Quicksheets Flashcards
What does the parasympathetic nervous system do?
The parasympathetic nervous system is focused on “rest-and-digest” responses. Think “para” for stop in spanish (parar).
What does the sympathetic nervous system do?
The sympathetic branch of the nervous system is focused on “fight-or-flight” responses.
What are the the three regions of the brain? What structures do they contain?
Hindbrain: contains the cerebellum, medulla oblongata, and reticullar formation
Midbrain: contains the inferior and superior colliculi
Forebrain: contains the thalamus, hypothalamus, basal ganglia, limbic system, and cerebral cortex
What does each region of the forebrain do?
Thalamus
Hypothalamus
Basal ganglia
Limbic system
Thalamus: relay station for sensory information (except olfactory)
Hypothalamus: maintains homeostasis and integrates with the endocrrine system through the hypophyseal portal system that connects it to the anterior pituitary
Basal ganglia: smoothens movements and helps maintain postural stability
Limbic system: contains emotion and memory. Includes septal nuclei (pleasure seeking), amygdala (fear and aggression), hippocampus (memory), and fornix (helps with communication via the limbic system)
List the divisions (lobes) of the cerebral cortex and identify their functions.
Frontal: Executive function, impulse control, long-term planning (prefrontal cortex), motor function (primary motor cortex, precentral gyrus), speech production (Broca’s area)
Parietal: Sensation of touch, pressure, temperature, and pain (somatosensory cortex); spatial processing, orientation, and manipulation
Occipital: Visual processing
Temporal: Sound processing (auditory cortex), speech perception (Wernicke’s area), memory, and emotion (limbic system)
Name the seven major neurotransmittters and some of their functions. (Specifically, their influences on behavior)
Acetylcholine: Voluntary muscle control, parasympathetic nervous system, attention, alertness
Norepinephrine and Epinephrine: Fight-or-flight responses, wakefulness, alertness
Dopamine: Smooth movements, postural stability
Serotonin: Mood, sleep, eating, dreaming
GABA: Brain “stabilization”, anti-anxyolitic
Endorphins: Natural painkillers
Identify two main theories regarding the development of individual traits.
Nature: Genetics.
Nurture: Environment.
Methods for study include family, twin, and adoption studies.
Sensation vs. Perception
Sensation: The conversion of physical stimuli into neurological signals
- Sensory receptors respond to stimuli (afferent) and trigger electrical signals.
- Sensory neurons transmit information from sensory receptors to the CNS.
- Sensory stimuli are transmitted to projection areas in the brain, which further analyze sensory input.
Perception: The processing of sensory information to make sense of its significance.
Sensory thresholds and their relation to a law regarding the nature of a changing stimulus and its effects on perception.
The minimum stimulus that causes a change in signal transduction.
Weber’s law states that the just-noticable difference for a stimulus is proportional to the magnitude of the initial stimulus. This proportion is constant over most of the range of possible stimuli.
Describe signal detection theory, response bias, and adaptation
Signal detection theory is in regard to the effects had by nonsensory factors, such as experiences, motives, and expectations, on perception of stimuli
Response bias: examined using signal detection experiments with the below structure
Adaptation: a decrease in response to a stimulus over time
Describe the structures of the eye, how it detects light, and the visual pathway.
The eye is an organ specialized to detect light in the form of photons.
Visual Pathway: retina -> optic nerve -> optic chiasm -> optic tracts -> lateral genitculate nucleus (LGN) of thalamus -> visual radiations -> visual cortex
Describe the process surrounding audition and the auditory pathway. Name some significant structures.
The ear transduces sound waves into electrical signals that can be interpreted by the brain.
Cochlea: Detects sound via fluid oscillations after the ossicles mechanically vibrate the oval window, that vibration is reverberated through fluid contained in the cochlea that vibrate hair fibers on the organ of corti.
Utricle and saccule: detect linear acceleration (housed in the vestibules)
Semicircular canals: detect rotational acceleration
Auditory pathway: cochlea -> vestibulocochlear nerve -> medial geniculate nucleus of the thalamus -> auditory cortex
Describe the senses smell, taste, somatosensation, and kinesthetic sense
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 modalitties (pressure, vibration, pain, and temperature)
Kinesthetic sense (proprioception): ability to tell where one’s body is in space
Describe the the two types of object recognition/visual processing.
Bottom-up (data-driven) processing: recognition of objects by parallel processing and feature detection. Slower, but less prone to mistakes.
Top-down (concept-driven) processing: recognition of an object by memories and expectations, but little attention to detail. Faster, but more prone to mistakes.
Gestal principles: ways that the brain can infer missing parts of an image when it is incomplete.
