Human Genome and Karyotype

3.2x10^9

# of base pairs of DNA in a haploid cell in our body

22,000

# of genes in the human genome

LTR, LINE, SINE

3 types of retrotransposons 1) ____ (long terminal repeats) similar to retrovirus insertions except lacking in envelope proteins required for forming infectious viral particles 2) ____ (long interspersed nuclear elements); mRNAs encoding reverse transcriptase; the only type of retrotransposon that is functional 3) ____ (short interspersed nuclear elements; copies of a short cellular RNA (<500bp); do not encode RT. Most common are Alu elements

nucleosome

DNA wrapped twice around 8 core histone proteins = a ____

genome size (C)

The amount of DNA contained in ONE copy of a genome aka the (___) value; (haploid cells/ germ cells). Diploid have 2 copies of this humans have 3.2 x 10^9 base pairs of DNA in each haploid cell of our bodies approximately 22,000 genes; protein coding portion and associated regulatory sequences

Robertsonian translocation

Translocation in which the long arms of two acrocentric chromosomes become joined to a common centromere, resulting in a chromosome with two long arms ; short arms often lost, but non-lethal (short arms of acrocentric autosomal chromosomes contain only genes for ribosomal RNA) rare, unbalanced. Breakpoints occur within the centromeres of acrocentric chromosomes with fusion of chromosomes and loss of p arms. Carrier has normal (balanced) phenotype. No loss of DNA from q arms. Short arms are often lost but is non-lethal. Are normal because have 2 normal copies, but when breed, pairing of homologous chromosomes will occur between 3 chromosomes- 2 normal and 1 translocation; meiosis of leads to genetic abnormalities

RNA, DNA

__ may be older than ____ (nucleic acids) first blank- may have preceded second in evolution. Is more complex and diverse in its functions (ribozymes can catalyze reactions), BUT second blank has more chemical stability (first blank is easy to degrade) and thus provides evolutionary advantages

genomic DNA

___ ___; primary coding sequence that every cell has. protein coding (transcribed into mRNA and then protein) regulatory (promoters, enhancers, etc); control transcription of RNA long non-coding (lnc); RNA transcribing ; don't code for protein, RNA of unknown function short non-coding RNA transcribing (tRNA, miRNA, etc) unknown function

repetitive sequences

___ ____ ; common in the human genome. often occur as "tandem repeats" (adjacent to one another) repeats - often where recombination occurs (due to similar or identical nucleotide sequence) increasing the chance of structural change in chromosomes. practical considerations- repeats are difficult to sequence; multiple reads of small segments of DNA needed types: large repeats, short repeats, retrotransposons

FISH, fluorescent in situ hybridization

___ aka ____ ___ ___ ____. a type of karyotyping technique chromatin or chromosomes are fixed to slide probe (~20bp long) binds to DNA of complementary sequence; fluorescently labeled limited to ~20pb long and must know sequence of probe. for smaller proteins faster on interphase cells (chromatin) (lower resolution because DNA not condensed; don't have address/ position that chromosomes can provide); can be done directly on clinical samples. Faster, often done on prenatal diagnosis vs. on chromosomes- requires cell culture to amplify number for incubation in colchicine but higher resolution; can give you location. used to identify common trisomies in fetus. Check right number in parent. Can tell normal number of chromosomes on gross level, doesn't tell if problems within. Can also use to look at entire chromosomes; Family of probes needed can identify DiGeorge syndrome but nothing less specific (ie small mutation or small deletion) ADVANTAGES AND DISADVANTAGES- detects alterations too small to be seen by G-banding, but requires a specific probe. Only detects presence/ absence/ position of DNA to which the probe binds. Must know the sequence or chromosome you are looking for. A normal result with one probe doesn't rue out a genetic defect elsewhere. Single probes detect presence of an exon or gene, but can't detect single nucleotide changes. Basket of probes can detect a single chromosome or region. Resolution decreases as number of probes increases. Whole-Chromosome FISH lacks the resolutionn of gene- or exon-specific probes.

