Download Genetics Ch 2 [10-23

Genetics Ch 2 Notes
Basic cell biology: structure and function of genes and chromosomes
Genes, the basic unit of inheritance, are contained in chromosomes and consist of DNA
-each somatic cell contains 23 pair of chromosomes (46 total)
 1 set of 23 from mother; other from father; 1 pair of sex chromosomes
 other chromosome pairs are autosomes (are homologs—similar DNA)
 somatic cells are diploid-maintained by mitosis
 gametes are haploid (23 chromosomes)-generated via meiosis
DNA, RNA, and proteins: heredity at the molecular level
DNA
 Nucleotide (DNA subunit)=pentose sugar (deoxyribose), phosphate group, nitrogenous
base
 Bases: thymine, cytosine=pyrimidines (single ring); adenine, guanine=purines (double
ring)
 Watson and CrickDNA double helix model
 Sugar backbone held together w phosphodiester bonds; projecting bases “rungs of the
ladder” are held together via relatively weak hydrogen bonds
 BASES:

DNA coiling: wound around histone (140-150 BP w 20-60 BP spacer), forms
nucleosomehelical solenoid (each solenoid turn=~6 nuclosomes)solenoids org into
chromatin loops attached to protein scaffold (~100,000 [100 kilobases) BP/loop)
REPLICATION
 Begins as hydrogen bonds separatecomplementary strand built on single-strand
templateend result is 2 DNA helices each w one old and one “new” strand of nucleotides
 DNA polymerase: travels along template adding nucleotides to 3’ end of new strand; also
proofreads-can excise inappropriate base and add correct base (if this error
persists=mutation)
 REPLICATION ALWAYS 5’-3’; 5’=upstream, 3’=downstream
 Replication origins—many places along length of DNA where replication begins-many of
them=increased rate of replication; replication bubbles—resulting separations of DNA
hydrogen bonds
FROM GENES TO PROTEINS
 DNA replication-takes place in nucleus; protein synthesis-takes place in cytoplasm
 DNA is transcribed into mRNAmoves out of nucleus; mRNA is translated into proteins
 RNA is similar to DNA; sugar=ribose instead of deoxyribose; uracil replaces thymine; RNA
is usually SS (DNA usually DS)
TRANSCRIPTION
 Process by which an RNA sequence if formed from DNA template
 RNA pol II binds promoter; pulls portion of DNA strand apart; one strand will be template
(template determined by promoter sequence-orients pol II [synthesis ONLY 5’-3’)
 TEMLATE strand=ANTISENSE strand; pol II adds bases complementary to
antisense=sequence of the SENSE strand (strand opposite the template) except uracil in
place of thymine
 After RNA synth begins, 5’ end is capped by modified guanine (5’ cap-prevents RNA from
being degraded during synthesis; indicates starting position for translation)
 Transcription stops at termination sequence poly A tail addition to 3’ end (100-200
adenine nucleotides added) stabilizes mRNA (prevents breakdown in cytoplasm)
 mRNA separates from DNA; is primary transcript
*promoters can exist at several places within a gene-one gene sequence can code for
various proteins (depending where you begin transcription)
TRANSCRIPTION AND REGULATION OF GENE EXPRESSION
 Housekeeping genes-genes that are transcribed in all cells in the body; encode proteins for
cell maintenance and metabolism
 In most cells very few genes are transcribed—many cell types making different gene
products even though they have the same DNA (liver cells vs blood cells)
 General/basal and specific transcription factors-proteins that participate in transcription
 specific only act on certain genes at certain times
 RNA pol II-binds promoter but cannot find on its own or produce mRNA in mass quantities
on its own; general TF facilitate binding to promoter
 Enhancers: increase transcriptional activity of specific genes; can be far up or downstream;
enhancer is bound by specific TF (the activator)binds co-activator (second class of
specific TF)bind general TF complexacts on gene itself
 Silencers: act similarly to enhancers to silence/reduce transcription activity of specific
