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Fluid Mosaic Model

Since the forces holding the entire membrane together are intermolecular, the membrane is fluid; its parts can move laterally but cannot separate. This is reflected in the asymmetrical layout of the integral membrane proteins.
-> In eukaryotic membranes, cholesterol moderates membrane fluidity (prokaryotic -> hopanoids).

1

Facilitated Diffusion

Makes the membrane selectively permeable because it is able to select between molecules of similar size and charge. Must occur down the electro-chemical gradient of all species involved.

2

Smooth ER

Distal to the nucleus. The site of lipid synthesis including steroids. Helps to detoxify some drugs.

3

Peroxisomes

Vesicles in the cytosol. Grow by incorporating lipids and proteins from the cytosol. Self-replicate instead of budding off of other membranes. Involved in the production and breakdown of hydrogen peroxide. Inactivate toxic substances such as alcohol, regulate oxygen concentration, play a role in synthesis and breakdown of lipids and in the metabolism of nitrogenous bases and carbohydrates.

4

Mitochondria

Have their own circular DNA. Antibiotics that block translation by prokaryotic ribosomes but not eukaryotic ribosomes also block translation by mitochondrial ribosomes. Mitochondria are inherited from the mother. Have an inner and outer membrane.

5

Cristae

The internal compartments formed by the inner membrane of the mitochondria. Studded with proteins including ATP synthase and a variety of cytochromes. Increases surface area for chemical reactions, where cellular respiration (aerobic since mitochondria require oxygen) occurs.

6

Interstitial Fluid

Fluid between the cells.

7

Glycolysis

First stage of aerobic and anaerobic respiration. Occurs in the cytosol.

Glucose + 2ADP + 2P(i) + 2H2O + 2NAD+ ---> 2 pyruvate + 2ATP + 2NADH

Can be performed by any cell (vs gluconeogenesis: formation of glucose from noncarbohydrate precursors - occurs mainly in the liver).
*The addition of a second phosphate to glucose commits it to the glycolytic pathway! (fructose 1,6-bisphosphate)

8

Fermentation

Anaerobic respiration. Includes glycolysis, reduction of pyruvate to ethanol (yeast) or lactic acid (human muscle cells), and oxidation of NADH back to NAD+.

9

Substrate-Level Phosphorylation

An energy-rich intermediate transfers its phosphate group to ADP, forming ATP, without requiring oxygen. As opposed to using energy from diffusion.
Ex: glyceraldehyde 3-phosphate (G3P or PGAL) in glycolysis, phosphocreatine in skeletal muscles

10

Cofactors

Metal ions or coenzymes that activate an enzyme by binding tightly to it.

11

Krebs (Citric Acid) Cycle

Aerobic respiration. The oxidation of glucose and reduction of oxygen (as the final electron acceptor --> H2O). Occurs in mitochondrial matrix (inside both membranes) with products of glycolysis (pyruvate and NADH). Once inside matrix, pyruvate is converted to acetyl CoA in a rxn that produces NADH and CO2. During the cycle, two carbons are lost as CO2 and oxaloacetic acid is reproduced to begin the cycle over again.
ATP is produced by substrate-level phosphorylation.

Glucose (C6H12O6) + 6O2 --> 6CO2 + 6H2O
(combustion rxn)

Produces 36 net ATP btwn cycle and ETC (and 2 from glycolysis).

One glucose produces two cycles. One cycle produces 1 ATP, 3 NADH, and 1 FADH2.
H from NADH and FADH2 go on to ETC, where O2 is reduced to H2O.

Can use:
-Triglycerides --> fatty acids --(-1 ATP)-> acyl CoA --(-2C)-> acetyl CoA
-Amino acids --(deamination in liver)-> deaminated pdt --> pyruvic acid or acetyl CoA

12

Oxidative Phosphorylation

The production of ATP via the electron transport chain and ATP synthase.

13

Organism Classification

1. Energy source
- Phototrophs: light
- Chemotrophs: oxidation of organic or inorganic matter
2. Carbon source
- Autotrophs: CO2 exclusively
- Heterotrophs: organic matter

CO2 fixing: reducing it and using the carbon to create organic molecules

-> Only prokaryotes can acquire energy from an inorganic source other than light.

14

Prokaryote

No membrane bound nucleus; instead, have a single, circular double stranded molecule of DNA. Have nucleoids and ribosomes, just no complex, membrane bound organelles. No centrioles.
Split into two domains:
- Bacteria
- Archaea (have more in common with eukaryotes)

15

Nucleoid

Irregular shaped area inside a prokaryotic cell formed from the genetic material (DNA, RNA and protein complex) and serves as a nucleus. NOT membrane-bound.
AKA chromatin body, nuclear region, or nuclear body.

16

The Central Dogma (of gene expression)

All organisms use the same method of gene expression:
DNA --> RNA --> proteins

17

Nucleotide

Always made up of 3 parts:
1) Phosphate group
2) 5 C sugar
3) Nitrogenous base

18

DNA Structure

Nucleotides are held together by phosphodiester bonds between the 3rd C (3') hydroxyl of one deoxyribose and the 5th C (5') phosphate of another deoxyribose. The backbone of a single strand of DNA has 5' -> 3' directionality.

19

Purines

Two-ring structures: adenine and guanine.

20

Pyrimidines

One-ring structures: cytosine and thymine (and uracil).

(think: pyrimidine has a 'y' and so do cytosine and thymine)

21

Base-pairing

The hydrogen bonding between nitrogenous bases to form the double stranded structure of DNA.

A and T form 2 H bonds --> A2T
C and G form 3 H bonds --> C3G
(why complementary strands match up)

The length of a strand of DNA is measured in base-pairs (bp).

22

RNA

Identical to DNA in structure except that:
1. C2 on the pentose sugar is not "deoxygenated" (has hydroxyl group attached).
2. RNA is single-stranded.
3. RNA contains the pyrimidine uracil instead of thymine (similarity between the two is a common cause of mutations).

DNA is produced by replication, RNA is produced by transcription.
In animals, DNA is only in the nucleus and mitochondrial matrix, RNA can move through nuclear pores so it is also in the cytoplasm.

3 types of RNA: mRNA, rRNA, tRNA

23

Messenger RNA (mRNA)

A form of RNA that carries the instructions for making a protein (amino acids) from a gene (DNA) and delivers it to the site of translation (cytosol).

24

Ribosomal RNA (rRNA)

RNA molecules that bind with proteins to form ribosomes as the site of translation of proteins (amino acids). rRNA is synthesized in the nucleolus (an area inside the nucleus, ribosomes are assembled; not separated by a membrane; disappears during prophase).

25

Transfer RNA (tRNA)

A single strand of RNA that sequesters the appropriate amino acids (dictated by mRNA) in the cytosol and transfers them to the site of translation (ribosomes) for incorporation into a protein.

26

Lagging Strand

New DNA strand whose polymerization is continuously interrupted and restarted with a new primer.

27

Leading Strand

The continuously-synthesized new strand of DNA.

28

Bidirectional Replication

All eukaryotic DNA replication begins at an origin of replication and continues along the chromosome in opposite directions.

29

Semiconservative Replication

When a new DNA strand is created, it contains one strand of the original DNA and one strand of newly synthesized DNA.

30

Nucleic Acid Hybridization

Complementary strands of nucleic acids will spontaneously bind in any combination:
DNA-DNA
DNA-RNA
RNA-RNA

--> Enables the identification of unknown nucleotide sequence by binding it with a known sequence.

31

Denaturization

To split the double helix of DNA into two strands.

32

5 Steps of Replication

Prokaryotes and eukaryotes:
1. Helicase unzips the double helix.
2. RNA primase builds a primer.
3. DNA polymerase (III) assembles the leading and lagging strands.
4. Primers are removed (DNA pol I).
5. Okazaki fragments are joined (Ligase).

Very fast and accurate.

33

DNA Polymerase

The enzyme that builds the new DNA strand; requires an RNA primer on which to add new nucleotides.

Reads the parental strand 3' -> 5' (upstream) and creates the new complementary strand 5' -> 3' (downstream).
(Think: DNA is complicated to understand so reading it is like paddling upstream. Once it is read, creating it is downstream.)

34

Okazaki Fragments

The series of disconnected strands that make up the lagging strand.

35

Telomeres

Repeated six-nucleotide units that protect the chromosomes from being eroded through repeated rounds of replication.

36

Genetic Code

The amino acids and "start" and "stop" signals that are coded for by each of the 64 possible mRNA codons (4 possible nucleotides can be placed in each of 3 positions --> 4^3 = 64).

The genetic code is:
1. Degenerative: more than one series of three nucleotides may code for any amino acid.
2. Unambiguous: any single series of nucleotides will code for one and only one amino acid.
3. Almost universal: nearly every living organism uses the same code.

37

RNA polymerase

A required enzyme that adds and links complementary RNA nucleotides during transcription.

38

Transcription

Process by which all RNA is manufactured from a DNA template (in nucleus or mitochondrial matrix where DNA is). 10x slower than replication.

1. Initiation: requires a promoter (sequence of nucleotides) on the DNA strand to tell the RNA polymerase where to begin transcription (vs. primer in replication). RNA polymerase unzips the DNA double helix.
2. Elongation: RNA polymerase transcribes only one strand of the DNA nucleotide sequence into a complementary RNA nucleotide sequence.
(RNA polymerase reads DNA 3' -> 5' and builds new RNA 5' -> 3' like DNA polymerase. No proof reading mechanism like replication but errors are not mutations, not as harmful.)
3. Termination: requires stop signal and proteins to separate RNA polymerase from DNA.

39

Primary Transcript

Initial mRNA nucleotide sequence arrived at through transcription. Processed post-transcriptionally in 3 ways:
1. Addition of nucleotides.
2. Deletion of nucleotides.
3. Modification of nitrogenous bases.

40

Introns

Long segments of nucleotides that have no coding information; between adjacent genes. Remain in the nucleus. Intron sequences are generally much longer than exon sequences.

41

Exons

Portions of the gene that exit the nucleus to be translated (expressed) into proteins. May be spliced together in different orders to form different polypeptides.

42

snRNPs

Small nuclear ribonucleoproteins; enzyme-RNA complexes which recognize nucleotide sequences at the ends of introns. They loop the introns, bringing the exons together. Then they excise the introns and splice the exons together.

43

Post-Transcriptional Processing (of RNA)

Occurs in prokaryotes and eukaryotes.
Prokaryotes - occurs in all tRNA and rRNA, but almost all mRNA is directly translated to proteins.
Eukaryotes - occurs in each type of RNA and allows for additional gene regulation.

44

Complementary DNA (cDNA)

DNA that has been reverse transcribed from mRNA using reverse transcriptase. Adding DNA polymerase to cDNA produces a double strand of the desired DNA.

--> useful for cloning eukaryotic DNA with bacteria because bacteria have no mechanism for removing introns.

45

Translation

The mRNA transcribed from the DNA template brings the complementary genetic code to the cytoplasm to be read and made into proteins from the complementary amino acids.

