The Central Dogma:

| Ch. 12 - The Cell Cycle | | Ch. 16 - The Molecular Basis of Inheritance | Ch. 6 - A Tour of the Cell | Ch. 17 - From Gene to Protein

Ch. 12 - The Cell Cycle

Must Know:
- structure of replicated chromosome
- stages of mitosis
- kinases and cyclin in regulation of cell cycle

Cell Cycle:
- life of cell from formation to its own division

- a cell's endowment of DNA
- must be duplicated before division

- eukaryotes have characteristic number of chromosomes, ex. humans have 46

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Sister Chromatids
- duplicated chromosome
- identical DNA
- attached by a centromere
- in cell division, separate and mote into new cells

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- division of the cell's nucleus

- division of the cell's cytoplasm
- in plant cells, cell plate forms
- in animal cells, cleavage furrow forms

Primary Events of Interphase (90% of cell cycle)

G1 Phase:
- cell grows while carrying out cell functions

G1 Phase Checkpoint:
- most important
- if gets go ahead signal, completes whole cell cycle and divides
- if not, enters nondividing phase called G0 Phase

S Phase:
- continues function
- duplicates chromosomes

G2 Phase:
- after chromosomes have been duplicated
- just before mitosis

- protein enzymes that control cell cycle
- active only when connected to cyclin proteins
- cyclin-dependent kinases (cdk)
- give go-ahead signals at G1 and G2 checkpoints

Key Characteristics of Cell Division:

1. Density-Dependent Inhibition
- crowded cells stop dividing

2. Anchorage Dependency
- normal cells must be attached to a substratum, like extracellular matrix of a tissue, to divide

- cancer cells exhibit neither

- process that changes normal cell to cancer cell

- mass of abnormal cells
- benign if remains at original site
- malignant if invasive enough to impair functions of organs

- when cancer cells enter blood or lymph vessels

Ch. 16 - The Molecular Basis of Inheritance

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Double Helix:
- twisted ladder with rigid rungs
- backbone made of sugar-phosphate
- rungs made of pairs of nitrogenous bases

Nitrogenous Bases:
- adenine and thymine
- guanine and cytosine

- right side is in reading position, left side upside down
- reading position - 5' to 3'
- opposite strand - 3' to 5'
- always antiparallel, whether DNA/DNA, DNA/RNA, RNA/RNA

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- double ring, pairs with pyrimidine
- adenine, guanine

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- single ring, pairs with purine
- thymine, cytosine

- thymine and adenine have double hydrogen bonds
- guanine and cytosine have triple hydrogen bond

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- making of DNA from existing DNA strand
- semiconservative: each daughter molecule has one old, one new strand
1. begins at sites called origins of replication
2. initiation proteins bind to origin of replication, separate two strands, form replication bubble, replication proceeds in both directions along DNA strand
3. group of enzymes called DNA polymerases catalyze elongation of new DNA at replication fork
4. DNA polymerase adds nucleotides one by one in 5' to 3' direction
5. replication occurs continuously on 5' to 3' leading strand, copied in segments on 3' to 5' lagging strand
6. lagging strand synthesized in separate pieces called Okazaki fragments, sealed together by DNA ligase

Accuracy of DNA replication:
- base pairing, A-T, G-C
- mismatch repair, repair enzymes fix incorrectly paired nuceotides
- nucleotide excision repair, incorrectly placed nucleotides are excised by enzymes called nucleases, gap filled with correct nucleotides
- telomeres, short repetitive nucleotide sequences that do not contain genes, cap chromosomes to avoid losing terminal genes, since tip of chromosome is removed when replicated

DNA Replication Terms:

DNA Ligase - linking enzyme essential for DNA replication, catalyzes covalent bonding fo 3' end of new fragment to 5' end of growing chain

DNA Polymerase I - catalyzes elongation at replication fork, removes RNA primer from lagging strand and replaces with nucleotides of Okazaki fragments

DNA Polymerase III - catalyzes elongation at replication fork, adds nucleotides to 3' end of DNA or RNA primer

Helicase - untwists double helix at replication forks

Nuclease - team of enzymes that DNA and RNA into component nucleotides, involved in nucleotide excision repair

Primase - enzyme that joins RNA nucleotides to make primer

Primer - already existing RNA chain bound to template DNA to which DNA nucleotides are added

Single Strand Binding Protein (SSBP) - molecules line up along unpaired DNA strands, holding them apart during replication

Telomerase - catalyzes lengthening of telomeres

Telomere - protective structure at end of eukaryotic chromosome, random repetitive DNA at end of DNA molecule

Topoisomerase - helps relieve strain from untwisting of DNA strands in front of helicase

