4 Flashcards
Hindsight bias
In retrospect, events seem more predictable and obvious
- Very common in medicine
Causation bias
Thinking that events closely related in time share a causal link
- post hoc ergo propter hoc
- after this, therefore because of this fallacy
Mistake correlation for causation
Heurisitics
Mental shortcuts and problem solving methods
- fixed, rigid processes to arrive at a quick answer, even from incomplete information
Examples of heuristics refer to ways that we assess probability of certain outcomes
Biases
General cognitive patterns that affect our decision making processes
Representative heuristic
Making decisions based on prototypical examples
- usually when estimating probability in everday life
- ex. looking like a criminal
Availability heuristic
How likely we think something is to occur
Influenced by readily available info
ex. Rare crime news stories, thinking they could happen to us
Second year syndrome
Learning about rare syndromes and thinking any symptom could be caused by it
Intelligence
Ability to:
- Detect patterns
- Process and store info
- Understand ideas
- Solve problems
Charles Spearman
Noticed correlation in performance in different subjects
- children who did well in history did well in math
- not a perfect correlation
General intelligence (g factor)
Underlying capacity that drives performance in may fields
- about 50% heritable
Francis Galton
Inspired by work of Charles Darwin, laid foundation for eugenics which embraced selective breeding
- endorsed racist ideas
- provided framework for unethical practices
- wrong turn in biology and anthropolgy
However wrote book about hereditary genius
Alfred Binet
The IQ scale, estimation of a child’s mental age relative to their chronological age
- mental age/chronological age x 100
Doesn’t apply well for adults
In adults, IQ is an estimate of geneal intelligence
IQ distribution
Normal distribution, few people have extreme low or high
68% within 1 SD of mean
95% of pop within 2 SD of mean
SD is +/- 15 points
Mean is 100
IQ controversy
IQ tests are high stakes
Can influence education a child receives
Flynn effect
flynn effect: describes how IQ scores increased in developed countries in 20th century
Howard gardner multiple intelligences
Make up g-factor
- Musical
- Visual-spatial
- Verbal-linguistic
- Logical-mathematical
- Bodily-kinesthetic
- Interpersonal
- Intrapersonal
*8. Naturalistic- relate to/pick up patterns in natural world
Emotional intelligence
Recognition of one’s own emotions and those of others
- emotional self regulation
- proposed it was an equal counterpart to traditional intelligence
- EQ
Language
Structure and underlying similarities of all human languages
- cognitive aspects of learning and using linguistic systems
Phonetics
Study of physical production and reception of speech sound
- anatomical parts of speech and hearing
Phonology
Organization of sounds into meaningful units
Morphology
Study of word formation
ex. eat –> ate
Syntax
How words are joined together to form phrases/sentences
Semantics
Literal meaning
Pragmatics
Non-literal meaning
- depends on context, body language, time
American sign language has its own
Grammar and words
Behaviorism
B.F. Skinner
observable behavior
Learning theory of language
Nativist theory
Generative linguistics
Interactionist Theory
Learning Theory of Language
Language as behavior based on environmental input
- no innate language capacity
Nativist Theory
Noam Chomsky
Humans have innate (genetic) capacity for language
Generative linguistics:
grammatical rules which govern sentences, certain sentence structures don’t work
Interactionist Theory
Language is acquired during social interaction
- language leaning is interactive and functional
Benjamin Whorf
Sapir-Whorf
Studied Hopi language
No past/future tenses, no sense of time passing continuously
Sapir-Whorf (linguistic relativity): grammatical categories and vocabulary influence thought
Linguistic determination
Grammatical categories determine thought
Aphasia
Wernicke’s aphasia
Broca’s aphasia
An impaired ability to communicate
Wernicke’s aphasia: impaired language comprehension aka fluent aphasia
Broca’s aphasia: understand language but impaired speech production
Arcuate fasciculus
Connects broca’s and wernickes areas
conductive aphasia: arcuate fasciculus lesions cause difficulties with repeating other peoples words
RNA world hypothesis
RNA stored info and catalyzed reactions before DNA
Transcription
Similar to replication
- Copying DNA into complementary strand, both occur in nucleus
- Don’t have to worry about lagging or leading strands or replicating ends of chromosomes
- Douple helix unzipped by helicase, kept open by single stranded binding proteins (SSBP)
2. Tension created upstream relieved by topoisomerase enzyme
- RNA pol catalyzes transcription; locates specific sequences for genes its interested in
- upstream promoter TATA box, A-T rich sequence recognized by RNA pol
- bonds with the help of transcription factors
** Reads DNA template 3’ to 5’, makes mRNA 3 to 5
- Reaches transcription terminator sequence
RNA pol proofreading ability is
Not as accurate as DNA polymerase
Error rate higher, not as high of a risk
Template (antisense) strand
Strand being read by RNA pol in transcription
Coding (sense) strand
Sequence identical to new RNA with thymine instead of Uracil
RNA pol I
RNA pol II
RNA pol III
Synthesizes rRNA in nucleolus
Synthesizes hnRNA (heteronuclear)(mRNA precursor)
SYnthesizes tRNA, some rRNA
Prokaryotic transcription and translation occur…
In prokaryotes, new RNA is immediately ready to be translated
- Transcription and translation occur simultaneously on same RNA molecule
Prokaryotic RNA is polycistronic, can code for multiple proteins
heteronuclear hnRNA posttranscriptional modification
polyA tail
5’ cap
splicing
pre mRNA that undergoes posttranscriptional modification
- RNA gains polyA tail at 3’ end: facilitates binding to nuclear export proteins, assist with mRNA translocation through pores in nuclear membrane
- main purpose is to protect mRNA from degradation in cytosol when going from nucleus to cytosolic ribosomes
- degradation by 3’ exonucleases
- more adenine residues = better defense
- 5’ cap: one nucleotide modification, triphosphate linkage
- protects mRNA against degradation, facilitates nuclear export (recognized by tranport proteins)
- also recognition for ribosomes
- RNA splicing- splicing introns
pre mRNA splicing
Enzyme?