37

___ known genes in mitochondria; have distinct DNA. NOT associated with chromosomes

red-green color blindness

___-___ ___ ____ ; because of large repeats; is caused by recombination between duplicated genes with almost identical sequence identity on the X chromosome. Have red receptor gene and green receptor gene on same chromosome; only 1 or 2 bp different between the two genes --> misalignment in meiosis follows by recombination; deletes one gene from the X chromosome if get an X with only a single receptor gene- inability to distinguish red/greed (colorblind male) ; have only one receptor- can't distinguish red from green / long from medium wavelength light. x with 1 red + 2 green receptor genes will be a normal male. in males because presumably normal other x in females. long wavelength = red, short = green

comparative genome hybridization, CGH

____ ____ ______ (____); a type of karyotyping technique is an array of oligonucleotides immobilized at different positions on a glass slid/ microarray, complementary to sequences spaced across genome. Compare PCR- amplified patient genome (test) DNA with reference genome (control) in ability to hybridize with oligonucleotides. Used to identify deletions and duplications. If yellow- equal, more red (or whatever standard labeled), deletion, if more green (or whatever test labeled), duplication. detects very small changes anywhere in the genome. Do NOT need to know where to look. BUT, only detects increases/ decreases in copy number; cannot detect rearrangements without gain or loss (translocations, inversions)

gene

____; a segment of DNA that includes protein coding and associated regulatory sequences

chromatin

____= DNA + histones; DNA in the nucleus is organized into. ; the state DNA usually exists in

karyotyping

______ techniques; techniques used for visual identification of chromosomes and to detect changes in their structure 1) G-banding; Giemsa staining creates pattern of dark and light bands unique to each chromosome 2) Fluorescent in situ hybridization (FISH); detects changes in chromosome structure too small to see by G-banding. LOCATION MUST BE KNOWN TO DESIGN PROBE 3) comparative genomic hybridization (CGH); detects deletions or duplications EVEN IF LOCATION IS NOT KNOWN; uses microarray approaches

Idiograms

a depiction of the spread of human chromosomes. Aligned from large to small with sex chromosomes displayed separately (from g-banding) can also align by centromere

G-banding

a type of karyotyping technique ; Giemsa staining creates a pattern of dark and light bands unique to each chromosome cells incubated with colchicine (binds tubular, prevents spindle formation, arrests cells in metaphase) (isolated from mitotically active source); lymphocytes, fibroblasts, aminocqytes, placenta, bone marrow, etc. chromosomes condense steadily during prolonged metaphase. With time, the number of cells in mitosis increases but the number of visible bands decreases staining with Giemsa dye heterochromatic regions (tightly packed- may contain fewer genes) are enriched for A-T nucleotides; stain more darkly (vs C-G that stain less darkly) standard karyotype- 500-800 bands per haploid set of chromosomes chromosomes can be identified by 1) size (1 largest, 22 smallest), 2) centromere position, 3) banding pattern centromere contains repetitive satellite DNA (low AT content, appear light) can use these karyotypes to determine deletions in some chromosome (align chromosomes based on centromeres and size, can see if a part is missing) ; ID ABNORMALITIES IN GENE THAT CONSIST OF MANY GENES. detects only large changes in chromosome structure (but irregardless of its nature/ location), lower resolution limit is one band, 500-800 bands for metaphase G-banding. 1 band = 4-7Mb, 45 of so genes. Each chromosome has on average ~1000 genes. To detect smaller changes, FISH or CGH required.

large repeats

a type of repetitive sequence ____ ____; divergence of ___ ___ (same ) sequences over time;. recent repeats have > 90% sequence identity vs. older where have more differences recombination is more likely between THESE sequences recombination can occur between widely diverse chromosomal regions on same chromosome or between chromosomes recombination can cause inversions, duplications, or deletions depending on the position and orientation of the repeats examples of recombination of ____ ___ (same) leading to disease - red-greed color blindness, Rh-factor, velocardiofacial syndrome, hemophilia A

short repeats

a type of repetitive sequence satellite sequences- tandem repeats of sequences of a few hundred base pairs long. Hundreds to thousands of copies in genome. Mostly found at centromeres and telomeres; may have structural role in chromosome organization microsatellites- repeats of a few nucleotides like (CA)n dinucleotides. Copy number (n) highly variable. Can be used to identify specific chromosomes because often each of the four parental copies will be different; run separately than the DNA in the sample.