Describe habituation and dishabituation.
Habituation: The process of becoming used to a stimulus.
Dishabituation: Occurs when a second stimulus intervenes, causing a resensitization to the original stimulus.
Describe two types of learning.
Observational learning: the acquisition of behavior by watching others
Associative learning: pairing together stimuli and responses, or behaviors and consequences (reinforcement)
Describe classical conditioning.
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
Describe operant conditioning.
Operant conditioning: a form of associative learning in which the frequency of a behavior is modified using reinforcement (increases behavior) or punishment (decreases behavior)
Describe EEG waves for consciousness and each of the stages of sleep. Additionally describe features of each sleep stage.
Sleep disorders including dysomnias (amount or timing of sleeep), such as insomnia, narcolepsy, sleep apnea, and sleep deprivation; and parasomnias (odd behaviors during sleep), such as night terrors and sleepwalking (somnambulism)
Describe the subcomponents of memory and the tasks each is assigned.
Facts are stored via semantic networks. Retrieval of information is often based on prriming interconnected nodes of the semantic network.
Recognition information is stronger than recall.
Describe Piaget’s Stages of Cognitive Development.
Identify components crucial to 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 or examples).
Heuristics are simplified principles used to make decisions (rules of thumb), but biases, intuition, and emotions may contribute to the decision-making process.
Define selective attention and divided 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
Identify the three language areas in the brain & what occurs if each is damaged.
Detail the four 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 (see Yerkes-Dodson law)
Drive reduction theory: individuals act to relieve internal states of tension
Maslow’s hierarchy of needs: prioritizes needs into five categores (highest -> lowest)
- physiological needs
- safety and security
- love and belonging
- self-esteem
- self-actualization
Identify the seven universal emotions and the three theories of emotion, as well as their postulates.
Seven universal emotions: happiness, sadness, contempt, fear, surprrise, disgust, anger
Define stress, the steps for appraisal, stressors, and the three stages of the general adaptation syndrome.
Stress: physiological and cognitive response to challenges or life changes
Primary appraisal: classifying a potential stressor as irrelevant, benign-positive, or stressful
Secondary appraisal: directed at evaluating whether the organism can cope with the stress, based on harm, threat, and challenge
Stresssor (eustress or distress): anything that leads to a stress response
General adaptation syndrome: alarm, resistance, and exhaustion
Self-concept and Identity: define the following terms
- Self-concept
- Identities
- Self-esteem
- Self-efficacy
- Locus of Control
Describe schizophrenia and give examples of positive and negative symptoms.
Schizophrenia: psychotic disorder characterized by distortions of rerality and disturbances in content and form of thought, perception, and behavior
Positive: hallucinations, delusions, and disorganized thought and behavior
Negative: disturbance of affect and avolition
Identify & outline the three depressive disorders.
Major depressive disorder: contains at least one major depressive episode
Pervasive depressive disorder: a depressed mood (either dysthymia or major depression) for at least two years
Seasonal affective disorder: the colloquial name for major depressive disorder with seasonal onset, with depression occurring during winter months
Name and describe the bipolar disorders.
Bipolar I disorder: contains at least one manic episode
Bipolar II disorder: contains at least one hypomanic episode and at least one major depressive episode
Cyclothymic disorder: conatins hypomanic episodes with dysthymia (persistent mild depression)
Detail Freud’s stages of psychosexual development
Based on tensions caused by the libido, with failure at any stage leading to fixation
Describe Erikson’s stages of psychosocial development
Stem from conflicts that are the result of decisions we are forced to make about ourselves and the environment around us at each phase of our lives
Stages are:
- trust vs. mistrust
- autonomy vs. shame and doubt
- initiative vs. guilt
- industry vs. inferiority
- identity vs. role confusion
- intimacy vs. isolation
- generativity vs. stagnation
- integrity vs. despair
Describe Kohlberg’s theory of moral reasoning development
Describes the approaches of individuals to resolving moral dilemmas
Six stages are divided into three main phases: preconventional, conventional, and postconventional
Describe Vygotsky’s theory of cultural and biosocial development
Describes development of language, culture, and skills
Describe the following anxiety disorders: GAD, specific phobias, social anxiety disorder, agooraphobia, panic disorder, OCD, and body-dismorphic disorder
Describe the psychoanalytic and humanistic perspectives
Psychoanalytic: personality results from unconscious urges and desires
Humanistic: emphasizes internal feelings of healthy individuals as they strive towards happiness and self-realization (Maslow: hierarchy of needs, Rogers: unconditional positive reward)
Define Type and Trait theory as well as some examples
Type and trait theory: personality can be described as a number of identifiable traits that carry characteristic behaviors. Some types: ancient Greek humorrs, Sheldon’s somatotypes, division into Types A and B, and the Myer-Briggs Type Inventory
