4 Flashcards

1
Q

Hindsight bias

A

In retrospect, events seem more predictable and obvious
- Very common in medicine

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2
Q

Causation bias

A

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

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3
Q

Heurisitics

A

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

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4
Q

Biases

A

General cognitive patterns that affect our decision making processes

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5
Q

Representative heuristic

A

Making decisions based on prototypical examples

  • usually when estimating probability in everday life
  • ex. looking like a criminal
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6
Q

Availability heuristic

A

How likely we think something is to occur

Influenced by readily available info

ex. Rare crime news stories, thinking they could happen to us

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7
Q

Second year syndrome

A

Learning about rare syndromes and thinking any symptom could be caused by it

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8
Q

Intelligence

A

Ability to:

  • Detect patterns
  • Process and store info
  • Understand ideas
  • Solve problems
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9
Q

Charles Spearman

A

Noticed correlation in performance in different subjects

  • children who did well in history did well in math
  • not a perfect correlation
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10
Q

General intelligence (g factor)

A

Underlying capacity that drives performance in may fields

  • about 50% heritable
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11
Q

Francis Galton

A

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

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12
Q

Alfred Binet

A

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

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13
Q

IQ distribution

A

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

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14
Q

IQ controversy

A

IQ tests are high stakes

Can influence education a child receives

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15
Q

Flynn effect

A

flynn effect: describes how IQ scores increased in developed countries in 20th century

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16
Q

Howard gardner multiple intelligences

A

Make up g-factor

  1. Musical
  2. Visual-spatial
  3. Verbal-linguistic
  4. Logical-mathematical
  5. Bodily-kinesthetic
  6. Interpersonal
  7. Intrapersonal

*8. Naturalistic- relate to/pick up patterns in natural world

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17
Q

Emotional intelligence

A

Recognition of one’s own emotions and those of others

  • emotional self regulation
  • proposed it was an equal counterpart to traditional intelligence
    • EQ
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18
Q

Language

A

Structure and underlying similarities of all human languages

  • cognitive aspects of learning and using linguistic systems
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19
Q

Phonetics

A

Study of physical production and reception of speech sound

  • anatomical parts of speech and hearing
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20
Q

