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MCAT-study guide for medical students, Study Guides, Projects, Research of Biology

It's an MCAT study guide 2022.

Typology: Study Guides, Projects, Research

2020/2021

Uploaded on 04/19/2022

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Memory

Human Memory

Sensory Memory

Short-term Memory

Long-term Memory (< 1 sec)

Explicit Memory (conscious)

Declarative Memory (facts, events)

Episodic Memory (events, experiences)

Semantic Memory (facts, concepts)

Procedural Memory (skills, tasks)

Implicit Memory (unconscious)

(< 1 min) (lifetime)

Working Memory

  • Encoding: the process of putting new information into memory Facts are stored via semantic networks. retrieval of information is often based on priming interconnected nodes of the semantic network. recognition of information is stronger than recall.

other Senses

  • Smell: detection of volatile or aerosolized chemicals by olfactory chemoreceptors ( olfactory nerves )
  • taste: detection of dissolved compounds by taste buds in papillae
  • Somatosensation: four touch modalities (pressure, vibration, pain, and temperature)
  • kinesthetic sense (proprioception): ability to tell where one’s body is in space

object recognition

  • Bottom-up (data-driven) processing: recognition of objects by parallel processing and feature detection. Slower, but less prone to mistakes
  • top-down (conceptually-driven) processing: recognition of an object by memories and expectations, with little attention to detail. Faster, but more prone to mistakes
  • gestalt principles: ways that the brain can infer missing parts of an image when it is incomplete

Piaget’s Stages of Cognitive Development

  • Sensorimotor stage: focuses on manipulating the environment to meet physical needs through circular reactions ; object permanence ends this stage
  • Preoperational stage: focuses on symbolic thinking , egocentrism (inability to imagine what another person thinks or feels), and centration (focusing on only one aspect of a phenomenon)
  • Concrete operational stage: focuses on understanding the feelings of others and manipulating physical (concrete) objects
  • formal operational stage: focuses on abstract thought and problem-solving

Problem-Solving and Decision-Making

Problem-solving techniques include trial-and- error , algorithms , deductive reasoning (deriving conclusions from general rules) and inductive reasoning (deriving generalizations from evidence). Heuristics (simplified principles used to make decisions, “rules of thumb”), biases, intuition, and emotions may assist decision-making, but may also lead to erroneous or problematic decisions.

Attention

  • Selective attention: allows one to pay attention to a particular stimulus while determining if additional stimuli require attention in the background
  • Divided attention: uses automatic processing to pay attention to multiple activities at one time

language Areas in the Brain

  • Wernicke’s area: language comprehension; damage results in Wernicke’s aphasia (fluent, nonsensical aphasia with lack of comprehension)
  • Broca’s area: motor function of speech; damage results in Broca’s aphasia (nonfluent aphasia in which generating each word requires great effort)
  • Arcuate fasciculus: connects Wernicke’s and Broca’s areas; damage results in conduction aphasia (the inability to repeat words despite intact speech generation and comprehension)

Motivation

Motivation is the purpose or driving force behind our actions.

  • Extrinsic: based on external circumstances
  • Intrinsic: based on internal drive or perception

Motivation theories

  • Instinct theory: innate, fixed patterns of behavior in response to stimuli
  • Arousal theory: the state of being awake and reactive to stimuli; aim for optimal level of arousal for a given task (Yerkes–Dodson law) Strong

Weak Low High Arousal

Optimal arousal Optimal performance

Impaired performance because of strong anxiety

Increasing attention and interest

Performance

MotIvAtIon, EMotIon, AnD StrESS

Consciousness

Stage EEg Waves features Awake Beta and alpha

Able to perceive, process, access, and express information 1 Theta Light sleep 2 Theta Sleep spindles and K complexes 3/4 Delta Slow-wave sleep; dreams; declarative memory consolidation; some sleep disorders rEM Mostly beta

Appears awake physiologically; dreams; paralyzed; procedural memory consolidation; some sleep disorders Sleep disorders include dyssomnias (amount or timing of sleep), such as insomnia, narcolepsy, sleep apnea, and sleep deprivation; and parasomnias (odd behaviors during sleep), such as night terrors and sleepwalking (somnambulism).

Consciousness-Altering Drugs

Drug addiction is mediated by the mesolimbic pathway , which includes the nucleus accumbens, medial forebrain bundle , and ventral tegmental area. Dopamine is the main neurotransmitter.

Drug group function Depressants (alcohol, barbiturates, benzodiazepines)

Sense of relaxation and reduced anxiety

Stimulants (amphetamines, cocaine, ecstasy)

Increased arousal

opiates/opioids (heroin, morphine, opium, pain pills)

Decreased reaction to pain; euphoria

hallucinogens (LSD, peyote, mescaline, ketamine, psilocybin- containing mushrooms)

Distortions of reality and fantasy; introspection

Marijuana has some features of depressants, stimulants, and hallucinogens (in very high doses).

CognItIon, ConSCIouSnESS, AnD lAnguAgE

learning

  • habituation: the process of becoming used to a stimulus
  • Dishabituation: occurs when a second stimulus intervenes, causing a resensitization to the original stimulus
  • observational learning: the acquisition of behavior by watching others
  • Associative learning: pairing together stimuli and responses, or behaviors and consequences
  • Classical conditioning: a form of associative learning in which a neutral stimulus becomes associated with an unconditioned stimulus such that the neutral stimulus alone produces the same response as the unconditioned stimulus; the neutral stimulus thus becomes a conditioned stimulus

UCS (food) UCR No Response

Neutral stimulus (bell)

CR (salivation)

CS (bell)

UCS (food) UCR No Response

Neutral stimulus (bell)

CR (salivation)

CS (bell)

  • operant conditioning: a form of associative learning in which the frequency of a behavior is modified using reinforcement (increases behavior) or punishment (decreases behavior) Stimulus Added Removed

Negative reinforcement

Positive reinforcement

Behavior

Continues

Stops

Positive punishment

Negative punishment

lEArnIng AnD MEMorY

Somatic symptom and related disorders

  • Somatic symptom disorder: at least one somatic symptom, which may or may not be linked to an underlying medical condition, that causes disproportionate concern
  • Illness anxiety disorder: preoccupation with having or coming down with a serious medical condition
  • Conversion disorder: unexplained symptoms affecting motor or sensory function

Personality disorders

Patterns of inflexible, maladaptive behavior that cause distress or impaired functioning

  • Cluster A (odd, eccentric, “weird”): paranoid, schizotypal, schizoid
  • Cluster B (dramatic, emotional, erratic, “wild”): antisocial, borderline, histrionic, narcissistic
  • Cluster C (anxious, fearful, “worried”): avoidant, dependent, obsessive–compulsive

Social Behavior

  • Interpersonal attraction: influenced by physical, social, and psychological factors
  • Aggression: behavior with the intention to cause harm or increase social dominance
  • Attachment: an emotional bond to another person; usually refers to the bond between a child and a caregiver
  • Altruism: helping behavior in which the person’s intent is to benefit someone else at a personal cost

SoCIAl thInkIng

  • Cultural relativism: studying social groups and cultures on their own terms
  • Discrimination: when prejudicial attitudes cause differences in treatment of a group

Social Class

Social stratification is based on socioeconomic status (SES).

  • Class: a category of people with shared socioeconomic characteristics
  • Power: the capacity to influence people through real or perceived rewards and punishments
  • Social capital: the investment people make in society in return for economic or collective rewards
  • Social reproduction: the passing on of social inequality, especially poverty, to other generations
  • Poverty: low SES; in the US, the poverty line is the government’s calculation of the minimum income requirements to acquire the minimum necessities of life

Epidemiology

Incidence:

new cases population at risk

per time

Prevalence:

number of cases(new or old)

total population

per time

Morbidity: the burden or degree of illness associated with a given disease Mortality: deaths caused by a given disease

SoCIAl StrAtIfICAtIon

-

Elements of Social Interaction

  • Status: a position in society used to classify individuals. Can be ascribed (involuntarily assigned), achieved (voluntarily earned), or master (primary identity)
  • role: set of beliefs, values, and norms that define the expectations of a certain status
  • group: two or more individuals with similar characteristics who share a sense of unity
  • network: observable pattern of social relationships between individuals or groups
  • organization: group with a structure and culture designed to achieve specific goals; exists outside of each individual’s membership within the organization

Self-Presentation and Interacting with others

  • Display rules: unspoken rules that govern the expression of emotion
  • Impression management: maintenance of a public image through various strategies
  • Dramaturgical approach: individuals create images of themselves in the same way that actors perform a role in front of an audience

SoCIAl IntErACtIon

Sociology: theories and Institutions

  • functionalism: focuses on the function and relationships of each component of society
  • Conflict theory: focuses on how power differentials are created and how they maintain order
  • Symbolic interactionism: the study of how individuals interact through a shared understanding of words, gestures, and other symbols
  • Social constructionism: explores how individuals and groups make decisions to agree upon a given social reality