- Eysenck’s three major traits: psychoticism, extraversion, neuroticism
- Trait theorists’ Big Five: openness, conscientiousness, extraversion, agreeableness, and neuroticism (OCEAN)
- Allport’s three basic types of traits: cardinal, central, and secondary
Describe personality disorders and the “clusters” associated with them
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
Define social facilitation
Social facilitation: tendency to perform at a different level (better or worse) when others are around
Define deindividuation
Deindividuation: loss of self-awareness in large groups; can lead to drastic changes in behavior
Define peer pressure
Peer pressure: social influence placed on an individual by other individuals they consider equals
Define group polarization
Group polarization: tendency towards making decisions in a group that are more extreme then the thoughts of the individual group members
Define groupthink
Groupthink: tendency to make decisions based on ideas & solutions that arise within the group without considering outside ideas
Define assimilation
Assimilation: one culture begins to melt into anotherr
Define multiculturalism
Multiculturalism: encouragement of multiple cultures within a community to enhance diversity
Define subculture
Subculture: a group that distinguishes itself from the primary culture to which it belongs
Define socialization
Socialization: the process of developing and spreading norms, customs, and beliefs
Define stigma
Stigma: extreme disapproval or dislike of a person or group based upon perceived differences
Define deviance
Deviance: any violation of norms, rules, or expectations within a society
Define conformity
Conformity: changing beliefs or behaviorrs in order to fit into a group or society
Define compliance
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
Define obedience
Obedience: change in behavior based on a command from someone seen as an authority figure
Define status, role, group, network, and organization
Define display rules
Display rules: unspoken rules that govern the expression of emotion
Define impression management
Impression management: maintenance of a public image through various strategies
Define dramaturgical apprroach
Dramaturgical approach: individuals create images of themselves in the same way that actors perform a role in front of an audience
Define aspects of Social Behavior, including:
- interpersonal attraction
- aggression
- attachment
- altruism
Define attribution theory and its componeents (dispositional, situational, Corrrespondent inference theory, and fundamental attribution error)
Attribution theory: focuses on the tendency for individuals to infer the causes of other people’s behavior
- Dispositional causes relate to the features of the person being considered
- Situational causes relate to featurers of the surroundings or context
- Correspondent inference thteory: describes attributions made by observing the intentional (especially unexpected) behaviors performed by another person
- Fundamental attribution error: bias toward making disposittional attributions rather than situational attributions
Define self-fulfilling prophecy
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
Define stereotype threat
Stereotype threat: a feeling of anxiety about confirming a negative stereoype
Define prejudice
Prejudice: an irrrrationally based attitude prior to actual expeerience
Define ethnocentrism
Ethnocentrism: the practice of making judgements about other culturers based on the values and beliefs of one’s own culture (in-group vs. out-group).
Describe each of these four theories for social structures:
- functionalism
- conflict theory
- symbolic interactionism
- social constructionism
Define symbolic and material culture.
Symbolic culture: the ideas associated with a cultural group
Material culture: physical items one associates with a given group (art, clothing, foods, buildings)
Define demographic transition
Demographic transition: a model used to represent drops in birth and death rates as a result of industrialization
Define social class/stratification based on socioeconomic status and these factors:
- Class
- Power
- Social Capital
- Social Reproduction
- Poverty
- Class: a category of people with shared socioeceonomic 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
Define these four components of epidemiology:
- Incidence
- Prevalence
- Morbidity
- Mortality
Name the amino acids that fit into each of the following groups: (i) Nonpolar, nonaromatic, (ii) Aromatic, (iii) Polar, (iv) Negatively charged, (v) Positively charged
Additionally identify the chirality of each amino acid -> what’s the exception?
Describe the reaction for that occurs between two amino acids when they’re connected. How is this bond broken?
Peptide bond formation is a condensation (dehydration) reaction with a nucleophilic amino group attaching an electrophilic carbonyl. Peptide bonds are broken by hydrolysis.
Identify the four levels of protein structure and describe each of their characteristics.
Describe structural and binding proteins.
Structural proteins: generally fibrous, include collagen, elastin, keratin, actin, and tubulin.
Binding proteins: bind to a specific substrate, either to sequester it in the body or hold its concentration at steady state
Describe motor proteins and how they function.
Motor proteins: capable of force generation through a conformational change, include myosin, kinesin, and dynein.
Describe cell adhesion molecules and antibodies.
