Misc. III
dsDNA
Double stranded DNA.
What is the critical region on chromosome 21 responsible for the trisomy in Downs?
Down sydrome critical region (DSCR)
How does the phospholipid bilayer form?
Due to the hydrophobic effect the hydrophilic head align towards the water, excluding the hydrophibic heads in the middle of the layer.
gene for gene hypothesis
During evolution of host parasite system, complementary genetic systems are developed where the host developed a defense gene and the parasite matches it by developing an attack gene
psudeogene
Dysfunctional relatives of a genes that have lost their protein or coding ability or are no longer expresses.
Which site is missing in the prokayote ribosome?
E is missing
E1, E2, E3
E1: U-activating enzyme E2: U-conjugating enzyme E3: U-protein ligase
electric field
E=F/q=-dU/ds=-DU
Aminoacyl tRNAs are deliverd to the A-site by ...
EF-Tu (EF-T recharges EF-TU with GTP..only GTP bound EF-Tu''s will bind charged aminoacyl tRNA's, it doesn't interact with fMet-tRNA)
GIve the 3 elongation of polypeptide factors and their function.
EF-Tu-binds GTP, miated aminoacyl-tRNA entry tot the A site of ribosome EF-Ts-generates active EF-Tu EF-G-stimulates translocation; GTP-dependent
How can the following chemicals alter bases? EMS HNO2 NH2OH
EMs->cause alkylation of G, making ehtylguanine bind to T Nitrous acid->causes deamination of C, making a U that binds to A hydroxylamie->hydroxylation of C, making hyd. C bind to A
EPSP and ISPSP typlically increase what to depolarize (EPSP) or hyperpolerizae (IPSP)
EPSP-increae gNA or decrease gK IPSP increases gCL or gK
cyclic adenosine monophosphate
"Cyclic adenosine monophosphate; a small molecule, derived from ATP, that is widely used by cells in signal transduction and transcriptional control."
constitutive gene
("housekeeping gene")-expressed all the time, not regulated by environmental conditions
constitutive gene
("housekeeping gene")-expressed all the time, not regulated by the environmental conditions
deletion
(1) A deficiency in a chromosome resulting from the loss of a fragment through breakage. (2) A mutational loss of one or more nucleotide pairs from a gene.
n
(2n+1)=distinct phynotypes 1/4^n=number of F2 individuals with either homogoneoous extreme
lacZ
(B-galactosidase)-converts lactose into galatose and glucose
lacY
(B-glactoside permease)-allows lactose ot be taken up into the cell
reciprocal translocation
(Cytogenic Effects) Multi-hit chromosome aberrations that require karyotyopic analysis for detection deal with this type...
biological species concept (BSC)
(Mayr) A group of interbreeding natural populations that are reproductively isolated from other such groups
DNA finerprinting
(PCR-base)
allosteric effect
- allosteric enzyme oscillates between two configuration (active site that can catalyze a reaction and inactive site that can't, an agent that alters the function of an enzyme by changing the shape of the active site
mesoderm
- musculoskeletal system, circulatory system, excretory system, gonads, connective tissue throughout the body and portions of digestive and respiratory organs
State the free energy rules for when Gibbs free energy is -, +, or 0.
- thermodynamically favorable 0 reversible; at equilibrium + thermodynamically unfavorable; reverse process is favorable
Pribnow Box
-10 region where TATAAT is found
TTGACA
-35 consensus sequence
Energy release from ATP hydrolysis?
-7.3 kcal/mol
types of nerve fibers, rank from largest to smallest and state their physiological fundtion
-Aa: somativ motor -Ad: pain, sharp -C: pain, ache
carboxamide
-CO-NH2
base excision repair
-DNA glycosylases recognizes specifically damged bases -repair of APsites or sites of DNA damage->(cut back bone, dRpase remove DNA stretch) -polymerase sythnsizes new -ligase seals
direct reversal of DNA damage
-DNA poly. preefreading (fixes most mismatches) -reapir UV induce pyrimidine dimers (photoreatic repair) -repair of alkylation (O6-methylG methyltransfersa...aka...MGMT)
What are the basic functional groups?
-NH2 imidazole guanidinium
thioether
-S-CH3
C complex
-U6 and U2 base pair during rearrangement allowing catalysis of 1st transesterfication -free 3' OH on exon 1 attacks 3' splice site
What are the 3 basic things DNA synthesis needs?
-a template -free -OH at the 3' end -deoxyribonucleoside triphosphat to extend DNA and exclusively in the 5' to '3 direction
4 mechanism GRPs act as repressors
-activaotro repressor competition -act. rep. inhibition -direct repression -indirect represion (HDA or HMT silencing gene expression)
What other genes, besides lac, does CAP control?
-activates transcription of many genes that encode other proteins that utilize sugurs other than glucose -works with repressors to control express of those other genes
What are predictions of the hary-wienberg model
-allele freq in pop do not change over time -after one generation of random mating, genotypic feq can be predicted from alleleic freq
name some neurological diseased associated with protein misfolings and aggregation
-alzheimer -parkinson -huntington -prion
aneuploidy
A chromosomal aberration in which one or more chromosomes are present in extra copies or are deficient in number
monosomic
A chromosomal condition in which a particular cell has only one copy of a chromosome, instead of the normal two; the cell is said to be monosomic for that chromosome.
coefficient of inbreeding
A coefficient of inbreeding can be calculated to give the probability that two alleles of a given gene in an individual are identical because they are descended from the same single copy of the allele in an ancestor.
selection
A composite of all the forces that cause differential survival and differential reproduction among genetic variants (artificial selection vs. natural selection); a key mechanism of evolution
Down Syndrome
A condition of retardation and associated physical disorders caused by an extra copy of chromosome 21.
Down Syndrome
A critical region of chromosome 21 contains the genes that are dosage sensitive in this trisomy and are responsible for many of the phenotypes: Down syndrome critical region (DSCR) An extra copy of the DSCR1 associated with ~10% decreased risk of some cancers Prominent epicanthic fold in each eye • Flat face, round head, short stature with protruding tongue • Short, broad hands with characteristic palm and fingerprint pattern • Mental retardation, average life span 50 years.
nucleoid
A dense region of DNA in a prokaryotic cell.
fragile x
A disorder produced by injury to a gene on the x chromosome, producing mild to moderate mental retardation.
karyotype
A display of the chromosome pairs of a cell arranged by size and shape.
allopolyploid
A fertile individual that has more than two chromosome sets as a result of two different species interbreeding and combining their chromosomes.