Culture

  • Material culture: physical items one associates with a given group (art, clothing, foods, buildings)
  • Symbolic culture: the ideas associated with a cultural group

Demographics

Demographics: the statistical arm of sociology Migration refers to the movement of people into (immigration) or out of (emigration) a geographical location. Demographic transition: a model used to represent drops in birth and death rates as a result of industrialization

SoCIAl StruCturE AnD DEMogrAPhICS

group Psychology

  • Social facilitation: tendency to perform at a different level (better or worse) when others are around
  • Deindividuation: loss of self-awareness in large groups; can lead to drastic changes in behavior
  • Bystander effect: in a group, individuals are less likely to respond to a person in need
  • Peer pressure: social influence placed on an individual by other individuals they consider equals
  • group polarization: tendency towards making decisions in a group that are more extreme then the thoughts of the individual group members
  • groupthink: tendency to make decisions based on ideas and solutions that arise within the group without considering outside ideas

Culture

  • Assimilation: one culture begins to melt into another
  • Multiculturalism: encouragement of multiple cultures within a community to enhance diversity
  • Subculture: a group that distinguishes itself from the primary culture to which it belongs

Socialization

  • Socialization: the process of developing and spreading norms, customs, and beliefs
  • norms: boundaries of acceptable behavior within society
  • Stigma: extreme disapproval or dislike of a person or group based on perceived differences
  • Deviance: any violation of norms, rules, or expectations within a society
  • Conformity: changing beliefs or behaviors in order to fit into a group or society
  • Compliance: individuals change behavior based on the request of others; techniques for gaining compliance include foot-in-the- door , door-in-the-face , lowball , and that’s- not-all
  • obedience: change in behavior based on a command from someone seen as an authority figure

SoCIAl ProCESSES, AttItuDES, AnD BEhAvIor

Attribution theory

Focuses on the tendency for individuals to infer the causes of other people’s behavior

  • Dispositional (internal) causes relate to the features of the person who is being considered
  • Situational (external) causes relate to features of the surroundings or social context
  • Correspondent inference theory: describes attributions made by observing the intentional (especially unexpected) behaviors performed by another person
  • fundamental attribution error: bias toward making dispositional attributions rather than situational attributions

Stereotypes, Prejudice, and Discrimination

  • Stereotypes: attitudes and impressions that are made based on limited and superficial information
  • Self-fulfilling prophecy: the phenomenon of a stereotype creating an expectation of a particular group, which creates conditions that lead to confirmation of this stereotype
  • Stereotype threat: a feeling of anxiety about confirming a negative stereotype
  • Prejudice: an irrationally based attitude prior to actual experience
  • Ethnocentrism: the practice of making judgments about other cultures based on the values and beliefs of one’s own culture ( in-group vs. out-group )

SoCIAl PErCEPtIon AnD BEhAvIor

Once replicated, the bacterial cells can be used to create a protein of interest, or can be lysed to allow for isolation of the fragment of interest from the vector.

DNA libraries are large collections of known DNA sequences.

  • Genomic libraries contain large fragments of DNA, including both coding and noncoding regions of the genome. They cannot be used to make recombinant proteins or for gene therapy.
  • cDNA libraries ( expression libraries ) contain smaller fragments of DNA, and only include the exons of genes expressed by the sample tissue. They can be used to make recombinant proteins or for gene therapy.

Hybridization is the joining of complementary base pair sequences.

Polymerase chain reaction ( PCR ) is an automated process by which millions of copies of a DNA sequence can be created from a very small sample by hybridization.

DNA molecules can be separated by size using agarose gel electrophoresis.

Southern blotting can be used to detect the presence and quantity of various DNA strands in a sample. After electrophoresis, the sample is transferred to a membrane that can be probed with single-stranded DNA molecules to look for a sequence of interest.

DNA sequencing uses dideoxyribonucleotides , which terminate the DNA chain because they lack a 3 ' –OH group.

Central Dogma: DNA → RNA → proteins

The Genetic Code

Degenerate code allows multiple codons to encode for the same amino acid.

  • Initiation: AUG
  • Termination: UAA, UGA, UAG
  • Redundancy and wobble (third base in the codon) allow mutations to occur without affecting the protein.

Point mutations can cause:

  • Silent mutations, with no effect on protein synthesis
  • Nonsense (truncation) mutations, which produce a premature stop codon
  • Missense mutations, which produce a codon that codes for a different amino acid
  • Frameshift mutations , which result from nucleotide addition or deletion and change the reading frame of subsequent codons

RNA is structurally similar to DNA except:

  • Substitution of a ribose sugar for deoxyribose
  • Substitution of uracil for thymine
  • Single-stranded instead of double-stranded

There are three major types of RNA in transcription:

  • Messenger RNA (mRNA): carries the message from DNA in the nucleus via transcription of the gene; travels into the cytoplasm to be translated
  • Transfer RNA (tRNA): brings in amino acids; recognizes the codon on the mRNA using its anticodon
  • Ribosomal RNA (rRNA): makes up much of the ribosome; enzymatically active

RNA AND THE GENETIC CODE

Transcription

Figure I-3-4. Expression of a Prokaryotic Protein Coding Gene

3 ' untranslated region (UTR)

5 ' 3 '

5 ' 3 '

3 ' 5 '

5 ' UTR 3 ' UTR

–10 coding region

transcription

promoter

TGA

transcription

translation

ATG

coding region

UGA GC-rich stem AUG and loop

transcription terminates

H 2 N–protein–COOH

5 ' untranslated region (UTR)

TATA box

UUUUUU

Shine–Dalgarno sequence

DNA

mRNA

Steps:

  • Helicase and topoisomerase unwind DNA double helix.
  • RNA polymerase II binds to TATA box within promoter region of gene (25 base pairs upstream from first transcribed base).
  • hnRNA synthesized from DNA template (antisense) strand. Posttranscriptional modifications:
  • 7-methylguanylate triphosphate cap added to 5 ' end
  • Polyadenosyl (poly-A) tail added to 3 ' end
  • Splicing done by spliceosome ; introns removed and exons ligated together. Alternative splicing combines different exons to acquire different gene products.

Translation

Occurs at the ribosome.

U A C

Met

A U G C C G U A U G C U

P site A site

U A C

Met

G G C

Pro

A U G C C G U A U G C U

G G C Pro incoming tRNA^ }

anticodon

Three stages: initiation , elongation , termination Posttranslational modifications:

  • Folding by chaperones
  • Formation of quaternary structure
  • Cleavage of proteins or signal sequences
  • Covalent addition of other biomolecules (phosphorylation, carboxylation, glycosylation, prenylation)

Control of Gene Expression in Prokaryotes

Operons (Jacob–Monod model) are inducible or repressible clusters of genes transcribed as a single mRNA.

inducible system repressible system

regulator

RNA polymerase

promoter operator structural

repressor I I R

R

R

repressor inducer—repressor complex cannot bindto operator—structural genes are transcribed

inducer

binds R R C RC

regulator

repressor

corepressor (end product)

repressor—corepressorcomplex binds to operator and repressesenzyme synthesis repressor cannotbind to operator by itself

RNA polymerase

promoter operator structural

Control of Gene Expression in Eukaryotes

Transcription factors search for promoter and enhancer regions in the DNA.

  • Promoters are within 25 base pairs of the transcription start site.
  • Enhancers are more than 25 base pairs away from the transcription start site.

Membrane Transport

Osmotic pressure , a colligative property , is the pressure applied to a pure solvent to prevent osmosis and is related to the concentration of the solution. Π = iM R T Passive transport does not require ATP because the molecule is moving down its concentration gradient or from an area of higher concentration to an area of lower concentration.

  • Simple diffusion does not require a transporter. Small, nonpolar molecules passively move from an area of high concentration to an area of low concentration until equilibrium is achieved.
  • Osmosis describes the diffusion of water across a selectively permeable membrane.
  • Facilitated diffusion uses transport proteins to move impermeable solutes across the cell membrane. Active transport requires energy in the form of ATP ( primary ) or an existing favorable ion gradient ( secondary ). Secondary active transport can be further classified as symport or antiport.

molecules (^) transport proteins

cell membrane

concentration gradient simple diffusion facilitated diffusion passive transport active transport Figure 1.5 Movement Across Memberances

energy (ATP or ion gradient)

Endocytosis and exocytosis are methods of engulfing material into cells or releasing material to the exterior of cells, both via the cell membrane. Pinocytosis is the ingestion of liquid into the cell from vesicles formed from the cell membrane and phagocytosis is the ingestion of solid material.