genes at specific times
 DNA binding motifs: allow TFs to locate specific DNA sequences; configurations in TF
proteins allowing them to fit snugly and stably into a unique portion of DA double helix
HMG (high-mobility group) of DNA-binding motifs: bend DNA to facilitate interxn btw
distant enhancer and appropriate basal TFs
The major classes of DNA-binding motifs found in TFs [Boxes in the Genetics book are money]
Motif
Description
Examples in Human disease
Helix-turn-helix
2 α helices connected by short chain of AA
(the turn); the carbonyl-terminal helix is
recognition helix that binds DNA major
groove
2 α helices (one short, one long) conn by
flexible loop allowing helices to fold back
and interact w one another; can bind DNA
or other helix-loop-helix structures
Zinc molecs used to stabilize AA
structures (ex α helices, β sheets) w
binding of α helix to DNA major groove
Helix-loop-helix
Zinc finger
Leucine Zipper
2 leucine rich α helices held together by
AA side chain; α helices form y-shape
whose side chains bind DNA major groove
Side chains extend forming 2-stranded β
sheet to form contacts w DNA helix
β Sheets




Homeodomain proteins (HOX genes);
mutations in human HOXD13 and
HOXA13=synpolydactyly and handfoot-genital syndrome, respectively
Mutations in TWIST gene cause
Saethre-Chotzen syndrome
(acrocephalosyndactyly type III)
BRCA1 (breast cancer gene); WT1
(Wilms tumor gene); GL13 (Grieg
syndrome); vit D receptor gene
(mutations=rickets)
RB1 (retinoblastoma gene); JUN and
FOS oncogenes
TBX family; TBX 5 (Holt-oram
syndrome); TBX3 (ulnar-mammary
syndrome)
Chromatin-combination of DNA and histone proteins
Euchromatin-open/decondensed chromatin; typically characterized by histone
acetylation (attachment of acetyl groups to lysine residues in histones)
 acetylation of histones reduces their affinity for DNAdecondenses
chromatin
 -euchromatin is transcriptionally active!
Heterochromatin-less acetylates; more condensed; txn-ally inactive
MicroRNA (miRNA): small RNA (17-20 nucleotides); NOT translated—can bind to
and downregulate specific complement mRNAs lowering their expression levels
GENE SPLICING
 Primary transcript is complementary to template (antisense)
 Sections of RNA are removed by nuclear enzymes; remaining sections spiced
together to form fcnal RNA
 introns: excised sequences; exons: sequences left to code for protein
 After gene splicing=mature transcriptcytoplasm
 Alternative splice sites: allow same primary transcript to be spliced different
waysdifferent protein products can come from the same gene
*replication errors, gene splicing errors=forms of mutation
THE GENETIC CODE
 Amino acidspolypeptidesproteins
 20 amino acids—AA sequence designated by DNA after transcription




Codons—base triplets specifying AA; correspondence btw codons and AA=genetic
code
Stop codons: UAA, UGA, UAG
Genetic code is degenerate: AA can be specified by more than one codon but one
codon does NOT specify more than one AA
Genetic code is universal (virtually the same In all organisms) EXCEPT mitochondria
TRANSLATION
 Process by which mRNA provides a template for the synth of polypeptides; mRNA
cannot directly bind AA—uses tRNA (cloverleaf shaped RNA strands ~80
nucleotides)
 tRNA: have 3’ attachment for AA (covalent bond); 3 nucleotide anticodon
(complementary BP w mRNA codon)
 -attached AA is transferred to polypeptide
 Ribosome: cytoplasmic site of protein synthesis; contains enzymatic proteins and
rRNA
 rRNA binds mRNA and tRNA to the ribosome
 Ribosome first binds the initiation side of mRNA—AUG (methionine—usually
excised)
 THEN tRNA binds to its surface (so BP can happen btw mRNA and tRNA)
 ribosome moves along mRNA seq in 5’-3’ direction
 Ribosome provides enzyme catalyzing formation of covalent peptide
bondspolypeptide
 Stop codon terminates translation
 amino terminus of polypeptide=5’ end of mRNA