Cell adhesion molecules (CAMs): bind cells to other cells or surfaces, include cadherins, integrins, and selectins.
Antibodies (or immunoglobulins, Ig): target a specific antigen, which may be a protein on the surface of a pathogen (invading organism) or a toxin
Identify the eight types of enzymes.
Specify the two models surrounding enzyme-substrate bindings.
Lock and key theory, as well as induced fit model.
What function do enzymes have? What are their effectts on a reaction? Do they alter free energy or enthalpy?
Enzymes, like all catalysts, lower the activation energy necessary for reactions. They do not alter the free energy or enthalpy change that accompanies the reactiton nor the final equilibrium position; rather, they change the rate (kinetics) at which equilibrium is reached.
Identify the binding site, impact on Km, and impact on Vmax of competitive, noncompetitive, mixed, and uncompetitive enzyme inhibitors.
Identify the three types of ion channels.
Ion channels can be used for regulating on flow into or out of a cell. There are three main types of ion channels: ungated channels, voltage-gated channels, and ligand-gated channels.
What do enzyme-linked receptors do?
Enzyme-linked receptors participate in cell signaling through extracellular ligand binding and initiation of second messenger cascades.
Describe G protein-coupled receptors and how they function.
G protein-coupled receptors have a membrane bound protein associated with a trimeric G protein. They also initiate second messenger systems.
Visualize a Michealis-Menten plot.
Note this would be sigmoidal for a cooperative enzyme (e.g., Hb).
Visualize a Lineweaver-Burk plot.
Outline the process for carbohydrate classification. How are sugars labeled L- or D-? What is an epimer? An anomer?
What three reactions can monosaccharides undergo?
Oxidation-reduction, esterification, and glycoside formation. Glycoside formation is the basis for building complex carbohydrates and requires the anomeric carbon to link with another sugar.
Sugars with a -H replacing an -OH group are termed deoxy sugars.
List some common disaccharides and their formal names.
- sucrose (glucose-α-1,2-fructose)
- lactose (galactose-β-1,4-glucose)
- maltose (glucose-α-1,4-glucose)
Describe the three main polysaccharides.
1. Cellulose: main structural component of plant cell walls; main source of fiber in the human diet
2. Starches (amylosse and amylopectin): main energy storage forms for plants
3. Glycogen: a major energy storage form for animals
Visualize the structure of adenosine tri-phosphate. Where are the high-energy bonds?
What is a nucleoside? What is a nucleotide? How do nucleotides differ between RNA and DNA?
A nucleoside contains a five-carbon sugar bound to a nitrogenous base; nucleotides are nucleosides with one to three phosphate groups added.
Nucleotides in DNA contain deoxyribose; in RNA, they contain ribose.
Describe the Watson-Crick Model
Some core components:
- The DNA backbone is composed of alternating sugar and phosphate groups, and is always read 5’ to 3’.
- There are two strands with antiparallel polarity, wound into a double helix.
- Purines (A and G) always pair with pyrimidines (C, U, and T). In DNA, A pairs with T (via two H bonds) and C pairs with G (via three H bonds). In RNA, A pairs with U (via two hydrogen bonds).
- Chargaff’s rules: purines and pyrimidines are equal in number in a DNA molecule. The amount of A equals the amount of T, and the amount of C equals the amount of G.
- DNA strands can be pulled apart (denatured) and brought back together (reannealed).
Describe the storage of DNA in eukaryotic (human) cells. What is transcriptionally active and inactive DNA called? What are telomeres?
In eukaryotes, DNA is wound around histone proteins (H2A, H2B, H3, and H4) to form nucleosomes, which may be stabilized by another histone protein (H1). DNA and its associated histones make up chromatin in the nucleus.
- Heterochromatin is dense, transcriptionally silent DNA.
- Euchromatin is less dense, transcriptionally active DNA.
- Telomeres are the ends of chromosomes -> They contain a high GC-content to prevent unraveling of the DNA (three hydrogen bonds = strong).
What are centromeres?
Centromeres are located in the middle of chromosomes and hold sister chromatids together until they are separated during anaphase in mitosis. They also contain a high GC-content.
Describe each of the steps in DNA replication and the differences between Prokaryotic Cells and Eukaryotic Cells (Nuclei).
How conseervative is DNA replication? What is the role of DNA polymerase? In what order is the template strand read? In what order is the new strand synthesized?
DNA replication is semiconservative; one old parent strand and one new daughter strand is incorporated into each of the two new DNA molecules.
DNA polymerase synthesizes new DNA strands, reading the template DNA 3’ to 5’ and synthesizing the new strand 5’ to 3’.
