Final Flashcards by caitlin quave

four criteria necessary for genetic material:

information
replication
transmission
variation

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building blocks of DNA and RNA; covalently bonded

nucleotides

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linear polymer strand of DNA and RNA

strand

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two strands of DNA

double helix

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DNA associated with an array of different proteins into a complex structure

chromosomes

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complete complement of genetic material in an organism

genome

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formed from nucleotides (A, T, C, G)
nucleotides composed of three components: phosphate group, pentose sugar, and nitrogenous base

DNA

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adenine (A) and guanine (G)

purine

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cytosine (C) and thymine (T) and uracil (U)

pyrimidines

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formed from nucleotides (A, G, C, U)

RNA

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phosphate group links two sugars

phosphodiester bond

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formed from phosphates and sugars

DNA backbone

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proposed the structure of DNA double helix (1953)
- used Paulings method of ball and stick model
- Franklins x-ray diffraction results were crucial

Watson and Crick

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analyzed base composition of DNA from many different species
- A=T
- C=G

Chargoff (base pairing)

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features of DNA (7 total)

double stranded
antiparallel strands
right handed helix
sugar phosphate backbone
bases on inside
stabilized by H bonding
specific base pairing

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proteins bind to affect gene expression

major groove

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narrower

minor groove

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DNA replication produces DNA molecules with 1 parental strand and 1 newly made daughter strand

semiconservative mechanism

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DNA replication produces 1 double helix with both parental strands and the other with 2 new daughter strands

conservative mechanism

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DNA replication produces DNA strands in which segments of new DNA are interspersed with the parental DNA

dispersive mechanism

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conclusion: semiconservative DNA replication
- uses nitrogen in light and heavy forms

Meselson and Stahl experiment

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two parental strands separate and serve as template strand
new nucleotides must obey the AT/GC rule
end result: two new double helices with same base sequences as original

DNA replication

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provides an opening called a replication bubble that forms two replication forks
- bacteria have single origin
- eukaryotes have multiple origins

origin of replication

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binds to DNA and travels 5’ to 3’ using ATP to separate strands and move fork forward (protein necessary for replication)

DNA helicase

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relives additional coiling ahead of replication fork (protein necessary for replication)

DNA topoisomerase

keep parental strands open to act as template (protein necessary for replication)

single strand binding protein

- covalently links nucleotides - deoxynucleoside triphophates - can't begin synthesis on a bare template strand (requires primer, DNA primase makes primer from RNA, RNA primer is removed and replaced with DNA later) - only works 5' to 3'

DNA polymerase

- free nucleotides with three phosphate groups - breaking covalent bond to release pyrophosphate (two phosphate) provides energy to connect nucleotides

deoxynucleoside triphosphate

- DNA synthesized as one long molecule - DNA primase makes a single RNA primer - DNA polymerase adds nucleotides in a 5' to 3' direction as it slides forward

leading strand

- DNA synthesized 5' to 3' but as Okazaki fragments - Okazaki fragments consist of RNA primers plus DNA

lagging strand

covalently attaches adjacent Okazaki fragments in the lagging strand (protein involved in replication)

DNA ligase

synthesizes short RNA primers (protein involved in replication)

DNA primase

three mechanisms of accuracy (replication):

1. hydrogen bonding between A and T and G and C is more stable than mismatched combinations 2. active site of DNA polymerase is unlikely to form bonds if pairs mismatched 3. DNA polymerase can proofread to remove mismatched pairs

multiple subunits, responsible for majority of replication

DNA polymerase III

single subunit, rapidly removed RNA primers and fills in DNA

DNA polymerase I

DNA repair and can replicate damaged DNA

DNA polymerases II, IV, and V

makes RNA primers and synthesizes short DNA strand

DNA polymerase alpha

replicates the mitochondrial DNA

DNA polymerase gamma

displaces DNA polymerase alpha and then replicates DNA at a rapid rate

DNA polymerase delta and epsilon

- series of short nucleotide sequences repeated at the ends of chromosomes is eukaryotes - specialized form of DNA replication only in eukaryotes - at 3' does not have a complementary strand and is called 3' overhang

telomeres

- DNA wrapped around histones to form nucleosome - shortens length of DNA molecule 7 fold

DNA wrapping (DNA compaction)

- current model suggest asymmetric, 3D zigzag of nucleosomes - shortens length another 7 fold

30 nanometer fiber (DNA compaction)

not as compact (preparing to divide)

euchromatin

much more compact (preparing to divide)

hetrochromatin

- interaction between 30 nanometer fibers and nuclear matrix - each chromosome located in discrete territory

radial loop domain

-wildtype: can grow on minimal medium - mutant strains: unable to grow unless supplemented with specific substances - conclusion: supports one gene, one enzyme