 carboxyl terminus of polypep=3’end of mRNA
 Polypeptide released into cytoplasm
 Posttranslational modification
 cleavage into smaller polypeptide
 combination to form larger protein
 addition of carbohydrate side chains
*may be essential for proper folding
Clinical Commentary 2-1
Osteogenesis Imperfecta, an Inherited Collagen Disorder
-AKA “brittle bone disease”
-~90% are defects in type 1 collagen—major component of bone
acts as steel bars reinforcing concrete
-results in easy fracturesvery variable (hundreds of fractures over lifetime or just a few)
-other effects: short stature, hearing loss, abnormal tooth dev (dentiogenesis imperfect), blueish
sclerae, various bone deformities
-subtypes P 17 in textbook
Process of collagen 1 formation
-type 1 collagen: trimeric protein, triple helix structure; formed from type 1 procollagen
2 subunits from gene on chromosome 12; other from gene on chromosome 7
-mature mRNA moves to cytoplasm for posttranslational modification
-many proline and lysine residues (AA that has been incorporated into the polypep chain)
are hydroxylated (mutations in this step=OI type VII)
-3 polypeptides begin association at carboxyl ends—stabilized by sulfide bonds
-triple helix formation is zipper-like COOHNH2
-some hydroxylysines are glycosylated (via ER)
-hydroxyprolines form H-bonds; stabilize helix
**glycine at every 3rd position on each polypeptide=critical to proper folding
-once folding is finished, protein moves from ERgolgi (then is secreted from cell)
-formation of mature type 1 collagen molecule: cleavage of procollagen via protease near
the COOH and NH2 ends
-collagen assembled into fibrils, form covalent X-links
-common mutation: replace glycine w something else=severe forms of OI (v poor fibril formation)
The structure of genes and the genome
Figure 2.14
INTRONS AND EXONS
 Intron-exon structure (disc 1977) is major distinguishing factor btw prok and euk
 Introns are spliced out of mRNA before it leaves nucleus; under precise control
 Consensus sequences: direct enzymes for splicing to appropriate location (common in ALL
euk)
 consensus sequences are adjacent to each exon
 Speculated potential function of introns (fcn is unknown)
 by lengthening genes, they encourage shuffling during meiosis
 modify amount of time needed for replication and txn
 Some introns contain transcribed genes unrelated to the gene in which they’re contained
 introns in human neurofibromatosis type 1 (NF1) contains 3 genes transcribed in
the opp direction that are not functionally related to NF1
 Factor VIII (F8) gene on human X chromosome has similar inserts
TYPES OF DNA
 Only 1% of DNA is codes for protein; large amt transcribed into mRNA that does not make
protein
 Most genetic material has no known function
 Many classes of DNA
 Single-copy DNA
 usually seen only once (maybe a couple times) in genome
 ~45% of genome
 includes protein coding genes
 most single-copy DNA is in introns
 Repetitive DNA
 remaining 55% of genome
 repeated, often thousands of times, in genome
 2 classes: dispersed repetitive DNA and satellite DNA


dispersed repeats tend to be scattered singly throughout genome; do
not occur in tandem
 Short interspersed elements (SINEs)
 90-500 BP
 Alu repeats; ~300 BP; contain DNA sequence that can
by cut by Alu restriction enzyme; family of genes (all
have slightly similar DNA sequences); ~1 million
throughout genome; ~10% of all DNA
 Alu repeats can generate copies of themselves that can
insert in other parts of genome—if it interrupts a
protein-coding region, can cause genetic disease
 Long interspersed elements (LINEs)
 can be as large as 7000 BP
 some LINEs can generate copies of themselves that can
insert in other parts of genome—if it interrupts a
protein-coding region, can cause genetic disease
Satellite repeats are clustered together in certain chromosome
locations; tend to be in tandem
*because of their composition, satellite sequences can be easily