F factor
A fertility factor in bacteria, a DNA segment that confers the ability to form pili for conjugation and associated functions required for the transfer of DNA from donor to recipient. It may exist as a plasmid or integrated into the bacterial chromosome.
active tension
A force that occurs in a muscle with contraction is called ___________
binary fission
A form of asexual reproduction in single-celled organisms by which one cell divides into two cells of the same size
biotechnology
A form of technology that uses living organisms, usually genes, to modify products, to make or modify plants and animals, or to develop other microorganisms for specific purposes.
non-crossover gamete
A gamete whose chromosomes have undergone no genetic recombination, Gametes which result in the same chromosomal genotype as the parental generation
hemizygous
A gene present on the X chromosome that is expressed in males in both the recessive and dominant condition
episome
A genetic element that can exist either as a plasmid or as part of the bacterial chromosome.
strain
A genetically related bloodline possessing distinguishing characteristics such as type, color, or coat, and the ability to pass the characteristics to the offspring.
macular degeneration
A gradual loss of acute, central and color vision in the elderly, possible RNAi therapy
clone
A group of genetically identical cells or organisms derived from a single cell or individual by some kind of asexual reproduction
syndrome
A group of symptoms typical of a particular disease or condition
gamete
A haploid cell such as an egg or sperm. Gametes unite during sexual reproduction to produce a diploid zygote.
nuclear membrane
A highly-porous membrane that separates the nucleus from the cytoplasm
microtubules
A hollow rod of the protein tubulin in the cytoplasm of all eukaryote cells that make up cilia, flagella, spindle fibers, and other cytoskeletal structures of cells
epitope
A localized region on the surface of an antigen that is chemically recognized by antibodies; also called antigenic determinant
enzyme
A macromolecule serving as a catalyst, a chemical agent that changes the rate of a reaction without being consumed by the reaction.
bicoid
A maternal effect gene that codes for a protein responsible for specifying the anterior end in Drosophila. (the other end is nanos)
GLUT4
A membrane-bound, insulin-stimulated glucose transport protein required to transport glucose from plasma to muscle and adipose tissue.
beta oxidation
A metabolic sequence that breaks fatty acids down to two-carbon fragments which enter the Krebs cycle as acetyl CoA.
Amphipathic
A molecule that has both a hydrophilic region and a hydrophobic region.
amphipathic
A molecule that has both a hydrophilic region and a hydrophobic region.
isometric
A muscle contraction in which the body part affected by the muscle does not move is called
nonsense mutation
A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein.
introns
A non-coding, intervening sequence within a eukaryotic gene
nucleoid
A non-membrane-bounded region in a prokaryotic cell where the DNA is concentrated.
How is transcription terminated?
A nucleotide sequence of ~40 bps is added to the transcript, forming a hairpin secondary structure that signals termination. -sometimes dependent on Rho enzyme
model organism
A particular species chosen for research into broad biological principles because it is representative of a larger group and usually easy to grow in a lab
anagenesis
A pattern of evolutionary change involving the transformation of an entire population, sometimes to a state different enough from the ancestral population to justify renaming it as a separate species; also called phyletic evolution.
interphase
A period between two mitotic or meiotic divisions during which the cell grows, copies its DNA, and synthesizes proteins
carrier
A person whose genotype includes a gene that is not expressed in the phenotype.
genomic imprinting
A phenomenon in which expression of an allele in offspring depends on whether the allele is inherited from the male or female parent
genetic anticipation
A phenomenon where the onset of symptoms of a hereditary disease appears to occur at progressively earlier ages in successive generations within a particular lineage
cloning
A process in which a cell, cell product, or organism is copied from an original source
natural selection
A process in which individuals that have certain inherited traits tend to survive and reproduce at higher rates than other individuals because of those traits.
mitosis
A process of nuclear division in eukaryotic cells conventionally divided into five stages: prophase, prometaphase, metaphase, anaphase, and telophase. Mitosis conserves chromosome number by equally allocating replicated chromosomes to each of the daughter nuclei.
epigenetic regulation
A process that affects the expression of specific genes and is inherited by daughter cells, but is NOT the result of a change in DNA sequence
electrophoresis
A process where DNA fragments are separated according to size using electrical charges
phenylketonuria
A rare inborn error of phenylalanine metabolism. Inherited as an autosomal recessive trait. Accumulation of phenylalanine in untreated cases causes CNS toxicity, most notably mental deficiency; organ damage; unusual posture; and can, in cases of maternal, severely compromise pregnancy
transcription factor
A regulatory protein that binds to DNA and affects transcription of specific genes
sexual reproduction
A reproductive process that involves two parents that combine their genetic material to produce a new organism, which differs from both parents
systematics
A scientific discipline focused on classifying organisms and determining their evolutionary relationships.
operon
A segment of DNA containing adjacent genes including structural genes and an operator gene and a regulatory gene
gene
A segment of DNA on a chromosome that codes for a specific trait
plasma membrane
A selectively-permeable phospholipid bilayer forming the boundary of the cells
patau syndrome
A short life-span, missing parts of the brain, a severe cleft palate, and malformed genitalia are all symptoms of _____________ ______________.
Alkaptonuria
A single-gene disorder identified by Archibald Garrod that is characterized by dark urine. Garrod first coined the term "inborn error in metabolism" to describe this and other congenital, inherited disorders that affect metabolic pathways.
corepressor
A small molecule that cooperates with a repressor protein to switch an operon off
inducer
A small molecule that inactivates the lac repressor which can bind to the operon and switching the operon off. The inducer prevents this by binding to the repressor.
plasmid
A small ring of DNA that carries accessory genes separate from those of the bacterial chromosome
plasmid
A small, circular section of extra DNA that confers one or more traits to a bacterium and can be reproduced separately from the main bacterial genetic code.
centromere
A specialized condensed region of each chromosome that appears during mitosis where the chromatids are held together to form an X shape.
kinetochore
A specialized region on the centromere that links each sister chromatid to the mitotic spindle.
operator
A specific DNA nucleotide sequence where transcriptional regulatory proteins can bind.
promoter
A specific nucleotide sequence in DNA that binds RNA polymerase and indicates where to start transcribing RNA.
codon
A specific sequence of three adjacent bases on a strand of DNA or RNA that provides genetic code information for a particular amino acid
nucleoside
A structure composed of a ribose molecule linked to one of the aromatic bases. In a deoxynucleoside, the ribose is replaced with deoxyribose.
endoplasmic reticulum
A system of membranes that is found in a cell's cytoplasm and that assists in the production, processing, and transport of proteins and in the production of lipids
x-ray crystallography
A technique that depends on the diffraction of an X-ray beam by the individual atoms of a crystallized molecule to study the three-dimensional structure of the molecule.
conjugation
A temporary union of two organisms for the purpose of DNA transfer.
conjugation
A temporary union of two organisms for the purpose of DNA transfer., In bacteria, the direct transfer of DNA between two cells that are temporarily joined.
adaption
A trait that helps an organism survive and reproduce
retrotransposon
A transposable element that moves within a genome by means of an RNA intermediate, a transcript of the retrotransposon DNA.
mRNA
A type of RNA, synthesized from DNA, that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein.
map unit
A unit of measurement of the distance between genes. One map unit is equivalent to a 1% recombination frequency. 300 recombinant offspring, out of 2000 total offspring. Map distance is calculated as (# Recombinants)/(Total offspring) X 100. So our map distance is (300/2000)x100, or 15 LMU.
bacteriophage
A virus that infects bacteria
Name the 5 noncoezyme vitamins and give their functions
A vision, growth, and reproduction C antioxidant D regulation of calcium and phosphate metabolism E antioxidant K blood coagulation
triploidy
A zygote with three copies of each chromosome, so with a total of 69 chromosomes.
oxidation 1
Acyl CoA + E-FAD trans-D2-enoyl CoA + E-FADH2
genome
All the genetic information in an organism; all of an organism's chromosomes.