1. mRNA carries the genetic information from the nucleus to the cytoplasm in the form of codons.
2. tRNA carries the complementary nucleotides (anticodons) and sequesters the amino acids that correspond to the anticodon.
3. rRNA binds with proteins to make up the ribosome, which provides the site for translation to take place.

46

Ribosome

Site of translation. Made up of a small subunit and a large subunit of rRNA and many separate proteins.

--> synthesized by the nucleolus (not found in prokaryotes, although synthesis is similar). Ribosome is assembled in nucleolus but small and large subunits are exported separately to the cytoplasm.

47

Codon

A series of three-nucleotide sequences on the mRNA; each corresponds to an amino acid or signifies a "start" or "stop" signal for translation.

48

Anticodon

A three-nucleotide sequence on a tRNA that is complementary to an mRNA codon.

49

Start Codon

AUG

--> signals the beginning of protein synthesis.

50

Stop Codons

UAA, UAG, UGA

--> signal an end to protein synthesis.

51

Initiation

The first step of translation.

1. 5' of mRNA attaches to the small subunit of the ribosome.
2. A tRNA possessing the 5'-CAU-3' anticodon (to start codon 5'-AUG-3' from mRNA) sequesters the amino acid methionine and settles in at the P site (peptidyl site).
3. This signals the large subunit to join and form the initiation complex.

52

Elongation

The second step of translation; elongation of the polypeptide.

1. A tRNA with its corresponding amino acid attaches to the A site (aminoacyl site) of ribosome at the expense of two GTPs.
2. The carboxyl end of methionine attaches to the amine end of the amino acid in a dehydration reaction.
3. Translocation: the ribosome shifts 3 nucleotides along the mRNA towards the 3' end and the tRNA that carried methionine moves to the E site (exit site) where it can exit the ribosome. The tRNA carrying the newly formed dipeptide moves to the P site, clearing the A site for the next tRNA.
--> requires the expenditure of another GTP

Elongation is repeated until a stop codon reaches the P site.

53

Termination

The third step of translation.

1. A stop codon reaches the A site and proteins (release factors) bind to the A site allowing a water molecule to attach to the end of the polypeptide chain.
2. The polypeptide is freed from the tRNA and ribosome, and the ribosome breaks up into its subunits to be used again later.

54

Post-Translational Modifications

Sugars, lipids, or phosphate groups are added to the amino acids; the polypeptide may be cleaved in one or more places; separate polypeptides may join to form the quarternary structure of a protein.

55

Signal Peptide

Directs a ribosome to attach to the rough ER. Without a signal, the ribosome remains floating in the cytosol. Depends on where the resulting protein will need to go.

56

Point Mutations

Mutation that changes a single base-pair of nucleotides in a double strand of DNA.

57

Base-Pair Substitution Mutation

One base-pair is substituted for another.

A-T --> C-G
C-G --> A-T

58

Missense Mutation

A base-pair substitution that changes the amino acid coding sequence of a gene to code for another amino acid.

59

Nonsense Mutation

A base-pair mutation that results in a stop codon. Prevents translation of a functional protein (serious).

60

Insertion or Deletion Mutation

Insertion or deletion of a base-pair, results in a frame shift mutation (when it occurs in multiples other than 3). Often result in a completely nonfunctional protein (vs. non-frame shift - may result in partially or even completely active protein).

61

Wild Type

The original state of an organism.

62

Forward Mutation

Shifts an already mutated organism further from its original state.

63

Backward Mutation

Shifts an already mutated organism back closer to its original state.

64

Nucleosome

Eight histones wrapped in the DNA.

65

Chromatin

The entire DNA-protein complex (many nucleosomes).

66

Chromosome

The chromatin associated with each of the 46 double stranded DNA molecules in human cells.

67

Homologues

Two chromosomes that code for the same traits but do not necessarily have the same genes (alleles).

-diploid: a cell with homologous pairs
-haploid: a cell without homologous pairs

68

Centromeres

A group of proteins located toward the center of the chromosome; where microtubules attach (to kinetochore protein -> kinetochore microtubules).

69

Chromatids

Identical sister sets resulting from chromosome (DNA) replication; attached at the centromere. The cell is still considered to have the same number of chromosomes.

70

Tetrads

When duplicated homologous chromosomes line up next to each other for a total of 4 chromatids.

71

Crossing Over

In prophase I, homologous chromosomes may exchange sequences of DNA (genetic recombination).

72

Chiasma

The single point where chromosomes are attached during crossing over.

73

Nondisjunction

When the centromere of any chromosome does not split during anaphase I or II.

Primary nondisjunction: anaphase I - all gametes affected. Two have an extra chromosome and two are missing a chromosome.
Secondary nondisjunction: anaphase II - half the gametes affected. One has an extra chromosome and one is missing a chromosome.

(can also occur in mitosis but consequences are not as severe since the genetic info in the new cells is not passed on to every cell in the body)

74

Chromosomal Deletion

Part of the chromosome breaks off or is lost during homologous recombination and/or crossing over.

--> can occur with entire chromosomes or even entire sets of chromosomes (nondisjunction).

75

Chromosomal Duplication

When a DNA fragment breaks free of one chromosome and is inserted in the homologous chromosome.

--> can occur with entire chromosomes or even entire sets of chromosomes (nondisjunction).

76

Inversion

Mutation when the orientation of a section of DNA is reversed on the chromosome.

77

Translocation

Mutation when a segment of DNA from a chromosome is inserted into a nonhomologous chromosome.

78

Transposable Elements (Transposons)

DNA segments that can excise themselves from a chromosome and reinsert themselves in a different location. Can contain one gene, several genes, or just a control element. Flanked by identical nucleotide sequences.

Transposition can cause translocation and inversion.

--> one mechanism by which a somatic cell of a multicellular organism can alter its genetic makeup without meiosis.

79

Centrosome

The major microtubule organizing center (MTOC) in mitosis in animal cells.

80

Centrioles

The barrel-shaped structures of microtubules arranged perpendicularly in the centrosome.

81

9 + 2 Microtubule Arrangement

The arrangement of microtubules in the axoneme of eukaryotic flagella or cilia. 9 pairs of microtubules form a circle around two lone microtubules. Dynein cross bridges connect each of the outer pairs of microtubules to their neighbor, which causes the microtubule pairs to slide past each other and move the flagella or cilia in a whip-like motion.

In humans, cilia are found only in the Fallopian tubes and respiratory tract.

Prokaryotes: flagella are made of a single strand of protein called flagellin and they move by rotation.

82

Asters

Microtubules radiating from the centrioles.

83

Kinetochore

A structure of protein and DNA located at the centromere of the joined chromatids of each chromosome.

84

Ionizing radiation can cause double stranded breaks in the DNA. Eukaryotes are able to repair some of these breaks, but prokaryotes are not. Which of the following gives the most likely explanation for this difference?

A. Prokaryotes do not possess a ligase enzyme to join the separated DNA molecules.
B. Prokaryotic DNA is single stranded.
C. Eukaryotes have matching pairs of chromosomes to act as a template for repair.
D. Eukaryotes have more DNA making the consequences of a break less severe.

Answer: C

85

Restriction Enzymes

Cut the nucleic acids according to palindromic nucleotide sequences. Usually cuts the DNA unevenly.

86

Recombinant DNA

Two DNA fragments that were cut by the same restriction endonuclease and can (artificially) recombine regardless of the origin of the DNA.

87

Probe

The radioactively labeled complementary sequence of the desired DNA fragment.

--> used in library screening.

88

Southern Blot

Used for detection of a specific DNA sequence in DNA samples. It combines transfer of electrophoresis-separated DNA fragments to a filter membrane and subsequent fragment detection by probe hybridization.

vs. Northern (RNA), Western (proteins - uses antibodies), etc.

89

Polymerase Chain Reaction (PCR)

A fast way to "clone" DNA. The method relies on repeated heating and cooling of the reaction for DNA denaturization and enzymatic replication of the DNA. Primers (short DNA fragments) containing sequences complementary to the target region along with a DNA polymerase (after which the method is named) enable selective and repeated amplification. As PCR progresses, the DNA generated is itself used as a template for replication, setting in motion a chain reaction in which the DNA template is exponentially amplified.

90

RFLP (Restriction Fragment Length Polymorphism)

Identifies individuals as opposed to specific genes.
DNA of different individuals possesses different restriction sites and different distances between restriction sites. After fragmenting a DNA sample with endonucleases, a band pattern unique to an individual is revealed on radiographic film via southern blotting.

--> RFLPs are the DNA tests used to identify criminals in court cases.

91

Operon

The genetic unit usually consisting of the operator, promoter, and genes that contribute to a single prokaryotic mRNA.

92

Lac Operon

The operon that controls the metabolism of lactose in E. coli.

93

Operator

The piece of DNA in the lac operon that overlaps the promoter site and serves as the on-off switch.

94

Repressor

A protein that binds to an operator and physically blocks the RNA polymerase from binding to a promoter site, stopping the transcription of the genes in the operon.

95

Vector

A DNA molecule used as a vehicle to transfer foreign genetic material into another cell.

96

Plasmid

Double-stranded, generally circular DNA sequences that are capable of automatically replicating in a host cell. Incubating bacteria with plasmids generates hundreds or thousands of copies of the vector within the bacteria in hours (transformation).

97

Screening

Not all bacteria in a library will have the vector and not all vectors will have the DNA. To screen for the appropriate bacteria, use the lacZ gene and an antibiotic resistant gene when originally preparing the clone. Use an endonuclease that will insert the DNA fragment into the middle of the lacZ gene and inactivate it.
--> clones with an active lacZ gene turn blue in the presence of X-gal.
--> clones without resistance to the antibiotic will be eliminated.

98

Bacteria Shapes

Cocci: round
Bacilli: rod-shaped
Spirilla: rigid helical-shaped
Spirochetes: non-rigid helical-shaped
-> certain species of spirochetes may have given rise to eukaryotic flagella through a symbiotic relationship.

--> name of bacteria often reveals its shape: spiroplasma, staphylococcus, pneumococcus, etc.

99

Bacterial Envelope

A cell wall on the exterior of the plasma membrane which prevents the protoplast (the bacterial plasma membrane and everything inside of it) from bursting since most bacteria are hypertonic. As the cell fills with water and the hydrostatic pressure builds, it eventually equals the osmotic pressure and the filling stops (equilibrium).

100

Peptidoglycan

A series of disaccharide polymer chains with amino acids, three of which are not found in proteins. The chains are connected by their amino acids or are crosslinked by an interbridge of more amino acids. Makes up the cell wall of bacteria from continuous chains that form a single molecular sac around the bacterium.
More elastic than cellulose (plant cell wall).
Porous so it allows large molecules to pass through.
Many antibiotics (penicillin) attack the amino acid cross links. Cell wall is disrupted, cell lyses killing the bacterium.
Lysozyme (enzyme produced by humans) attacks the disaccharide linkage. Cell wall is disrupted, cell lyses killing the bacterium.