separated using centrifugation in cesium chloride density
gradient
*NOT the same as microscopic satellites on certain
chromosomes
 ~10% of genome and further subdivided
 α-satellite DNA=tandem repeats of 171 BP sequences
 found near centromeres of chromosomes
 extend several million BP or longer
 Minisatellites=blocks of tandem repeats 14-500 BP
 extend for a few thousand BP
 Microsatellites=1-13 BP long
 total length usually <100 BP
 *mini- and micro- satellites vary in length btw individuals;
used for gene mapping; one is found usually every 2kb and
they account for ~3% of genome
THE CELL CYCLE
 Development=single-celled zygote (egg fertilized by sperm)organism w 100 trillion cells
 Cell regeneration is imperative—few cells last a lifetime
 MITOSIS: cell division process creating new diploid cells from existing ones
 mitosis=nuclear division; cytokinesis=cytoplasmic division
 Interphase: time before division when cell duplicates its contents (cell spends most of life
here)
 Cell cycle: alteration of interphase and mitosis
 G1 (gap 1)—synthesis of RNA and proteins
 S (synthesis)—DNA replication
 G2 (gap 2)—some DNA repair, preparation for mitosis
*by the time cell reaches G2, cell has 2 identical copies of each of 46 chromosomes
 Sister chromatids: identical chromosome copies
 Sister chromatid exchange: sister chromatids often exchange genetic info during interphase



Different types of cells have different length of cell cycle—these variations are due to
length of G1
G0—stage when cells stop dividing for long period of time (terminal division) exs: skeletal
muscle cells and neurons
Cell division occurs in response to internal cues and environmental factors
 cells must respond to demand w increased or decreased rates of division
 cyclin dependent kinases (CDKs)—family of kinases that phosphorylate other
regulatory proteins at key stages of cell cycle (important molecules for regulation of
cell division)
 form complexes w various cyclins (proteins that are synth at specific cellcycle stages and are degraded when CDK action is no longer needed)
*cyclin and CDK malfunction can lead to cancer
Mitosis
-
requires only 1-2 hours for completion; divided into stages
Prophase
1.
2.
3.
4.
chromosomes condense and coil—become visible under light microscope
sister chromatids are attached at center point called centromere
nuclear membrane disappears
spindle fibers form and radiate from centrioles at the poles of the elongating
cell
5. spindle fibers become attached to centromeres (and eventually pull sister
chromatids in opposite directions-anaphase)
Metaphase
1. chromosomes reach their most condensed state (easiest visualization)
2. diagnosis of chromosome disorders usually based on metaphase
chromosomes
3. spindle fibers begin to contract, pulling centromeres f chromosomes
4. chromosomes arranged in middle of spindles on equatorial plane of cell
Anaphase
1. centromere of each chromosome splits; sister chromatids separate
2. chromosomes pulled, spindle first, along spindle fibers toward opposite
poles of cell
3. at end of anaphase, cell contains 92 chromosomes (one set at each pole)
Telophase
1. formation of new nuclear membranes around each of the two sets of 46
chromosomes
2. spindle fibers disappear
3. chromosomes begin to decondense
4. at completion, two diploid daughter cells (identical to parent cell) have been
formed
*cytokinesis usually occurs after nuclear division and results in ~equal distribution of cytoplasm
Meiosis
- primary mechanism by which haploid gametes are formed from diploid precursor cells
2 cell divisions occur
Meiosis 1—reductive division; two haploid cells (oogonia-female, spermatogoniamale) formed from one diploid
Meiosis 2—equatorial division; each haploid cell is replicated
Interphase 1 – replication of chromosomal DNA
Prophase 1 (key elements distinguishing mitosis from meiosis)
1. chromatin strands coil and condense, becoming visible