Phonology

A

Organization of sounds into meaningful units

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21
Q

Morphology

A

Study of word formation

ex. eat –> ate

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22
Q

Syntax

A

How words are joined together to form phrases/sentences

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23
Q

Semantics

A

Literal meaning

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24
Q

Pragmatics

A

Non-literal meaning

  • depends on context, body language, time
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25
American sign language has its own
Grammar and words
26
Behaviorism
**B.F. Skinner** observable behavior Learning theory of language Nativist theory Generative linguistics Interactionist Theory
27
Learning Theory of Language
Language as behavior based on environmental input * no innate language capacity
28
Nativist Theory
**Noam Chomsky** Humans have innate (genetic) capacity for language
29
Generative linguistics:
grammatical rules which govern sentences, certain sentence structures don't work
30
Interactionist Theory
Language is acquired during social interaction * language leaning is interactive and functional
31
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
32
Linguistic determination
Grammatical categories determine thought
33
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
34
Arcuate fasciculus
Connects broca's and wernickes areas **conductive aphasia:** arcuate fasciculus lesions cause difficulties with repeating other peoples words
35
RNA world hypothesis
RNA stored info and catalyzed reactions before DNA
36
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 1. Douple helix unzipped by **helicase,** kept open by **single stranded binding proteins (SSBP)** **2.** Tension created upstream relieved by **topoisomerase** enzyme 3. **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 4. Reaches transcription terminator sequence
37
RNA pol proofreading ability is
Not as accurate as DNA polymerase Error rate higher, not as high of a risk
38
Template (antisense) strand
Strand being read by RNA pol in transcription
39
Coding (sense) strand
Sequence identical to new RNA with thymine instead of Uracil
40
RNA pol I RNA pol II RNA pol III
Synthesizes rRNA in nucleolus Synthesizes hnRNA (heteronuclear)(mRNA precursor) SYnthesizes tRNA, some rRNA
41
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
42
heteronuclear hnRNA posttranscriptional modification polyA tail 5' cap splicing
pre mRNA that undergoes **posttranscriptional modification** 1. 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 2. **5' cap:** one nucleotide modification, triphosphate linkage * protects mRNA against degradation, facilitates nuclear export (recognized by tranport proteins) * also recognition for ribosomes 3. RNA splicing- splicing introns
43
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
44
Ribozymes
RNA components capable of enzymatic activity
45
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
46
**Degeneracy**
Multiple codons can correspond to one amino acid
47
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
48
wobble hypothesis:
1 tRNA can recognize several codons, usually where 3rd amino differs -- creates same amino
49
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
50
Steps of Translation - Initiation
1. 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**
51
Steps of Translation - Elongation
1. 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 2. 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
52
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
53
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** **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
54
phosphorylation:
adding high energy phosphate group to proteins or other molecules by **kinase** enzymes
55
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
56
Ubiquitation:
addition of ubquitin proteins, used to designate proteins for degradation in the cell
57
After synthesis, proteins folded into 3D conformation by
**Chaperone proteins** in cytoplasm or ER
58
Posttranslational modification Disulfide bonds
Bonds between neaby cysteine residues, linking two parts of a protein - Maintaining tertiary structure
59
Posttranslational modification Proteolytic processing
Cleaved at specific sites, sometimes to generate two separate peptides with unique functions - Also activates proteins sometimes
60
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
61
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
62
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
63
Types of stem cells
**Mesenchymal stem cells:** produce fat, bone, and liver cells **Intestinal stem cells** **Hematopoietic:** generate blood cells
64
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
65
Apoptosis
Programmed cell death, intentional * critical role in embryonic development * ex. webbed fingers before apoptosis Checkpoint for when things go wrong
66
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**
67
lac Operon
Negative inducible; expression induced by removal of repressor **negative inducible:** default is off, expression induced by specific signal removed repressor
68
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
69
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
70
**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
71
**Silencers**
Gene expression Sequence that when bound by a repressor, silence or repress expression of genes
72
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
73
Epigenetics
Heritable changes that affect gene expression without directly changing the genetic sequence - Can be transmitted through multiple generations
74
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
75
Fertilization of an egg by sperm occurs in the
Fallopian tubes, unless in vitro fertilization
76
Fertilization steps up until zygote
1. Mature egg released from ovary into abdominal cavity before being swept up by cilia into fallopian tubes 2. 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 3. 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**
77
Sperm contain abundant
Mitochondria to power long journey - Any sperm mitochondria that enter egg are destroyed, _mitochondria inherited maternally_
78
Because the body only wants ONE sperm to interact with egg... ## Footnote **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
79
At the 16 cell stage (after cleavage of zygote), embryo is known as **morula** What happens next?
1. Continues to divide into **blastula** * has fluid filled cavity called **blastocoel** * outer layer of cells surrounding blastocoel is the **trophoblast** * **​**forms the _placenta_ * _​​_**inner cell mass:** mass of cells at one pole of the cell, develops into cells of **fetus** 2. 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 3. Trophoblast begins forming placenta, inner cell mass begins to form **yolk sac** and **amnion** which become the amniotic sac 4. Firmly implanted in uterine wall, blastula differentiates into a **gatrula - undergoes gastrulation**
80
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
81
Amniotic sac
yolk sac and amnion Membranous sac containing **amniotic fluid** which the fetus develops in
82
Gastrulation