BIOLOGICAL MEMBRANES

Glycolysis

Occurs in the cytoplasm of all cells, and does not require oxygen. Yields 2 ATP per glucose. Important enzymes include:

  • Glucokinase: present in the pancreatic β -islet cells as part of the glucose sensor and is responsive to insulin in the liver
  • Hexokinase: traps glucose
  • Phosphofructokinase-1 ( PFK-1 ) : rate-limiting step
  • Phosphofructokinase-2 ( PFK-2 ) : produces F2,6-BP, which activates PFK-
  • Glyceraldehyde-3-phosphate dehydrogenase: produces NADH
  • 3-phosphoglycerate kinase and pyruvate kinase: perform substrate-level phosphorylation Glucokinase/hexokinase, PFK-1, and pyruvate kinase catalyze irreversible reactions. The NADH produced in glycolysis is oxidized aerobically by the mitochondrial electron transport chain and anaerobically by cytoplasmic lactate dehydrogenase.

CARBOHYDRATE METABOLISM

Pyruvate Dehydrogenase

  • Converts pyruvate to acetyl-CoA. Stimulated by insulin and inhibited by acetyl-CoA.

The Citric Acid Cycle

Takes place in mitochondrial matrix. Main purpose is to oxidize acetyl-CoA to CO 2 and generate high- energy electron carriers (NADH and FADH 2 ) and GTP.

Figure I-13-1. Citric Acid Cycle

Fatty acids Ketones Alcohol

Citrate

Acetyl-CoA

Pyruvate Glucose Amino acids PDH

synthaseCitrate

cis-Aconitase Isocitrate

α-Ketoglutarate α -Ketoglutarate dehydrogenase Succinyl-CoA

NAD+ NAD+

NAD+

GTP

FADH (^2) FAD

Fumarate

Fumarase

Malate

Malate dehydrogenase

GDP + Pi

NADH

NADH

NADH

CO (^2)

Succinyl-CoA synthetase

Succinate

Succinate dehydrogenase (complex II)

Oxaloacetate

Isocitrate dehydrogenase CO 2

The Electron Transport Chain

Takes place on the matrix-facing surface of the inner mitochondrial membrane. NADH donates electrons to the chain, which are passed from one complex to the next. Reduction potentials increase down the chain, until the electrons end up on oxygen, which has the highest reduction potential.

Complex I Complex II Complex III Complex IV

centers^ Fe-S 4 H+^ 2 H+ FMN NADH NAD+^ + H +

2 e

QH^ Q 2 QH 2 2 H + Heme

Fe

FAD FADH 2 Succinate Fumarate + 2 H +

centersFe-S

2 H+

2 H+

Cyt c(ox) Cyt c(red) Q Q

Cyt c(ox) Cyt c(red) Q Q

Step 1 Step 2 1 e – 1 e

1 e – 1 e

4 × 4 ×

2 H+

2 H+

4 H+^ + O 2

Fe Fe

Cu Cu

Cyt c(ox)

Cyt c(red) 4 e

2 H 2 O

2 H+ Q QH (^2) Q QHQH (^2 )

NADH cannot cross the inner mitochondrial membrane, so must use one of two shuttle mechanisms to transfer its electrons to energy carriers in the mitochondrial matrix: the glycerol 3-phosphate shuttle or the malate–aspartate shuttle.

Oxidative Phosphorylation

The proton-motive force is the electrochemical gradient generated by the electron transport chain across the inner mitochondrial membrane. The intermembrane space has a higher concentration of protons than the matrix; this gradient stores energy, which can be used to form ATP via chemiosmotic coupling. ATP synthase is the enzyme responsible for generating ATP from ADP and an inorganic phosphate (Pi ). Summary of the energy yield of the various carbohydrate metabolism processes:

  • Glycolysis: 2 NADH and 2 ATP
  • Pyruvate dehydrogenase: 1 NADH (2 NADH per molecule of glucose because each glucose forms two molecules of pyruvate)
  • Citric acid cycle: 3 NADH, 1 FADH 2 , and 1 GTP (6 NADH, 2 FADH 2 , and 2 GTP per molecule of glucose) - Each NADH: 2.5 ATP; 10 NADH form 25 ATP - Each FADH 2 : 1.5 ATP; 2 FADH 2 form 3 ATP - GTP are converted to ATP. - 2 ATP from glycolysis + 2 ATP (GTP) from citric acid cycle + 25 ATP from NADH + 3 ATP from FADH 2 = 32 ATP per molecule of glucose (optimal). 30–32 ATP per molecule of glucose is the commonly accepted range for energy yield

Glycogenesis and Glycogenolysis

Glycogenesis (glycogen synthesis) is the building of glycogen using two main enzymes:

  • Glycogen synthase , which creates α-1, glycosidic links between glucose molecules. It is activated by insulin in the liver and muscles.
  • Branching enzyme , which moves a block of oligoglucose from one chain and connects it as a branch using an α-1,6 glycosidic link. Glycogenolysis is the breakdown of glycogen using two main enzymes:
  • Glycogen phosphorylase , which removes single glucose 1-phosphate molecules by breaking α-1,4 glycosidic links. In the liver, it is activated by glucagon to prevent low blood sugar. In exercising skeletal muscle, it is activated by epinephrine and AMP to provide glucose for the muscle itself.
  • Debranching enzyme , which moves a block of oligoglucose from one branch and connects it to the chain using an α-1,4 glycosidic link.

Gluconeogenesis

Occurs in both the cytoplasm and mitochondria, predominantly in the liver. Most of gluconeogenesis is just the reverse of glycolysis, using the same enzymes. The three irreversible steps of glycolysis must be bypassed by different enzymes:

  • Pyruvate carboxylase and PEP carboxykinase bypass pyruvate kinase
  • Fructose-1,6-bisphosphatase bypasses phosphofructokinase-
  • Glucose-6-phosphatase bypasses hexokinase/ glucokinase

The Pentose Phosphate Pathway

Occurs in the cytoplasm of most cells, generating NADPH and sugars for biosynthesis. Rate-limiting enzyme is glucose-6-phosphate dehydrogenase , which is activated by NADP+^ and inhibited by NADPH and insulin.

Lipid Transport

Lipids are transported via chylomicrons , VLDL , IDL , LDL , and HDL.

TGLCE

Liver

Adipose

Cholesterol

Chylomicron(lymph) Chylomicron(blood)

Chylomicronremnant

Triacylglycerol Glucose

Fatty acids

Triacylglycerol

Glycerol 3-P

Glycerol 3-P

Fatty acids

TGLCE

IDL

(blood)VLDL

TGLchol

TGLCE

TGLchol

(epithelium)^ Intestine Lipoproteinlipase

Lipoproteinlipase

Cholesterol Metabolism

  • Cholesterol may be obtained through dietary sources or through synthesis in the liver.
  • The key enzyme in cholesterol biosynthesis is HMG-CoA reductase. Palmitic acid , the only fatty acid that humans can synthesize, is produced in the cytoplasm from acetyl-CoA transported out of the mitochondria. Fatty acid oxidation occurs in the mitochondria, following transport by the carnitine shuttle, via β -oxidation. Ketone bodies form ( ketogenesis ) during a prolonged starvation state due to excess acetyl-CoA in the liver. Ketolysis regenerates acetyl-CoA for use as an energy source in peripheral tissues.

Protein Catabolism

Protein digestion occurs primarily in the small intestine. Carbon skeletons of amino acids are used for energy, either through gluconeogenesis or ketone body formation. Amino groups are fed into the urea cycle for excretion.

LIPID AND AMINO ACID METABOLISM

Insulin Glucagon

Gluconeogenesis

Glycogenolysis Lipolysis Protein catabolism Ureagenesis

Glycogensynthesis

synthesisProtein

synthesisLipid

Cellular glucoseuptake

Glucose efflux Ketogenesis

Plasma glucose

utilizationGlucose

Stimulates Inhibits

Tissue-Specific Metabolism

  • Liver: maintains blood glucose through glycogenolysis and gluconeogenesis. Processes lipids, cholesterol, bile, urea, and toxins.
  • Adipose: stores and releases lipids
  • Resting muscle: conserves carbohydrates as glycogen and uses free fatty acids for fuel
  • Active muscle: may use anaerobic metabolism, oxidative phosphorylation, direct phosphorylation (creatine phosphate), or fatty acid oxidation
  • Cardiac muscle: uses fatty acid oxidation
  • Brain: uses glucose except in prolonged starvation, when it can use ketolysis

Metabolic States

  • In the postprandial/well-fed (absorptive) state , insulin secretion is high and anabolic metabolism prevails.
  • In the postabsorptive (fasting) state , insulin secretion decreases while glucagon and catecholamine secretion increases.
  • Prolonged fasting ( starvation ) dramatically increases glucagon and catecholamine secretion. Most tissues rely on fatty acids.

BIOENERGETICS AND REGULATION OF METABOLISM

Direct hormones directly stimulate organs; tropic hormones stimulate other glands. Mechanisms of hormone action: peptides act via second messengers and steroids act via hormone/receptor binding to DNA. Amino acid-derivative hormones may do either.