2. synapsis occurs-homologous chromosomes pair up side-by-side in perfect
alignment (except X-Y in male—they line up end to end)
3. chromatids intertwine forming bivalents (2 chromosomes) or tetrads (4
chromatids)
4. formation of chiasmata (plural; chiasma-singular)—each chiasma includes a
point where homologous chromosome exchange genetic material (crossing
over)
5. crossing over produces chromosomes that consist of combination of parts of
the original chromosomes
a. chromosomal shuffling is important for increasing combinations of
genes in each gamete and increases possible combinations of each
human trait
b. also important for inferring the order of genes along the chromosome
6. at end of prophase 1, bivalents begin to move toward equatorial plane,
spindle apparatus begins to form in cytoplasm, and nuclear membrane
disappears
Metaphase 1
1. completion of spindle formation
2. alignment of bivalents (still attached at chiasmata) in equatorial plane
3. centromeres of each bivalent lie on opposite sides of equatorial plane
Anaphase 1
1. chiasmata disappear
2. homologous chromosomes pulled by spindle fibers to opposite poles of cell
*centromeres to NOT divide and duplicate SO only half of the chromosomes
migrating twd each pole—ONE member of each pair of autosomes and ONE
of the sex chromosomes
Telophase 1
1. chromosomes reach opposite sides of cell
2. slight uncoiling of chromosomes
3. new nuclear membrane begins to form
4. in MALES: cytoplasm divided equally btw two cells; in FEMALES: nearly all
cytoplasm goes to one cell ,while the other cell becomes a polar body (small,
non functional cell that eventually degenerates)
Interphase II
1. very brief; NO genetic replication
Prophase II
1. similar to mitotic prophase except each cell is haploid
2. chromosomes thicken as they coil
3. nuclear membrane disappears
4. new spindle fibers formed
Metaphase II
1. spindle fibers pull chromosomes into alignment on equatorial plane
Anaphase II
1. centromeres split and each carries a single chromatid toward a pole of the
cell
2. chromatids now separated, but (bc of chiasma formation and cross-over) the
newly separated sister chromatids are probably not identical
Telophase II
1. chromosomes reach opposite poled of the cell
2. new nuclear membranes formed around each group of chromosomes;
cytokinesis occurs
3. in MALE gametes: cytoplasm equally divided; in FEMALE gametes: unequal
cytoplasmic division resulting in an egg cell and another polar body
*males produce 4 functional daughter cells w equal cytoplasm; female
produce 1 egg, and 2 or 3 polar bodies (polar body from meiosis 1 might
undergo another division)
-most chromosome disorders are result in meiosis; chomosome may be missing or have extra
chromosome or chromosome w/ altered structure
-early mitotic errors in development can cause significant disease
-mitotic errors at any point in ones lifetime can cancer
The relationship between mitosis and gametogenesis
Spermatogenesis
in mature males, seminiferous tubules of testes are populated by diploid spermatogonia
which undergo division to becomeprimary spermatocytes (diploid) which undergo
meiosis 1secondary spermatocytes (w 23 DS chromosomes) that undergo meiosis
IIspermatids (haploid) which lose most of their cytoplasm and develop tailssperm cells
Oogenesis
much of female oogenesis is completed before birth
- diploid oogonia divide mitoticallyprimary oocytes by 3rd month of fetal dev (6 million
oocytes formed during gestation)—these cells suspended in prophase 1 at birth;
meiosis continues only when a mature primary oocyte is ovulated; in meiosis 1, a
primary oocyte prodces1 secondary oocyte and one polar body; the secondary oocyte
emerges from follicle and proceeds down fallopian tube w attached polar body; IF
FERTILIZED you have meiosis IImature ovum and another polar body; polar bodies
degenerate; sperm and ovum fusediploid zygote which undergoes mitotic division
and becomes an embryo