Formation of 3 primary germ layers 1. **endoderm:** internal derm, gives rise to many of internal organs * urinary bladder and gastrointestinal and respiratory tracts, epithelial linings 2. **mesoderm:** means to move, gives rise to connective tissue, muscle, circulatory system, kidneys, adrenal glands, and gonads 3. **ectoderm:** external derm, gives rise to nervous system, skin, eyes, ears, nose, hair, and teeth enamel * **neurulation:** early development of nervous system
83
Neurulation
Gives rise to nervous system 1-3 weeks after fertilization 1. 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_
84
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
85
Vitamin D
help the body absorb and retain calcium and phosphorus; both are critical for building bone
86
thyrotropin releasing hormone (TRH)
Hypothalamic hormone tells anterior pituitary to release thyroid stimulating hormone (TSH) which tells thyroid to produce T3 and T4
87
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
88
ex. corticotropin-releasing hormone (CRH),
Hypothalamic hormone releases adrenocorticotropic hormone (ACTH) which travels to adrenal cortex and produces corticosteroids: stress response and circadian rhythms
89
Organic separation and purification techniques take advantage of
Polarity, solubility, boiling point
90
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
91
Can you separate two different acids using extraction?
Only if one of the acids is much stronger than the other (lower pKa)
92
Volatile substance
easily transitions from liquid to gas phase
93
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 1. Round bottom flask with mixture is heated 1. Liquid becomes gas and rises up to a condensor 2. Cold water around condensor changes gas back to liquid Doesn't always separate perfectly --\> REPEAT DISTILLATIONS
94
Molecules with the highest boiling points have
Highest polarity: trong hydrogen bonding or dipole-dipole interactions Largest molecular weight (not as much of priority)
95
Fractional distillation
Uses fractional distillation to separate liquids with close boiling points 1. Increases vertical distance that vapor travels 2. Allows vapor to recondense and revaporize repeatedly
96
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**
97
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
98
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" 1. Spots are placed at bottom of stationary phase plate and just above mobile phase solvent 2. 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
99
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) 1. **size exclusion:** separate components based on physical size 1. stationary phase has pore studded beads, _larger molecules pass through faster_ (OPPOSITE of what we'd think) 2. **cation exchange:** traps positive molecules, negatively charged stationary phase 3. **anion exchange:** opposite 4. **afffinity:** ligands designed to bind to molecule of interest are attached to stationary phase 1. once solution has passed through, dissociate bound compound of interest 5. **gas-liquid:** gas mobile phase and sample, liquid is stationary phase 1. time spent in compound depends on volatility and affinity 2. smaller compounds have earlier peaks when analyzed
100
Technique used to purify impure crystalline structures that precipitate out of solution Ideal solvent??
**Recrystallization** 1. Solid product placed in liquid solvent and heated to dissolve 2. Mixture cooled again and solid allowed to reform 1. 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
101
To begin crystallization and recrystallization, requires initial...
**Nucleation** Nucleus or tiny seed crystal initiates crystallization Scratch side of glass
102
Spectroscopy
Analysis of molecules based on interaction with electromagnetic radiation
103
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
104
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
105
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
106
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)
107
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
108
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
109
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
110
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
111
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 4. **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
112
**13CNMR**
Uses carbon and isotope carbon 13 Same as HNMR except no splitting 1. FIRST STEP: determine number of equivalent carbons * Equivalent carbons are a single peak * carbonyl carbon will be much further downfield * terminal carbons are upfield
113
Mass spectroscopy What is most important?
Uses magnetism to determine mass 1. First step is ionization using an electron beam 1. creates ions and can break apart molecules 2. **parent ion**: ion created by loss of just one electron and no fragmentation **M+** 1. maintains parent molecular weight but is charged 2. Accelerate into magnetic field and uses Fb = Bqvsin0 to determine the angle of deflection 1. 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
114
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
115
What does SDS do to proteins (SDS-PAGE)
Gives them a uniform negative charge for gel electrophoresis
116
Hybridization lab technique
ssDNA or RNA to bond with cDNA or cRNA Used to anneal DNA strands and artificially replicate DNA
117
Blotting
Transfer of DNA or protein from a gel to another membrane where molecules of interest can be visualized * Southern * Northern * Western 1. Sample undergoes gel electrophoresis (proteins mix w/ SDS to neutralize charge) and separation is BY SIZE 2. Contents transferred to nitrocellulose membrane 3. Use hybridization to tag sample with visual marker either cDNA/cRNA or a tagged antibody for proteins 4. Detect molecule of interest with conjugated probe
118
SNOWDROP
Southern Northern o Western DNA RNA o Protein
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DNA microarrays
Uses hybridization to analyze tens of thousands of genes simultaneously on a chip ex. cancer cells vs healthy cells
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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
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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 1. Reaction heated to 95 deg C to denature two strands of DNA 2. Cooled to allow primers to anneal to template strands 3. Heated again to initiate synthesis by DNA polymerase = **Taq polymerase** Heating and cooling done by **thermocyclers**
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Protein Purification steps
1. 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 2. Separation by centrifugation * **pellet:** heavy dense particles * **supernatant:** proteins usually stay in solution or by solubility: changing salt concentrations of surroundings 3. Use chromatography to isolate desired protein
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Retention factor (thin layer chromatography)
High value is nonpolar Low value is polar
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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
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Primary and secondary antibodies
Used for tagging proteins in separation techniques = western blotting
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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
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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
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Publication bias
Only significant or interesting results are published