101

Gram Staining

A staining technique used to prepare bacteria for viewing under the light microscope. Stains two major cell wall types differently:
1. Gram-positive bacteria: the thick peptidoglycan cell wall prevents the gram stain from leaking out. These cells show up purple. Gram-positive bacteria have a cell wall approx 4x thicker than the plasma membrane.
2. Gram-negative bacteria: the thin peptidoglycan cell wall allows most of the gram stain to be washed off. These cells show up pink. Outside of the cell wall, gram-negative bacteria have a phospholipid bilayer that is more permeable than the first (even glucose passes through). The outer membrane protects against certain antibiotics such as penicillin.

102

Bacterial Flagella

Made from the globular protein flagellin. NOT to be confused with eukaryotic flagella, which is composed of microtubules! It is propelled using the energy from a proton gradient rather than ATP.

103

Bacterial Reproduction

Do not reproduce sexually. They have three alternative forms of genetic recombination:
1. Conjugation
2. Transformation
3. Transduction

Or binary fission (asexual).

104

Binary Fission

The circular DNA is replicated: two DNA polymerases begin at the same point on the circle (origin of replication) and move in opposite directions making complementary single strands that combine with their template strands to form two complete DNA double stranded circles. The cell divides making two identical daughter cells.

105

Conjugation

A method of genetic recombination which requires that one of the bacterium have a plasmid (small circle of DNA that exists/replicates independently of the bacterial chromosome) with the gene that codes for the sex pilus (a hollow protein tube that connects two bacteria to allow the passage of DNA). This is called the F plasmid (fertility factor, F factor).
The DNA passage is not always from the cell containing the plasmid to the cell that does not.
One end of the plasmid strand begins to separate from its complement as its replacement is replicated. The loose strand is then replicated and fed through the pilus.

106

R Plasmid

Donates resistance to certain antibiotics. Can also initiate conjugation.

--> prescribing multiple antibiotics for patients to take at one time promotes conjugation of different R plasmids providing different resistances to antibiotics to produce a super-bacterium that contains many antibiotic resistances on one or more R plasmids. Some R plasmids are readily transferred between species, further promoting resistance and causing serious health problems for humans.

107

Transformation

The process by which bacteria may incorporate DNA from their external environment into their genome; may be initiated due to external environment in the lab or lyses of other bacteria.

Ex: mix heat-killed virulent bacteria with harmless living bacteria. The living bacteria receive the genes of the heat-killed bacteria through transformation and become virulent.

108

Transduction

The transfer of DNA via a virus. The capsid of a bacteriophage mistakenly encapsulates a DNA fragment of the host cell. When these virions infect a new bacterium, they inject harmless bacterial DNA fragments instead of virulent viral DNA fragments. This is mediated by a virus vector. Can be mediated artificially in a lab.

109

Virus

Consists of a capsid protein coat that contains the nucleic acid (either DNA or RNA, never both).
Most animal viruses surround themselves with a lipid-rich envelope either borrowed from the membrane of their host cell or synthesized in the host cell cytoplasm; it typically contains some virus-specific proteins.
All organisms experience viral infections.
A viral infection begins when a virus adsorbs to a specific chemical receptor (usually a glycoprotein) site on the host. Then the nucleic acid of the virus penetrates into the cell.
Viruses are very small -> a bacterium is the size of a mitochondrion, and hundreds of viruses may fit within a bacterium.

110

Virion

The inert form of a virus that exists outside the host cell.

111

Bacteriophage

A virus that infects bacteria, injects its nucleic acid through the tail after viral enzymes (from within the capsid) have digested a hole in the cell wall.
Structure: tail, base plate, and tail fibers.
1. Viral DNA is injected into the host cell.
2. Viral DNA is transcribed and replicated.
3. The capsid is formed.
4. The host cell lyses releasing hundreds of viral progeny.

112

Prophage

The name of the virus when it is incorporated into the host cell's DNA.

113

Lytic Infection

The virus commandeers the cell's reproductive machinery and begins reproducing new viruses. The cell may fill with new viruses until it lyses or it may release the new viruses one at a time in a reverse endocytotic process.
Latent period: the period from infection to lysis.
Virulent virus: a virus following a lytic cycle.

114

Lysogenic Infection

The viral DNA is incorporated into the host genome, or, if the virus is an RNA virus and it possesses the enzyme reverse transcriptase, DNA is reverse-transcribed from RNA and then incorporated into the host cell genome.
Temperate virus: a virus in the lysogenic cycle.
Provirus: the infected cell while the viral DNA remains incorporated in the host DNA and the virus is dormant/latent (prophage if the host cell is a bacterium).
The dormant virus may become active when the host cell is under stress (like exposure to UV light and other carcinogens). When it becomes active, it becomes virulent.

(think: lysogenic is a longer word than lytic, it is also a longer cycle; lyso"gen"ic incorporates its genes.)

115

Classification of Viruses by Nucleic Acid

Plus-strand RNA: proteins can be directly translated from the RNA.
Ex: common cold, retroviruses (carry reverse transcriptase) like HIV

Minus-strand RNA: the complement to mRNA must be transcribed to plus-RNA before being translated.
Ex: measles, rabies, the flu

Double stranded RNA

Single and double stranded DNA

116

Vaccine

Either an injection of antibodies or an injection of a non-pathogenic virus with the same capsid or envelope.

117

Carrier Population

An animal that carries a virus without any adverse symptoms which maintains the virus's ability to reinfect another animal population.

118

Fungi

Multicellular (except yeast), eukaryotic heterotrophs that spend most of their lives in the haploid state. They can reproduce sexually or asexually. May contain one or more nuclei which may or may not be identical. Lack centrioles. Mitosis takes place entirely in nucleus and the nuclear envelope never breaks down.

-exodigesters: digest their food while it is outside of their bodies and then absorb the nutrients.
-saprophytic: consume dead or decayed organic matter.

-septa: cell walls made of the polysaccharide chitin; usually perforated to allow exchange of cytoplasm between cells (allows rapid growth).
-chitin: more resistant to microbial attack than cellulose, same substance of which the exoskeleton of arthropods is made.

--> more similar to human cells than bacteria so drugs that attack fungi are more likely to affect human cells than antibiotics.

119

Mycelium

The tangled mass of multiple branched thread-like structures (hyphae) of fungi in their growth state.

120

Asexual Reproduction of Fungi

*When conditions are good! If good for the parent, will be good for asexually produced offspring that are exactly like the parent.
-> Hyphae are haploid and some may form reproductive structures that release haploid spores that give rise to new mycelia. In yeasts, asexual reproduction occurs by budding (aka cell fission) in which a smaller cell pinches off from the single parent cell.

Note: spore formation is not always via asexual reproduction.

121

Sexual Reproduction of Fungi

*When conditions are tough! If bad for the parent, may not be bad for sexually produced offspring that are different from the parent.
-> Occurs between hyphae from two mycelia of different mating types + and -. The two hyphae grow towards each other and form a conjugation bridge. They each produce a gamete and their nuclei fuse to produce a (dormant) diploid zygote. When activated by the appropriate environmental conditions, it undergoes meiosis to produce haploid cells, one of which immediately begins to asexually produce many spores.

122

Cytoplasmic Streaming

The directed flow of cytosol and organelles around large fungal and plant cells through the mediation of actin.

123

Endocytosis

Pathway of cell bringing substances into the cell.
-Phagocytosis: cell membrane protrudes outward to engulf the particulate matter. Only a few specialized cells do this. Need membrane protein receptors for the particulate matter.
-Pinocytosis: extracellular fluid is engulfed by small invaginations of the membrane. Performed by most cells; nonselective.
(-Receptor mediated: uses clathrin-coated vesicles, specifically brings in ligands.)

124

Neuronal Communication

Rapid, direct, and specific.

125

Hormonal Communication

Slower, spread throughout the body, affects many cells and tissues in many different ways.

126

Dendrites

Receive the signal to be transmitted. Connected to cell body.

127

Axon Hillock

Region of the neuron between the dendrite and the axon where the action potential is initiated.

128

Resting Potential

Using Na+/K+ pumps, 3 Na+ are pumped out of the cell while 2 K+ are pumped in, making the outside of the cell slightly positive and the inside slightly negative.

129

Depolarization

The voltage across the membrane is disturbed and voltage gated Na+ channels change configuration, allowing Na+ to flow into the cell for a fraction of a second. Na+ influx causes more voltage change, changing the configuration of more Na+ channels and bringing more Na+ in (positive feedback). Since [Na+] moves towards equilibrium while internal [K+] remains the same (high), the membrane potential reverses polarity -> positive inside and negative outside.

130

Repolarization

Voltage gated K+ channels are less sensitive to voltage changes so they open much slower. By the time they begin to open, most Na+ channels are closing. Now K+ flows out of the cell, making the inside more negative (comparatively).

131

Hyperpolarization

The K+ channels are so slow to close that, for a fraction of a second, the inside of the membrane becomes even more negative than the resting potential. Passive diffusion returns the membrane to resting potential.

132

Electrical Synapses

Uncommon, composed of gap junctions between cells. Don't involve diffusion of chemicals so they transmit much faster than chemical synapses and in both directions.

Ex: cardiac muscle, visceral smooth muscle, very few neurons in CNS

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Chemical Synapses

Slowest step in the transfer of a nervous signal. More common, unidirectional. Called a "motor end plate" when connecting neuron to muscle. Small vesicles filled with neurotransmitter rest just inside presynaptic neuron. When an action potential arrives at a synapse, the large concentration of Ca2+ voltage gated channels are activated, allowing influx of Ca2+ which allows some of the neurotransmitter vesicles to be released via exocytosis into the synaptic cleft.

Neurotransmitter diffuses across synaptic cleft via Brownian Motion (random motion of molecules).

Post synaptic membrane contains neurotransmitter receptor proteins. When bound, this membrane becomes even more permeable to ions which move across the membrane, completing the neural impulse. This way, the impulse will not meet electrical resistance as it travels to the next cell. If a cell is fired too often, it will not be able to replenish its supply of neurotransmitter vesicles.

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Neurotransmitter

Attaches to receptor for a fraction of a second and is released back into synaptic cleft. If it remains there, the post synaptic cell will be continuously stimulated. To prevent this, the neurotransmitter may be:
1. Destroyed by an enzyme and its parts are recycled back to the presynaptic neuron.
2. Directly absorbed by the presynaptic cell via active transport.
3. Diffuse out of the synaptic cleft.

135

Alpha-subunit of G-proteins

A G-protein is attached to the receptor protein on the postsynaptic neuron. When the receptor is stimulated by a neurotransmitter, the alpha-subunit breaks off. Can activate:
1. Separate specific ion channels.
2. A second messenger (cAMP or cGMP).
3. Intracellular enzymes.
4. Gene transcription.

136

Myelin

Increases the rate at which axons can transmit signals. In CNS, produced by oligodendrocytes. In PNS, produced by Schwann cells. Vertebrates only. "White matter".

Nodes of Ranvier: tiny gaps between myelin.

137

Saltatory Conduction

An action potential travels down a myelinated axon by jumping from one Node of Ranvier to the next as quickly as the disturbance moves through the electric field between them. Much faster because of reduced internal resistance.

138

Sensory (Afferent) Neurons

Receive signals from a receptor cell that interacts with its environment and then transfer this signal to other neurons. Most sensory input is discarded by the brain. Located dorsally (towards back) to spinal cord.

*sensory receptors transduce physical stimulus to neural signals!