Ectoderm “Attract”oderm

Nervous system, epidermis, lens of eye, inner ear Endoderm “Endernal” organs

Lining of digestive tract, lungs, liver and pancreas Mesoderm “Means”oderm

Muscles, skeleton, circulatory system, gonads, kidney

I Rest All gates closed II Depolarization Na gates open+ III Repolarization Na gates inactivate+ K gates open+ IV Hyperpolarization All gates closed

Blood type

RBC antigen

Antibodies Donates to:

Receives From: A A anti-B A, AB A, O B B anti-A B, AB B, O AB A, B None AB only All O None anti-A, B All O only

Enzyme Production Site Function Site Function Pepsin Gastric glands(chief cells) Stomach Hydrolyzes specific peptide bonds

Trypsin Pancreas Small Intestine

Hydrolyzes specific peptide bonds Converts chymotrypsinogen to chymotrypsin Chymotrypsin Hydrolyzes specific peptide bonds Carboxypeptidases A and B Hydrolyzes terminal peptide bond at C-terminus Aminopeptidase Intestinal glands

Hydrolyzes terminal peptide bond at N-terminus Dipeptidases Hydrolyzes pairs of amino acids Enteropeptidase Converts trypsinogen to trypsin

Table 1 Surface Colony Growth Starch Digestion A B C A B C Strain 1 + + + – – – Strain 2 + + – + + – key: + = growth; – = no growth

Table 2 Surface Colony Growth Deep-Agar Colony Growth Strain 1 + – Strain 2 + + key: + = growth; – = no growth

Hormone Source Action F ollicle-stimulating (FSH)

Anterior pituitary

Stimulates follicle maturation; spermatogenesis L uteinizing (LH) Stimulates ovulation; testosterone synthesis A drenocorticotropic (ACTH) Stimulates adrenal cortex to make and secrete glucocorticoids T hyroid-stimulating (TSH) Stimulates the thyroid to produce thyroid hormones P rolactin Stimulates milk production and secretion E ndorphins Inhibits the perception of pain in the brain G rowth hormone Stimulates bone and muscle growth/lipolysis Oxytocin Hypothalamus; stored in posterior pituitary

Stimulates uterine contractions during labor, milk secretion during lactation Antidiuretic (ADH, vasopressin) Stimulates water reabsorption in kidneys Thyroid hormones (T 3 , T 4 ) (^) Thyroid Stimulates metabolic activity Calcitonin Decreases (tones down) blood calcium level Parathyroid hormone Parathyroid Increases blood calcium level Glucocorticoids (^) Adrenal cortex Increases blood glucose level and decreasesprotein synthesis; anti-inflammatory Mineralocorticoids Increases water reabsorption in kidneys Epinephrine, Norepinephrine Adrenal medulla Increases blood glucose level and heart rate

Glucagon Pancreas

Stimulates conversion of glycogen to glucose in the liver; increases blood glucose Insulin (^) Lowers blood glucose; increases glycogen stores Somatostatin Supresses secretion of glucagon and insulin Testosterone Testes Maintains male secondary sexual characteristics Estrogen (^) Ovary/Placenta Maintains female secondary sexual characteristics Progesterone Promotes growth/maintenance of endometrium Melatonin Pineal Regulates sleep–wake cycles Atrial natriuretic peptide Heart Involved in osmoregulation and vasodilation Thymosin Thymus Stimulates T-cell development

Enzyme Production Site Function Site Salivary amylase (ptyalin) Salivary glands^ Mouth Pancreatic amylase Pancreas Small intestine Maltase Intestinal glands Small intestine Sucrase Intestinal glands Small intestine Lactase Intestinal glands Small intestine

Hydrolysis Reaction

Starch → maltose Starch → maltose Maltose → 2 glucoses Sucrose → glucose, fructose Lactose → glucose, galactose

ENDOCRINE SYSTEM

The functional unit is the neuron: cell body

dendrites

Schwann cells nodes ofRanvier myelinsheath axon (^) nerve terminals

Resting Potential:

  • 3 Na+^ pumped out for every 2 K+^ pumped in

Action Potential:

  • Stimulus acts on the neuron, depolarizing the membrane of the cell body

Impulse Propagation:

  • Depolarization (Na+^ rushing into axon) followed by repolarization (K+^ rushing out of axon) along the nerve axon

The Synapse:

  • At the synaptic knob, voltage-gated Ca2+ channels open, sending Ca2+^ into the cell.
  • Vesicles fuse with presynaptic membrane sending the neurotransmitter across the synaptic cleft.
  • Neurotransmitter binds to receptors on the postsynaptic membrane, triggering depolarization.

ACTION POTENTIAL

Ectoderm “Attract”oderm

Nervous system, epidermis, lens of eye, inner ear Endoderm “Endernal” organs

Lining of digestive tract, lungs, liver and pancreas Mesoderm “Means”oderm

Muscles, skeleton, circulatory system, gonads, kidney

I Rest All gates closed II Depolarization Na gates open+ III Repolarization Na gates inactivate+ K gates open+ IV Hyperpolarization All gates closed

Blood type

RBC antigen

Antibodies Donates to:

Receives From: A A anti-B A, AB A, O B B anti-A B, AB B, O AB A, B None AB only All O None anti-A, B All O only

Enzyme Production Site Function Site Function Pepsin Gastric glands(chief cells) Stomach Hydrolyzes specific peptide bonds

Trypsin Pancreas Small Intestine

Hydrolyzes specific peptide bonds Converts chymotrypsinogen to chymotrypsin Chymotrypsin Hydrolyzes specific peptide bonds Carboxypeptidases A and B Hydrolyzes terminal peptide bond at C-terminus Aminopeptidase Intestinal glands

Hydrolyzes terminal peptide bond at N-terminus Dipeptidases Hydrolyzes pairs of amino acids Enteropeptidase Converts trypsinogen to trypsin

Hormone Source Action F ollicle-stimulating (FSH)

Anterior pituitary

Stimulates follicle maturation; spermatogenesis L uteinizing (LH) Stimulates ovulation; testosterone synthesis A drenocorticotropic (ACTH) Stimulates adrenal cortex to make and secreteglucocorticoids

T hyroid-stimulating (TSH) Stimulates the thyroid to produce thyroid hormones P rolactin Stimulates milk production and secretion E ndorphins Inhibits the perception of pain in the brain G rowth hormone Stimulates bone and muscle growth/lipolysis Oxytocin Hypothalamus; stored in posterior pituitary

Stimulates uterine contractions during labor, milk secretion during lactation Antidiuretic (ADH, vasopressin) Stimulates water reabsorption in kidneys Thyroid hormones (T 3 , T 4 ) (^) Thyroid Stimulates metabolic activity Calcitonin Decreases (tones down) blood calcium level Parathyroid hormone Parathyroid Increases blood calcium level Glucocorticoids (^) Adrenal cortex Increases blood glucose level and decreasesprotein synthesis; anti-inflammatory Mineralocorticoids Increases water reabsorption in kidneys Epinephrine, Norepinephrine Adrenal medulla Increases blood glucose level and heart rate

Glucagon Pancreas

Stimulates conversion of glycogen to glucose in the liver; increases blood glucose Insulin (^) Lowers blood glucose; increases glycogen stores Somatostatin Supresses secretion of glucagon and insulin Testosterone Testes Maintains male secondary sexual characteristics Estrogen (^) Ovary/Placenta Maintains female secondary sexual characteristics Progesterone Promotes growth/maintenance of endometrium Melatonin Pineal Regulates sleep–wake cycles Atrial natriuretic peptide Heart Involved in osmoregulation and vasodilation Thymosin Thymus Stimulates T-cell development

Enzyme Production Site Function Site Salivary amylase (ptyalin) Salivary glands^ Mouth Pancreatic amylase Pancreas Small intestine Maltase Intestinal glands Small intestine Sucrase Intestinal glands Small intestine Lactase Intestinal glands Small intestine

Hydrolysis Reaction

Starch → maltose Starch → maltose Maltose → 2 glucoses Sucrose → glucose, fructose Lactose → glucose, galactose

action potential

action potential

action potential

- - - - - - - - - - - - -

+ + + + + +

- – + + + + + + - + Na+ **+

  • +**

K +

K +

**+

+**

+ +

- - - - - - - **-

  • – + + + +**

+ + – – + + + +

+

- **Na+

  • –**

K +

K +

**+

+**

+ +

+ +

+ +

**- – – –

-**

+ +

+ + + + – –

+

- **Na+

  • –**

axon

NERVOUS SYSTEM

Four Stages of Menstrual Cycle:

  1. Follicular: FSH causes growth of a follicle
  2. Ovulation: LH causes follicle to release egg
  3. Luteal: corpus luteum forms
  4. Menstruation: endometrial lining sheds Hypothalamus GnRH

FSH

follicle begins to mature estrogen uterus vascularization of uterine wall

LH surge follicle^ ruptures-egg released(ovulation) corpus luteum pr ogesterone

pr egnancy corpus luteum atrophies(inhibition stops, cycle starts anew)

day 0

ovary

pituitary (prevents multiple egg development)

day 14

early in cycle later in cycle

LH

uterine wallmaintains

no pregnancy

zygote hCG (LH analog)

Sarcomere

  • Contractile unit of the fibers in skeletal muscle
  • Contains thin actin and thick myosin filaments

Contraction

Initiation:

  • Depolarization of a neuron leads to an action potential. Sarcomere shortening:
  • Sarcoplasmic reticulum releases Ca2+.
  • Ca2+^ binds to troponin on the actin filament.
  • Tropomyosin shifts, exposing myosin-binding sites.
  • Myosin binds, ATPase activity allows myosin to pull thin filaments towards the center of the H zone, and then ATP causes dissociation.
  • Ca 2+

tropomyosin

actin filament (^) troponin

calcium myosin binding site

Relaxation:

  • Ca 2+^ is pumped back into the sarcoplasmic reticulum.