Pribnow Box
Also known as the -10 sequence, consists of a sequence TATAAT that is used as a promoter for DNA transcription.
Pribnow box
Also known as the -10 sequence, consists of a sequence TATAAT that is used as a promoter for DNA transcription. Generally it is homologous iwht the consensus sequence.
ribozyme
An RNA molecule that functions as an enzyme, catalyzing reactions during RNA splicing
ribozymes
An RNA molecule that functions as an enzyme, catalyzing reactions during RNA splicing
retrovirus
An RNA virus that reproduces by transcribing its RNA into DNA and then inserting the DNA into a cellular chromosome; an important class of cancer-causing viruses.
duplication
An aberration in chromosome structure due to fusion with a fragment from a homologous chromosome, such that a portion of a chromosome is duplicated.
allotetraploid
An allopolyploid containing two genomes derived from different species
allele
An alternative form of a gene.
autosome
Any chromosome that is not a sex chromosome
pili
Appendages that allow bacteria to attach to each other and to transfer DNA
bioinformatics
Application of mathematics and computer science to store, retrieve, and analyze biological data
amino acid attachment site
Binds amino acid corresponding to the codon it recognizes, CCA terminus (3' end)
chromosome
Bodies within the nucleus made in DNA and proteins called the histones
glycogenolysis
Breakdown of glycogen into glucose
rosalind franklin
British scientist; use X-ray diffraction on a DNA molecule; research wasn't clear; she was not credited with the discovering of the double helix
What corn produces what bacteria that produces toxins harmful to insects that include rootworm?
Bt corn Bacillus thurigiensis
Amino acids are added to the __-terminus, giving directionto protien synthesis
C
imino tautomer C
C without one of its double bonds
The bases in tRNA can bind differnt bases. List the base of the anticodon and what it can pair with
C-G A-U U-A or G G-U or C I-U, C, or A
GC box
DNA sequence - GGGCGG - approx position at -70 to -200
cis-acting elements
DNA sequences in the vicinity of the structural portion of a gene that are required for gene expression
cis-acting
DNA sequences that exert their effect only on nearby genes (TATA box, enhancers, silencers)
consensus sequences
DNA sequences to which RNA polymerases bind; identical in many organisms
CTD
C-terminal domain of RNA polymerase II -contains series of repeats: YSPTSPS- Y,S,&T get phosphorylated (lysine, serine, threonine) -phosphorylation of CTD causes general transcription factor dissociation
capacitance of parallel plates
C=Q/V=eoA/D D=delta=distance between plates A=area
What seq is prone to errors
CAG
What is the binding site that activates transcription of the Lac operon?
CAP-binding site
Which cyclins regulate which phase of the cell cylce?
CKD2 -Cyclin A-S -Cyclin B-S, G2, and M -Cyclin E-G1 and S CDK4,5 -Cyclin D-G1
What is the primary buffer int he blood?
CO2-carbonic acid-bicarbonate keeping it at pKa=6.4 blood pH=7.4...at 7.35 acidosis is present
13 loci STR database
CODIS STRs, hetttetrameriepeats
What kind of reaction does Creatine phosphate undergo?
CP+ADP->ATP+creatine
____ carries long-chain activated fatty acids into the mitochondria
Carnitine
chylomicrons
Carry dietary triglycerides from the intestine to other tissues
Name 6 functions of proteins.
Catalyze chemical reactions: enzymes Transport: hemoglobin and myoglobin Participate in contraction: myosin and actin Provide protection: antibodies, interferon and fibrin Hormones: insulin, luteinizing hormone, FSH Detect and transmit signals: receptors and G proteins Control growth and differentiation: transcription factors
lactate dehydrgenase (LDH)
Catalyzes the reaction of pyruvate to lactate and vice versa in the Citric Acid Cycle Genes: LDH-A (11p15.1) LDH-B (12p12.1) LDH-C (11p15.1) Difference based on location within the human body Skeletal muscle Cardiac muscle Testes
cri du chat syndrome
Caused by absence of the short arm of 5th chromosome (5p), high-pitched cry of long duration, like a cat, low-set ears, narrow oral cavity, laryngeal hypoplasia, microcephaly, hypertelorism (wide-set eyes), micrognathia, oral clefts, intellectual disability
What is the 4 component of tryp synth. rxn?
CdRP (1-(o-carboxyphenylamino)-1deoxyribulose 5-phosphate)
diploid number
Cell condition in which two of each type of chromosome are present, The total number of chromosomes in a cell (2n).
sarcolemma
Cell membrane of a muscle cell
Hfr
Cells contain an F factor that is integrated into the bacterial chromosome, integrated F plasmids integrated into the host chromosome
translocation
Change to a chromosome in which a fragment of one chromosome attaches to a nonhomologous chromosome
ordered genetic code
Chemically similar amino acids often share 1 or 2 "middle" bases in the different triplets encoding them hydrophobic (U or C in 2nd position) hydrophilic (G or C in 2nd position)
column chromatography
Chromatography in which the substances to be separated are introduced onto the top of a column packed with an adsorbent (as silica gel or alumina), pass through the column at different rates that depend on the affinity of each substance for the adsorbent and for the solvent or solvent mixture, and are usually collected in solution as they pass from the column at different times
homologous
Chromosomes that have the same sequence of genes and the same structure
homologous chromosomes
Chromosomes that have the same sequence of genes and the same structure
______ serves as a carrier to transport acetyl units from the mitochondrion to the cytosol for fatty acid synthesis
Citrate
CPSF
Cleavage and polyadenylation specificity factor, Binds to the AAUAA consensus sequence to start the poly A tail
CstF
Cleavage stimulation facto, What binds U/GU sequence - promotes polyadenylation
lipoproteins
Clusters of lipids associated with proteins that serve as transport vehicles for lipids in the lymph & blood.
complete linkage
Complete linkage describes the inheritance patterns for 2 genes on the same chromosome when the observed frequency for crossover between the loci is zero.
amino acids
Compounds with an amino group on one end and a carboxyl group on the other end., Building blocks of protein
compare the function and work ofr the 3 types of contraction
Concentric: acceleration, W=F*D Isometric: fixation, W=0 Eccentric: deceleration, W=F*(-D)
polyploidy
Condition in which an organism has extra sets of chromosomes
RNase P
Consists of an RNA dimer complexed with a dimer of a small protein, it is a ribozyme. Cleaves tRNA
tetany
Constant muscle contractions; associated with hypocalcemia and hypoparathyroidism.
nucleus
Controls the cells function, contains the cells DNA, RNA comes out, contains genetic material
DNA is methylated at __ dinucleotides
CpG
____ _____ serves as a reservoir of phosphoryl groups that can be readily transferred to ATP.
Creatine phosphate
Lambda repressor represses __ transcription by binding OR1, and activates lambda transcription by binding OR2
Cro
synapsis
Pairing of homologous chromosomes
oxidative phosphorylation
Part of the electron transport chain. A process occurring in the mitochondria that results in the formation of ATP from the flow of electrons across the inner membrane to bind with oxygen.
trisomy 13
Patau Syndrom
gyrase
Relieves tension in an unwinding DNA strand, A prokaryotic enzyme used to twist teh single circular chromosome of prokaryotes upon itself to form supercois. Supercoiling helps to compact prokaryotic DNa and make it sturdier.
asexual reproduction
Process by which a single parent reproduces by itself
polyploidization
Process by which an individual is formed with extra sets of chromosomes in cells due to accidents during cell division
crossing over
Process in which homologous chromosomes exchange portions of their chromatids during meiosis.