- The leading strand requires only one primer and can then be synthesized continuously.
- The lagging strand requires many primers and is synthesized in discrete sections called Okazaki fragments.
What is Recombinant DNA? DNA cloning? What can be done after a bacteria is altered?
Recombinant DNA: DNA composed of nucleotides from two different sources.
DNA cloning: introduces a fragment of DNA into a vector plasmid. A restriction enzyme (restriction endonuclease) cuts both the plasmid and the fragment, leaving them with sticky ends, which can bind.
These bacterial cells can then replicate via binary fission to create a protein of interest or lysed to allow for isolation of the fragment of interest from the vector.
What are DNA Libraries (genomic) and cDNA libraries (expression libraries)?
Genomic libraries: these 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): these 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.
What is PCR and hybridization?
Hybridization: the joining of complementary base pair sequences.
Polymerase chain reaction (PCR): an automated process by which millions of copies of a DNA sequence can be created from a very small sample by hybridization.
How can DNA molecules be separated?
Agarose gel electrophoresis can be used to separate DNA molecules by size.
What is southern blotting? What is it used for?
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.
What are dideoxyribonucleotides?
DNA sequencing uses dideoxyribonucleotides which terminate the DNA chain becausee they lack a 3’ -OH group.
What is the initiation codon? Termination? What do redundancy and wobble mean?
Initiation: AUG
Termination: UAA, UGA, UAG
Redundancy and wobble (third base in the codon) allow mutations to occur without affecting the protein.
List the point mutations and their effects.
- 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
How is RNA different structurally from DNA?
- Substitution of a ribose sugar for deoxyribose.
- Substitution of uracil for thymine.
- Single-stranded instead of double-stranded.
What are the 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
Outline the steps of transcription.
- 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.
What are the main posttranscriptional modifications?
- 7-methylguanylate triphosphate cap added to the 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.
Outline translation (the three stages) and posttranslational modifications.
Three stages: initiation, elongation, and 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)
What are transcription factors? What role do they play in the control of gene expression for Eukaryotes?
Transcription factors search for promotor and enhancer regions in the DNA.
- Promotors are within 25 base pairs of the transcription start site.
- Enhancers are more than 25 base pairs away from the transcription start site.
What model describes control of gene expression in prokaryotes? What does it say?
Operons (Jacob-Monod model) are inducible or repressible clusters of genes transcribed as a single mRNA.
What is osmotic pressure?
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 = iMRIT
What is passive transport? What are its forms?
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 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.
What is active transport? What types are there? How can a cell ingest?
Active transport reequires 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.
Endocytosis and exocytosis are methods of engulfing material into cells or releasing material to the exterior of the cells, both via the cell membrane.
Pinocytosis is the ingestion of liquid into the cell from vesciles formed from the cell membrane and phagocytosis is the ingestion of solid material.
Where does glycolysis occur? How many ATP does it yield and from what molecule?
Glycolysis occurs in the cytoplasm of all cells, and does not require oxygen. 2 ATP are yielded per glucose.
Name six important enzymes for glycolysis.
- Glucokinase: present in the pancreatic Beta-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 fructose-2,6-bisphosphate, which activates PFK-1
- Glyceraldehyde-3-phosphate dehydrogenase: produces NADH
- 3-phosphoglycerate kinase and pyruvate kinase: perform substrate-level phosphorylation
Gluco/hexokinase, PFK-1, and pyruvate kinase catalyze irreversible reactions.
The NADH produced in glycolysis is oxidized aerobically by the mitochondrial ETC and anerobically by cytoplasmic lactate dehydrogenase.
What does pyruvate dehydrogenase do?
Pyruvate dehydrogenase converts pyruvate to acetyl-CoA. Stimulated by insulin and inhibited by acetyl-CoA.
What is the Citric Acid Cycle? Where dooes it occur? What is its main purpose?
Takes place in the mitochondrial matrix. Main purpose is to oxidize acetyl-CoA to CO2 and generate high-energy electron carriers (NADH and FADH2) and GDP for the electron transport chain.
Where does the ETC take place? Roughly, how does it function?
ETC takes place on the matrrix-facing surface of the inner mitochondrial membrane.
Rough process: 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.
NADH cannot cross the inner mitochondrial membrane, so must use one of the two shuttle mechanisms to transfer its electrons to energy carriers in the mitochondrial matrix: the glycerol 3-phosphate shuttle or the malate-aspartate shuttle.
What is the proton-motive force? Where are protons concentrated? By what mechanism is ATP formed and with what enzyme?
The proton-motive force is the electrochemical gradient generated by the ETC across the inner mitochonodrial 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).