introns: intervening sequences of noncoding, spliced
exons: expressed sequences which are ligated back together
Catalyzed by splicosome made up of proteins and snRNA which combine to form snRNP (small nuclear ribonuclear proteins)
- snRNPs recognize marker sequences at end of introns, pulling them together to form lariat loop
One mRNA precursor can be spliced to code for different proteins
Ribozymes
RNA components capable of enzymatic activity
Translation - protein from RNA
secreted vs. cytoplasmic proteins
Ribozyme?
RNA nucleotides arranged in triplet codons and code for aminos
secreted proteins: membrane bound ribosomes on rough ER, fed into ER then directed to golgi apparatus -> secretory vesicles
cytoplasmic proteins: come from free ribosomes in cytoplasm
Ribosomal rRNA: ribozymal component of ribosomes, catalyzes formation of peptide bonds
Degeneracy
Multiple codons can correspond to one amino acid
tRNA:
clover leaf hairpin secondary structure, recognize triplet codons on mRNA and attach corresponding amino acids to growing chain
each tRNA has unique anticodon complementary to mRNA codon
tRNA becomes “charged” when bound to corresponding amino
- to charge tRNA with correct amino
-
amino acyl-tRNA synthetase links C-terminus of aminos to 3’ end of tRNA
- requires ATP, which energy is later harnessed to create peptide bond
-
amino acyl-tRNA synthetase links C-terminus of aminos to 3’ end of tRNA
wobble hypothesis:
1 tRNA can recognize several codons, usually where 3rd amino differs – creates same amino
Synthesizing protein is
Expensive to cell in terms of ATP (charging tRNAs)
- *One reason gene expression is tightly regulated, so ATP isn’t wasted
- Makes only necessary proteins
Steps of Translation - Initiation
- Small ribosomal subunits recognize and binds specific mRNA sequence
- in prokaryotes, location is the Shine-Dalgarno sequence in 5’ untranslated region upstream of start
- In eukaryotes, recognize 5’ cap and intiator tRNA binds to start codon AUG
- tRNA is always charged with methionine first
2. initiation factors facilitate binding of large subunit to small, forming initiation complex
Steps of Translation - Elongation
- Ribosome with elongation factors read mRNA 5’ to 3’
- one triplet codon at a time
- Ribosome synthesizes polypeptide from N-terminus to C-terminus
- N-C polarity of all aminos
- Ribosome assemply has 3 binding site for tRNA: A acceptor site, P peptidyl site (forms peptide bond), E exit site, uncharged tRNA leaves
* tRNAs move over exposing A site
Steps of Translation - Termination
Occurs when ribosome encounters 1 of 3 stop codons: UAA, UAG, UGA
Don’t code for an amino, instead recognized by release factors at P site
Ribosome evicts protein and moves onto next mRNA
Where does postranslational modification occur?
Types?
Mostly in rough ER and golgi apparatus
- addition of carbohydrates and some protein cleavage
- proteins can be covalently linked to variety of functional groups
- ex.
- phosphorylation: adding high energy phosphate group by kinase enzymes
- ex.