Bone Formation and Remodeling

  • Osteoblast: builds bone
  • Osteoclast: breaks down bone
  • Reformation: inorganic ions are absorbed from the blood for use in bone
  • Degradation (resorption): inorganic ions are released into the blood

MUSCULOSKELETAL SYSTEM

Circulatory Pathway Through Heart

pulmonary veins L. pulmonary artery

R. pulmonary artery

aorta

superior vena cava inferior vena cava

R. atrium

L. atrium mitral valve L. ventricle

tricuspid ValveR. ventricleseptum

Superior and inferior vena cava → right atrium → right ventricle → pulmonary arteries → lungs→ pulmonary veins → left atrium → left ventricle → aorta → body Three portal systems: Blood travels through an extra capillary bed before returning to the heart.

  • Liver (hepatic), kidney, and brain (hypophyseal)

Fetal Circulation

  • Foramen ovale: connects right and left atria
  • Ductus arteriosus: connects pulmonary artery to aorta. Along with foramen ovale, shunts blood away from lungs
  • Ductus venosus: connects umbilical vein to inferior vena cava, connecting umbilical circulation to central circulation

Blood Components

Plasma: aqueous mix of nutrients, wastes, hormones, blood proteins, gases, and salts Erythrocytes (red blood cells): carry oxygen

  • Hemoglobin: four subunits carry O 2 and CO 2. Iron controls binding and releasing.
  • Oxygen–hemoglobin dissociation: Factors leading to right shift of curve:
  • ↑ Temperature
  • Bohr Effect ↓ pH, ↑ PCO 2
  • O 2 release to tissues enhanced when H+ allosterically binds to Hb. ↑ PCO 2 leads to ↑ [ H+]: carbonic anhydrase CO 2 + H 2 O ⇋ H 2 CO 3 ⇋ H+^ + HCO 3 –

Leukocytes (white blood cells): function in immunity Platelets: clotting

  • Platelets release thromboplastin, which (along with cofactors calcium and vitamin K) converts inactive prothrombin to active thrombin.
  • Thrombin converts fibrinogen into fibrin, which surrounds blood cells to form the clot.

Blood Typing

Antigens are located on the surface of red blood cells.

Ectoderm “Attract”oderm

Nervous system, epidermis, lens of eye, inner ear Endoderm “Endernal” organs

Lining of digestive tract, lungs, liver and pancreas Mesoderm “Means”oderm

Muscles, skeleton, circulatory system, gonads, kidney

I Rest All gates closed II Depolarization Na gates open+ III Repolarization Na gates inactivate+ K gates open+ IV Hyperpolarization All gates closed

Blood type

RBC antigen

Antibodies Donates to:

Receives From: A A anti-B A, AB A, O B B anti-A B, AB B, O AB A, B None AB only All O None anti-A, B All O only

Hormone Source Action imulating (FSH)

Anterior pituitary

Stimulates follicle maturation; spermatogenesis g (LH) Stimulates ovulation; testosterone synthesis rticotropic (ACTH) Stimulates adrenal cortex to make and secrete glucocorticoids timulating (TSH) Stimulates the thyroid to produce thyroid hormones Stimulates milk production and secretion ns Inhibits the perception of pain in the brain ormone Stimulates bone and muscle growth/lipolysis

Hypothalamus; stored in posterior pituitary

Stimulates uterine contractions during labor, milk secretion during lactation ic (ADH, sin) Stimulates water reabsorption in kidneys ormones (T 3 , T 4 ) (^) Thyroid Stimulates metabolic activity Decreases (tones down) blood calcium level id hormone Parathyroid Increases blood calcium level ticoids (^) Adrenal cortex Increases blood glucose level and decreasesprotein synthesis; anti-inflammatory orticoids Increases water reabsorption in kidneys

ine, Norepinephrine Adrenal medulla Increases blood glucose level and heart rate

Pancreas

Stimulates conversion of glycogen to glucose in the liver; increases blood glucose Lowers blood glucose; increases glycogen stores atin Supresses secretion of glucagon and insulin one Testes Maintains male secondary sexual characteristics

rone Ovary/Placenta^ Maintains female secondary sexual characteristicsPromotes growth/maintenance of endometrium Pineal Regulates sleep–wake cycles iuretic peptide Heart Involved in osmoregulation and vasodilation Thymus Stimulates T-cell development

Production Site Function Site

mylase (^) Salivary glands Mouth

amylase Pancreas Small intestine Intestinal glands Small intestine

Hydrolysis Reaction

Starch → maltose Starch → maltose Maltose → 2 glucoses

Blood cells with Rh factor are Rh+; these individuals produce no anti-Rh antibody. Rh –^ blood cells lack the antigen; these individuals produce an antibody if exposed.

CIRCULATION

0

20

20

40

40

60

60

80

80

100

100

% saturation of hemoglobin

P (^) O 2 (mmHg)

35 25 curve shifts to the RIGHT pH shifts DOWN

Gas Exchange

  • Exchange occurs across the thin walls of alveoli.
  • Deoxygenated blood enters the pulmonary capillaries that surround the alveoli.
  • O 2 from the inhaled air diffuses down its gradient into the capillaries, where it binds with hemoglobin and returns to the heart.
  • CO 2 from the tissues diffuses from the capillaries to the alveoli, and is exhaled.

Fetal Respiration

  • Fetal hemoglobin has a higher affinity for oxygen than adult hemoglobin.
  • Gas and nutrient exchanges occur across the placenta.

RESPIRATION

diaphragm alveoli

trachea

bronchus

bronchiole

  • The body distinguishes between “self” and “nonself” (antigens).

Humoral Immunity (Specific Defense)

B-lymphocytes memory cells remember antigen, speed up secondary response

plasma cells make and release antibodies ( IgG , IgA , IgM , IgD , IgE ), which induce antigen phagocytosis

  • Active imumunity: antibodies are produced during an immune response
  • Passive immunity: antibodies produced by one organism are transferred to another organism

Cell-Mediated Immunity (Specific Defense)

T-lymphocytes cytotoxic T-cells destroy cells directly helper T-cells activate B- and T-cells and macrophages by secreting lymphokines

suppressor T-cells regulate B- and T-cells to decrease anti-antigen activity

memory cells

Nonspecific Immune Response

Includes skin, passages lined with cilia, macrophages, inflammatory response, and interferons (proteins that help prevent the spread of a virus)

Lymphatic System

  • Lymph vessels meet at the thoracic duct in the upper chest and neck, draining into the left subclavian vein of the cardiovascular system.
  • Vessels carry lymph (excess interstitial fluid), and lacteals collect fats by absorbing chylomicrons in the small intestine.
  • Lymph nodes are swellings along the vessels with phagocytic cells (leukocytes); they remove foreign particles from lymph.

IMMUNE SYSTEM

small intestine

colon

pancreas

stomach

esophagus

anus rectum

duodenum

gallbladder

liver

pharynx

trachea

tongue

oral cavity

DIGESTION

Lipid Digestion

  • When chyme is present, the duodenum secretes the hormone cholecystokinin (CCK) into the blood.
  • CCK stimulates the secretion of pancreatic enzymes and bile, and promotes satiety.
  • Bile is made in the liver and emulsifies fat in the small intestine; it’s not an enzyme.
  • Lipase is an enzyme made in the pancreas that hydrolyzes lipids in the small intestine.