What are the yields from the various carbohydrate metabolism processes?
Glycolysis: 2 NADH and 2 ATP
Pyruvate dehydrogenase: 1 NADH (2 NADH for each glucose because each glucose forms two pyruvate)
Citric acid cycle: 3 NADH, 1 FADH2, and 1 GTP (6 NADH, 2 FADH2, and 2 GTP per glucose)
How many ATP are formed from each NADH? Each FADH2? What is the total ATP yield per molecule of glucose?
- Each NADH: 2.5 ATP
- Each FADH2: 1.5 ATP
- 2 ATP from glycolysis + 2 ATP from citric acid cycle + 25 ATP from NADH + 3 ATP from FADH2 = 32 ATP per glucose. (30-32 is normal)
What is glycogenesis? What are the main enzymes?
Glycogenesis is the building of glycogen using two main enzymes:
- Glycogen synthase, which creates α-1,4-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.
What is glycogenolysis? What are the main enzymes?
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.
What is gluconeogenesis and where does it occur? Which three irreversible steps of glycolysis must be bypassed by different enzymes?
Gluconeogensis is the generation of glucose. It occurs in both the cytoplasm and mitochondria, predominantly in the liver. Most of gluconeogenesis is just the reverse of glycolysis, using the same enzymes. Three steps must use different enzymes, as they’re irreversible from a glycolytic perspective.
- Pyruvate carboxylase and PEP carboxykinase bypass pyruvate kinase.
- Fructose-1,6-bisphosphatase bypasses phosphofructokinase-1
- Glucose-6-phosphatase bypasses hexokinase/glucokinase
What is the pentose phosphate pathway?
It occurs in the cytoplasm of most cells and generates NADPH and sugars for biosynthesis. The rate-limiting enzyme is glucose-6-phosphate dehydrogenase, which is activated by NADP+ and inhibited by NADPH and insulin.
What are the three-ish metabolic states and what occurs during them?
- Postprandial/well-fed (absorptive) state: insulin secretion is high and anabolic metabolism prevails.
- Postabsorptive 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.
Describe the process by which lipids are transported. What is necessary?
Chylomicrons, VLDL, IDL, LDL, and HDL each transport lipids.
Where is cholesterol synthesized? What is the key enzyme?
Cholesterol may be obtained through dietary sources or through synthesis in the liver. The key enzyme in cholesterol biosynthesis is HMG-CoA reductase.
What is the only fatty acid that humans can synthesize? Where is it produced and from what?
Palmitic acid is the only FA that humans can produce. It is synthesized in the cytoplasm from acetyl-CoA transported out of the mitochondria.
Where does FA oxidation occur? By what process? How are FAs transported?
Fatty acid oxidation occurs in the mitochondria, following transport in via the carnitine shuttle, via β-oxidation.
How are ketone bodies made/degraded? When are they made?
Ketone bodies form via ketogenesis during prolonged starvation due to excess acetyl-CoA in the liver. Ketolysis regeneerates acetyl-CoA for use as an energy source in peripheral tissues.
Where does protein digestion occur? Which parts are used for what?
Protein catabolism 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 extraction.
Describe tissue-specific metabolic processes for each of the following:
Liver
Adipose
Resting muscle
Active muscle
Cardiac muscle
Brain
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
What is the nucleus?
Nucleus: contains all of the genetic material necessary for replication of the cell
What is the mitochondrion?
Mitochondrion: location of many metabolic processes (pyruvate dehydrogenase, citric acid cycle, ETC, oxidative phosphorylation, B-oxidation, some of gluconeogenesis, urea cycle) and ATP production
What are lysosomes?
Lysosomes: membrane-bound structures containing hydrolytic enzymes capable of breaking down many different substrates
What is the rough endoplasmic reticulum?
Rough endoplasmic reticulum: interconnected membranous structure with ribosomes studding the outside; site of synthesis of proteins destined for insertion into a membrane or secretion
What is the smooth endoplasmic reticulum?
Smooth endoplasmic reticulum: interconnected membranous structure where lipid synthesis and detoxification occurs
What is the golgi apparatus?
Golgi apparatus: membrane-bound sacs where posttranslational modification of proteins occurs
What are peroxisomes?
Peroxisomes: organelle containing hydrogen peroxide; site of B-oxidation of very long chain fatty acids
What are the steps of cell division?
G1: cell increases its organelles and cytoplasm
S: DNA replication
G2: same as G1
M: the cell divides in two
Mitosis = PMAT (prophase, metaphase, anaphase, telophase)
Meiosis = PMAT X 2
Describe meiosis I and meiosis II.