Glycolysation: addition of carbohydration moieties, often catalyzed in golgi apparatus
Ubiquitation: addition of ubquitin proteins, used to designate proteins for degradation in the cell
Protein folding, disulfide bonds, proteolytic processing
phosphorylation:
adding high energy phosphate group to proteins or other molecules by kinase enzymes
Glycolysation:
addition of carbohydration moieties to proteins after translation, often catalyzed in golgi apparatus
- relevant for ABO blood typing; based on presence/absence of A and B glycoproteins on red blood cells
Posttranslational modification
Ubiquitation:
addition of ubquitin proteins, used to designate proteins for degradation in the cell
After synthesis, proteins folded into 3D conformation by
Chaperone proteins in cytoplasm or ER
Posttranslational modification
Disulfide bonds
Bonds between neaby cysteine residues, linking two parts of a protein
- Maintaining tertiary structure
Posttranslational modification
Proteolytic processing
Cleaved at specific sites, sometimes to generate two separate peptides with unique functions
- Also activates proteins sometimes
Peptide prohormones cleavage
Why?
Preprohormone which is cleaved into prohormone which is cleaved into hormone before relased from cell
** Prevents premature activation, which can be dangerous
ex. Pancreas contains host of proteolytic enzymes for digestion in dormant state
- only activated in small intestine for digesting proteins
- in acute pancreatitis become prematurely activated; rampant proteolytic activity
Cells contain same genome but are expressed and regulated differently
Diploid human cell contains about 20,000 genes but only express specific subsets at specific times in response to specific stimuli
During development, complex signaling patterns induce cell differentiation
Stem cells into diff tissues and specialized cell types
stem cells: relatively undifferentiated cells capable of differentiating
- embryonic and somatic
Types of stem cells
Mesenchymal stem cells: produce fat, bone, and liver cells
Intestinal stem cells
Hematopoietic: generate blood cells
Stem cell potency
Limits to their cell differentiation
totipotent: can differentiate to any type of cell
- in humans, only embryos up to morula or 16 cell stage
pluripotent: capable of differentiating into many different cell types
- ectoderm, mesoderm, endoderm (primary germ layers)
- can’t differentiate into cells of placent
multipotent: adult, limited subset of cell types within germ layer
Totipotent and pluripotent can be used for generating tissue and organ grafts, controversial
- cancer cells can become less differentiated and pluripotency can be artificially induced
Apoptosis
Programmed cell death, intentional
- critical role in embryonic development
- ex. webbed fingers before apoptosis
Checkpoint for when things go wrong
Prokaryotic Gene Expression
Operon: genetic system used by prokaryotes to regulate the expression of specific genes; under positive or negative control
- contains regulatory sequence with promoter, and operator
positively controlled gene: genes expressed when activator present
- activator molecule binds to regulatory gene
negatively controlled gene: genes expressed unless repressor present
- repressor binds to operator
lac Operon
Negative inducible; expression induced by removal of repressor
negative inducible: default is off, expression induced by specific signal removed repressor
trp Operon
PROKARYOTES (has operon)
Expression is repressed by binding of repressor
- negative repressible: default is on
Contains genes for synthesis of amino acid tryptophan
- abundant supply tryptophan represses transcription
Eukaryotic Gene Regulation/Expression
Much more complex. Short sequences recognized by mediator proteins which recruit RNA pol III
TATA box bound by TATA binding protein which associates with other proteins to act as a transcription factor for RNA polymerase
-
transcription factors: bind to specific DNA sequences to regulate gene expression; recruit other regulatory proteins that make chemical modifications to DNA
- *play pivotal role in activity/identity of given cell
Enhancers
Gene expression
Sequences which promote enhanced expression of genes in response to stimuli, can be upstream or downstream
- bind to transcription factors known as activators which twist DNA into a hairpin
- brings enhancer region closer to gene sequence to facilitate intiation of transcription
ex. estrogen binding its nuclear estrogen receptor, which then binds enhancers
Silencers
Gene expression
Sequence that when bound by a repressor, silence or repress expression of genes
Types of DNA modification
In nucleus, DNA is wound around histones and then condensed further into tightly packed heterochromatin or relatively loose euchromatin
Acetylation/deactylation: certain enzymes can modify histones by adding/removing acetyl groups
- affect how easy DNA is accessed
-
histone acetyltransferases: add acetyl groups, makes DNA more accessible for transcription
- histone deacetyltransferases reduce transcription
Methylation: add methyl groups to cytosine or adenine
- deactivates gene sequences, preventing their expression
Epigenetics
Heritable changes that affect gene expression without directly changing the genetic sequence
- Can be transmitted through multiple generations
RNA interference
Non coding RNA that can interfere with gene expression
- Degrade mRNA prior to translation
- siRNA (double stranded) and microRNA (ss)
siRNA or microRNA incorporated into RNA induced silencing complex (RISC)
- pairs with complementary target mRNA transcipt, cleaves it
Fertilization of an egg by sperm occurs in the
Fallopian tubes, unless in vitro fertilization
Fertilization steps up until zygote
- Mature egg released from ovary into abdominal cavity before being swept up by cilia into fallopian tubes
- As egg is being transported to uterus, sperm makes its way up fallopian tubes
- at this point egg is secondary oocyte (undergone meiosis I and stalled at metaphase in meiosis II)
- Sperm must pass through corona radiata layer of follicular cells and then zona pellucida layer of glycoproteins
- When sperm head makes contact with particular glycoprotein, triggers the acrosome reaction
- release of digestive enzymes that permit entry of sperm and nuclueus into egg
- When sperm head makes contact with particular glycoprotein, triggers the acrosome reaction
- Secondary oocyte proceeds to complete meiosis II, forming a polar body and a mature, fertilized ovum
* haploid nuclei of sperm and ovum fuse to form diploid called ZYGOTE
Sperm contain abundant
Mitochondria to power long journey
- Any sperm mitochondria that enter egg are destroyed, mitochondria inherited maternally
Because the body only wants ONE sperm to interact with egg…
Cortical reaction
Once one reaches egg, egg releases cortical granules which cause surface glycoproteins to form cross links which prevent polyspermy
- fertilization by multiple sperm
At the 16 cell stage (after cleavage of zygote), embryo is known as morula
What happens next?