Carbohydrate Digestion

Ectoderm “Attract”oderm

Nervous system, epidermis, lens of eye, inner ear Endoderm “Endernal” organs

Lining of digestive tract, lungs, liver and pancreas Mesoderm “Means”oderm

Muscles, skeleton, circulatory system, gonads, kidney

I Rest All gates closed II Depolarization Na gates open+ III Repolarization Na gates inactivate+ K gates open+ IV Hyperpolarization All gates closed

Blood type

RBC antigen

Antibodies Donates to:

Receives From: A A anti-B A, AB A, O B B anti-A B, AB B, O AB A, B None AB only All O None anti-A, B All O only

Enzyme Production Site Function Site Function Pepsin Gastric glands(chief cells) Stomach Hydrolyzes specific peptide bonds

Trypsin Pancreas Small Intestine

Hydrolyzes specific peptide bonds Converts chymotrypsinogen to chymotrypsin Chymotrypsin Hydrolyzes specific peptide bonds Carboxypeptidases A and B Hydrolyzes terminal peptide bond at C-terminus Aminopeptidase Intestinal glands

Hydrolyzes terminal peptide bond at N-terminus Dipeptidases Hydrolyzes pairs of amino acids Enteropeptidase Converts trypsinogen to trypsin

Table 1

Hormone Source Action F ollicle-stimulating (FSH)

Anterior pituitary

Stimulates follicle maturation; spermatogenesis L uteinizing (LH) Stimulates ovulation; testosterone synthesis A drenocorticotropic (ACTH) Stimulates adrenal cortex to make and secrete glucocorticoids T hyroid-stimulating (TSH) Stimulates the thyroid to produce thyroid hormones P rolactin Stimulates milk production and secretion E ndorphins Inhibits the perception of pain in the brain G rowth hormone Stimulates bone and muscle growth/lipolysis Oxytocin Hypothalamus; stored in posterior pituitary

Stimulates uterine contractions during labor, milk secretion during lactation Antidiuretic (ADH, vasopressin) Stimulates water reabsorption in kidneys Thyroid hormones (T 3 , T 4 ) (^) Thyroid Stimulates metabolic activity Calcitonin Decreases (tones down) blood calcium level Parathyroid hormone Parathyroid Increases blood calcium level Glucocorticoids (^) Adrenal cortex Increases blood glucose level and decreasesprotein synthesis; anti-inflammatory Mineralocorticoids Increases water reabsorption in kidneys Epinephrine, Norepinephrine Adrenal medulla Increases blood glucose level and heart rate

Glucagon Pancreas

Stimulates conversion of glycogen to glucose in the liver; increases blood glucose Insulin (^) Lowers blood glucose; increases glycogen stores Somatostatin Supresses secretion of glucagon and insulin Testosterone Testes Maintains male secondary sexual characteristics Estrogen (^) Ovary/Placenta Maintains female secondary sexual characteristics Progesterone Promotes growth/maintenance of endometrium Melatonin Pineal Regulates sleep–wake cycles Atrial natriuretic peptide Heart Involved in osmoregulation and vasodilation Thymosin Thymus Stimulates T-cell development

Enzyme Production Site Function Site Salivary amylase (ptyalin) Salivary glands^ Mouth Pancreatic amylase Pancreas Small intestine Maltase Intestinal glands Small intestine Sucrase Intestinal glands Small intestine Lactase Intestinal glands Small intestine

Hydrolysis Reaction

Starch → maltose Starch → maltose Maltose → 2 glucoses Sucrose → glucose, fructose Lactose → glucose, galactose

Protein Digestion

Ectoderm “Attract”oderm

Nervous system, epidermis, lens of eye, inner ear Endoderm “Endernal” organs

Lining of digestive tract, lungs, liver and pancreas Mesoderm “Means”oderm

Muscles, skeleton, circulatory system, gonads, kidney

I Rest All gates closed II Depolarization Na gates open+ III Repolarization Na gates inactivate+ K gates open+ IV Hyperpolarization All gates closed

Blood type

RBC antigen

Antibodies Donates to:

Receives From: A A anti-B A, AB A, O B B anti-A B, AB B, O AB A, B None AB only All O None anti-A, B All O only

Enzyme Production Site Function Site Function Pepsin Gastric glands(chief cells) Stomach Hydrolyzes specific peptide bonds

Trypsin Pancreas Small Intestine

Hydrolyzes specific peptide bonds Converts chymotrypsinogen to chymotrypsin Chymotrypsin Hydrolyzes specific peptide bonds Carboxypeptidases A and B Hydrolyzes terminal peptide bond at C-terminus Aminopeptidase Intestinal glands

Hydrolyzes terminal peptide bond at N-terminus Dipeptidases Hydrolyzes pairs of amino acids Enteropeptidase Converts trypsinogen to trypsin

Hormone Source Action F ollicle-stimulating (FSH)

Anterior pituitary

Stimulates follicle maturation; spermatogenesis L uteinizing (LH) Stimulates ovulation; testosterone synthesis A drenocorticotropic (ACTH) Stimulates adrenal cortex to make and secrete glucocorticoids T hyroid-stimulating (TSH) Stimulates the thyroid to produce thyroid hormones P rolactin Stimulates milk production and secretion E ndorphins Inhibits the perception of pain in the brain G rowth hormone Stimulates bone and muscle growth/lipolysis Oxytocin Hypothalamus; stored in posterior pituitary

Stimulates uterine contractions during labor, milk secretion during lactation Antidiuretic (ADH, vasopressin) Stimulates water reabsorption in kidneys Thyroid hormones (T 3 , T 4 ) (^) Thyroid Stimulates metabolic activity Calcitonin Decreases (tones down) blood calcium level Parathyroid hormone Parathyroid Increases blood calcium level Glucocorticoids (^) Adrenal cortex Increases blood glucose level and decreasesprotein synthesis; anti-inflammatory Mineralocorticoids Increases water reabsorption in kidneys Epinephrine, Norepinephrine Adrenal medulla Increases blood glucose level and heart rate

Glucagon Pancreas

Stimulates conversion of glycogen to glucose in the liver; increases blood glucose Insulin (^) Lowers blood glucose; increases glycogen stores Somatostatin Supresses secretion of glucagon and insulin Testosterone Testes Maintains male secondary sexual characteristics Estrogen (^) Ovary/Placenta Maintains female secondary sexual characteristics Progesterone Promotes growth/maintenance of endometrium Melatonin Pineal Regulates sleep–wake cycles Atrial natriuretic peptide Heart Involved in osmoregulation and vasodilation Thymosin Thymus Stimulates T-cell development

Enzyme Production Site Function Site Salivary amylase (ptyalin) Salivary glands^ Mouth Pancreatic amylase Pancreas Small intestine Maltase Intestinal glands Small intestine Sucrase Intestinal glands Small intestine Lactase Intestinal glands Small intestine

Hydrolysis Reaction

Starch → maltose Starch → maltose Maltose → 2 glucoses Sucrose → glucose, fructose Lactose → glucose, galactose

Regions of Electron Density Example

Geometric Arrangement of Electron Pairs around the Central Atom

Shape Angle betweenElectron Pairs

Complex Ion (Coordination Compound)

A Lewis acid–base adduct with a cation bonded to at least one electron pair donor (including water). Donor molecules are called ligands and use coordinate covalent bonds. The central cation can be bonded to the same ligand multiple times in a process called chelation.

Intermolecular Forces

  1. Hydrogen bonding: The partial positive charge of the hydrogen atom interacts with the partial negative charge located on the electronegative atoms (F, O, N) of nearby molecules.

δ+ δ+

δ–

δ+^ δ+

δ–

  1. Dipole–dipole interactions: Polar molecules orient themselves such that the positive region of one molecule is close to the negative region of another molecule.

δ+ H (^) Cl

δ+

δ– δ+

H (^) Cl δ–

H (^) Cl δ–

  1. Dispersion forces: The bonding electrons in covalent bonds may appear to be equally shared between two atoms, but at any particular point in time they will be located randomly throughout the orbital. This permits unequal sharing of electrons, causing transient polarization and counterpolarization of the electron clouds of neighboring molecules, inducing the formation of more dipoles.

δ+^ δ–

δ+^ δ–^ δ+^ δ–

nucleus

electron

symmetrical distribution

asymmetrical distribution

A mole is the amount of a substance that contains the same number of particles that are found in a 12.000 g sample of carbon-12. The molecular or formula weight is measured in amu per molecule (or formula unit). The molar mass is measured in grams per mole. Combustion reactions: A fuel, such as a hydrocarbon, is reacted with an oxidant, such as oxygen, to produce an oxide and water. CH 4 ( g ) + 2 O 2 ( g ) → CO 2 ( g ) + 2 H 2 O ( g )

Combination reactions: Two or more reactants form one product. S ( s ) + O 2 ( g ) → SO 2 ( g )

Decomposition reactions: A compound breaks down into two or more substances, usually as a result of heating or electrolysis. 2 HgO ( s ) → 2 Hg ( l ) + O 2 ( g ) Single-displacement reactions: An atom (or ion) of one compound is replaced by an atom of another element. Zn ( s ) + CuSO 4 ( aq ) → Cu ( s ) + ZnSO 4 ( aq ) Double-displacement reactions: Also called metathesis reactions; elements from two different compounds displace each other to form two new compounds. CaCl 2 ( aq ) + 2 AgNO 3 ( aq ) → Ca(NO 3 ) 2 ( aq ) + 2 AgCl ( s )

Net ionic equations: These types of equations are written showing only the species that actually participate in the reaction. Consider the following equation: Zn ( s ) + Cu 2+^ ( aq ) + SO 4 2–^ ( aq ) → Cu ( s ) + Zn2+^ ( aq ) + SO2– 4 ( aq ) The spectator ion (SO 4 2–) does not take part in the overall reaction, but simply remains in solution throughout. The net ionic equation would be: Zn ( s ) + Cu 2+^ ( aq ) → Cu ( s ) + Zn2+^ ( aq )

Neutralization reactions: These are a specific type of double-displacement reactions that occur when an acid reacts with a base to produce a solution of a salt (and, usually, water): HCl ( aq ) + NaOH ( aq ) → NaCl ( aq ) + H 2 O ( l ) Factors affecting reaction rates: reactant concentrations, temperature, medium, catalysts Catalysts are unique substances that increase reaction rate without being consumed; they do this by lowering the activation energy.