RNA editing
Process whereby the genetic information is changed at the level of mRNA. It is revealed by situations in which the coding sequence in the RNA differs from the sequences of DNA from which is was transcribed.
How does prokaryote and eukaryote chromosomal structure differ and what does this mean for transcription?
Prokaryote DNA is circular. Transcription and translation are linked and is thereby much faster than eukaryotic transcription which is not linked ot transcription, has a linear chromosomal structure, and must pass the mRNA through the nucleus.
Promoter regions in prokaryotes and eukaryotes?
Prokaryotes -10 Pribnow box (TATAAT) -35 (TTGACA) Eukaryotes -25 TATA box/Hogness box (TATAAA) -75 CAAT box (GGNCAATCT)
What are the regulatory regions on the lac Operon and what do they do?
Promotor (P) and Operator (O) binding sites for proteins that affect gene expression
pyrin
Protein domain located in NOD receptors and other receptors involved in inflammation and host cell death, play role in sensing intracellular pathogens
Chromodomain
Protein structural motif that recognizes and binds certain methylated Lys residues in proteins.
Proteins, fats, and carb metabolism
Proteins Amino acids as fuels Protein synthesis Nitrogen metabolism Fats Fatty acids as fuels Stored as triacylglycerols Lipid synthesis Carbohydrates Carbohydrates as fuels Stored as glycogen Converted to glycerol Glycosylate proteins
Poiseuille's law
Qv=pia^4/8n *(DP/Dx) Qv=flow of volume through a narrow tube without any turbulance pi=geometric ratio a=radius n=viscosity DP=change in pressure Dx=length of tube
SINES
Repeated DNA sequences of 300 base pairs in length that are interspersed throughout the human genome. An example is the alu sequences.
sister chromatid
Replicated forms of a chromosome joined together by the centromere and eventually separated during mitosis or meiosis II.
snRNA
RNA which help with splicing of pre-mRNA
ribozyme
RNA with catalytic activity ex. splicesome
RNA world hypothesis is suppored by
RNA's abilty to store, transit and dulpicate gnetic infomration
RISC
RNA-induced silencing complex binding prior to promoter causes degredation, after inhibits translation
palindromic
Reading the same forward and backward; some DNA sequences are palindromic because the base sequence of one strand is the reverse of the base sequence in its complement; for example, the complement of 5'-GAATTC-3' is 3'-CTTAAG-5'.
DNA synapsis is catalyzed by
RecA/Rad5
restriction endonucleases
Recognizeand cut DNA in a specific and reproducible fashion. They do not have methylase activity and thus very useful for DNA manipulation
types of GRPs
Repressors-turn gene expression off (-regulation_ activators-turn gene expression on (+regulation_
haploid number
Refers to the number of chromosomes found in gametes. It is half the chromosome number found in normal body cells.(n)
minimal promoter
Region which contains all the necessary sites to support efficient and controlled transcription
key techniques in recombinatn dna tech
Restriction-enzyme analysis; Separating DNA fragments by gel-electrophoresis; Solid-phase synthesis of nucleic acids; Blotting techniques; Polymerase chain reaction (PCR); Rapid DNA sequencing.
___ turn transcription off prematurely by producing a terminator.
Riboswitches
B-DNA
Right-handed helical structure of DNA that exists when water is abundant; the secondary structure described by Watson and Crick and probably the most common DNA structure in cells.
dsRNA
Rotavirus
Gauss's Law for a sphere
S E.ds=q/eo E=kq/r^2
sympatric speciation
The formation of a new species as a result of a genetic change that produces a reproductive barrier between the changed population (mutants) and the parent population. No geographic barrier is present.
DNA gyrase
Relaxes supercoiling ahead of the replication fork
allopatric speciation
The formation of a new species as a result of an ancestral population's becoming isolated by a geographic barrier.
quarternary structure
The fourth level of protein structure; the shape resulting from the association of two or more polypeptide subunits.
What 4 transcription factors induce pluripotent stem cells?
Sox-2, Oct-4, cMyc, and Klf4
alternative splicing
Splicing of RNA transcripts from the same gene in different ways, each of which produces a distinct protein.
alternative splicing
Splicing of introns in a pre-mRNA that occurs in different ways, leading to different mRNAs that code for different proteins or protein isoforms. Increases the diversity of proteins.
Name the Start and Stop codons.
Start: AUG Stop: UAA, UAG, UGA
molecular genetics
Study of DNA structure and function on the molecular level
genomics
Study of genes, diagnose disease before tissue damaged
Affinity chromatography often exploits what pairs/
Substrate / Enzyme; Short DNA / DNA-binding protein; Antibodies / Antigen;
Why is ATP a good source of high energy phosphoryl bonds?
The high phosphoryl-transfer potential of ATP results from structural differences between ATP and its hydrolysis products -electron repulsion -resonance stabilization (product isn't resonance stabilized) -stabilization due to hydration
Wobble Hypothesis
The hypothesis that some tRNA molecules can pair with more than one mRNA codon, tolerating some variation in the third base, as long as the first and second bases are correctly matched. 4^3=64, 61 of 64 cod for amino acids
trisomy 18
Edward Syndrome
zygotic mortality
Egg is fertilized, but zygote does not develop.
histone code
The hypothesis that specific combinations of chemical modifications of histone proteins contain information that influences gene expression.
capacitance expressions
Electrical: Q=CV (Farada=coulumbs/volt) Thermal Capacitance: CpM=H/T (J/K) Chemical Capacitance, (V=volume), V=M/C (moles/molarity=>L) Mechanical Capacitance (C=compliance), C=V/P (volume/pressure->m^3/Pa)
endoderm
Embryonic germ layer; forms the lining of the digestive tube and its associated structures.
lacA
Encodes a transacetylase enzyme that modifies lactose and lactose analogs.
lac Z
Encodes the enzyme beta-galactosidase which breaks down lactose to form glucose and galactose.
lac z
Encodes the enzyme beta-galactosidase which breaks down lactose to form glucose and galactose.
lac Y
Encodes the enzyme permease which transports lactose into the cell.
peptidase
Enzyme that breaks down peptides into amino acids
DNase
Enzyme that breaks down the polymer DNA into the monomer or nucleotides
restriction enzymes
Enzyme that cuts DNA at a specific sequence of nucleotides
argonaute
Enzyme that cuts target RNA molecule
dna polymerase I
Enzyme. Removes RNA primers and replaces them with the appropriate nucleotides during DNA replication.
dna polymerase i
Enzyme. Removes RNA primers and replaces them with the appropriate nucleotides during DNA replication.