- Continues to divide into blastula
- has fluid filled cavity called blastocoel
- outer layer of cells surrounding blastocoel is the trophoblast
- forms the placenta
- outer layer of cells surrounding blastocoel is the trophoblast
- inner cell mass: mass of cells at one pole of the cell, develops into cells of fetus
- As it reaches the uterus, blastula implants itself into uterine wall
- if zygote implants in fallopian tube or cervix = ectopic pregnancy
- nonviable and can be dangerous for mother
- Trophoblast begins forming placenta, inner cell mass begins to form yolk sac and amnion which become the amniotic sac
- Firmly implanted in uterine wall, blastula differentiates into a gatrula - undergoes gastrulation
Implantation
What tissue does embryo implant in?
Requires reciprocal cooperation between embryo and uterine tissue which undergo structural changes and responds to hormonal signals as embryo implants in uterine endometrium in cervix
Trophoblast then begins forming placenta
Amniotic sac
yolk sac and amnion
Membranous sac containing amniotic fluid which the fetus develops in
Gastrulation
Formation of 3 primary germ layers
-
endoderm: internal derm, gives rise to many of internal organs
* urinary bladder and gastrointestinal and respiratory tracts, epithelial linings - mesoderm: means to move, gives rise to connective tissue, muscle, circulatory system, kidneys, adrenal glands, and gonads
-
ectoderm: external derm, gives rise to nervous system, skin, eyes, ears, nose, hair, and teeth enamel
* neurulation: early development of nervous system
Neurulation
Gives rise to nervous system 1-3 weeks after fertilization
- Rod of mesodermal cells form notochord which induces the formation of neural plate from ectoderm cells
* neural plate invaginates to form neural folds and a central neural groove
2. continues to fold until folds meet and form neural tube
- neural tube gives rise to central nervous system (brain and spinal cord)
- neural crest cells will migrate from neural folds to form peripheral nervous system
Fertilization cell cycle
1. Mature egg
2. Secondary oocyte once in fallopian tubes (undergone meiosis I, stalled at metaphase in meiosis II)
3. Fetilized ovum once gone through meiosis II
4. Zygote: haploid nuclei of sperm and ovum fuse to form diploid
5. Morula: after cleavage
6. Blastula after more division
7. Gastrula once implanted in uterine endometrium in cervix
Vitamin D
help the body absorb and retain calcium and phosphorus; both are critical for building bone
thyrotropin releasing hormone (TRH)
Hypothalamic hormone
tells anterior pituitary to release thyroid stimulating hormone (TSH) which tells thyroid to produce T3 and T4
ex. gonadotropin releasing hormone (GnRH)
Hypothalamic hormone which tells anterior pituitary to release LH and FSH which play roles in reproduction and growth
- in males LH, stimulates Leydig cells in testes to release testosterone and FSH promotes spermatogenesis
- in females, LH stimulates estrogen production from ovaries, FSH promotes maturation of ovarian follicles
ex. corticotropin-releasing hormone (CRH),
Hypothalamic hormone
releases adrenocorticotropic hormone (ACTH) which travels to adrenal cortex and produces corticosteroids: stress response and circadian rhythms
Organic separation and purification techniques take advantage of
Polarity, solubility, boiling point
Extraction (separation technique)
Takes advantage of two liquid phases: polar aqueous phase (usually water) and relatively nonpolar organic phase (organic solvent, immiscible with water (don’t mix))
- liquid half in separatory funnel, denser liquid at the bottom
Like dissolves like, shaking the funnel separates them into polar and nonpolar solutes
**If compound is uncharged and has both polar and nonpolar groups, non polar groups win
- by using acid base properties, you can add protons to create polarity
Can you separate two different acids using extraction?