COMPOUNDS & STOICHIOMETRY

E auncatalyzed

reaction coordinate

free energy

E acatalyzed catalyzed

uncatalyzed

Law of Mass Action

a A + b B  ⇀↽  c C + d D

K c =

[ ] [ ]

[ ] [ ]

c d a b

C D

A B

K c is the equilibrium constant (c stands for concentration).

Properties of the Equilibrium Constant

Pure solids and liquids don’t appear in expressions. K eq is characteristic of a given system at a given temperature. If K eq >> 1, an equilibrium mixture of reactants and products will contain very little of the reactants compared to the products. If K eq << 1, an equilibrium mixture of reactants and products will contain very little of the products compared to the reactants. If K eq is close to 1, an equilibrium mixture of products and reactants will contain approximately equal amounts of the two. Le Châtelier’s principle is used to determine the direction in which a reaction at equilibrium will proceed when subjected to a stress, such as a change in concentration, pressure, volume, or temperature. The key is to remember that a system to which these kinds of stresses are applied tends to change so as to relieve the applied stress.

In a nutshell:

n – 1

Experimental determination of rate law: The values of k , x , and y in the rate law equation (rate = k [A] x [B] y ) must be determined experimentally for a given reaction at a given temperature. The rate is usually measured as a function of the initial concentrations of the reactants, A and B.

Efficiency of Reactions

E aforward

reaction coordinate

free energy Δ G

H 2 + Cl 2 E areverse

2 HCl

KINETICS & EQUILIBRIUM

The law of conservation of energy dictates that energy can be neither created nor destroyed, but that all thermal, chemical, potential, and kinetic energies are interconvertible.

Systems:

Isolated: no exchange of energy/matter with the environment. Bomb calorimetry creates a nearly isolated system. Closed: can exchange energy but not matter with the environment Open: can exchange both energy and matter with the environment. Human beings are open systems because they can take in energy and matter (eat), release matter into the environment (respiration, urination, defecation), and release energy into the environment (heat transfer from the skin and mucous membranes).

THERMOCHEMISTRY

Osmotic pressure

∏ = M R T

Vapor pressure lowering (Raoult’s law)

P A = X A P A˚; P B = X B P ˚B

Solutions that obey Raoult’s Law are called ideal solutions.

heating of ice

heating of water

heating of water vapor

heat used to melt ice to water

heat used to vaporize water towater vapor

0

25

50

75

100

125

temperature (˚C)

heat added (each division = 4 kJ)

Graham’s law of diffusion and effusion

Diffusion: occurs when gas molecules distribute through a volume by random motion

Effusion: the flow of gas particles under pressure from one compartment to another through a small opening:

Both diffusion and effusion have the same formula: r r

1 2

1 2

m m 2 1

 

 

 

 

  1. All salts containing alkali metal (Group 1) or ammonium (NH 4 +) cations are water-soluble.
  2. All salts containing the nitrate (NO 3 – ) or acetate (CH 3 COO–) anions are water-soluble.
  3. All chlorides, bromides, and iodides are water- soluble, with the exception of Ag+, Pb2+, and Hg2+.
  4. All salts of the sulfate ion (SO 4 2–) are water- soluble, with the exception of Ca2+^ , Sr2+, Ba2+, and Pb2+^.
  5. All metal oxides are insoluble, with the exception of the alkali metals and CaO, SrO, BaO, all of which hydrolyze to form solutions of the corresponding metal hydroxides.
  6. All hydroxides are insoluble, with the exception of the alkali metals and Ca2+, Sr2+, and Ba2+.
  7. All carbonates (CO 3 2–), phosphates (PO 4 3–), sulfides (S 2–), and sulfites (SO 3 2–) are insoluble, with the exception of the alkali metals and ammonium.

Units of Concentration

Percent composition by mass:

= Mass of solute× Mass of solution 100%

Mole fraction:

of mol of compound

total # of moles in system

×100%

Molarity: # of mol of solute liter of solution

Molality: # of mol of solute kg of solvent

Normality:

of gram equivalent weights of solute

liter of solution

SOLUTIONS

Arrhenius definition: An acid is a species that produces excess H +^ (protons) in an aqueous solution, and a base is a species that produces excess OH –^ (hydroxide ions). Brønsted–Lowry definition: An acid is a species that donates protons, while a base is a species that accepts protons. Lewis definition: An acid is an electron pair acceptor, and a base is an electron pair donor.

Properties of Acids and Bases

pH = –log[H+^ ] = log( 1 [H+]

pOH = –log[OH – ] = log( 1 [OH^ − ]

H 2 O ( l )  ⇀↽ ^ H +^ ( aq ) + OH–^ ( aq ) K w = [H+][OH–] = 10– pH + pOH = 14

Weak Acids and Bases

HA ( aq ) + H 2 O ( l ) ↽  ⇀^ H 3 O+^ ( aq ) + A–^ ( aq )

K a =

[H O 3 ][A ]

[HA]

K b =

[B ][OH ]

[BOH]

Salt formation: Acids and bases may react with each other, forming a salt and (often, but not always) water in a neutralization reaction. HA + BOH → BA + H 2 O Hydrolysis: This is the reverse reaction, where the salt ions react with water to give back the acid and base. Amphoteric species: is one that can act either as an acid or a base, depending on its chemical environment

Titration and Buffers

strong acid and strong base

weak acid and strong base Henderson–Hasselbalch equation: is used to estimate the pH of a solution in the buffer region where the concentrations of the species and its conjugate are present in approximately equal concentrations

pH = p K a + log [conjugate base] [weak acid]

pOH = p K b + log [conjugate acid] [weak base]

ACIDS AND BASES

Titration is a procedure used to determine the molarity of an acid or base by reacting a known volume of a solution of unknown concentration with a known volume of a solution of known concentration. The half- equivalence point defines pH = p K a

B A S IC

A C ID IC

3 3

2 3 4 4

Oxidation: loss of electrons

Reduction: gain of electrons Oxidizing agent: causes another atom to undergo oxidation, and is itself reduced Reducing agent: causes another atom to be reduced, and is itself oxidized

Galvanic Cells

A redox reaction occurring in a galvanic cell has a negative ∆ G and is therefore a spontaneous reaction. Galvanic cell reactions supply energy and are used to do work. This energy can be harnessed by placing the oxidation–reduction half-reactions in separate containers called half-cells. The half-cells are then connected by an apparatus that allows for the flow of electrons.

Electrolytic Cells

e

e

A redox reaction occurring in an electrolytic cell has a positive ∆ G and is therefore nonspontaneous. In electrolysis, electrical energy is required to induce a reaction. The oxidation and reduction half-reactions are usually placed in one container. Reduction potential of each species is defined as the tendency of a species to acquire electrons and be reduced. Standard reduction potential, E ˚, is measured under standard conditions: 25˚C, 1 M concentration for each ion in the reaction, a partial pressure of 1 atm for each gas and metals in their pure state. Standard reduction potentials are used to calculate the standard electromotive force (emf or E (^) cell˚ ) of a reaction, the difference in potential between two half-cells. emf = E red, cathode˚ – E red, anode˚

Gibbs free energy , ∆ G , is the thermodynamic criterion for determining the spontaneity of a reaction. ∆ G = – n F E cell

REDOX REACTIONS & ELECTROCHEMISTRY

Carboxylic acids have p K a values around 4.5 due to resonance stabilization of the conjugate base. Electronegative atoms increase acidity with inductive effects. Boiling point is higher than alcohols because of the ability to form two hydrogen bonds.

