleep
Dyssomnias
Parasomnias
Disorders impairing ability to fall/stay asleep
Parasomnias: disorders involving abnormal behavior while asleep
- sleepwalking (somnabulism)
- night terrors - sleeper suddenly plunged into fight or flight response
- nightmares
Dream Content (Freud)
Manifest: surface level details
Latent: underlying meaning
Wish fulfillment: resolution of respressed conflict
Activation/synthesis model (dreams)
Neurons activate during REM and synthesize experience
Problem-solving theory (dreams)
Dreams as a way of processing/resolving real world problems
Cognitive Theory (dreams)
Dreams are a visualization of our cognitive processes
Hypnosis
Hypnotist induces a hyper suggestive state in a subject
- extremely responsive to certain suggestions even after session
- Receives considerable skepticism
Meditation
Has been a part of religious traditions
- quieting the mind, focusing attnetion
- Beginners experience alpha waves, more experienced practitioners have theta waves
Included in wellness approaches
Consciouness altering drugs
Caffeine
Caffeine- stimulant, increase activity in CNS
- mimic sympathetic NS response, fight or flight
Antagonizes (blocks) adenosine (sleepiness) receptors
Addiction
Pattern of compulsive behavior that repeatedly engages reward pathway
- behavior persists despite negative consequences
- dependence: absence of drug causes withdrawal symptoms
*biggest difference is compulsion and negative consequences
tolerance: heavy users need more of a drug for same effect
Stimulants
Nicotine
Amphetamines
MDMA
Cocaine
Nicotine
highly addictive
15% of adults smoke
Amphetamines
Increased energy and alterness
- concetration and focus
- appetite reduction
- mood swings, psychosis
Medication for ADHD
MDMA
Ecstacy or molly
- empathy and pleasure
- energy, focus, appetite reduction
- Promotes serotonin, norepinephrine, dopamine release
- depletes serotonin reserves
Cocaine
Strong stimulant, blocks serotonin, dopamine, norepinephrine reuptake causing buildup in brain
- often inhaled, processed to smokable form of crack
Depressants
Reduce activity in central NS; psychological and physiological effects, lowers heart rate, blood pressure, etc
Alcohol
Barbiturates and Benzodiazepines
Opioids
Endorphins
Hallucinogens
Marijuana
Alcohol
Enhances action of GABA receptors (main inhibitory neurotransmitter)
- makes neurons fire less often, slowing brain down
- Low doses reduce conscious inhibitions and planning activity
Higher doses affect speech, motor function, cognition, memory, etc.
- anterograde amnesia: blackouts, inability to create new memories
Long term alcohol use elevates risk of cardiovascular disease/cancer
Once dependent on alcohol, stopping can lead to unpleasant or fatal withdrawal
- hallucination anxiety seizures
Alcohol overdose
Breathing stops –> death
acute alcohol intoxication
Korsakoff syndrome
Associated with chronic alcoholism
- anterograde amnesia: events starting after syndrome develops
- retrograde amnesia: events before can’t recall
confabulation: invented memories
Barbiturates and benzodiazepines
Increase GABA receptor (inhibitory) activity
- Treat anxiety and insomnia
- HIgh risk of overdose, addiction, and withdrawals
- Don’t mix with alcohol
Opioids
symptoms, types
Cause sedation, sleepiness, respiratory depression
Pain relief, euphoria
Bind opioid receptors on neurons
morphine: derived from opium poppy
heroin: synthetic morphine derivative
- makes you feel heroic
- thought to be non addictive
Codeine, hydrocodone, oxycodone, fentanyl
Endorphins
Produced by body, naturally interact with opioid receptors
Block pain, induce euphoria
- runners high
- morphine and heroin are extremely potent endorphin agonists
Hallucinogens
Distort perceptions, enhance sensation, promote introspection
- LSD, ketamine, peyote, psilocybin, PCP
- Complex mechanisms
Marijuana
THC (tetrahydrocannabinol) is the psychoactive component of marijuana
- Bind with cannabinoid receptors in brain
- Body naturally produces endocannabinoids
- processes of appetite, mood and pain sensation
CBD: non psychoactive cannabinoid in marijuna
Complex profile of effects- stimulant, depressant, hallucinogenic
Addiction
Compulsive behavior that triggers reqard pathway and is repeated pathologically despite negative consequences
- mesolimbic pathway = reward pathway
prefrontal cortex: decision making
nucleus accumbens: dopamine uptake and motivation; associated with otivation and reinforcement learning
amygdala: memory and emotion
ventral tegmental area: dopamine release
Dependence
Someone requires a drug to function normally
- more stable than addiction, without the compulsivity
- discontinuing may lead to withdrawal
Attention
ability to direct our awareness to a single aspect of external stimuli
Selective attention
Can be thought of as a spotlight
focus: full attention
fringe area: no attention
margin: partial attention
Donald Broadbent - attention
Basic sensory info enters a sensory buffer
- from the sensory buffer, the mind selects something to focus on and process
- other info decays
Dichotic listening task- only pay attention to audo from one side of the headphones
shadowing: repeating words instantly, no memory component
We process info we are focuing on much more than other info
Cocktail Party Effect
Can “tune in” to a particular stimulus, like a name being said from across the room
Background info is processed to some degree even if not the center of focus
Treisman Model
Unattended info is attenuated (reduced in intensity)
- intense/important info can come to attention
- explains cocktail party effect
Inattentional Blindness
Direct attention causes people to miss things happening in the background
- Invisible gorilla experiment
Change Blindness
Failure to notice changes that take place
Unattended Stimuli
Color and design might subconsciously affect our mood and behavior
Multitasking
Can we do it?