Only if one of the acids is much stronger than the other (lower pKa)
Volatile substance
easily transitions from liquid to gas phase
Simple Distillation (for very different boiling points)
Separates liquid by their boiling point using votality and vapor pressure
vapor pressure: pressure exerted by liquid molecules
- Round bottom flask with mixture is heated
- Liquid becomes gas and rises up to a condensor
- Cold water around condensor changes gas back to liquid
Doesn’t always separate perfectly –> REPEAT DISTILLATIONS
Molecules with the highest boiling points have
Highest polarity: trong hydrogen bonding or dipole-dipole interactions
Largest molecular weight (not as much of priority)
Fractional distillation
Uses fractional distillation to separate liquids with close boiling points
- Increases vertical distance that vapor travels
- Allows vapor to recondense and revaporize repeatedly
Boiling point
How can you lower the boiling point of a liquid?
Vapor pressure of liquid reaches atmospheric pressure
Lower the boiling point by lowering the ambient pressure = vacuum distillation
Chromatography
In all chromatography, two phases:
Mobile phase: moving fluid or gas
Stationary phase: immobile substance that retains some molecules moving through the mobile phase
Solutes travelling at different speeds based on affinity for mobile and stationary phases
Thin Layer Chromatography
Can be used to detect impurities in a sample
Stationary phase: glass or plastic plate coated with a thin layer of absorbent material like silica gel (HIGHLY POLAR)
Mobile phase: nonpolar solvent such as hexane, referred to as “eluent”
- Spots are placed at bottom of stationary phase plate and just above mobile phase solvent
- Capillary action pulls mobile phase up the plate, compounds in the sample will also travel upward
Nonpolar particles travel further than polar (have higher affinity for plate and don’t want to move)
Allows us to make rough measurements of polarity of compounds using Retention Factor (Rf) = distance travelled by compound/distance travelled by solvent
- nonpolar compounds have higher Rf typically
Column Chromatography
Different types
For larger quantities of material
Stationary phase: solid adsorbent packed in vertial column, sample is added here
Mobile phase: solvent poured through column (eluent)
-
size exclusion: separate components based on physical size
- stationary phase has pore studded beads, larger molecules pass through faster (OPPOSITE of what we’d think)
- cation exchange: traps positive molecules, negatively charged stationary phase
- anion exchange: opposite
-
afffinity: ligands designed to bind to molecule of interest are attached to stationary phase
- once solution has passed through, dissociate bound compound of interest
-
gas-liquid: gas mobile phase and sample, liquid is stationary phase
- time spent in compound depends on volatility and affinity
- smaller compounds have earlier peaks when analyzed
Technique used to purify impure crystalline structures that precipitate out of solution
Ideal solvent??
Recrystallization
- Solid product placed in liquid solvent and heated to dissolve
- Mixture cooled again and solid allowed to reform
- typically excludes many impurities present before
Ideal solvent is one in which desired product is soluble at high temperature, relatively insoluble in low temp
Often repeated many times over
To begin crystallization and recrystallization, requires initial…
Nucleation
Nucleus or tiny seed crystal initiates crystallization
Scratch side of glass
Spectroscopy
Analysis of molecules based on interaction with electromagnetic radiation
Electromagnetic radiation and how different types of light interact with molecules
- Lower energy waves, like microwaves, can rotate molecules
- Infrared waves can cause bonds to stretch and bend
- Visible and UV waves can excite electrons to higher energy levels
- some are ionizing, can remove electrons
- All X-rays and gamma rays are ionizing, which can cause DNA damage
Infrared spectroscopy
Uses infrared radiation and molecule interactions ***different bonds have distinct ways of interacting with IR radiation
- ** must be a dipole present, usually polar covalent bonds
- vibrational frequencies: even those with dipole present, requires specific frequency of IR radiation to stretch or bend
x-axis: differenw wavelengths of IR radiation
y-axis: transmittance (low transmittance means high absorption)
PEAKS ONLY HELPFUL FROM 1500-4000
For IR spectroscopy, double bonds with carbon appear at ____
****Carbonyl
Triple bonds are at ___
***O-H bonds are at ___
N-H bonds ____
Low frequency (below 2000)
*** Carbonyl at 1650, SHARP PEAK
Medium frequency (low 2000s)
3100-3500 BROAD AND WIDE
3300-3500
UV/Vis spectroscopy
y-axis x-axis
Electron excitement due to UV light (electrons move to higher energy orbitals)
UV and visible light usually absorbed by molecules with non-bonding or pi electrons
- conjugated compounds (alternating single and double bonds) are fantastic at absorbing UV light
- overlapping p orbitals which delocalize
Each molecule has peak absorption values that correspons to wavelengths of light most readily absorbed (opposite of IR transmittance)
y-axis: percent absorbance= proportion of light absorbed by sample
x-axis: wavelength (nm)
Beer’s Law (UV/Vis spectroscopy)
absorbance is proportional to the path length, b, through the sample and the concentration of the absorbing species, A= α b · c.