139

Interneurons

Transfer signals from neuron to neuron. Make up 90% of the neurons in the human body.

140

Motor (Efferent) Neurons

Carry signals to a muscle or gland called the "effector". Located ventrally (toward front) from spinal cord.

141

Nerves

Neuron processes (dendrites and axons) bundled together.

142

Somatic Nervous System (SNS)

Voluntary branch of the PNS. Primarily responds to the external environment. Contains sensory and motor functions - motor neurons innervate only skeletal muscle. Neurons synapse directly on their effectors and use acetylcholine as neurotransmitter.

Cell bodies of somatic motor neurons are located in the ventral horns of the spinal cord.
--> responsible for the simple reflex arc!

143

Autonomic Nervous System (ANS)

Involuntary branch of the PNS. Sensory portion receives signals mainly from the organs in the ventral cavity. The motor portion conducts signals to the smooth muscle, cardiac muscles, and glands. Most preganglionic neurons use acetylcholine. Controlled mainly by the hypothalamus.

Sympathetic NS: fight or flight. Postganglionic neurons use epinephrine or norepinephrine.

Parasympathetic NS: rest and digest. Postganglionic neurons use acetylcholine.
-> acetylcholine binds to muscarinic receptors which stimulate the opening of K+ channels, inhibiting depolarization -> increases the time between heartbeats.

*does NOT indicate stimulatory vs. inhibitory! Both symp/para do both.

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The Lower Brain

Consists of the medulla (breathing), hypothalamus, thalamus, and cerebellum (coordinated muscle movements)
(Not as important: pons, mesencephalon, and basal ganglia.)
In the CNS, it integrates subconscious activities such as respiratory system, arterial pressure, salivation, emotions, and reactions to pain and pleasure.

145

The Higher Brain

AKA the cortical brain. Consists of the cerebrum, or cerebral cortex. The cerebral cortex stores memories and processes thoughts. It cannot function without the lower brain.

146

Path of Light Entering the Eye

Cornea -> lens -> vitreous chamber -> retina (rods and cones)

147

Lens

A converging lens. Would be spherical but has ligaments attached to ciliary muscles. When ciliary muscles contract, the lens becomes more like a sphere and brings the focal point closer. Relaxing flattens the lens and moves the focal point further away.

-> aging reduces the muscle elasticity making it difficult to see objects up close.

148

Rods and Cones

Photosensitive cells. The tips of these cells contain light sensitive photochemicals (pigments) that go through a chemical change when one of their electrons is struck by a single photon. The photon isomerizes (same atoms, just rearranged) the pigments, causing the membrane to be less permeable to Na+ and hyperpolarize. The hyperpolarization is transduced into a neural action potential and the signal is sent to the brain.

Cones -> colors
Rods -> no colors - sense all photons with wavelengths in the visible spectrum.

Vitamin A is a precursor to all pigments in the rods and cones.

149

Iris

The colored part of the eye that creates the opening called the pupil. Made from circular and radial muscles.
-> In a dark environment, the sympathetic NS contracts the radial muscles of the iris, dilating the pupil and allowing more light to enter the eye.
-> In a light environment, the parasympathetic NS contracts the circular muscles of the iris, constricting the pupil and screening out light.

150

Outer Ear

The skin and cartilage flap (auricle or pinna) directs the sound wave into the external auditory canal which carries the wave to the "tympanic membrane" AKA eardrum.

151

Middle Ear

Begins at the tympanic membrane, which brings the sound wave to the three small bones: malleus, incus, and stapes which bring the wave to the oval window.
They act as a lever system and change the combination of force and displacement from the inforce to the outforce (decreases displacement which increases force -> W = Fd). Additionally, the oval window is smaller than the tympanic membrane, acting to increase the pressure (P = F/A).
-> increase in force is necessary because the wave is being transferred from air in the outer ear to a more resistant fluid within the inner ear.

152

Inner Ear

The wave moves from the oval window through the "cochlea" to the center of the spiral, then spirals back out to the round window (positioned inferior to oval window). The change in pressure as the wave moves through the cochlea moves a membrane (vestibular membrane) in and out. This movement is detected by the "hair cells" (actually specialized microvilli) of the Organ of Corti and is transduced into neural signals which are sent to the brain.

153

Semicircular Canals

In the inner ear; responsible for balance. Each canal contains fluid and hair cells. Movement changes the momentum of the fluid which impacts on the hair cells and the body senses motion.
-> the canals are oriented at right angles to each other in order to detect movement in all directions.

154

Exocrine Glands

Release enzymes to the external environment through ducts.

Ex: sweat, oil, and digestive glands

155

Endocrine Glands

Release hormones directly into body fluids.

Ex: insulin and glucagon released by pancreas directly into the blood (pancreas also acts as exocrine gland - releases digestive enzymes through pancreatic duct).

Tend to over secrete their hormones so typically, some aspect of their effect on the target tissue will inhibit this secretion through negative feedback.
--> *the control point of this negative feedback is the conduct of the effector, NOT the concentration of the hormone (aka gland lags behind effector).

Ex: High insulin levels do not typically create low blood glucose. High insulin levels are caused by high blood glucose. High blood glucagon levels are caused by low blood glucose. A patient has high blood glucose. Would you expect to see high levels of insulin or glucagon?
Answer: Insulin - the hormone responding to the condition, not creating it.

156

Endocrine System

Alters metabolic activities, regulates growth and development, and guides reproduction. Works in conjunction with the nervous system, although it is much slower, less direct, and has longer lasting effects. Many endocrine glands are stimulated by neurons to secrete their hormones.

157

Hormone Receptor

A hormone receptor may act in several ways:
1. Act as an ion channel, increasing membrane permeability to a specific ion, or
2. Activate/deactivate other intrinsic membrane proteins also acting as ion channels.
3. Activate an intracellular second messenger (such as cAMP, cGMP, or calmodulin) which activates/deactivates enzymes/ion channels and creates a cascade of chemical rxns that amplifies the hormone's effect.

158

Effector

The "target cell" of the hormone; the cell that the hormone is meant to affect.

159

Adipocytes

Fat cells, cytoplasm contains mostly triglycerides (aka triacylglycerols) which have a 3 C "glycerol" back bone attached to 3 fatty acids (carbon chain with carboxylic acid end). Store energy, provide thermal insulation and padding.

Note: phospholipids also have a glycerol backbone, but one fatty acid is replaced by a phosphate group.

160

Micelle

Spherical structure resulting from amphipathic phospholipids being placed in an aqueous solution and spontaneously aggregating (polar ends towards solution, non polar ends inwards).

161

Peptide Hormones

Derived from peptides (water soluble), may be large or small, often include carbohydrate portions. Manufactured in the rough ER, typically as an inactive form that is larger than the active form. Modified in ER lumen/Golgi, packaged by Golgi into secretory vesicles to be released by exocytosis upon stimulation by another hormone or a nervous signal.

-> water soluble - move freely in blood but need membrane-bound receptor to get into cells.

162

Tertiary/Quarternary Structure of Peptides

Held together by 5 forces:
1. Covalent disulfide bonds between two cysteines on different parts of the chain (denatured by mercaptoethanol)
2. Electrostatic (ionic) interactions mostly between acidic and basic side chains (denatured by salt or change in pH)
3. Hydrogen bonds (denatured by urea)
4. Van der Waals forces
5. Hydrophobic side chains pushed away from water and towards the center of the peptide (denatured by organic solvents)

All denatured by heat.

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Anterior Pituitary

Anterior pituitary is located in the brain beneath the "hypothalamus". The hypothalamus controls the release of anterior pituitary hormones with releasing and inhibiting (tropic) hormones of its own. The release of these hormones is controlled by nervous system signals.

Peptide hormones: FSH, LH (later w reproduction), hGH, ACTH, TSH, Prolactin

Tropic hormones: have other endocrine glands as their target. Most released by ant pituitary.

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Human Growth Hormone (hGH)

Peptide; stimulates growth in almost all cells of the body. *all other hormones of the anterior pituitary have specific target tissues.
-Stimulates growth by increasing episodes of mitosis, cell size, rate of protein synthesis, as well as mobilizing fat stores, increasing use of fatty acids for energy and decreasing the use of glucose.
-Effects on proteins is accomplished by increasing amino acid transport across the cell membrane, increasing translation and transcription, and decreasing breakdown of protein and amino acids.

165

Adrenocorticotropic Hormone (ACTH)

Peptide; stimulates the adrenal cortex to release glucocorticoids via second messenger system using cAMP.
-> Release of ACTH is stimulated by many types of stress. Glucocorticoids are stress hormones (secreted by adrenal cortex).

166

Thyroid-Stimulating Hormone (TSH)

Peptide; aka thyrotropin, stimulates the thyroid to release T3 and T4 via second messenger system using cAMP. Increases thyroid cell size, number, and rate of secretion of T3 and T4.
--> *T3 and T4 concentrations have a negative feedback effect on TSH release, both at anterior pituitary and hypothalamus (see effects of T3 and T4).

167

Prolactin

Peptide, promotes lactation (milk production, NOT ejection). Typically, progesterone and estrogen inhibit milk production. Hypothalamus mainly has stimulatory effects but it inhibits the release of prolactin. Suckling stimulates the hypothalamus to stimulate the anterior pituitary to release prolactin (also inhibits menstrual cycle - not known whether this is directly due to prolactin).

168

Posterior Pituitary

Composed mainly of support tissue for nerve endings extending from the hypothalamus. Releases the peptide hormones oxytocin and ADH after synthesis in the neural cell bodies of the hypothalamus.

169

Oxytocin

Peptide; increases uterine contractions during pregnancy and causes milk to be ejected (NOT produced) from the breasts.

170

Antidiuretic Hormone (ADH)

Peptide; AKA vasopressin. Causes the collecting ducts of the kidney to become permeable to water concentrating/reducing the amount of urine. Also increases blood pressure since fluid is reabsorbed.
-> coffee and beer are ADH blockers that increase urine volume.

171

Parathyroid

Consists of four small parathyroid glands attached to the back of the thyroid. Releases parathyroid hormone.

172

Parathyroid Hormone (PTH)

Peptide; increases blood calcium.
Increases osteocyte absorption of calcium and phosphate from the bone and stimulates proliferation of osteoclasts.
Increases renal calcium reabsorption and renal phosphate excretion.
Increases calcium and phosphate uptake from the gut by increasing renal production of a steroid derived from vitamin D.
-> secretion is regulated by the calcium ion plasma concentration, and parathyroid glands shrink or grow accordingly.
Note: opposite effect of calcitonin.

173

Insulin

Peptide hormone released by the *pancreas. Associated with energy abundance in the form of high energy nutrients in the blood. Released when blood levels of carbohydrates or proteins are high - affects carbohydrate, fat, and protein metabolism. In presence of insulin, carbs stored as glycogen in liver and muscles, fat stored in adipose tissue, and amino acids taken up by body cells and made into proteins.
--> net effect: lower blood glucose levels.

Insulin binds to membrane receptor -> cascade of rxns inside cell.
-cells of body (not neurons) become highly permeable to glucose and amino acids.
-Intracellular metabolic enzymes are activated and (slowly) even translation and transcription rates are affected.