Who is credited with allopatric speciation?
Ernst Mayr
How does eukaryotic gene expression control compare to that in prokaryotes?
Eukaryotes have multiple levels of gene expression control. Prokaryotes control via transcription.
pulse chase experiment
Experiment where they found RNA is the carrier of genetic code from DNA. As it leaves the nucleus and appears into the cytoplasm and the genetic material is in protein the final product. They labeled it, like a snapshot before & after.
allopolyploidy
Extra sets of chromosomes come from different species, arise from hybridization, new chromosomes have no homologues, can create new species if followed by autopolyploidy
donor in conjugation
F+ present as separate circular DNA F' present as separate circular DNA, carrying some bacterial genes
recipient in conjugation
F-
...
F/A=n dv/dy
Coulomb's Law
F=q1q2/(4pi*eo*r^2) F12=q1q2r12/(k4pi*eo*r^3)=-F21 r12=distan between particles eo=8.85*10^-12 C^2/(Nm) k=dielectric constant
What are the by products of B-oxidation?
FADH2 and NADH+H 2 Acetyl CoA's
True or False? Helicases do not require ATP.
FALSE
True or False? The promoter is part of the RNA-coding region and is transcribed into the RNA transcript.
FALSE
What 3 primary molecular components make up DNA?
Sugar, Base, and Phosphate
Examples of rare base pairings
T and keto G C (imino) and A (amino)
List the conserved promoter elements and their location.
TATA box -30 (consensus sequence) CCAAT box -70 to -100 bp CG-rich region -100 to -100 bp
What is the eukaryotic equivalent of the Pribnow box?
TATA box -30 region
Name 2 consensus sequences found in bacteria.
TATAAT in -10 region & TTGACA in -35 region
leader region
The leader region can form two different conformations, depending on the presence or absence of tryptophan
euchromatin
The less condensed form of eukaryotic chromatin that is available for transcription.
True or False? Another action potential can fire while another is still firing on the axon?
False
True or False? Most eukaryotic genes are colinear.
False A triplet can be interrupted by an intron.
true or False? Eukaryotic chromosomes contain one replication origin.
False they contain multiple
True or False? constitutive mutants express genes of the lac operon if an inducer is present.
False Constitutive mutants do not need an inudcer. They are expressed all the time regardless of environemntal conditions.
True or False? The structurla genes are always transcribed if lactose is present.
False Glucose must be absent too
True or False? Insertion of 9 base pairs alter the reading frame.
False. Insertions that are multiples of 3 do not change the reading frame even though they change the length.
True or False? AUG is the start codon for RNA synthesis?
False. It's the start codon for protein synthesis. DNA does not contain uracil. TAG is the complement to AUG.
True or False? Iron metabolism is transcitipionally regulated.
False..it's translationally
Force cause by electric field
Fe=Bv B=drag coeff v is terminal velocity
zygote
Fertilized egg
spindle fibers
Fibers that appear during mitosis. Chromosomes attach to the spindle fibers at the centromere and move back and forth between the poles on the fibers.
Flow vs Flux
Flow=Q Flux=J J=Q/A (A=area)
ploidy
The number of complete chromosome sets present. Haploid refers to a ploidy of 1; diploid refers to a ploidy of 2; triploid, a ploidy of 3; and tetraploid, a ploidy of 4
FISH
Fluorescent DNA or RNA probe binds to specific gene of interest - used for specific localization of genes and direct visualization of anomalies, like microdeletions, at molecular level
stabilizing selection
Form of natural selection by which the center of the curve remains in its current position; occurs when individuals near the center of a distribution curve have higher fitness than individuals at either end, Natural selection that favors intermediate variants by acting against extreme phenotypes
CAAT box
Found in eukaryotes, it's found 70-85 bp upstream of the initial transcription site and serves as a consensus sequence. Used as a binding site for General Transcription Factors.
What mathematical model is used to elucidate the model from a difraction pattern of an x-ray?
Fourier transform
Who provided the experimental proof fro the triplet nature of the genetic code and how was it done?
Francis Crick and ccolleagues a phage T4 was used to study the effects of frame shift mutations 1 or 2 deletions caused a change in the reading, but 3 caused a shift results also suggested degeneracy of the code
penetrance
Frequency with which a heritable trait is exhibited by individuals carrying the gene or genes that determine that trait.
What are the two classes of RNA?
Functional RNA & Messenger RNA
How do you calculate actual free energy change?
G=Go+RTln([B]/[A]) B=products A=reactants [B]/[A]=Keq RT=2.47
Constitutive genes tent to have __ boxes.
GC
The intron in the major splicing pathway begins with a __ and ends with an __
GU, AG
pseudodominance
The phenotypic expression of a single recessive allele resulting from deletion of a dominant allele on the homologous chromosome
Which is larger, the pre-mRNAs or RNAs? What happens to extra parts that don't get translated?
The pre-mRNAs are larger. They are only found inside the nucleus. They are part of a group of molecules call hnRNA (when attached to proteins they are called hnRNPs). 25% of hnRNAs get converted to mRNA. The rest is spliced out, leaving behind split genes.
shine-dalgarno sequence
The prokaryotic ribosome-binding site on mRNA, found 10 nucleotides 5' to the start codon.
shine-dalgarno sequences
The prokaryotic ribosome-binding site on mRNA, found 10 nucleotides 5' to the start codon.
chromosome theory of inheritance
Generalization that genes are located on chromosomes and that the behavior of chromosomes during meiosis and fertilization accounts for inheritance patterns
constitutive genes
Genes that are always "on"
inducible genes
Genes whose expression is turned on by the presence of some substance. Regulate catabolic pathways.
What distinguishes the template strand form the coding strand?
The template strand contains the promoter (start site).
character displacement
The tendency for characteristics to be more divergent in sympatric populations of two species than in allopatric populations of the same two species.
N-terminal rule
The tendency of the N-terminal amino acid of a protein to influence protein stability.
sucrose
Glucose + Fructose
lactose
Glucose + Galactose
meselson and stahl experiment
Grew bacteria in 15N then place them in 14N and let them replicate. They saw two bands of DNA. One hybrid 15-14N band and one 14N band. Proves semiconservation.
genetic counseling
Guidance for prospective parents on the likelihood of genetic disorders in their future children
What percentage of a C-C bond stength (~350 kJ/mol) are H-bonds and hydrophobic interactions?