A = absorbance
α = molar absorptivity
b = length of light path
c = concentration
Absorbance proportional to concentration
Aromatic amino acids and UV/Vis spectroscopy
Tryptophan, Tyrosine, Phenylalanine all capable of absorbing UV light through aromatic ring structures (with conjugated pi electrons)
- each has different spectrum
*** UV spectrum of any peptide depends on aromatic amino content
Absorption
UV/Vis spectroscopy
Colored compounds absorb some wavelengths of light and reflect others; we perceive an object to have color of the wavelength it reflects
- UV/Vis spectroscopy is basically identifying compounds based on their color
Nuclear Magnetic Resonance (NMR) spectroscopy
2 types
Characterizing a molecules atoms (unlike IR which characterizes bonds) by how they interact with magnetic field
- either spin with field at lower energy or against it
Protons and neutrons have opposite spins that cancel out, if atom as even number than won’t show up on NMR; requires net magnetic moment from unequal spins
1HNMR and 13CNMR
Location on graph depends on shielding and deshielding of nucleus; carboxylic acids and electronegative atoms are deshielding and to the left on graph
HNMR steps
1. Number of signals (equivalence, H’s bonded to same carbon count as 1)
2. Position of signals relative to most electronegative atoms (oxygens for example)
- Most shielded are further from EN groups, further right on graph
3. Size of signal: height is proportional to number of protons represented by signal
- Shape of signal (splitting): caused by interference with neighboring protons (bonded to a different adjacent carbon)
- n+1
- each peak split into number corresponding to hydrogen atoms nearby
13CNMR
Uses carbon and isotope carbon 13
Same as HNMR except no splitting
- FIRST STEP: determine number of equivalent carbons
- Equivalent carbons are a single peak
- carbonyl carbon will be much further downfield
- terminal carbons are upfield
Mass spectroscopy
What is most important?
Uses magnetism to determine mass
- First step is ionization using an electron beam
- creates ions and can break apart molecules
-
parent ion: ion created by loss of just one electron and no fragmentation M+
- maintains parent molecular weight but is charged
- Accelerate into magnetic field and uses Fb = Bqvsin0 to determine the angle of deflection
- separated by mass to charge ratio
y axis is relative abundance, x axis is m/z
*** M+ is the peak furthest to the right and thats how you determine the molecular mass
Gel electrophoresis
Which way days DNA migrate
Charged macromolecules like DNA or protein are suspended in agarose gel and migrate due to application of electric current
Separates by size or charge
- Cathode: negative charge
- Anode: positive charge
DNA negative phosphate groups move towards anode
Can isolate to just size by negating charge of proteins using SDS (anionic detergent) which UNFOLDS and makes neutral charge
- requires reducing agent to fully denature quaternary/tertiary structure
What does SDS do to proteins (SDS-PAGE)
Gives them a uniform negative charge for gel electrophoresis
Hybridization lab technique
ssDNA or RNA to bond with cDNA or cRNA
Used to anneal DNA strands and artificially replicate DNA
Blotting
Transfer of DNA or protein from a gel to another membrane where molecules of interest can be visualized
- Southern
- Northern
- Western
- Sample undergoes gel electrophoresis (proteins mix w/ SDS to neutralize charge) and separation is BY SIZE
- Contents transferred to nitrocellulose membrane
- Use hybridization to tag sample with visual marker either cDNA/cRNA or a tagged antibody for proteins
- Detect molecule of interest with conjugated probe
SNOWDROP
Southern
Northern
o
Western
DNA
RNA
o
Protein
DNA microarrays
Uses hybridization to analyze tens of thousands of genes simultaneously on a chip
ex. cancer cells vs healthy cells
Sanger Sequencing Method
Replication of DNA fragment sample is prematurely terminated using one of the 4 labeled ddNTPs (dideoxynucleoside triphosphates) which each stop for a different nucleotide
- *** lacks 3’ OH required to extend nucleotide chain
Then different sized strands separated by gel electrophoresis
Requires large number of genetic copies of same sequence – PCR
Polymerase Chain Reaction
Repeated cycles of DNA sequencing that doubles them each time
- Can also amplify RNA if it is reverse transcribed
Primers specific to target sequence
- Reaction heated to 95 deg C to denature two strands of DNA
- Cooled to allow primers to anneal to template strands
- Heated again to initiate synthesis by DNA polymerase = Taq polymerase
Heating and cooling done by thermocyclers
Protein Purification steps
- Extract by lysing cellular membranes either by freezing and thawing, solvents, detergents
- often treated with protease inhibitors to keep lysed proteins from degrading other cells