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Observational study design can't determine
Causation
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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
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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
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Ways to increase validity of experiment
Randomization Blinding Controls Large sample
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Mediating variable
Provide mechanistic link between independent and dependent variables Help explain relationship
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Moderating variables
Affect the strength of a relationship Age, gender, socioeconomic class
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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
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Systematic review / meta analysis
Analyzing the results of multiple randomized controlled trials would give even more confidence in results
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Non associative learning
instances in which an animal's behaviour toward a stimulus changes in the absence of any apparent associated stimulus or event
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Baddeley’s model, working memory includes:
Phonological loop and visuospatial sketchpad
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Impulse
product of force and time (kg\*m) / s
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Common types of enzymes
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Acetyl Group
Acetyl group contains a methyl group single-bonded to a carbonyl
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How to know how many stereoisomers there are?
If there are 5 chiral centers, 25 2n
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Temperature and Resistance
As temp increases, resistance increases linearly
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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
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Best primers for PCR consist of
Best primers for PCR have a high GC content and CG bases in 5′ and 3′
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In which phase of meiosis does nondisjunction occur?
Anaphase I
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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.
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mercapto-
indicates presence of a thiol group
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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.
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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
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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.
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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
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Electric field can be given in (units)
V/m
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The period T and frequency f of a tone are related by
T = 1/f.
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Methylation of DNA
Methylation: add methyl groups to cytosine or adenine * deactivates gene sequences, preventing their expression
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Sn2 reactions cause
an inversion of stereochemistry (R to S or vice versa)
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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
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In glycogen, branching is due to the formation of ## Footnote Which type of bond is formed by glycogen synthase upon release of UDP?
α−1, 6-glycosidic bonds α-1,4-Glycosidic bond
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Type II errors are
false negatives
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Two types of sensory memory
Echoic memory: the ultra-short-term memory for things you hear. Iconic memory: involves the memory of visual stimuli.
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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.
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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
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Parent chain =
Longest/most C's in a way that results in lowest possible #'s for substituents
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GLUT 1 transporter
Nearly all tissues, especially fetal, erythrocytes, and cancer cells - Baseline cellular uptake, expression increases when glucose is low
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GLUT 2 transporter
Liver, kidney, pancreatic B cells - Bidirectional transport for glycolysis, glycogenesis, gluconeogenesis - Uptake and export
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GLUT 3 transporter
Neurons, placenta - High glucose affinity, transports glucose into cell even when extracellular concentration is low
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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
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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
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Peptide bond resonance
Resonance in peptide bonds causes: * planar geometry * restricted rotation of peptide bonds * exceptional stability of amides
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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
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Priority from highest to lowest
**1. Carboxylic acid** carboxy- -oic acid **2. Ester RCOOR**' oxycarbonyl- -oate **3. Acid halides****RCOX** 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**
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Ring nomenclature Benzene substituent nomenclature
cyclopropane (3 carbons), cyclobutane * constrained rings highly unstable - phenyl
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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
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Halides are
very reactive, great leaving groups
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Alkenes and alkynes are more ____ than alkanes
REACTIVE Double and triple bonds have extra electron density, act as nucleophiles in reactions
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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
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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
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Epigenetics
Changes to genome that don't involve changing actual nucleotide content ex. methylation of cytosine silences specific genes - stress, exercise, heritable
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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
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Study design for heritability (nature vs. nurture)
Twin studies - monozygotic and dizygotic Adopted children- genetics of real parent but environment of foster
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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
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Molecular geometry chart regions of electron density -2, 3, 4, 5, 6