Beadle and Tatum

- produces a transcript (RNA copy) of a gene - messenger RNA (mRNA) specifies the amino acid sequence of a polypeptide

transcription

process of synthesizing specific polypeptides on a ribosome using the mRNA template

translation

organized unit of base sequences that enables a segment of DNA to be transcribed into RNA and ultimately results in the formation of a functional product

gene

translates mRNA into amino acids - cloverleaf structure - anticodon - acceptor stem for amino acid binding

transfer RNA (tRNA)

part of ribosomes

ribosomal RNA (rRNA)

transcription stage 1 - recognition step - in bacteria: sigma factor causes RNA polymerase to recognize promoter region - stage completed when DNA strands separate near promoter to form open complex

initiation (transcription)

transcription stage 2 - RNA polymerase synthesizes RNA - template or coding strand used for RNA synthesizes (noncoding stand is not used) - synthesized 5' to 3' and DNA template strand reads 3' to 5' - uracil substituted for thymine

elongation (transcription)

transcription stage 3 - RNA polymerase reaches termination sequence - causes both the polymerase and newly made RNA transcript to dissociates from DNA

termination (transcription)

transcribes mRNA - requires 5 general transcription factors to initiate transcription

RNA polymerase II

transcribes nonstructural genes for rRNA and tRNA

RNA polymerase I and III

transcribed but not translated - found in many eukaryotic genes

introns (RNA modification)

coding sequence found in mature mRNA

exons (RNA modification)

removal on introns by splicing - composed of snRNPs (small nuclear RNA and proteins)

spliceosome (RNA modification)

-modified guanosine attached to 5' end - needed for mRNA to exit nucleus and bind ribosome

capping (RNA modification)

-100 to 200 adenine nucleotides added to 3' end - increases stability and lifespan in cytosol - not encoded in gene sequence

poly A tail (RNA modification)

splicing can occur more than one way to produce different products

alternative splicing

sequence of bases in an mRNA molecule

genetic code

more than one codon can specify the same amino acid

degenerate code

- catalyzes attachment of amino acids to tRNA - reactions results in tRNA with amino acid attached

aminoacyl tRNA synthase

-mRNA, first tRNA and ribosomal subunits assemble - requires help of ribosomal initiation factors - also requires input of energy (GTP hydrolysis)

initiation (translation)

synthesis from start codon to stop codon

elongation (translation)

complex disassembles at stop codon releasing the completed polypeptide - 3 stop codons: UAA, UAG, UGA - release factor binds to stop codon at the A site - bond between polypeptide and tRNA hydrolyzed to release polypeptide

termination (translation)

- ribosomal binding sequence helps the mRNA binds to small ribosomal subunit - initiator tRNA recognizes the start codon, a few nucleotides downstream - large ribosomal subunit associates - at the end the initiator tRNA is in the P site

initiation in bacteria (translation)

two differences: - instead of ribosomal binding sequence, mRNAs have guanosine cap at 5' end (recognized by cap binding proteins) - position of start codon more variable (first AUG codon used as start codon)

initiation of eukaryotes (translation)

step 1 - aminoacyl tRNA brings a new amino acid to the A site - binding occurs due to codon/anticodon recognition - elongation factors hydrolyze GTP to provide energy to bind tRNA to A site - peptidyl tRNA is in the P site - aminoacyl tRNA is in the A site

elongation step 1 (translation)

step 2 - peptide bond is formed between the amino acid at the A site and the growing polypeptide chain - polypeptide is removed from the tRNA in the P site and transferred to the amino acid at the A site - called the peptidyl transfer reaction - rRNA catalyzes peptide bond formation (the ribosome is a ribozyme)

elongation step 2 (translation)

step 3 - movement or translocation of the ribosome toward the 3' end of the mRNA by one codon - shifts tRNAs at the P and A sites to the E and P sites - the next codon is now at the A spot - uncharged tRNA exits from E spots

elongation step 3 (translation)

process where gene is turned on and information used to make a protein

gene expression

process controlling which genes are turned on or off (timing, amount)

gene regulation

genes that are turned on constantly (metabolic genes)

constitutive genes

- repressor binds to operator - RNA polymerase can't read operon genes

lactose absent

- allolactose binds to repressor - repressor comes off operator - RNA polymerase can start reading operon genes

lactose present

- repressible - small effector molecule (Trp) turns the operon off - positive control: when low- turn on genes, when high- turn off genes

Trp operon

- add methyl group to cytosine base - block transcription or attract protein complex to block transcription

methylation

- changes in gene expression - heritable in daughter cells - does not change DNA base sequence - DNA methylation - chromatin remodeling - x chromosome inactivation - maternal or paternal gene silencing

epigenetic changes

regulatory segments of RNA - small - binding will prevent mRNA from being translated