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Glucagon

Peptide hormone released by the *pancreas. Effects nearly opposite to insulin. Stimulates glycogenolysis (breakdown of glycogen) and gluconeogenesis in the liver. Acts via second messenger cAMP. In higher concentrations, breaks down adipose tissue, increasing fatty acid level in blood.
-> net effect: raise blood glucose levels.

175

Tyrosine Derivative Hormones

Formed by enzymes in the cytosol or on the rough ER.

Thyroid hormones:
T3 (triiodothyronine, 3 iodine atoms) and T4 (thyroxine, 4 iodine atoms). Their general effect is to increase the basal (resting) metabolic rate.
-> *Lipid soluble, must be carried in blood by plasma protein carriers. Slowly released to target tissues, brought to receptors inside *nucleus. High affinity to binding proteins in plasma and nucleus create a latent period in their response and increase duration of effect. Increase *transcription of large numbers of genes in nearly all cells of the body.
-> Controlled by negative feedback involving TSH from the anterior pituitary.

Adrenal Medulla hormones:
Catecholamines - epinephrine and norepinephrine.
-> Stress hormones, contribute to 'fight or flight' response with sympathetic NS.
-> *Water soluble (dissolve in blood), bind to receptors on target tissue and act mainly through second messenger cAMP.

176

Thyroid

Located along the trachea just in front of the larynx. Secretes T3 and T4 (tyrosine derivatives - also lipid soluble), and calcitonin (peptide).

177

Calcitonin

Peptide hormone released by the thyroid gland. Slightly decreases blood calcium by decreasing osteoclast activity and number.

-> calcium levels can be effectively controlled in humans in the absence of calcitonin.

Note: opposite effect of parathyroid hormone.

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Steroid Hormones

Derived from and often chemically similar to cholesterol. Formed mainly in smooth ER and mitochondria.
Come only from adrenal cortex, gonads, and placenta.

-> lipids - require protein transport molecule to dissolve into bloodstream. Diffuse through cell membrane of effector.
Once inside, combine with a receptor in the *cytosol which transports steroid into nucleus where steroid acts at the *transcription level --> typical effect is to increase certain membrane or cellular proteins within effector.

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Adrenal Glands

On top of kidneys.
Adrenal Cortex:
Outside portion of the gland, secretes only STEROID hormones (also a small amount of sex hormones). 2 types:
-mineral corticoids - aldosterone: affects electrolyte balance in blood.
-glucocorticoids - cortisol: increases blood glucose concentration, affects fat and protein metabolism.

Adrenal Medulla:
Synthesizes the TYROSINE DERIVATIVE catecholamines - epinephrine and norepinephrine. Effects of these two are similar to those in sympathetic NS but last much longer. Stress hormones - fight or flight. Vasoconstrictors of most internal organs and skin but vasodilators of skeletal muscle.

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Aldosterone

Steroid, a mineral corticoid that increases Na/K membrane proteins in distal convoluted tubule to increase Na+ and Cl- reabsorption and K+ and H+ secretion. Creates net gain in particles in the plasma which results in eventual increase in blood pressure. Same, but smaller, effect on sweat glands, salivary glands, and intestines.

*Primary effect: Na+ reabsorption and K+ secretion in collecting tubule of kidney.
Secondary effect: increase in blood pressure.

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Cortisol

Steroid; a glucocorticoid that increases blood glucose levels by stimulating "gluconeogenesis" (creation of glucose and glycogen from amino acids, glycerol, and/or lactic acid) in the liver.
1. Degrades adipose tissue to fatty acids to be used for cellular energy.
2. Causes a moderate decrease in use of glucose by cells.
3. Causes the degradation of nonhepatic proteins, a decrease of nonhepatic amino acids and a corresponding increase in liver and plasma proteins and amino acids.
-> a stress hormone: diminishes capacity of the immune system to fight infection. Anti-inflammatory properties.

182

Human Chorionic Gonadotropin (HCG)

Peptide hormone, secreted by the embryo upon implantation. Prevents the degeneration of the corpus luteum and maintains its secretion of estrogen and progesterone. HCG in the blood and urine of the mother is the first outward sign of pregnancy.

183

Follicle Stimulating Hormone (FSH)

Peptide, stimulates (sertoli cells) surrounding and nurturing cells of spermatocytes and spermatids.
Stimulates the growth of (granulosa cells) around the primary oocyte (where eggs are arrested at birth) which secrete the viscous "zona pellucida" around the egg.

184

Luteinizing Hormone (LH)

Peptide, stimulates (leydig cells) in interstitium between the tubules to release testosterone.
Stimulates (theca cells) to secrete androgen which is converted to estradiol (type of estrogen) by the granulosa cells in presence of FSH and secreted into the blood.

185

Gonadal Hormones

Steroid hormones: estrogen and progesterone (also produced by placenta), testosterone.

186

Testosterone

Steroid, primary androgen (male sex hormone) which stimulates germ cells to become sperm. Responsible for development of secondary sex characteristics. Stimulates growth spurt at puberty as well as the closure of the epiphyses of the long bones, ending the growth stature.
Synthesized by adrenal cortex.

187

Estradiol

Steroid hormone, prepares the uterine wall for pregnancy. Inhibits LH secretion by the anterior pituitary. However, levels rise rapidly just before ovulation (bursting of the follicle) causing a dramatic increase in LH secretion - "luteal surge" - positive feedback loop of rising estrogen levels increasing LH, increasing estrogen --> causes follicle to burst, releasing the egg into body cavity.

188

Spermatogonia

Male germ cells located in seminiferous tubules, arise from epithelial tissue and undergoes meiosis to become
1. Spermatocytes,
2. Spermatids, and
3. Spermatozoa: loses cytoplasm, forms the head, midpiece and tail -> sperm cell.
Head has nuclear material and enzymes to penetrate egg; midpiece contains many mitochondria to provide energy for movement of the tail. Only nuclear portion enters egg.

After DNA replication in S phase of interphase, it is called a primary spermatocyte (diploid, 46).

After cytokinesis, it is called a secondary spermatocyte (haploid, 23).

189

Seminiferous Tubules

In the testes; where sperm production occurs.

190

Epididymus

Where the spermatozoon is carried to mature after freed into the tubule lumen. *Site where gametes become motile and capable of fertilization.

191

Vas Deferens

Vessel leading to the urethra through which spermatozoa are propelled upon ejaculation.

192

Semen

Complete mixture of spermatozoa and fluid from the seminal vesicles, prostate, and bulbourethral glands (aka Cowper's glands).

193

Oogonia

Female germ cells located in the ovaries, arise from epithelial tissue and undergoes meiosis to become
1. Oocytes,
2. Ootids, then
3. Ovum: egg cell. Fusion of ovum and sperm nuclei result in "fertilization".

After DNA replication in S phase of interphase, it is called a primary oocyte (diploid, 46).

After cytokinesis, it is called a secondary oocyte (haploid, 23).

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Corpus Luteum

The remaining portion of the follicle left behind after the egg is released during ovulation. Secretes estradiol and progesterone throughout pregnancy or, with no pregnancy, for about 2 weeks until the corpus luteum degrades into the "corpus albicans"; progesterone levels decrease.

195

Placenta

Formed from the tissue of the egg and the mother, takes over the job of hormone secretion. Reaches full development by the end of the first trimester and begins secreting its own estrogen and progesterone while lowering its secretion of HCG.

196

Determination

The process where a cell becomes committed to a specialized development path. Occurs as the embryo develops past the eight-cell stage and cells become different from each other due to cell-cell interactions.

197

Differentiation

The specialization that occurs at the end of development forming a specialized tissue cell.

198

Induction

Occurs when one cell type affects the direction of differentiation of another cell type.

199

Morula

A zygote comprised of eight or more cells due to cleavage. First eight cells are equivalent in size and shape and have the potential to express any of their genes (totipotent).

200

Blastocyst

The fluid filled ball resulting from four days of the morula dividing. Lodges in the uterus, "implantation," 5-7 days after ovulation (in Fallopian tube prior to this). Now female is considered pregnant.

201

Gastrula

Forms from a process called "gastrulation" in the second week after fertilization. Cells begin to slowly move about the embryo for the first time. The three primary germ layers are formed:
1. Ectoderm: outer coverings of body - skin, nails, tooth enamel, and the cells of nervous system and sense organs.
2. Mesoderm: muscle, bone, stuff that lies between the inner and outer covering of the body.
3. Endoderm: lining of digestive tract and into much of the liver and pancreas.

202

Neurula

Formed in process called "neurulation" in the third week. The notochord (made from mesoderm) "induces" the overlying ectoderm to thicken and form the (neural plate) which eventually becomes the spinal cord, brain, and most of the nervous system.

203

Alpha-amylase

Enzyme in the saliva; begins digestion by breaking down the long straight chains of starch (the major *carbohydrate in the human diet) into polysaccharides. Chewing increases surface area of food.

204

Chyme

Semifluid mass consisting of food and stomach acid.

205

Mucous Cells

Stomach; secrete mucous (sticky glycoprotein and electrolytes - like sodium) which lubricates the stomach wall for food and protects the epithelial lining from the acidic environment.

206

Chief Cells

Stomach (in exocrine glands); secrete pepsinogen.

207

Pepsinogen

The zymogen (inactive enzyme) precursor to pepsin. Activated to pepsin by the low pH in the stomach. Once activated, pepsin begins *protein digestion.

208

Parietal Cells

Stomach (in exocrine glands); secrete hydrochloric acid (HCl) which diffuses to the lumen.
-> Requires a lot of energy to produce the concentrated acid. Uses CO2 to produce carbonic acid (H2CO3) inside the cell. One H is expelled to lumen and the bicarbonate ion is expelled to the interstitial fluid side.
--> net result: lower pH in stomach, higher pH in blood.

209

G Cells

Stomach; secrete gastrin into the interstitium.

210

Gastrin

A large peptide hormone that is absorbed into the blood and stimulates parietal cells to secrete HCl.

--> *acetylcholine increases the secretion of all cell types.

211

Villi

Finger-like projections from the wall of the small intestine that increase surface area allowing for greater digestion and absorption. Each villus contains a capillary network and a lymph vessel called a "lacteal," both of which are passed through by nutrients.

212

Microvilli

Much smaller finger-like projections on the apical (lumen) surface of the cells of each villus. Further increase the surface area of the small intestinal wall.

213

Brush Border

The "fuzzy covering" of the microvilli which contains membrane bound digestive enzymes (for carbs, proteins, and nucleotides). Also further increases surface area.

214

Goblet Cells

Make up some of the epithelial cells in the small intestine. Secrete mucous to lubricate the intestine and help protect the brush border from mechanical and chemical damage.

215

Pancreas

Secretes bicarbonate ions into the duodenum, giving it a pH of 6. Releases several major enzymes: *trypsin, *chymotrypsin, pancreatic *amylase, *lipase, ribonuclease, and deoxyribonuclease.

216

Trypsin and Chymotrypsin

Released by pancreas into the small intestine. Degrade proteins into small polypeptides which then continue to the brush border to be reduced to amino acids, dipeptides and tripeptides before they're absorbed into the enterocytes (reduce everything to amino acids).