H-bonds 6% (20 kJ/mol) hydrophobic interactions 2% (8 kJ/mol)
Silver-Russel syndrome
H19 and IGF-2 and imprinting
Epigenetics
HERITABLE changes in expression of a gene that changes phenotype but not the DNA itself... just changes in chromatin structure ex. methylation on cytosing residues (CpG), imprinting, histone modificiation, chromatin remodeling, gene silencing, RNAi, inactivatio of X chromosome
broad sense-heritability
H^2=Vg/Vp
sickle cell anemia
Hb-A changes to mutant Hb-S when Glu changes to Val during missence mutation sdue to a RFLPing destruction of DdeI DdeI RFLP recognized the sickle cell anemia
high freq donar
Hfr present F facter, integrated into fact chrom
Histone variant
Histones with varying stabilities or specialist domains that alter the function of the nucleosome. They can replace one of the four standard histones to form alternat nucleosomes.
What are the 2 subunits of prokaryotes RNA polymerase?
Holoenzyme=core+sigma -core enzyme: a2BB' -sigma subunit
What type of human DNA does not follow the universal triplet code? Why might this be?
Human (and yeast) mitochondrial DNA (mtDNA) Changes in codon recognition may represent evolutionary trend toward reducing the # of tRNAs needed in mitochondria.
zymogen
Inactive enzyme precursor
pericentric inversion
Includes the centromere
optic neuritis
Inflammation of the optic nerve; can produce a sudden but reversible loss of sight, or demylinatinng that lead to MS
thalassemia
Inherited defect in ability to produce hemoglobin, disorder caused by a genetic defect resulting in low hemoglobin production (ANEMIA), caused by a splicing mutation (an AU after a stop codon in the intron frame is changed to GU...looking like a new 5' splice site, part of the intron with the stop get spliced into the mature mRNA which is then degraded)
cycloheximide
Inhibits elongation. Inhibits peptidyl transferase activity in eukaryotes only. Toxic to humans acts by interfering with proteinbiosynthesis
inosine
Inosine is commonly found in tRNAs and is essential for proper translation of the genetic code in wobble base pairs. it most closely resembles guanine and it can base pair with either A, U, or C which gives the tRNA's more flexibility.
in vivo
Inside the body
Transfer RNA forms an __ shape consisting of RNA double helices and loops.
L
Which isomer form do most amino acids take?
L
Into what shape dose the cloverleaf fold into?
L shape
Oxidation 2:______________ catalyzes the oxidation of thehydroxyl group at C3 into a keto group, generating NADH
L-3-hydroxyacyl CoA dehydrogenase
__ and __sequences are regulatory sequences within the first protion of the mRNA
Leader and attenuator
Heptad repeat
Leucine is always d(fourth) residue, a and d always have hydrophobic interactions, Repeating amino acid chain following abcdefg where a and d are hydrophobic. Forms an alpha helix with a twisting line of hydrophobicity. Two of these intertwine to form strong fibers
_____ are water-insoluble molecules that are highly soluble in organic solvents
Lipids
eugenics
Literally, "Good genes"; science of improving a breed through selection
How does linking, twist, and writhing number relate?
Lk=Tw+Wr
____ add or remove functional groups reactions, and this removes or forms double bonds
Lyases
Which of the following peptides will bind most tightly to anion-exchange column at pH 7.0? MDTDI SEASY CMVEA NSWER MVPAF AYMNG MPVKA FYWCR
MDTDI SEASY
ionophores
MOA - disrupts tranmembrane electrochemical gradients
Which of the following peptides will bind most tightly to a cation-exchange column at pH 7.0 and thus elute out the last? MATHISEASY HAVEANSWER MVPAFAYMIL MPVKAFYWCR
MPVKAFYWCR
Give the affinity tag for the following ligands. Metal ions Flag-Antibody Maltose IgG
Metal ions:Histidine residues (HHHHHH) Flag-Antibody:Flag peptide (DYKDDDK) Maltose:Maltose Binding Protein IgG: Protein A
What metal is found at the center of RNA polymerase? What kind of metal is it?
Mg2+ or Mn2+, divalent
mechanisms of gene conversion
Mismatch Repair Homologs in meiotic prophase Mismatches (heteroduplexes) form during recombination Excision of mismatches and repair of DNA (Russell 303) Remove one of the strands of the heteroduplex and use the other as a template Can convert one allele to the other allele
hershey-chase experiment
Mix radioactively labeled phages with bacteria. The phages infect the bacterial cells. Agitate in a blender to separate phages outside the bacteria from the cells and their contents. Centrifuge the mixture so bacteria form a pellet at the bottom of the test tube. Measure the radioactivity in the pellet and the liquid.
RNA processing
Modification of RNA transcripts, including splicing out of introns, joining together of exons, and alteration of the 5' and 3' ends
zinc finger motif
Motif where zinc binds to Cysteine-Cysteine or Cysteine-Histidine., Hormone Response Element; a-helix and b-sheet where 4 cystein/histidine bind zinc to expose DNA binding site; estrogen receptor
What are the special proteins required for mismatch repair and what do they do?
MutS: detecting and binding a mismatched base pair MutL: looking for GATC sequence that is close by (to distinguish the newly synthesized strand from the template strand) MutH: nicks the unmethylated GATC sequences (bacteria only)
What general transcription factors are necessary for the transcription of all protein coding genes?
TBP (tat box binding protein) and TAF (TBP-associated factors)-part of TFIID TFIIA TFIIB TFIIF TFIIE TFIIH
What do TBP and TAF stand for?
TBP: TATA box Binding Protein TAF: TBP Associated Factors
Name the transcripiton factors of RNA polymerase II. What is their function?
TFIIA-stabilizes the binding of TFIID TFIIB (binds to BRE)-accurately posititions RNA polymerase to the start of transcription TFIID (binds to INR & DPE) -TBP subunit (binds to TATA)-recognizes TATA box -TAF subunit-recognizes DNA seq. near the transciption start point, regulates DNA binding by TBP TFIIE-attracts and regulates TFIIH TFIIF-stabilizes RNA polymerase interaction with TBP and TFIIB; hellps attract TFIIE and TFIIH TFIIH-unwinds DNA at the start point, phosphorylates Ser5 of the RNA polymerase CTD; relases RNA polymerase fromt the promoter
What transcription factor can be missing and still have minimal transcription?
TFIIB, TFIIE, TFIIH
Give the function of the transcription factors in order of those that bind first.
TFIID -TBP-binds to TATA -TAF recognizes DNA region near the start site TFIIA-stabilizes binding to promoter TFIIB-bind to Bre if present, recruits TFIIF TFIIF-carry RNA pol to promoter, recruit TFIIE TFIIE-recruit and activate TFIIH TFIIH-helicase and kinase
What doe TFII D,A,B,F,E, and H do?
TFIID (TBP+TAFs) bind to core promoter elements TFIIA binds to TFIID TFIIB binds to BRE elements TFIIF and Mediator interat with RNA Pol II; this complex then binds to the promoter TFIIE adn TFIIH bind to complete the assembly o fthe pre-initiation complex
Which RNA pol II transcription factor remains attached ot the enzyme after intiation?
TFIIF
True or False? The terminator is part of the RNA-coding region ans is transcribed into the RNA transcript.
TRUE
True or False? Transcription and mRNA processing are coupled.