RNA interference (RNAi)

- mRNA in inactive state present at all times - IRP (iron regulatory protein) prevents translation

ferritin protein

change a specific nucleotide

point mutation

add or remove nucleotides

insertion or deletion

duplications, translocations, inversions

chromosomal changes

no change in amino acid sequence

silent

- changes a single amino acid - may or may not change protein

missence

changes codon to stop codon

nonsense

-insert or delete nucleotide - change all downstream amino acids

frameshift

can be passed to offspring

germ line mutations

- inherited by all daughter cells - depending on the type of mutation (silent, missense, nonsense, frameshift) it may or may not have an effect on the cell

somatic cell mutation

- resulting from normal cellular processes - DNA polymerase - reactive molecules - spontaneous changes in the structure of molecules

spontaneous mutation

- resulting from environmental damage - chemical and physical

induced mutation

agents chemical or physical that create mutations

mutagens

normal proof reading functions - direct repair (DNA polymerase) - base excision and nucleotide excision repair - methyl directed mismatch repair

DNA repair

- grow slowly - do not spread to other tissues in the body

benign tumor growth

- grow rapidly - invade other tissues - locally invasive: invade surrounding tissues - metastatic: send cells to other parts of the body

malignant tumor growth

hallmarks of cancer cells (six total):

1. self sufficiency in growth signals or response 2. insensitivity to growth inhibitory signals 3. evasion of programmed cell death 4. limitless reproductive potential 5. sustained angiogenesis 6. tissue invasion and metastasis

mutants form of normal proteins that control cell division (growth factors, receptors, transduction protein)

oncogenes

step 1: isolate the vector, identify gene of interest step 2: use restriction enzymes (cut vector DNA, isolate gene of interest)

recombinant DNA technology

separate macromolecules - DNA - protein - other organic molecules separation based on: - size - charge

gel electrophoresis

bacteria that have been transformed with vectors containing fragments of a genome

gene libraries

another way to amplify specific genes or regions of DNA - step 1: heat DNA to separate (denature) DNA - step 2: add primers and cool, primers will bind to specific sites - step 3: add taq polymerase, primers serve as starting points for DNA replication

polymerase chain reaction (PCR)

- use restriction enzymes to cut up entire genome - match overlapping regions

gene mapping

- DNA polymerase makes complementary DNA - use ddNTPs to color specific nucleotides

gene sequencing

- reproduction of cells - highly regulated series of events - 2 types of eukaryotes (mitosis, meiosis)

cell division

cells engage in their metabolic business

G1 (interphase)

time of synthesis (DNA replication)

S (interphase)

cell makes proteins that will drive cell division

G2 (interphase)

tangled mass of threadlike DNA in a nondividing cell

chromatin

condensed DNA molecules observed in dividing cells

chromosomes

cells have two (a pair) of each type of chromosome

diploid (2n)

cells have half the diploid number of chromosomes

haploid (1n)

chromosomes with the same length, shape, and set of genes; each individual receives one from their mother and one from their father

homologous chromosomes

each chromosome makes an exact copy of itself during the S phase of the cell cycle; these copies remain attached to one another

sister chromatids

division of nucleus to produce two identical nuclei - prophase - metaphase - anaphase - telophase - cytokinesis

mitosis

nuclear membrane disappears, centrosomes condense (coil up), spindle fibers appear

prophase (mitosis)

chromosomes line up at metaphase plate, associated with spindle fibers

metaphase (mitosis)

sister chromatids migrate to opposite poles, cytokinesis begins

anaphase (mitosis)

nuclear membranes form, spindle disappears, cytokinesis occurs

telophase (mitosis)

- spindle begins to disassemble - at the midpoint of the former spindle, a ring of actin and myosin filaments attached to the plasma membrane contracts - contractile ring pulls the cell surface inward as it shrinks - ring contracts until it pinches the cell in two

cytokinesis (mitosis)

cell division the results in four haploid daughter cells

meiosis

- homologous pairs of sister chromatids associate with each other, lying side by side form a bivalent or tetrad - process called synapsis

tetrad

- physical exchange between chromosome pieces of the tetrad - may increase the genetic variation of a species - chiasma: arms of chromosomes tend to separate but remain adhered at a crossover site - number of crossovers carefully controlled by cells

crossing over

- homologous chromosomes condense, pair up, and swap segments - spindle microtubules attach to chromosomes at the nuclear envelope breaks up

prophase I (meiosis I)

homologous chromosome pairs are aligned midway between spindle poles

metaphase I (meiosis I)

homologous chromosomes separate and begin heading toward the spindle poles

anaphase I (meiosis I)