217

Pancreatic Amylase

Released by pancreas into the small intestine. Hydrolyzes polysaccharides to disaccharides and trisaccharides like salivary amylase but much more powerful. Degrades nearly all carbs from the chyme into small glucose polymers. Brush border enzymes finish degrading these polymers to their respective monosaccharides before they are absorbed.

218

Lipase

Released by pancreas into the small intestine. Degrades fat, especially triglycerides.

219

Bile

Produced in the liver and stored in the gallbladder. Released into the duodenum to emulsify (breakdown, NOT digest) the fat to increase its surface area for digestion into fatty acids and monoglycerides. These products are shuttled to the brush border in bile micelles and then absorbed by the enterocytes. Much of the bile is reabsorbed by the small intestine and transported back to the liver.

220

Large Intestine

Major functions are water reabsorption and electrolyte absorption. Fails -> diarrhea. Contains the bacteria E. coli (mutualistic symbiosis) which gets our leftovers and provides us with vitamins.

221

Glycogenesis

The formation of glycogen (stored form of glucose). Stored mostly in the liver and muscles. When cells reach saturation point with glycogen, carbs are converted to fatty acids and then triglycerides in a process requiring a small amount of energy (long term storage).

-> relate to glycolysis in Krebs Cycle.

222

Glycogenolysis

The formation of glucose from glycogen when blood levels of glucose are low. Takes place in the liver.

223

Ammonia

NH3
-> by-product of gluconeogenesis from proteins. Nearly all is converted to urea by the liver and then excreted in the urine by the kidney.

224

Albumin

Osmoregulatory protein in the blood plasma. A fat carrier (like lipoproteins) that free fatty acids combine with in the blood for transportation. A single albumin molecule typically carries 3 fatty acids but can carry up to 30.

225

Liver

Functions:
1. Blood storage
2. Blood filtration (continues to vena cava)
3. Carb metabolism (gluconeogenesis, glycogenesis, storage of glycogen)
4. Fat metabolism: synthesizes bile from cholesterol and converts carbs and proteins into fat. Oxidizes fatty acids for energy, forms most lipoproteins.
5. Protein metabolism: deaminates amino acids, forms urea from ammonia in the blood. Synthesizes plasma proteins such as fibrinogen, prothrombin (clotting factors), albumin (osmoregulatory protein in blood), and most globulins (but not antibodies - made by plasma cells), and synthesizes nonessential amino acids.
6. Detoxification: detoxified chemicals are excreted by liver as part of bile or polarized so they may be excreted by the kidney.
7. Erythrocyte destruction (although mostly by spleen).
8. Vitamin storage: vitamin A, D, B12. Also stores iron and combines it with the protein.

--> *know that when the liver mobilizes fat or protein for energy, the blood acidity increases!

226

Kidney

Functions:
1. Excrete waste products such as urea, uric acid, ammonia, and phosphate.
2. Maintain homeostasis of body fluid volume and solute composition.
3. Help control plasma pH.

Has outer "cortex" and inner "medulla". Creates urine, empties into renal pelvis which empties to the bladder via the ureter. Bladder is drained by the urethra.

227

Nephron

Functional unit of the kidney. Contains (in order of flow): glomerulus, Bowman's capsule, proximal convoluted tubule, Loop of Henle, juxtaglomerular apparatus, distal convoluted tubule and collecting duct.

"Hydrostatic pressure" forces some plasma through "fenestrations" of the glomerular endothelium and into the Bowman's capsule.

228

Renal Corpuscle

The glomerulus and Bowman's capsule together.

229

Fenestrations of the Glomerulus

Function as a sieve to screen out blood cells and large proteins from entering the Bowman's capsule (only filtrate gets through).

230

Proximal Convoluted Tubule

Where filtrate goes after the Bowman's capsule. Where most of the reabsorption of glucose, most proteins, and other solutes takes place via secondary active transport proteins on the apical membrane of the tubules.
-> once these transport proteins are completely saturated with a solute, any additional solute is washed into the urine.

Some solutes not actively reabsorbed can be reabsorbed via passive or facilitated diffusion.
Water is reabsorbed across relatively permeable tight junctions due to the favorable osmotic gradient.

Drugs, toxins, and other solutes are secreted into the filtrate by the cells of the proximal tubule. H+ ions secreted through an "antiport" system with sodium, driven by Na+ conc gradient.

*net result of PCT: reduce amount of filtrate in nephron while changing the solute composition without changing the osmolarity.

--> if glucose appears in the urine, it must be because the glucose transporters in the PCT are unable to reabsorb all of the glucose from the filtrate (saturated).

231

Loop of Henle

Dips into medulla. Function is to increase solute conc, and thus osmotic pressure, of medulla.
-> as filtrate descends into medulla, water diffuses out of the loop and into medulla.

-descending loop: has low permeability to salt so filtrate osmolarity goes up.
-ascending loop: as filtrate rises out of medulla salt diffuses out of loop; passively at first then actively. Nearly impermeable to water.

A capillary bed surrounds the loop and helps maintain the conc of the medulla.

232

Distal Convoluted Tubule

Reabsorbs Na and Ca while secreting H, K, and (HCO3)-.
Aldosterone acts to increase Na and K membrane transport proteins.

*net effect: lower filtrate osmolarity.

At end of tubule, ADH increases permeability of cells to water --> in presence of ADH, water flows from tubule concentrating the filtrate.

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Juxtaglomerular Apparatus

Monitors filtrate pressure in distal tubule. Secretes enzyme Renin which initiates a regulatory cascade producing angiotensin (stimulates adrenal cortex to secrete aldosterone - increases Na/K membrane proteins in distal tubule).

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Renin

Catalyzes the conversion of angiotensin I to II which increases the secretion of aldosterone.
--> if blocked, aldosterone cannot cause increased synthesis of Na/K proteins, so Na reabsorption decreases. Blood pressure would decrease.

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Collecting Duct

Carries filtrate into the highly osmotic medulla. Impermeable to water but also sensitive to ADH.
--> in presence of ADH, duct becomes permeable to water, allowing it to diffuse into medulla, concentrating the urine.
(Many collecting ducts line up side by side in medulla to make up the renal pyramids. Leads to a renal calyx which empties into renal pelvis).

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Arterioles

Smaller branches of arteries, branch to capillaries

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Venules

Smaller branches of veins, branch from capillaries

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Systole

Pressure of ventricular contraction.

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Diastole

Pressure of atrial contraction following complete relaxation of the entire heart.

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Sinoatrial (SA) Node

Pacemaker in right atrium. A group of specialized cardiac muscle cells. Contracts by itself at regular intervals, spreading its contractions to surrounding cardiac muscles via "electrical synapses" made from "gap junctions". Pace of SA node is faster than normal heartbeats but parasympathetic "vagus nerve" innervates the node, slowing contractions.

-> action potential spreads around both atria causing them to contract and at the same time spreads to "AV node".

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Atrioventricular (AV) Node

In interatrial septa (wall between atria). Slower to contract, creating a delay to allow atria to finish their contraction and squeeze contents into ventricles before ventricles begin to contract.

-> action potential moves down "bundle of His"

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Bundle of His

Conductive fibers in the interventricular septa.

-> action potential branches via "Purkinje fibers"

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Purkinje Fibers

Conductive fibers that branch out through the ventricular walls. Allow for a more unified and stronger contraction.

-> action potential spreads through gap junctions from one cardiac muscle to the next.

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Vagus Nerve

Parasympathetic. Innervates the heart and digestive system. Slows the rate of heart contractions and increases digestive activity in the intestines.

245

Capillaries

4 methods for materials to cross capillary walls:
1. Pinocytosis
2. Diffusion or transport through capillary cell membranes
3. Movement through pores in the cells called fenestrations
4. Movement through the space between the cells

-> from arteriole to capillary: hydrostatic pressure > osmotic pressure, net fluid flow is out of capillary and into interstitium.
-> from capillary to venule: hydrostatic pressure < osmotic pressure, net fluid flow is into capillary and out of interstitium.
(osmotic pressure remains relatively constant, hydrostatic pressure changes)
-net result of fluid exchange: 10% loss of fluid to interstitium

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Respiratory Path

Nose -> pharynx -> larynx -> trachea -> bronchi -> bronchioles -> alveoli

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Nasal Cavity

Filters, moistens, and warms incoming air.
-"coarse hair" at front of cavity traps large dust particles.
-"mucus" secreted by goblet cells traps smaller dust particles and moistens the air.
-capillaries warm the air.
-cilia moves the mucus and dust back toward the pharynx so it can be removed by spitting or swallowing.

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Pharynx

Throat. Passageway for food and air.

249

Larynx

Voice box; contains vocal cords. Sits behind the "epiglottis" (prevents food from entering trachea). When no gaseous material enters the larynx, a coughing reflex is triggered to force material back out.

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Trachea

Windpipe. Lies in front of esophagus. Composed of ringed cartilage covered by ciliated mucous cells (collect dust and usher towards pharynx like in nasal cavity). Splits into right and left bronchi before entering the lungs.

*note: microtubules are found in cilia! Problem in microtubule production --> problem in breathing.

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Hemoglobin

Protein inside erythrocytes that binds rapidly and reversibly with 98% of the oxygen in the blood, forming "oxyhemoglobin". Composed of four polypeptide subunits, each with a single organic molecule with an atom of iron at its center (heme cofactor). Each iron atom can bind with one O2 molecule, and the binding of one accelerates the binding of the rest (same with release of O2).

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Oxygen Dissociation Curve

As O2 pressure increases, the O2 saturation of hemoglobin increases sigmoidally (flat portion of curve at about the normal 97% saturation shows that small fluctuations in oxygen pressure have little effect).
Saturation also depends on: CO2 pressure, pH, and temperature of the blood.
*shifted right by increase in CO2 pressure, H+ concentration, or temperature!
--> shows a lowering of hemoglobin's affinity for oxygen.

*CO has more than 200x greater affinity for hemoglobin than O2 but shifts curve left.
-> in CO poisoning, pure oxygen can be administered to displace the CO from hemoglobin.

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Carbon Dioxide

Carried by the blood in three forms:
1. In physical solution
2. As bicarbonate ion
3. In carbamino compounds (combined with hemoglobin and other proteins)

10x as much is carried as bicarbonate than as either of the other forms.
"carbonic anhydrase" is the enzyme that governs bicarbonate ion formation in the reversible rxn:
CO2 + H2O --> (HCO3)- + H+

Carbonic anhydrase is inside the red blood cells, not plasma, so when CO2 is absorbed in the lungs, bicarbonate ion diffuses into the cell (and chlorine moves out to balance electrostatic forces).

Reduced hemoglobin (without oxygen) acts as a blood buffer by accepting protons. It has a greater capacity to form carbamino hemoglobin.

Central and peripheral chemoreceptors monitor [CO2] in the blood and increase breathing when levels get too high (low blood pH).

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Lymphatic System

Collects excess interstitial fluid (from most tissues except CNS) and returns it to the blood; recycles interstitial fluid and monitors the blood for infection. Removes proteins and large particles that cannot be taken up by the blood. Takes excess fluid through lymph nodes on the pathway to the blood to illicit an immune response if necessary (from lymphocytes).
-reroutes low soluble fat digestates around the small capillaries of the intestine and into the large veins of the neck.