- cooled and pH maintained
- Separation by centrifugation
- pellet: heavy dense particles
- supernatant: proteins usually stay in solution
or by solubility: changing salt concentrations of surroundings
- Use chromatography to isolate desired protein
Retention factor (thin layer chromatography)
High value is nonpolar
Low value is polar
Isoelectric point
Isoelectric focusing
pH at which protein has a net charge of 0
Separates proteins of different charge states using special gel based on number of basic or acidic residues
- can be combined with SDS PAGE for 2D gel electrophoresis
Primary and secondary antibodies
Used for tagging proteins in separation techniques = western blotting
Immunoassays
Techniques that rely on binding specificities of antibodies to identify proteins
western blotting
radioimmunoassay: conc of protein in sample measured indirectly by looking at unlabeled proteins reacting with labeled antigens
ELISA: antigens in sample are attached to plate and antibodies apply; after washing, amount of bound antibody is measured with fluorescence
Replication Crisis
Results of many studies cannot be replicated or reproduced in efforts to repeat the studies
Due to methodology – need procedures to be airtight
Publication bias
Only significant or interesting results are published
Observational study design can’t determine
Causation
Representative sampling
Important goal in study design to ensure applicability to real populations (external validity)
Sampling bias: population sampled isn’t representative of population as a whole
The larger the sample size the more likely it is to represent the entire population – increases statistical power
To eliminate underlying variables, experimental design must contain
Control groups
- Equal number of sample receive control as do experiment
negative controls: expect a negative result
positive controls: expect a positive result
Ways to increase validity of experiment
Randomization
Blinding
Controls
Large sample
Mediating variable
Provide mechanistic link between independent and dependent variables
Help explain relationship
Moderating variables
Affect the strength of a relationship
Age, gender, socioeconomic class
Confounding variable
Affect both the independent and dependent variables; obscures the true relationship
- bigger problem with observational studies
Risk can be reduced by making statistical adjustments for possible confounding variables
Systematic review / meta analysis
Analyzing the results of multiple randomized controlled trials would give even more confidence in results
Non associative learning
instances in which an animal’s behaviour toward a stimulus changes in the absence of any apparent associated stimulus or event
Baddeley’s model, working memory includes:
Phonological loop and visuospatial sketchpad
Impulse
product of force and time
(kg*m) / s
Common types of enzymes
Acetyl Group
Acetyl group contains a methyl group single-bonded to a carbonyl
How to know how many stereoisomers there are?
If there are 5 chiral centers, 25
2n
Temperature and Resistance
As temp increases, resistance increases linearly
How can enzymes be used to form a single stereoisomer?
An enzyme is a chiral catalyst capable of preferentially forming one enantiomer because a lower energy chiral transition state leads to the preferred product
Best primers for PCR consist of
Best primers for PCR have a high GC content and CG bases in 5′ and 3′
In which phase of meiosis does nondisjunction occur?
Anaphase I
When a striated muscle cell metabolizes glucose in the complete absence of O2, which of the following substances is NOT produced in a significant amount?
If oxygen is scarce or absent, the product of glycolysis will be transformed into lactic acid instead of acetyl-CoA. Thus, the cell will produce less acetyl-CoA.
mercapto-
indicates presence of a thiol group
cAMP
regulates pivotal physiologic processes including metabolism, secretion, calcium homeostasis, muscle contraction, cell fate, and gene transcription. cAMP is a cyclic nucleotide that serves as a vital second messenger in several signaling pathways.
Red litmus paper
Red litmus paper is a base indicator. It turns blue at 8.1 pH and higher. While not a measure of pH levels, it’s a quick and accurate way to determine if a solution is alkaline
Transition metals and color
The color arises because nickel(II) ion has partially filled d orbitals and the electrons in the lower energy d orbitals absorb visible light to move to the higher energy d orbitals.
The retention factor of a particular material is the ratio of the distance the spot moved above the origin to the distance the solvent front moved above the origin
Lower for more polar molecules for a polar starting material
Electric field can be given in (units)
V/m
The period T and frequency f of a tone are related by
T = 1/f.