TRUE
linkage disequilibrium
Tendency for certain alleles at 2 linked loci to occur together more often than expected by chance. Measured in a population, not in a family, and often varies in different populations. whit tigers-slc45a2
template strand
The DNA strand that provides the template for ordering the sequence of nucleotides in an RNA transcript.
F factor
The ability of a donor E. coli cell to carry out conjugation is usually due to a specific piece of DNA called the ____ ______.
How is the termination sequence transcribed?
The approx. 40 bp sequence is transcribed into the RNA forming a secondary hairpin structure that is held together by H bonds. In some cases, termination is depended on the factor p (rho), a large hexameric protein that interacts with the growing RNA transcript.
allosteric
The binding of a regulatory molecule to a protein at one site that affects the function of the protein at a different site.
transmission genetics
The branch of genetics concerned with the mechanisms by which genes are transferred from parent to offspring.
protein turnover
The continuous breakdown and synthesis of body proteins involving the recycling of amino acids
mutagenesis
The creation of a mutation
luciferase
The enzyme that catalyses the oxidation of luciferin, a reaction that produces bioluminescence.
RNase
The enzyme that removes RNA primers at the end of replication
epigenetic reprogramming
The erasure and remodeling of epigenetic marks, eg. in germ cells and during early development of an embryo.
degeneracy of the code
The fact there are more triplets of coding than the number of amino acids in the genetic code.
primary structure
The first level of protein structure; the specific sequence of amino acids making up a polypeptide chain.
double helix
The form of native DNA, referring to its two adjacent polynucleotide strands wound into a spiral shape.
tertiary structure
The third level of protein structure; the overall, three-dimensional shape of a polypeptide due to interactions of the R groups of the amino acids making up the chain.
In which direction is hte polypeptide made?
N-terminus to C-terminus
electron carriers annd their precursors
NADH & NADPH (niacin) FADH2 (B2/riboflavin) FMNH2 (B2/ribflavin)
types of primary active transport mechanisms
Na-K ATPas (Na out, 2K in) PMCA (Ca out) H-K ATPase (H out K in) SERCA (Ca through ER membrane) Vacuolar H-ATPase (H into vesicle membrase) SPCA (Ca into golgi)
composition of Na_ channel and K+ channel
Na: TTX binding site, selectivity filter, activation gate, inactivation cate :K:s selectivity filter, activation gate
Which has an inactivation gate, Na or K channel?
NaChannel
autoploidy
Natural multiples of the same genome
directional selection
Natural selection in which individuals at one end of the phenotypic range survive or reproduce more successfully than do other individuals.
Fuel molecules transfer electrons to pyridine nucleotides (____) or flavins (____); these e- carriers then transfer e- to O2
Nicotinamide adenine dinucleotide (NAD+) Flavin adenine dinucleotide (FAD
What is PAGE and how does it work?
PAGE: PolyAcrylamide-Gel Electrophoresis 1. Proteins can migrate in an electric field 2. Migration rate of a protein depends on net charge, size, and shape 3. Solid support for protein migration: polyacrylamide - highly cross-linked polymer of acrylamide
What helps make many copies of a gene in vitro
PCR polymerase chain reaction -DNA copy number amplification -used to make cDNA lib -aplifies without cloning
seasonal isolation
Occurs when 2 closely related sympatric species breed during different seasons. Example: 2 sympatric termite species in souther florida. One breeds march-may, other in fall and winter---don't mate with each other.
how do you detect Rs (microsat.)
PCRs
Recognitions of __ ___ or the __ a.a. tirggers ubiqitination and subsequent degradation of the protein.
PEST domains, N-terminal
vicariance
Occurs when a physical barrier splits a widespread population into subgroups that are physically isolated from each other
What are the reprogramming factors used to induce pleuripotent cells?
Oct4 Sox2 Klf4 c-Myc
independent assortment
One of Mendel's principles that states that genes for different traits can segregate independently during the formation of gametes, the random distribution of the pairs of genes on different chromosomes to the gametes
ectoderm
One of the three primary (embryonic) germ layers formed during gastrulation. Ectoderm ultimately forms external structures such as the skin, hair, nails, and inner linings of the mouth and anus, as well as the entire nervous system.
splicing
One type of eukaryotic mRNA processing in which introns are removed from the primary transcript and exons are ligated together. SPlicing of transcripts can be different in different tissues.
siRNA
One type of ribonucleic acid coded for by the "junk DNA" is
What proteins is the NMR restricted to?
Only works well for smaller proteins with molecular weight less than 70 kilodaltons (kD).
transgenic organism
Organisms that contain functional recombinant DNA from a different organism
transgenic organsim
Organisms that contain functional recombinant DNA from a different organism.
___ powers the fomration of ATP
Oxidation
List the order of reaction in fatty acid degredation and when FADH2 and NADH are produced.
Oxidation (FADH2) Hydration Oxidation (NADH) Cleavage/Thiolysis
Intiation by bindin go the fMet begins in the _ site.
P
How is the trp operon organized?
P, O, trpL, attenuator, trpE, trpD, trpC, trpB, trpA
How does PKA affect other pathways?
PKA inactivates phosphofructokinase 2 in glycolysis/gluconeogenesis PKA inactivates pyruvate kinase in glycolysis PKA activates hormone-stimulated lipases in lipolysis
what makes CdRPA to lnGP?
PRA isom
What turns PRA to CdRP?
PRA isom. lnGP synth.
trpC
PRA isomerase lnGP synthetase
What types of hemaglobin do humans produce?
embryonic, fetal, and adult (express different a and B like chains by regulating transcription of their genes at the diff ddevelopmental stages)
retrotransposons
encode a reverse transcriptase for making DNA copies of tehir RNA transcripts, simlar to retrovirus (euk only)
maternal effect
encode for cytoplasmic determinants that initially establish the axes of the body of Drosophila
goblinn gene family
encode proteins with a heme-binding domain and cna bin oxygen..ex hemoglobin and myoclobin...thought hav arisen due to gen duplication of myoglobin which cam from another gene dup
mefv gne
encodes pyrin..mutations are missense...pyrin domain, pyd, is common to inflammasome complex
lacI gene
encodes the lac repressor
lacY
encodes the lactose permease, required for transport of lactose into the cell
restriction enzymes
endogenous to certain organisms, protect against viruses in lab they are used for cloning and DNA analyiss
While systems become more disorded with time, local order and complexity arise due to the input of __
energy
anabolism
energy and small molecules react to form complex molecules
anabolism
energy+small molec->complex molecules
____ stimulate transcription in specific cell types
enhancers
Hydration: _____ ____ ______ catalyzes the hydration of the trans double bond between C2 and C3. This reaction is ______.
enoyl CoA hydratase, sterospecefic
insulators (boundary elemnts)
ensure the activators act appropriately
histone acetyltransferase
enzyme acetylates histone arginine and lysine, removing the positive charge and weakening histone-DNA interactions, allowing proteins access to DNA
poly-A polymerase (PAP)
enzyme responsible for adding a string of adenine bases to the end of mRNA to protect it from degradtion later on
dna helicase
enzyme that move along and pry apart DNA helix using energy from hydrolisis of ATP
allozymes
enzyme variants
What is the largest group of proteins?