Meiosis I:
- Two pairs of sister chromatids form tetrads during prophase I
- Crossing over leads to genetic recombination in prophase I
- Homologous chromosomes separate during metaphase I
Meiosis II:
- Essentially identical to mitosis, but no replication
- Meiosis occurs in spermatogenesis (sperm formation) and oogenesis (egg formation)
Describe the Fluid Mosaic Model and Membrane Traffic
Three core tenents:
- Phospholipid bilayer with cholesterol and embedded proteins
- Exterior: hydrophilic phosphate head groups
- Interior: hydrophobic fatty acids
What are the four stages of early embryogenetic development?
- Cleavage: mitotic divisions (cleave -> without growth)
- Implantation: embryo implants into the endometrium during blastula stage
- Gastrulation: ectoderm, endoderm, and mesoderm form
- Neurulation: germ layers develop a nervous system
What do kidneys do? What is their functional unit? Describe it.
Kidneys regulate [salt] and [water] in the blood. Their functional unit is the nephron.
Outline the neuron.
Describe ion flow during impulse progogation/action potential.
Depolarization (Na+ rushing into the axon) followed by repolarization (K+ rushing out of the axon) along the nerve axon.
Describe the organization of the nervous system.
Describe the four stages of the menstrual cycle.
- Follicular: FSH causes growth of a follicle.
- Ovulation: LH causes follicle to release egg.
- Luteal: Corpus luteum forms.
- Menstruation: Endometrial lining sheds.
What is a sarcomere? What is it composed of?
A sarcomere is sthe contractile unit of the fibers in skeletal muscle.
It contains thin actin and thick myosin filaments.
Describe the Bohr Effect. What effects do high temperature/pH have on the oxyhemoglobin dissociation curve?
Factors leading to a right shift of the curve:
- Increase in temperature.
- The Bohr Effect: Decrease in pH, increase in pCO2
- O2 releases to tissues enhanced when H+ allosterically binds to Hb. Increase in pCO2 increases [H+]:
- CO2 + H2O <-> H2CO3 <-> H+ + HCO3-
What antigens on are located on the surface of which blood cell types? What is the role of Rh factor?
Describe the process surrounding gas exchange.
Describe the digestive tract. (i.e., the path food takes all the way through)
Describe humoral immunity (specific defense).
Describe cell-mediated immunity (specific defense).
Describe the law of segregation.
Describe the law of independent assortment.
Describe how the probability of producing a genotype that requires multiple events to occur can be calculated?
How about the probability of producing a genotype that can result from one of many events?
Describe genetic mapping.
Describe the core tenants of the Hardy-Weinberg equilibrium.
Describe transduction in the context of prokaryotic cells.
Transduction occurs when a bacteriophage acquires genetic information from a host cell. Sometimes, when the new virions are assembled in a host cell, some of the genetic material fromo the host cell is packaged along with the viral genetic material. Then, the bacteriophage infects another bacterium, resulting in transfer of bacterial genetic material.
What is atomic weight?
Atomic weight: The weighted average of the masses of the naturally occuring isotopes of an element (proportioned out), in amu per molecule or grams per mole
What is Bohr’s Model of the Hydrogen Atom?
What are the four quantum numbers? What character, symbol, and value do they refer to?
Describe roughly the relationship between position on the periodic table and (effective charge, ionization energy, electronegativity, and electron affinity) and atomic radius.
What is the octet rule? What are its exceptions?
Identify the sequence of orbitals electrons fill (s, p, d, and f).
What is a lewis structure? What are the steps for writing one?
What occurs in a polar covalent bond?
How can polarity of a molecule be determined?
The polarity of molecules depends on the polarity of the constituent bonds and on the shape of the molecule.
- Nonpolar bonds -> nonpolar molecule
- Polar bonds -> either polar or nonpolar molecule (see below)
Describe the five possible geometric arrangements of electron pairs around a central atom and give each of the angles between electron pairs.
What is a complex ion? (coordination compound)
How do hydrogen bonds give rise to intermolecular forces?
How do dipole-dipole interactions give rise to intermolecular forces?
How do dispersion forces give rise to intermolecular forces?
Describe the efficiency of reactions.
What is a combustion reaction?
What is a combination reaction?
What is a decomposition reaction?
What is a single-displacement reaction?
What is a double-displacement reaction?
What is a net ionic equation?
What is a neutralization reaction?
What does a catalyst do?
Catalysts are unique substances that increase reaction rate without being consumed; they do this by lowering activation energy.
What is the law of mass action?
Describe some properties of Keq. What if it is > 1? < 1? What if it equals 1?