Synthesis

Oxidation of primary alcohols with KMnO (^4)

OH

O OH

KMnO (^4)

Hydrolysis of nitriles

CH 3 Cl CH 3 CN CH 3 COH

O

  • NH+ 4

Reactions

Formation of soap by reacting carboxylic acids with NaOH; arrange in micelles

O —Na +

O

nonpolar tail polar head

Nucleophilic acyl substitution

  • Ester formation
  • Reduction to alcohols

Decarboxylation O C O

CARbOXyLIC ACIDS Carboxylic acid derivatives contain three bonds to heteroatoms (O, N, halides, and so forth). As such, they can be interconverted through nucleophilic acyl substitution by swapping leaving groups. Carboxylic acid derivatives can be ranked based on descending reactivity:

  • Acyl halides are the most reactive
  • Anhydrides
  • Carboxylic acids and esters
  • Amides are the least reactive A reaction that proceeds down the order of reactivity can occur spontaneously by nucleophilic acyl substitution. A reaction that proceeds up the order of reactivity requires special catalysts and specific reaction conditions.

Anhydrides

Synthesis via dehydration of two carboxylic acids

Intramolecular formation of a cyclic anhydride

ortho -phthalic acid

OH OH

O

O

O

O

O

  • H 2 O

phthalic anhydride

CARbOXyLIC ACID DERIVATIVES

Lactams

Cyclic amides are called lactams. These are named according to the carbon atom bound to the nitrogen: β-lactams contain a bond between the β-carbon and the nitrogen, γ-lactams contain a bond between the γ-carbon and the nitrogen, and so forth.

N H

O N H O N H O N H O β-lactam γ-lactam δ-lactam ε-lactam

Lactones

Cyclic esters are called lactones. These are named not only based on the carbon bound to the oxygen, but also the length of the carbon chain itself.

O

O O

O O O O

O

α-acetolactone β-propiolactone γ-butyrolactone δ-valerolactone

CyCLIC CARbOXyLIC ACID DERIVATIVES

Strecker Synthesis

Reagents: aldehyde, ammonium chloride (NH 4 Cl), potassium cyanide (KCN) R O NH+ 3

NH 2 NH+ 2 OH+ 2

H NH+^3 O+

NH 3 R H

−CN −H 2 O

protontransfer

R (^) N

R OH

R

NH (^2) R

N (^) NH+ H+^ H2 O

transferproton H H2 N O

OH

R NH

OH+ 2

NH

OH+ 2

OH NH+ 2

proton transfer

−NH

OH OH NH+ 3

−H+

O OH

OH+ OH

H 2 N R

H2 N R

H 2 N R

H2 N R

H2N R

H 2 N R

H 2 N R

Gabriel (Malonic-Ester) Synthesis

Reagents: potassium phthalimide, diethyl bromomalonate

O

S (^) N 2

O N K

phthalimidepotassium bromomalonatediethyl

CO 2 C 2 H 5 CO2C 2 H (^5)

CO2 C 2 H 5 CO2 C 2 H 5

base O

O CO 2 C 2 H 5 CO2C 2 H 5

R–Br

O

O −CO 2 C RH^3 O+,^ ∆ H

H 3 +NCO^2 H H 2 NCCO 2 R CO (^2) H^ NaOH 2 O, ∆ C O

O N R

CO 2 C 2 H (^5) CO 2 C 2 H 5

O

O N

O

O

  • (^) Br C H C H N C SN 2

NITROGEN-CONTAINING COMPOUNDS

  • Phosphoric acid is a phosphate group or inorganic phosphate ( Pi ). At physiologic pH, inorganic phosphate includes both hydrogen phosphate (HPO2– 4 ) and dihydrogen phosphate (H 2 PO– 4 ).
  • Pyrophosphate ( PPi ) is P 2 O 7 4–, which is released during the formation of phosphodiester bonds in DNA. Pyrophosphate is unstable in aqueous solution, and is hydrolyzed to form two molecules of inorganic phosphate.

O

O

O

O

O

O O

P P

  • Nucleotides with phosphate groups, such ATP, GTP, and those in DNA, are referred to as organic phosphates.

PHOSPHORUS-CONTAINING COMPOUNDS

Amides

Formation from an anhydride

O – O

O

H 2 N (^) H

O – O

O

H 3 N

O OH

O

O O NH 3 +

O NH (^2)

Formation from an ester

Hydrolysis (requires acid)

Reduction to an amine O

NH (^2)

LiAlH 4 NH (^2)

Esters

Transesterification

Hydrolysis

H 2 O O

H3O+

+OH

OH O OH (^) H

OH OH

    • OH

O + OH

OH O H O+H

H 2 O

Reduction

O

O LAH (^) OH + OH

Saponification

O

O

O

RC

RC

RC

O

O

O

RC O Na+

O

RC O Na+

O

RC O Na+

O

NaOH + HO HO

HO

triacylglycerol soap glycerol

Type of Chromatography Mobile Phase Stationary Phase Common Use Thin-layer or Paper Nonpolar solvent Polar card Identify a sample Reverse-phase Polar solvent Nonpolar card Identify a sample

Column Nonpolar solvent zPolar gel or powder Separate a sample into components Ion-exchange Nonpolar solvent Charged beads in column Separate components by charge

Size-exclusion Nonpolar solvent Polar, porous beads in column Separate components by size

Affinity (^) Nonpolar solvent

Beads coated with antibody or receptor for a target molecule

Purify a molecule (usually a protein) of interest

Gas (GC) Inert gas Crushed metal or polymer Separate vaporizable compounds

High-performance liquid (HPLC) Nonpolar solvent Small column with concentration gradient

Similar to column, but more precise

Extraction separates dissolved substances based on differential solubility in aqueous vs. organic solvents.

Filtration separates solids from liquids.

residue filter paper

to vacuum trap

clean filter flask

filtrate vacuum filtration

Chromatography uses a stationary phase and a mobile phase to separate compounds based on polarity and/or size.

thin-layer chromatograms

solvent front

Y

X

R f = (^) YX

11 22 33 11 22 333

solvent sand

sand

silica or alumina

glass wool or cotton stopcock to control flow

collection flask

column chromatography

PURIFICATION METHODS

Distillation separates liquids based on boiling point, which depends on intermolecular forces. Types are simple, fractional, and vacuum.

vacuum distillation

ice bath

vacuum adapter

to vacuum source

receiving flask

distilling flaskwater outlet water inlet

heat source

clamp clamp

condenser

thermometer

Column

fractional distillation

glass projection to hold up packing

Column packing

Simple distillation can be used to separate two liquids with boiling points below 150°C and at least 25°C apart. Vacuum distillation should be used when a liquid to be distilled has a boiling point above 150°C. To prevent degradation of the product, the incident pressure is lowered, thereby lowering the boiling point. Fractional distillation should be used when two liquids have boiling points less than 25°C apart. By introducing a fractionation column, the sample boils and refluxes back down over a larger surface area, improving the purity of the distillate. Recrystallization separates solids based on differential solubility in varying temperatures. Electrophoresis is used to separate biological macromolecules based on size and/or charge.

Infrared spectroscopy measures molecular vibrations of characteristic functional groups.

Alkanes 2800 — 3000 (^) C H 1200 C C Alkenes 3080 — 3140 C H (^1645) C C Alkynes (^2200) C C 3300 C H Aromatic 2900 — 3100^ C H 1475 — 1625 C C Alcohols 3100 — 3500 (^) O H (broad) Ethers 1050 — 1150 (^) C O Aldehydes 2700 — 2900 (O)C H 1700 — 1750 C O Ketones 1700 — 1750 C O Carboxylic acids 1700 — 1750 (^) C O 2800 — 3200 (^) O H (broad) Amines 3100 — 3500 N H (sharp)

Functional Group Wavenumber (cm–1) Vibration

UV spectroscopy involves passing ultraviolet light through a chemical sample and plotting absorbance vs. wavelength. It is most useful for studying compounds containing double bonds and heteroatoms with lone pairs. (^1) H–NMR is a form of nuclear magnetic resonance. Type of Proton Approximate Chemical Shift (ppm) Downfield from TMS RC H 3 RC H 2 R 3 C H –C H =C H –C≡ C H Ar– H –C H X –C H OH/–C H OR RC H O RC H CO– –C H COOH/–C H COOR –CHO H– C H 2 O H ArO H –COO H –N H 2

4.6– 2– 6–8. 2–4. 3.4– 9– 2–2. 2–2. 1–5. 4– 10.5– 1–

TMS

shielding

deshielding

8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 0. δ (ppm)

a

b (^) Cl C H (^) a Hb O C Hb Cl Hb

When analyzing an NMR spectrum, look for:

  • Types of protons: corresponds to the number of peaks seen in the spectrum
  • Position of peaks: the further left-shifted (downfield) the peak, the more deshielded the proton. Usually this corresponds to more electron-withdrawing groups
  • Integration of peaks: the larger the integration, the more protons contained under the peak
  • Splitting: hydrogens on adjacent carbons will split a peak into n + 1 subpeaks, where n is the number of hydrogens on the adjacent carbon

SPECTROSCOPy