What happens in our brain when we do?
Simultaneous or sequential attention
Most multi tasking is sequential attention (jumping back and forth)
- Might perceive it as simultaneous attention because the switching happens quickly
Multitasking degrades one’s ability to perform complex tasks in comparison to in isolation
We have a certain capacity for attention that we allocate among tasks - proposed by Daniel Kahneman
Allport’s module reesource theory
Attention comes from distinct, specialized modules of the brain
Multitasking easier with different types of tasks
Controlled processing
Conscious focus on a task
- skills often start out requiring controlled processing
Automatic processing
Unconscious work on a task, “autopilot”
- with practice, skills can become automatically processed
- Requires less attention, allows for more multitasking
Attention Deficit Hyperactivity Disorder (ADHD)
3 types
- Predominantly inattentive
- not paying close attention to details
- Trouble sustaining attention to details
- Easily distracted
- Predominantly hyperactive
* impulsive - Combined
Information processing model
Contrasts what model?
Mind is a computer that receives data, processes some of it, then decides what to do
- contrasts behaviorism: asserted only behavior can be studied scientifically
Jean Piaget - developmental psychologist of 20th century
1st developmental stage:
Proposed stages of childhood
1st developmental stage: sensorimotor
- birth to 2 y/o
- interact with world through processing sensory input and engaging in motor activities
Object permanence: things dont go away when you stop seeing them
Circular reactions: repitition of accidental or reactional actions
Stranger anxiety (8 or 9 months): strangers provoke intense worry
Jean Piagets developmental stage 2
Preoperational stage: 2 to 7
- represent objects symbolically with words/images
egocentrism: difficulty imaging the world from the perspective of others
centration: tendency to focus on a single property/parameter
ex. taller grass means more water
lack of conservation: same amount of substance is preserved in different shapes
Symbolic thought but minimal abstract reasoning
Jean Piagets developmental stage 3
Concrete Operational Stage- 7 to 11
- Develop an understanding of conservation
- Loss of egocentrism
- Develop logical reasoning skills
- Perform better at inductive rather than deductive tasks
Jean Piagets developmental stage 4
Formal Operational Stage: 11-16
Abstract logic
Can handle hypotheticals, reason abstractly, and make nuanced moral judgment
- nuanced: subtle shades of meaning or expression
Schema: cognitive framework that organizes info about things that one perceives in the outside world, with implications for the actions that can be taken in response
ex. encounter cow that is yellow; either cant be a cow = assimilation or cows can be different colors accomodation
Fluid vs. crystallized intelligence
fluid: problem solving skills that can be applied to new situations without any reliance on previous knowledge
crystallized intelligence: ability to deploy one’s knowledge and skills to solve problems
Age
Dementia
hepatic encephalopathy
Cognitive performance an decline with age
dementia: cognitive decline and memory impairments interfere with a person’s ability to function in the world
- multiple symptoms with multiple causes
- causes include Alzheimer’s disease (accumulation of B-amyloid plaques), tiny brain bleeds, etc.
hepatic encephalopathy: liver can no longer effectively remove toxins which impacts brain function
Trial and error
Try different options and see what works
- reflects lack of conceptual understanding, used when we have the timeresources to explore many possible solutions
Modern drug design
Thomas Edison
Algorithm
Involves applying a fixed set of steps
- designed with preparation and insight
- Application requires no conceptual understanding of the problem
Very specific instructions
ex. having a routine for solving physics problem but not understanding conceptually
Deductive reasoning
Top down
Applying general principles to a specific situation
Inductive reasoning
Bottom up
Successive observations extrapolated to identify general principles
- vulnerable to overgeneralizations
Analogies
Problem solving
Used to solve a porblem similar to one we’ve seen before
- closely related to intuition
Intuition
Gut sense of how to solve a problem
- corresponds to analogies that we aren’t consciously aware of
Mental set
The framework that we use for conceptualizing a problem and trying to solve it
Fixation
Functional fixedness
Getting stuck in existing ways of thinking about things
Functional: tendency to see objects as only having a certain function
Belief perserverance
Maintaining or strengthing beliefs in the face of contradictory evidence
Cognitive processes can be impeded by
cognitive biases: systemic, generally subconscious patterns of thought that skew reasoning
Confirmation bias
Reasoning in a way that favors info supporting our preexisting conclusions/beliefs
ex. more likely to notice news we agree with
Cell Cycle two parts:
Interphase
Mitosis