translocation, inversion, duplication, deletion

abnormalities of chromosome structure: ______; genetic material moved from one chromosome to another ; can be reciprocal (2 chromosomes exchange segments) or non-reciprocal : movement of DNA from 1 chromosome to another ____; segment of DNA inverted with respect to the rest of the chromosome: ABcdeFG --> ABedcFB ___ or ____ of part of a chromosome causes of these chromosome alterations- errors in cell division (meiosis/ mitosis), maternal age >35 years old, environmental factors (mutagens, ionizing radiation)

chromatids, centromere

after DNA is replicated chromosomes form a pair of sister ____ that are attached by the _____ visible in cell division

contiguous gene syndrome

aka micro deletion or segmental aneuploidy syndromes large blocks of DNA deleted, repeated etc. Recombination occurs between LARGE REPEATS resulting in deletion of a block of DNA that contains multiple genes. diagnosis by FISH with probe for deleted region. examples- DiGeorge/ Velocardiofacial syndrome: del22q11. Failure of pharyngeal pouches to develop; parathyroid, thymus, cardiac defects. Also trader-willi and angeman syndromes (del 15q11-13)

translocation

an abnormality of chromosome structure where genetic material moved from one chromosome to another ; can be reciprocal (2 chromosomes exchange segments) or non-reciprocal : movement of DNA from 1 chromosome to another most common between acrocentric autosomal chromosomes. extra chromosomes usually do not survive. Short p arms of these chromosomes contain only genes for ribosomal RNA considered balanced if no genetic material is lost or gained; or no signitifanct phenotype arises. designated by t(1;3) ; the 2 chromosomes affected. ex- 46, XY, t(1;3)(q31;q24) robertsonian- ; rare, unbalanced. Breakpoints occur within the centromeres of acrocentric chromosomes with fusion of chromosomes and loss of p arms. Carrier has normal (balanced) phenotype. No loss of DNA from q arms. Short arms are often lost but is non-lethal. Are normal because have 2 normal copies, but when breed, pairing of homologous chromosomes will occur between 3 chromosomes- 2 normal and 1 translocation; meiosis of leads to genetic abnormalities

yes, no

are mitochondria's DNA distinct? ____ are mitochondria's DNA associated with chromosomes? mitochondria DNA inherited solely from the mother (male mitochondria destroyed as sperm enters egg during fertilization)

metacentric, sub-metacentric, acrocentric

centromere position differs among chromosomes _____; centromere in middle of chromosome (but still have p and q arms) ___-____ ; centromere more differentially distributed ; higher up; smaller p but not super small _____ ; highly lateralized distribution; very small p, large q also telocentric where centromere at end of chromosome, but do not exist in humans.

chromosomes

chromatin (DNA+ histones) condenses into _____ during the prophase of mitotic cell division (after replication) visible only in cell division

outward

chromosome bands and numbering; chromosomes numbered on each arm ____ from the centromere divided with increasing resolution (second or 3rd number are subsets of the larger number that precedes (on left))

variations

common genome _____ in humans DNA sequence (genome) variations are responsible for both benign differences and some disease states among individuals types: single-nucleotide polymorphisms: A/T vs. G/C; single base pair substitution; many of benign (degenerate) but some have big change in. structural changes: few to millions of bp in size insertions and deletions: aka indels; even small change in sequence will affect protein. GcatT vs GT block substitutions GcatT vs. GttaT inversions: GcatT vs. GtacT copy number variations; small and large- varies from 3-14 tandem copies; may or may not affect protein function; GcatT vs. GcatcatT. Example - alpha amylase ___ ____

AT

dark staining in G-banding due to high ___ content

genes

differentiation and diversification of cell types occurs during embryogenesis. This process involves controlling which ___ are turned on and which are turned off. control expression of ___ (same) ; only a subset of genome expressed in each cell (depending on function of that cell) , but entire genome in nucleus of each cell. Expression depends on function. Development controls this process

chromosomes

during mitosis, DNA is packaged into _____ . Humans have 22 PAIRS of autosomal ____ (same) and 2 sex ____ (x or y) ; 46 in total

increases

genome size generally ____ (increases/ decreases) with an organisms complexity EXCEPT; the C-value enigma; wide variations exist between genome size and organism complexity.

junk, finely tuned

human genome does not consist of ____, but also does not consist of a ___ ___ genome.