What does Le Chatelier’s Principle say?
Le Chatlier’s Principle: 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. They key is to remember that a system to which these kinds of stresses are applied tends to change to relieve to the applied stress.
Describe the three types of thermodynamic systems and their characteristics.
What is heat? What happens with heat during endothermic and exothermic reactions?
Heat: the transfer of thermal energy from one object to another
Endothermic: reactions that absorb heat energy
Exothermic: reactions that release heat energy
What are states and state functions?
What is the Standard heat of reaction (∆H°rxn)?
What is bond dissociation energy?
What is bond enthalpy?
How many mmHg is 1 atm? Torr? Pa?
What is Boyle’s law?
What is Charle’s law?
What is Gay-Lussac’s law?
What is Avagadro’s principle?
What is the Combined Gas Law?
What is the Ideal Gas Law?
Describe what happens to real gases when decreasing total volume?
What is entropy (S)?
What is Gibbs free energy (G)?
What is a reaction quotient (Q)?
Describe the role of temperature and pressure in influencing the effects had by intermolecular forces on gas dynamics.
Describe the Van der Waals equation of state.
What is Dalton’s law of partial pressures?
What is the equation for average molecular speeds? For root-mean-square speed?
What are colligative properties? How can one calculate their effects on boiling/freezing points?
Colligative properties: These are physical properties derived solely from the number of particles present, not the nature of those particles. These properties are usually associated with dilute solutions. Molality (m) must be used, in addition to the van ‘t Hoff factor (i) for ionic compounds.
Solutions with small amounts of solute prefer to keep the solution in its liquid phase, thereby increasing the boiling temperature and decreasing the freezing temperature.
Describe vapor pressure lowering (Raoult’s law).
Define galvanic cells. In what direction do electrons flow?
A redox reaction occurring in a galvanic cell has a negative deltaG and is therefore a spontaneous reaction. Galvanic cell reactions supply energy and are used to do work.
The energy of these spontaneous reactions can be harnessed by placing the oxidation reduction half-reactions in seperate containers called half-cells. The half-cells are then connected by an apparatus that allows for the flow of electrons.
Note that a salt bridge prevents buildup of molecules on either side.
What does t-butyl look like?
What does neopentyl look like?
What does isopropyl look like?
What does sec-butyl look like?
What does isobutyl look like?
Identify the prefix and suffix for:
- Carboxylic acid
- Anhydride
- Ester
- Amide
- Aldehyde
- Ketone
- Alcohols
What is a stereoisomer? What is the difference between conformational and configurational isomers?
Describe the bond type, hybridization, and angles of single, double, and triple bonds.
Describe some of the differences between SN1 and SN2 reactions. Which occurs in one step, and which in two? Which one is favored in which solvent?
What effect can protic solvents have on nucleophiles? Which are the strongest nucleophiles in aprotic solvents? In protic solvents?
Define conformational isomers and their characteristics (i.e. group positioning around sigma bond).
How are configurational isomers interchanged? What are enantiomers? What are diastereomers?
Describe the two key characteristics of alcohols. How can they bee synthesized?
What characteristics make for good oxidizing agents?
What characteristics make for good reducing agents?
What does PCC do in this reaction?
What does Jones’s reagent, KMnO4 do in this reaction? (Or other alkali dichromate salts, in this case).
What does LiAlH4 (or NaBH4 or CaH2) do in this reaction?
What can be used as a protecting group for carbonyls?
What is a phenol? How acidic is a phenol?
What is synthesized when phenols are treated with oxidizing agents? Can they be oxidized further, and if so, to form what?
What is the Q cycle?
Describe an aldol condensation reaction.
What approximately is the pKa of carboxylic acids? Why? Where does their boiling point stand in regard to other functional groups?
Describe two mechanisms for synthesizing carboxylic acids.
What is a lactam?
What is a lactone?
Rank the following in terms of reactivity: Acyl halides, Amides, COOH, and Anhydrides
Describe the following phosphorus-containing compounds and their characteristics:
- Phospric acid
- Pyrophosphate
- Inorganic vs. Organic phosphates.
Describe extraction and when it is used.
Describe filtration and when it is used.
Describe chromatography (thin-layer and column) and when it is used.
Describe distillation and when it is used. Also describe the following: simple, vacuum, and fractional distillation.
What are recrystallization and electrophoresis? What are they used for?
What is infrared spectroscopy? Identify the Wavenumber (cm-1) of the main functional groups.
What is UV spectroscopy?
Identify the approximate chemical shift of some functional groups (their protons, specifically) for 1H-NMR.
What are the four things to look for when analyzing an NMR spectrum?