Methylation of DNA
Methylation: add methyl groups to cytosine or adenine
- deactivates gene sequences, preventing their expression
Sn2 reactions cause
an inversion of stereochemistry (R to S or vice versa)
The energy of electromagnetic radiation is directly proportional to
the number of photons, and the intensity of electromagnetic radiation is defined as energy emitted per unit time. Thus, intensity is directly proportional to the number of photons emitted
In glycogen, branching is due to the formation of
Which type of bond is formed by glycogen synthase upon release of UDP?
α−1, 6-glycosidic bonds
α-1,4-Glycosidic bond
Type II errors are
false negatives
Two types of sensory memory
Echoic memory: the ultra-short-term memory for things you hear.
Iconic memory: involves the memory of visual stimuli.
Fovea
a small depression in the retina of the eye where visual acuity is highest. The center of the field of vision is focused in this region, where retinal cones are particularly concentrated.
Nomenclature of alkanes
CH4 - methane
C2H6 - ethane
C3H8 - propane
C4H10 - butane
pentane, hexane, heptane, octane
Substituents in alphabetical order before parent chain
ex. 3-ethyl-4,5-dimethyloctane
Parent chain =
Longest/most C’s in a way that results in lowest possible #’s for substituents
GLUT 1 transporter
Nearly all tissues, especially fetal, erythrocytes, and cancer cells
- Baseline cellular uptake, expression increases when glucose is low
GLUT 2 transporter
Liver, kidney, pancreatic B cells
- Bidirectional transport for glycolysis, glycogenesis, gluconeogenesis
- Uptake and export
GLUT 3 transporter
Neurons, placenta
- High glucose affinity, transports glucose into cell even when extracellular concentration is low
GLUT 4 transporter
Skeletal and cardica 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
Bond order
Total number of bonds in molecules divided by the number of BOND GROUPS (i.e. one double bond and one single bond = 2 bond groups) they are connected to
Peptide bond resonance
Resonance in peptide bonds causes:
- planar geometry
- restricted rotation of peptide bonds
- exceptional stability of amides
Conjugation (pi systems)
3+ pi orbitals (double bonds) align with eachother
- Electrons delocalize throughout
- Absorbs UV light, easily detected by UV spectroscopy
Much more stable, lower energy
Priority from highest to lowest
1. Carboxylic acid carboxy- -oic acid
2. Ester RCOOR’ oxycarbonyl- -oate
3. Acid halidesRCOX halocarbonyl- -oyl halide
4. Amide carbomoyl- -amide
5. Aldehydes oxo- -al
6. Ketones oxo- -one
7. Alcohols hydroxy- -ol
8. Thiols mercapto- -thiol
9. Alkanes
10. Ethers
Ring nomenclature
Benzene substituent nomenclature
cyclopropane (3 carbons), cyclobutane
- constrained rings highly unstable
- phenyl
Branched alkanes have lower ____ than linear alkanes
boiling points
LARGER alkanes have higher boiling points
- Alkanes generally low melting and boiling points = VOLATILE
- only london dispersion forces
Halides are
very reactive, great leaving groups
Alkenes and alkynes are more ____ than alkanes
REACTIVE
Double and triple bonds have extra electron density, act as nucleophiles in reactions
Aromaticity and Huckels Rule
What molecules are aromatic
Electron delocalization, fully conjugated ring
- Huckels rule: 4n + 2π electrons
* each double bond is 2 pi electrons
Benzene has 3 double bonds, 6 pi electrons
4n + 2 = 6
n= 1
Environmental influence on behavior
Genes expressed more or less with environemtnal stimuli
- DNA promoters initiate expression of some genes
- Regulatory genes code for proteins that affect gene expression
Theory that variations could affect behavior
- ex. Allele in gene for promoting serotonin makes people susceptible to depression
Epigenetics
Changes to genome that don’t involve changing actual nucleotide content
ex. methylation of cytosine silences specific genes
- stress, exercise, heritable
Nature vs. Nurture
Characterizing heritability (how much is a trait determined by genes alone) of a trait
- Slope = 1
- all variation from genetics
- Slope = 0
- environmental factors/ chance
Pyschological trait heritability: .3-.6 (genetic and enviuronmental factors
- Schizophrenia = .8
Study design for heritability (nature vs. nurture)
Twin studies - monozygotic and dizygotic
Adopted children- genetics of real parent but environment of foster
monozygotic twins for zygotic twins
Monozygotic twins are formed by one sperm and one egg. Dizygotic twins are formed by two different sperm and two different eggs
Monozygotic = identical
Dizygotic = fraternal
Molecular geometry chart
regions of electron density -2, 3, 4, 5, 6