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- as DNA becomes more packaged, less accessible to transcription enzymes, reducing gene expression
- in interphase, chromatin in highly extended euchromatin, available for transcription
- heterochromatin, more condensed, inaccessible, not transcribed, ex. barr bodies

- DNA and protein packed together in eukaryotic cells

- 10nm fiber
- DNA and proteins called histones form "beads on a string"
- eight histone molecules
- basic unit of DNA packaging

Chromatin Fiber:
- 30nm
- string of nucleosome coils
- form seen during interphase

Looped Domains:
- 300nm
- seen during prophase
- loops attached to scaffold of nonhistone proteins

Metaphase Chromosome:
- maximally compacted chromosome
- two sister chromatids

Ch. 6 - A Tour of the Cell

Must Know:
- prokaryotic vs. eukaryotic cells
- structure/function of organelles in plant and animal cells
- structure/function of organelles exclusive to either

Plasma membrane
Cytosol w/ organelles
1-10 micrometers
10-100 micrometers
Internal Membranes

Prokaryotic Cells:
1. chromosomes grouped in nucleoid region, no nuclear membrane, no true nucleus
2. no membrane-bound organelles in cytosol (ribosomes not membrane-bound)
3. much smller than eukaryotes

Eukaryotic Cells:
1. membrane enclosed nucleus contains chromosomes
2. membrane-bound organelles in cytoplasm
3. much larger than prokaryotes


Animal Cells Only
Plant Cells Only
- lysosomes
- centrioles
- flagella (in some plant sperm)
- chloroplasts
- central vacuole and tonoplast
- cell wall
- plasmodesmata

Plasma Membrane:
- boundary of cell
- selectively permits materials into/out of cell
- made of phosphilipids, proteins, carbohydrates

- contains most of DNA
- control center of cell
- large relative size
- double membrane called nuclear envelope
- nuclear pores control what enters/leaves

- region of nucleus where ribosomal RNA (rRNA) complexes with proteins to form ribosomal subunits

- sites of protein synthesis
- large and small subunit
- floating free in cytosol (making proteins for use within cell) or bound to rough ER (proteins for export or cell membranes)

Endoplasmic Reticulum (ER):
- more than half of total membrane structure
- network of membranes and sacs, internal area called cisternal space
Smooth ER:
- synthesis of lipids, metabolism of carbohydrates, detoxification of drugs and poisons
Rough ER:
- associated ribosomes make it appear rough
- synthesize proteins secreted by cell
- polypeptide chains travel into cisternal space to be concentrated before moving to the Golgi apparatus

Golgi Apparatus:
- "postal system"
- proteins modified, stored, shipped
- flattened sacs of membranes, cisternae, arranged in stacks
- polarity, cis face receives vesicles, trans face ships vesicles

- cellular respiration
- ATP created
- "powerhouses" of cell

- metabolic functions, transfer of hydrogen from compounds to oxygen
- break down fatty acids
- detoxify alcohol

- network of protein fibers running through cytoplasm
- supporty, motility, regulating some biochemical activities
- made of microtubules, microfilaments, intermediate filaments

- near nucleus, where microtubules grow
- contain centioles in animal cells

- membrane bound sacs of hydrolytic enzymes
- digest large molecules: proteins, polysaccharides, fats, nucleic acids

- projections that increase cell's surface area

- long, few in number
- propel unicellular eukaryotic cells through water
- made of mcirotubules

- shorter, more numerous
- move fluid ofver surface of tissue
- used in locomotion

Extracellular Matrix (ECM):
- strengthens tissues, can turn genes on

Central Vacuoles:
- storage and breakdown of waste products
- as much as 80% of cell in plant cells
- tonoplast encloses central vacuole

- sites of photosynthesis

Cell Wall:
- protects plant, helps maintain shape
- made of cellulose

- channels that perforate adjacent plant cell walls
- allow passage of molecules from cell to cell

Ch. 17 - From Gene to Protein

Must Know:
- gene expression, transcription, translation
- how eukaryotic cells modify RNA after transcription
- how point mutagens can change the amino acid sequence of a protein

Gene Expression:
- process by which DNA directs synthesis of proteins

One Gene-One Polypeptide Hypothesis:
- each gene codes for a polypeptide, which can be or be part of a protein

- synthesis of RNA using DNA as template

Messenger RNA (mRNA):
- produced during transcription
- carries genetic message to ribosome, the protein-maker

RNA Processing:
- in eukaryotes, pre-mRNA processed to yield final mRNA
- in prokaryotes, transcription results directly in mRNA, processing not necessary

- production of polypeptide chain using mRNA transcript
- occurs in ribosomes

Triplet Code:
- series of three-nucleotide groups that code for polypeptide chain