-> an "open system": fluid enters one end and leaves at the other.
To enter: fluid flows between overlapping endothelial cells where large particles push their way in. Cells are overlapped in such a fashion that, once inside, large particles cannot push their way out.

Vessels have valves for one-way flow. Propelled by smooth muscle cells in vessel walls (contract when stretched) and squeezed by adjacent skeletal muscles, outside movement, compression, etc. -> flow greater in more active person.

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Interstitial Pressure

As interstitial pressure increases, lymph flow increases. Factors affecting interstitial pressure include: blood pressure, plasma osmotic pressure, interstitial osmotic pressure (from proteins, infection response, etc), and permeability of capillaries.

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Blood

Connective tissue (contains cells and a matrix). Regulates extra cellular environment of the body by transporting nutrients, waste productions, hormones, and even heat. Protects body from injury and foreign invaders. Three parts:
1. Plasma
2. White blood cells (buffer coat)
3. Red blood cells

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Blood Plasma

Contains matrix of the blood which includes water, ions, urea, ammonia, proteins, and other organic/inorganic compounds.
Important proteins (mostly formed in liver, act as source of amino acids for tissue protein replacement):
1. "albumin": transports fatty acids and steroids, regulates osmotic pressure of blood.
2. "immunoglobulins": aka "antibodies" (made in lymph tissue)
3. Clotting factors: like "fibrinogen" --> *plasma with fibrinogen removed is called "serum"

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Erythrocytes

Red blood cells. Like bags of hemoglobin with no nucleus or other organelles (no mitosis). Main function is to deliver oxygen and remove carbon dioxide. Filtered in spleen (mostly) and liver.

A common precursor, the "stem cell" in the bone marrow differentiates into all different blood cells.

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Leukocytes

White blood cells. Have organelles but no hemoglobin. Protect the body from foreign invaders. Formation of wbc is more complex than rbc due to the many different types.
-> some types have shorter lives (nonspecific, multiply quickly against any infection)
-> some types have longer lives (specific, fight one infection and hang around in case it returns)

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Platelets

Small portions of membrane-bound cytoplasm torn from megakaryocytes (which remain mainly in bone marrow). Similar to tiny cells without a nucleus. Contain actin and myosin, residuals of the Golgi, ER, mitochondria, and are capable of making prostaglandins and some important enzymes.
-> membrane is designed to avoid adherence to healthy endothelium while adhering to injured endothelium (upon contact, become sticky, swell, and release various chemicals to activate other platelets).

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Coagulation

Three steps:
1. A dozen or so coagulation factors form a complex (prothrombin activator)
2. Prothrombin activator catalyzes the conversion of prothrombin (a plasma protein) into thrombin
3. Thrombin governs the polymerization of the plasma protein fibrinogen to fibrin threads that attach to the platelets and form a tight plug.
-> this clot/coagulation appears within seconds in small injuries, 1-2 min in larger injuries.

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Innate Immunity

A generalized protection from most intruding organisms and toxins. Includes:
1. The skin as a barrier to organisms and toxins
2. Stomach acid and digestive enzymes to destroy ingested organisms and toxins
3. Phagocytotic cells
4. Chemicals in the blood

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Acquired Immunity

Protection against specific organisms or toxins. Develops after the body is first attacked. Two types:
1. Humoral (B-cell) immunity
2. Cell-mediated (T-cell) immunity

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Humoral (B-Cell) Immunity

Promoted by B lymphocytes which differentiate and mature in bone marrow and liver. Each is capable of making a *single type of "antibody" (or "immunoglobulin") which it displays on its membrane. Antibody recognizes the "antigen" with *specific binding.
If there is a match, the B lymphocyte, assisted by the "helper T cell," differentiates into "plasma cells" and "memory B cells".
-> plasma cells begin synthesizing free antibodies and releasing them into the blood. The antibodies may cause the antigen bearing cell to be perforated, mark the antigen for phagocytosis by macrophages (and natural killer cells), or cause the antigenic substances to "agglutinate" (clump) or even precipitate, or in the case of a toxin, the antibodies may block its chemically active portion.

--> effective against bacteria, fungi, parasitic protozoans, viruses, and blood toxins.

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Primary Response

The first time the immune system is exposed to an antigen. Requires 20 days to reach its full potential.

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Secondary Response

In the case of re-infection, memory B cells which have proliferated and remained in the body can be called upon to synthesize antibodies, resulting in a faster-acting and more potent effect. Requires approx 5 days to reach its full potential.

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Cell-Mediated (T-Cell) Immunity

Involves "T-lymphocytes" which mature in the thymus. Like B-lymphocytes, T-lymphocytes have an antibody-like protein that recognizes antigens however they never make free antibodies. In the thymus, they are tested by exposure to the body's normal cell antigens. If the T-lymphocyte binds to a self-antigen, it is destroyed. If not, it is released to lodge in lymphoid tissue or circulate between the blood and the lymph fluid.
-> T-lymphocytes that are not destroyed differentiate into "helper T cells, memory T cells, suppressor T cells, and killer (cytotoxic) T cells".

--> effective against infected cells.

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Helper T Cells

Assist in activating B lymphocytes as well as killer and suppressor T cells. The helper T cells are attacked by HIV.

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Killer T Cells

Bind to the antigen-carrying cell and release a protein (perforin) which punctures the antigen-carrying cell. Can attack many cells because they do not phagocytize their victims. Responsible for fighting some forms of cancer and for attacking transplanted tissue.

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Muscle

Three types:
1. Skeletal
2. Cardiac
3. Smooth

Contraction has four functions:
1. Body movement
2. Stabilization of body position
3. Movement of substances through the body (blood, lymph)
4. Generating heat to maintain body temperature

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Agonist Muscle

In skeletal muscle, the muscle responsible for the movement. Contracts.

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Antagonist Muscle

In skeletal muscle, the muscle that stretches when the agonist contracts.
-> when antagonist contracts, the bone moves in the opposite direction, stretching the agonist.
Ex: biceps and triceps

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Synergistic Muscle

Assist the agonist by stabilizing the origin bone (the larger one, remains relatively stationary) or by positioning the insertion bone (the smaller one, moves relative to larger bone upon muscle contraction) during movement.

*Skeletal muscles will likely be used for leverage physics problems. Most lever systems of the body typically act to *increase the required force of a muscle contraction. AKA a greater force than mg is required to lift a mass (m) -> done in order to reduce the bulk of the body and increase range of movement.
-> If the muscle has a shorter lever arm, it's closer to the body and creates less bulk.

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Sarcomere

The smallest functional unit of skeletal muscle. Composed of many strands of two protein filaments: the "thick and thin filaments" laid side by side to form a cylindrical segment. Surrounded by the "sarcoplasmic reticulum" - specialized ER of the muscle cell, lumen is filled with Ca2+ ions.

*in muscle contraction: H zone (open space between thin actin filaments) and I band (intersection of connecting thin actin filaments of separate sarcomeres) get smaller while A band (thick myosin filament) does not change size.

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Thick Filament

Made of the protein myosin. Several long myosin molecules wrap around each other to form one thick filament. Globular heads protrude along both ends of the thick filament.

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Thin Filament

Made of a polymer of the globular protein "actin". Attached to actin are the proteins (troponin) and (tropomyosin).

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Sarcolemma

A modified membrane that wraps several myofibrils (several sarcomeres positioned end to end) together to form a muscle cell or muscle fiber.

Human muscle cells are so specialized that they have lost the ability to undergo mitosis. Changes occur over time when the muscles are exposed to forceful, repetitive contractions: diameter of muscle fiber increases, the number of sarcomeres and mitochondria increases, and sarcomeres lengthen.

"Acetylcholine" released by the action potential of the neuron from the "neuromuscular synapse" activates ion channels in the sarcolemma of the muscle cell creating an action potential.
-> the action potential moves deep into the muscle cell via small tunnels in the membrane called "T-tubules".

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T-tubules

Small tunnels in the membrane of muscle cells. Allow for a uniform contraction of the muscle by allowing the action potential to spread through the muscle cell more rapidly. From here, action potential is transferred to the sarcoplasmic reticulum which suddenly becomes permeable to Ca2+ ions. The Ca2+ ions begin the 5 stage cycle.

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5 Stage Cycle of Skeletal Muscle Contraction

Each myosin head crawls along the actin.
1. Tropomyosin covers an active site on the actin preventing the myosin head from binding. The myosin head remains cocked in a high-energy position with a phosphate and ADP group attached.
2. In the presence of Ca2+, troponin pulls the tropomyosin back, exposing the active site, allowing the myosin head to bind to actin.
3. The myosin head expels a phosphate and ADP bends into a low-energy position, dragging the actin along with it -> called the power stroke because it causes the shortening of the sarcomere and the muscle contraction.
4. ATP attaches to the myosin head which releases the myosin from the active site, which is covered immediately by tropomyosin.
5. ATP splits to inorganic phosphate and ADP causing the myosin head to cock into the high-energy position.
The cycle is repeated many times to form a contraction.

At the end of each cycle, Ca2+ is actively pumped back into the sarcoplasmic reticulum.

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Motor Unit

From 2-2000 fibers spread throughout the muscle are innervated by a single neuron. Motor units are independent of each other. The force of a contracting muscle depends upon the number and size of the active motor units, and the frequency of action potentials in each neuron of the motor unit.
Typically, smaller motor units are first to be activated and larger units are recruited as needed -> results in a smooth increase in the force generated by the muscle.
-> muscle requiring intricate movements (finger muscles) have smaller motor units whereas muscles requiring greater force (back muscles) have larger motor units.

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Myoglobin

An oxygen storing protein similar to hemoglobin, but having only one protein subunit. Stores oxygen inside muscle cells (one molecule oxygen per molecule myoglobin). Has a hyperbolic O2 dissociation curve (vs. hemoglobin -> sigmoidal).

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Cardiac Muscle

"striated" - composed of sarcomeres, like skeletal muscle. Each cardiac muscle cell contains only *one nucleus (vs. *two nuclei in skeletal) and is separated from its neighbor by an "intercalated disc" - contains gap junctions which allow an action potential to spread from one cardiac cell to the next via electrical synapses.
Mitochondria of cardiac muscle cells are larger and more numerous.
Forms a net which contracts in upon itself like a squeezing fist (vs connection to bone like skeletal).
Grows similarly to skeletal.
The action potential of cardiac muscle exhibits a plateau after depolarization created by slow voltage-gated calcium channels which allow calcium to enter and hold the inside of the membrane at a positive potential difference, lengthening the time of contraction.

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Smooth Muscle

Innervated by autonomic NS (mainly involuntary). Cells contain only *one nucleus. Also contain thin and thick filaments, but not organized into sarcomeres.
Smooth muscle cells contain "intermediate filaments" - attached to thin and thick filaments. When thin and thick filaments contract, they cause intermediate filaments to pull their attached "dense bodies" together.
Upon contraction, smooth muscle cells shrink length-wise.
Cells can be connected by gap junctions to spread action potential from single neuron to a large group of cells, allowing cells to contract as single unit (intestines, uterus, etc.) or can be in a group of fibers each attached directly to a neuron that can contract independently of each other (multiunit) (bronchioles, pili muscles attached to hair follicles, iris).
Also contracts/relaxes in presence of hormones, or to changes in pH, O2 and CO2 levels, temperature, and ion concentrations.