dark, light

in g-banding regions with high AT content stain ____ ; pack more tightly; may contain fewer genes in g-banding regions with less AT content, stain _____

duplication, incorporation

increased genome complexity / size arises by 2 basic mechanisms 1) _____ (partial or whole); of existing sequences followed by divergence and selection; example- multigene families are common components of all genomes. Selected pressure may preserve as new. Proteins that are closely related to each other 2) ____ of DNA from other species (lateral transfer) ; viruses, bacteria (mitochondira/ chloroplasts); record of many of our past ancestor's diseases in our genome.

pericentric inversion

inversion that includes the centromere (one chromosome) vs. paracentric inversion where both breakpoints are in the SAME arm

visual, structure

karyotyping techniques techniques used for ____ identification of chromosomes and to detect changes in their ____ G-banding, FISH, comparative genomic hybridization (CGH)

retrotransposons

mobile DNA elements DNA --> RNA --> dscDNA by reverse transcriptase and reintegration of the DNA back into genome in new location. self-amplifying gene sequences account for up to 40% of the human genome ; they are preserved- unclear why. likely derived from past retrovirus infections; reverse transcriptase activity preserved. Only LINEs (type of these) thought to be active in humans, the rest tend to be inactive relation to disease- insertion of reverse-transcribed RNA into DNA can disrupt a gene at integration site 3 types- 1) LTR (long terminal repeat); similar to retrovirus insertions except lacking in envelope proteins required for forming infectious viral particles 2) LINE- long interspersed nuclear elements: mRNA's encoding reverse transcriptase; only one that is functional; encode reverse transcriptase 3) SINE; short interspersed nuclear elements; copies of a short cellular RNA (<500bp); do not encode RT. Most common are Alu elements.

C-value enigma

size of genome generally increases with an organisms complexity, EXCEPT wide variations exist between genome size and organism complexity; single celled protists bigger than humans

21

smallest human chromosome = chromosome ____

p arm

the __ ___ is the short arm of a chromosome

q arm

the ___ ___ is the long arm of a chromosome

ENCODE

the ___ project; found which elements of the genome are functional 21,000 protein-encoding genes but at least 70,000 promoters and 400,000 enhancers; regulatory elements direct the expression of the 21,000 genes. 60-75% of genome is transcribed into RNA ; only a subset of this goes to protein. Non-Coding transcripts, many predicted to have regulatory roles, are NEARLY AS ABUNDANT AS PROTEIN-ENCODING GENES not all regulatory regions are active in a given cell type; gene expression is different in different cells. Regulatory sequences control. ~80% of genome is functional; protein-encoding and "non-coding regions"; non-coding at least as important as protein-encoding long range influences over gene expression can be important in disease

ploidy

the number of each type of chromosome present; does not strictly correlate with genome size or complexity sperm are haploid (1N), with one copy of each chromosome. zygotes and somatic cells are diploid (2N) with 2 copies of each chromosome. In diploid cells, the 2 copies of each chromosome are homologues and form a homologous pair. One maternal, one paternal. Carry same genes in same order, but not necessarily identical alleles. Diploid with 2 maternal or 2 paternal chromosome sets not viable euploidy- normal number of chromosomes; 22 pairs of autosomes and one pair fo sex chromosomes aneuploidy- extra or missing chromosomes ; arise during meiosis. Missing chromosome (MONOSOMY (2N-1), extra chromosome (TRISOMY)(2N+1). Aneuploidy for most chromosomes is lethal. Exceptions- X,Y, trisomy for a few small autosomes, Down syndrome (trisomy 21) triploidy- 3N; 2 sperm fertilize one egg --> 3 complete chromosome sets; lethal

cytogenics

the study of the number and structure of chromosomes about 1.5% have an abnormality of chromosome number or structure should consider a diagnosis of chromosome abnormality when- - problems with physical or mental development of a fetus or child (congenital problems) - infertility, spontaneous abortion, stillbirth (especially if repeated) - pregnancy in a woman 35 years of age or older; accumulate abnormalities in chromosome number/ structure in germ line over life - cancer

centromere

when identifying abnormal chromosome identity, the number of chromosomes = the number of centromeres. The identity of a chromosome = told by the identity of its ______