- two clusters of chromosomes reach the spindle poles - new nuclear envelope forms around each cluster, so two haploid (n) nuclei form

telophase I (meiosis I)

- chromosomes condense - spindle microtubles attach to each sister chromatid as the nuclear envelope breaks up

prophase II (meiosis II)

(still duplicated) chromosomes are aligned midway between poles of the spindle

metaphase II (meiosis II)

- all sister chromatids separate - now unduplicated chromosomes head to spindle poles

anaphase II (meiosis II)

- cluster of chromosomes reaches each spindle pole - new nuclear envelope encloses each cluster, four haploid (n) nuclei form

telophase II (meiosis II)

- male germ cell develops into a primary spermatocyte (diploid) - undergoes meiosis I to form two secondary spermatocytes (haploid) - undergo meiosis II to form four haploid spermatids - spermatids mature into sperm

spermatogenesis

- female germ cell develops into a primary oocyte - undergoes meiosis I to form a secondary oocyte and a small polar body - undergoes meiosis II followed by unequal cytoplasm division to form an egg and another polar body

oogenesis

- occurs when homologous chromosomes fail to separate during anaphase I, or sister chromatids fail to separate during anaphase II - results in condition called aneuploidy (missing- monosomic or extra- trisomic)

nondisjunction

where the experimenter follows only a single trait - P generation: true breeding parent - F1 generation: offspring of P cross - F2 generation: F1 self fertilizes

single factor cross

two copies of a gene segregate from each other during the transmission from parent to offspring - can be explained by the pairing and segregation of homologous chromosomes during meiosis

Mendel's Law of Segregation

genetic composition of an individual

genotype

physical or behavioral characteristics that are the result of gene expression

phenotype

alleles of different genes assort independently of each other during gamete formation - can be explained by the behavior of chromosomes during meiosis

Mendel's Law of Independent Assortment

recessive trait disease (not everyone effected)

Cystic Fibrosis

dominant trait disease (everyone is effected)

Huntington disease

males XY and females XX

XY system

males X or XO and females XX

XO system

males ZZ and females ZW

ZW system

genes found on the X but not the Y

X linked genes

recessive allele does not affect phenotype of heterozygote - one gene, one trait

Simple Mendelian Inheritance

mutation in a single gene can have multiple effects on an individual's phenotype

pleiotropy

- heterozygote shows intermediate phenotype - neither allele is dominant

incomplete dominance

- multiple alleles: three or more variants in a population - phenotype depends on which two alleles are inherited

Codominance

single trait is controlled by two or more genes, each of which has two or more alleles

gene interaction

- alleles of one gene mask the expression of the alleles of another gene - often arise because two or more different proteins are involved in a single cellular function

epistasis

type of trait - clearly defined phenotypic variants - purple or white flowers, red or white eyes

discrete

type of trait - majority of traits - continuous variation over a range of phenotypes - usually polygenic: multiple genes involved - environmental influence - height, skin color, number of fruits on a tree

quantitative

deviation between observed and expected outcome - larger samples have smaller erros

random sampling error

genes are on the same chromosome

linked genes

- genetic code in not changed - only regulation of gene expression

epigenetic gene regulation

- all the descendants of a particular cell - offspring of an organism - over one or two generations

inheritance

- everyone needs one X chromosome - females inherit two X (randomly inactivate one, early in development, Barr body) - compaction of chromosome

X chromosome inactivation

- UBE3A gene - maternal expression - paternal silencing

Angelmann syndrome

- SNRPN gene - paternal expression - maternal silencing

Prader Willi

- genome: DNA or RNA - capsid: protein coat - viral envelope: lipid membrane from the host cell

viral structure

viral DNA inserted into host genome - prophage: viral DNA in a bacterial genome - provirus: viral DNA in an eukaryotic genome

lysogenic

- proceed directly to synthesis of viral components, assembly and release of virus - provirus or prophage can switch over to this cycle

lytic

- circular pieces of DNA: separate from chromosome, several dozen to hundreds of genes - independent replication: origin of replication, multiple copies

plasmids

results in two genetically identical daughter cells

binary fission

- daughter cells inherit genetic information from parental cell - in bacteria daughter cell chromosomes are genetically identical to parent cells - unless mutation occurs

vertical discent

- transfer of genetic information from one cell to another cell that is not its offspring - between bacteria of the same species - occasionally between bacteria of different species

horizontal transfer

bacteria- bacteria - direct contact - transfer DNA from one cell to another (plasmid)

conjugation

environmental DNA- bacterium - does not require direct contact - bacterium must be competent (genes that facilitate DNA uptake) - common technique in genetic engineering

transformation

bacterium- virus- bacterium - virus incorporates bacterial DNA into its own genome - transfers to another bacterium

transduction

Final Flashcards

(172 cards)