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Bone

Living tissue. Functions:
1. Support of soft tissue
2. Protection of internal organs
3. Assistance in movement of the body
4. Mineral storage
5. Blood cell production
6. Energy storage in the form of adipose cells in bone marrow

Contains four types of cells surrounded by an extensive matrix: (osteoprogenitor/osteogenic cells - differentiate into osteoblasts), osteoblasts, osteocytes, and osteoclasts.

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Osteoblasts

Secrete collagen and organic compounds upon which bone is formed. Incapable of mitosis. Release matrix materials around themselves, become enveloped by the matrix, and differentiate into osteocytes.

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Osteocytes

Exchange nutrients and waste materials with blood. Also incapable of mitosis.

*parathyroid hormone increases blood calcium by increasing osteocyte activity and osteoclast number.

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Osteoclasts

Resorb bone matrix, releasing minerals back into the blood. Believed to develop from the white blood cells called monocytes.

*parathyroid hormone increases blood calcium by increasing osteocyte activity and osteoclast number.

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Spongy Bone

Contains "red bone marrow" - the site of red blood cell development.

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Compact Bone

Surrounds the (medullary) cavity which holds "yellow bone marrow" - contains adipose cells for fat storage. Highly organized.
In a continuous remodeling process, *osteoclasts burrow tunnels called "Haversian (central) canals" through compact bone. Osteoclasts are followed by osteoblasts, which lay down a new matrix onto tunnel walls forming concentric rings called "lamellae". Osteocytes trapped between the lamellae exchange nutrients via "canaliculi" - canals through layers of lamellae.

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Osteon (Haversian System)

The entire system of lamellae and Haversian canals (parallel to lamellae coils). Tunnels through compact bone. Contain blood and lymph vessels, and are connected by crossing canals called "Volkmann's canals" (perpendicular to lamellae coils).

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Hydroxyapatite

Ca10(PO4)6(OH)2 in the bone matrix. How most of the Ca2+ in the body is stored.
Collagen fibers lie along the lines of tensile force of the bone, giving the bone great tensile strength. Hydroxyapatite crystals lie alongside collagen fibers, giving the bone greater compressive strength than the best reinforced concrete.

Since calcium salts are only slightly soluble, most calcium in the blood is not in the form of free calcium ions -> the [free Ca2+] in the blood is what is physiologically important. Too much -> membranes become hypo-excitable producing lethargy, fatigue, and memory loss. Too little produces cramps and convulsions.

Bone stores Ca2+ and (HPO4)2- (phosphate) in the form of the slightly soluble calcium salt CaHPO4 (calcium phosphate). It is these salts that buffer the PLASMA Ca2+ levels.

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Cartilage

Flexible, resilient connective tissue. Composed primarily of collagen and has great tensile strength. Contains NO blood vessels or nerves except in its outside membrane (perichondrium).
(hyaline - most common) cartilage reduces friction and absorbs shock in joints.

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Joints

Can be classified by structure:
1. (fibrous) between two bones held closely and tightly together by fibrous tissue permitting little or no movement.
Ex: between skull bones, between teeth and mandible.
2. (cartilaginous) between two bones tightly connected by cartilage, also allow little or no movement.
Ex: between ribs and sternum, between pubic symphysis and hip bone.
3. (synovial) between bones not bound directly by the intervening cartilage. Instead, separated by a capsule filled with (synovial) fluid. The fluid provides lubrication and nourishment to the cartilage, and contains phagocytotic cells that remove microbes and particles which result from wear and tear from joint movement. Allow for wide range of movement.
Ex: between humerus and shoulder.

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Skin

Important functions:
1. Thermoregulation: blood conducts heat from core to skin. Some heat can be dissipated by endothermic evaporation of sweat but most is dissipated by radiation (only effective if body is higher than room temp). Blood can also be shunted away from skin capillaries to reduce heat loss. Hairs can be erected (piloerection) via sympathetic stimulation trapping insulating air next to the skin. Skin has both warmth and cold receptors.
2. Protection: physical barrier to abrasion, bacteria, dehydration, many chemicals, and UV radiation.
3. Environmental sensory input: gathers info by sensing trmperature, pressure, pain, and touch.
4. Excretion: of water and salts. This water loss occurs by diffusion through the skin and is independent of sweating. Burning of the skin can increase this type of water loss dramatically.
5. Immunity: in addition to barrier, specialized cells of epidermis are components of immune system.
6. Blood reservoir: vessels in dermis hold up to 10% of resting blood.
7. Vitamin D synthesis: UV radiation activates a molecule in skin that is precursor to vitamin D. The activated molecule is modified by enzymes in the liver and kidneys to produce vitamin D.

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Epidermis

First principle part of skin. Avascular (no blood vessels) epithelial tissue. Consists of 4 major cell types:
1. (keratinocytes): 90% of epidermis. Produce the protein keratin that helps waterproof skin.
2. (melanocytes): transfer skin pigment (melanin) to keratinocytes.
3. (Langerhans cells): interact with the helper T-cells of the immune system.
4. (Merkel cells): attach to sensory neurons and function in the sensation of touch.

Has five strata/layers. Deepest layer contains Merkel cells and stem cells, which continually divide to produce keratinocytes and other cells. Keratinocytes are pushed to the top layer and as they rise they accumulate keratin and die, losing their cytoplasm, nucleus and other organelles. When the cells reach the outermost layer of skin, they slough off the body (2-4 weeks). The outermost layer of epidermis consists of 25-30 layers of flat, dead cells.
Exposure to friction or pressure stimulates the epidermis to thicken, forming a "callus".

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Dermis

Second principle part of skin. Connective tissue derived from mesodermal cells. Embedded by blood vessels, nerves, glands, and hair follicles. Collagen and elastic fibers provide skin with strength, extensibility, and elasticity.
Thick in the palms and soles.

(integumentary system): composed of the skin, hair, nails, glands, and some nerve endings.

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Mendelian Ratio

3:1 phenotype ratio of the possible offspring of heterozygous parents.

298

Hybrid

An individual with a heterozygous genotype for a trait.

299

Law of Segregation

Alleles segregate independently of each other when forming gametes. Any gamete is equally likely to posses any allele.
AKA homologous alleles separate independently of each other and do not blend but show complete dominance.

300

Law of Independent Assortment

Genes located on different chromosomes assort independently of each other. AKA genes that code for different traits (ex: pea shape and pea color) when located on different chromosomes do not affect each other during gamete formation.

*if two genes are located on the same chromosome, the likelihood that they will remain together during gamete formation is indirectly proportional to the distance separating them -> the closer they are in the chromosome, the more likely they will remain together.

301

Inbreeding

Mating relatives; does not change the frequency of alleles but does increase the number of homozygous individuals within a population. Can increase the frequency of the expression of inherited recessive diseases.

302

Outbreeding

AKA outcrossing. The mating of non relatives; often produces hybrids or heterozygotes.

303

Barr Body

In most somatic cells of a female (2 X chromosomes) one of the X chromosomes will condense and most of its genes will become inactive, forming a tiny dark object. Formed at random, so the active allele is split about evenly among the cells.
-> in most cases, the recessive phenotype is still only displayed in homozygous recessive individuals.

304

Gene Pool

The total of all alleles in the population.
-> "evolution" is the change in the gene pool.

305

Classification System of Animals

Kingdom
Phylum
Class
Order
Family
Genus
Species
(plants and fungi use divisions instead of phyla)

Know the subphylum "Vertebrata" which is in the phylum "Chordata".
All mammals belong to the class "Mammalia" and the phylum "Chordata"
-> all mammals probably share a common ancestor that they do not share with birds, which are also in the phylum Chordata but in the class Aves.

*Taxonomy of humans: animalia, chordata, mammalia, primata, homididae, Homo sapiens.

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Domains

New superkingdoms.
1. Bacteria
2. Archaea
3. Eukarya

-> puts the kingdoms of Protista, Fungi, Plantae, and Animalia into the domain Eukarya.
-> makes the kingdom Monera obsolete, dividing it into the domains of Bacteria and Archaea.
-> the two domains of Bacteria and Archaea are divided into several kingdoms each.
-> Archaea is more closely related to Eukarya than is Bacteria.

*when naming an organism, the genus and species name are given in order (both italics, Genus capitalized).

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Species

Loosely limited to, but not inclusive of, all organisms that can reproduce fertile offspring with each other. AKA if two organisms can reproduce fertile offspring, they might be the same species; if their gametes are incompatible, they are definitely not the same species.

308

Survival of the Fittest

Predicts that one species will exploit the environment more efficiently, eventually leading to the extinction of the other within the same "niche". No two species can occupy the same niche indefinitely.

309

r-selection

Producing large numbers of offspring that mature rapidly with little or no parental care. Generally have a high brood mortality rate. Population growth curves are EXPONENTIAL. Generally found in unpredictable, rapidly changing environments affected by (density independent) factors such as floods or drastic temperature change.

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K-selection

Produces small brood size with slow maturing offspring and strong parental care. Population growth curves are SIGMOIDAL -> levels off at "carrying capacity" (density dependent factor).

Most organisms have reproductive strategies somewhere between K- and r-selections.

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Speciation

The process by which new species are formed, like when gene flow ceases between two sections of a population. Factors which bring about speciation include: geographic, seasonal, and behavioral isolation.

312

Adaptive Radiation

Occurs when several separate species arise from a single ancestral species, such as the 14 species of Galapagos finches that all evolved from one ancestor.

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Evolutionary Bottleneck

A species faces a crisis so severe as to cause a shift in the allelic frequencies of the survivors of the crisis.

314

Divergent Evolution

When two or more species evolving from the same group maintain a similar structure from the common ancestor.

315

Convergent Evolution

When two species independently evolve similar structures.
Ex: wings evolved by bats and birds which did not receive them from a common ancestor.

316

Polymorphism

The occurrence of distinct forms such as having either red or white flower color with no intermediate colors.

317

Symbiosis

A relationship between two species.
1. Mutualism: beneficial for both.
2. Commensalism: beneficial for one and doesn't affect the other.
3. Parasitism: beneficial for one and detrimental to the other.

318

Hardy-Weinberg Equilibrium

Statistically, there should be no change in the gene pool of a sexually reproducing population possessing the five following conditions:
1. Large population
2. Mutational equilibrium (rate of forward mutations = rate of backward mutations)
3. Immigration or emigration must not change the gene pool
4. Random mating
5. No selection for the fittest organism

No real population ever possesses these characteristics completely.

Binomial theorem predicts the genotype frequency of a gene with only two alleles in a population in H-W equilibrium.

p^2 + 2pq + q^2

"p + q = 1" since there are only two alleles.

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Genetic Drift

One allele may be permanently lost due to the death of all members having that allele. Not caused by selective pressure so the results are random in evolutionary terms.