enzymes
recombination requires a hoste of ___ ad oher protein and uses __
enzymes, atp
What substance exposure can cause dna lesions
ethyl-methane sulfonate (EMS), and ethidium bromide
orgin of tetraploids
even number of chromosomes meas chromosome pairs can form in meosis produced eperimentally from diploid cells
Give some evidence of the genetic code being universal and state some exceptions to the rule.
evidence: eukaryotic genes can be inserted into bacterial cells and be transcribed and translated exceptions -mtDNA of yeast, humans -nuclear DNA of a bacterium and 3 protozoans
microevolution
evlutionary changes within populations of a species (changes in allele frequencies in a population)
evo-devo
evolutionary and developmental biology
macroevolution
evolutionary changes leading to speciation
Is ATP hydrolysis exergonic or endergonic?
exergonic (releases energy from bond breakage)
enhancer sequences
exert their stimulatory action over distances of several thousand base pairs
continuous varitiation
exhibit a continuous range of phenoteypes (ex. varying height)
How does mismatch repair wokr>
exonnuclease unwinds ad degrades DNA until mismatch is removed DNA poly. III replaced it with correct nt DNA ligase seasle the nixed DNA
Trans-splicing
exons from differnt RNA molecuels can e fused
lederberg-tatum experiment
experiment that showed when a mixture of two auxotrophic strains of E. coli were grown together, colonies appeared, but when grown separately, colonies did not appear; conclusion was that recombination had taken place
exonss
expressed sections of DNA, code for something
inducible gene
expressed when a certain chemical is present
N-formylmethionine
f-Met-t-RNA; the amino acid used in prokaryotes for initiation during protein synthesis.
trans-acting factors
factors, usually considered to be proteins, that bind to the cis-acting sequences to control gene expression
True or Fasle? genetic and environmental variance would create parallel lines
false..they cross
Explain the difference between fast fracture and fatigue fractures.
fast fracture -crack propegates quickly -stress above yield -typically due to trauma or imact fatigue fracture -repeated, cyclic stresses -stress below yield -seen in miltary bc of marching, ballet dancer, marathon runers
glucagon signals ___ & epinephrine induces ___
fasting state, release of glucose
Ketone bodies are formed in the liver when...
fat breakdown predominates. Ketone bodies can be regarded as a water-soluble, transportable form of acetyl units
unlike skeletal smooth muscle can go a long tie without...
fatiguing
fatty acid oxidation
fatty acid- acetyl CoA
In what form do lipid products pass from the lumen to the mucosal cell?
fatty acids + monacylglycerols-->form triacylglycerides on mucosal side
lipolysis gererates _____ ____ and _____
fatty acids, glycerol
eq for fitness
fecundityXsurvival
The weak interactions between biological molecules allows for ___ and a ___ nature, which is essential to functioning of many biological processes.
flexibility/dynamic
What conditions could result form nondisjuction in meiosis I?
for the trisomic, there would be a 47, XXX female or Klienfelter male (XXY) for the monosomic there would be a Turner female and the male monosomic would be lethal so there would be a 25% of a lethal inheritance
genetic units
form large intercomminicating gene pool
disruptive selection
form of natural selection in which a single curve splits into two; occurs when individuals at the upper and lower ends of a distribution curve have higher fitness than individuals near the middle
function of skull
form protective, supportive cavity -support facital struct -facial musc attachment
Rho-independent termination involves...
formation of a hair pin structure, followed by U's
angiogensis
formation of new capillary beds for wound healing
inversion loop
formed in the cells of an inversion heterozygote when the inverted region rotates to pair with the similar region in the normal homolog
High FMN (flavin mononucleotide), terminator ___, full mRNA ___ produced.
formed, isn't
Bacterial protein synthesis is initated by ________ tRNA
formylmethionyl
lampbrush chromosome
found especially in amphibian oocytes; chromosme in diplotene stage of first meiotic division characterized by paired lateral loops
What proteins are synthesize in free floating ribosomes and Er-bound ribosomes?
free-floating -cytoplasmic proteins -nucler proteins -mitochondrial proteins -choloroplast proteins ER-bound ribosomes -secretory proteins -lysosomal proteins -plasma membrane proteins
intercalary deletion
from the interior of the chromosome
GLUT5
frutose transporter in small intestine
catabolism
fuels (carbs, fats)-> CO2+H2O+energy
catabolism
fuels are broken down into useful energy and waste products (CO2, H2O)
assumptions of the onh
fully spherical vessel uniform thickness uniform material properties
reduction
gain of H loss of O part of anaboism
Lactose is the combination of ___ and ___.
galactose, glucose
life cylce
gametogenesis->fertilization->cleavage (zygote->bastula, localization of materal molec. in sea squirt)->gastrulation (cell signaling-induction)->
segmentation genes
gap genes, pair-rule genes, segment polarity genes
fragil siets
gaps, narrowings, or unstained areas in some regions of chromosome
slc45a2 mutation
gene enocdes 12-transmembrane transporter mut in white tigers change s ala-477 to val
positive control
gene espression is "off" by default; gene expression is turned on by a regulatory protein
Phospohlation on S 10 and acytelatio ofn K 14
gene expression
positive control
gene expression is "off" by default; gene expression is turned on by a regulatory protein
negative control
gene expression is "on" by default; gene expression is turned off by a regulatory protein
negative control
gene expresssion is "on" y default; gene expression is turned off by a regulatory protein
gene duplication and subsequent divergence give rise to ___. Duplications play a critical role in the evolution o fmultiple genes with related fuctions. Ex. ___
gene families -trypsin and chymotrypsin -hemoglobin and myoglobin
redundant genes
gene sequences present in more than one copy per haploid genome (ex. ribosomal genes)
histone variants
generally inserted into already-assembled chromatin by histone chaperones working with chromatin remodeling complexes (H2A.Z, H3.#)
unnatural bases
generated by deamination can easily detect
cistrons
genes in bacteria
marfan syndrom
genetic diseas from misfolidnig of fibrillin-I results in tall, ong arms, flat feet and long, thing fingers, heart palps
recombinant dna
genetically engineered DNA made by recombining fragments of DNA from different organisms
GWAS
genome wide association studies SNPs (500k+) in each study
advantage of genomic ibrary and cDNA library
genomic -cles represent all regions equally..the intact genome cDNA -clones reveal which parts of the genome cantian the information used in making the proteins in specific tissues, allows comparison of gene expression
Nonrandome mating changes ___ freq but not __ freq.
genotype, allele
polytene chromosome
giant chromosomes consisting of many identical chromatids lying in parallel register, chromosome bundles
mylination is through __ in the CNS and ____ in the PNS
glial cells, schwann cells
glycolysis
glucos->pyruvate
Does E. coli prefer glucose or lactose?
glucose
group-transfer reactions
glucose + ATP-> G-6P + ADP
maltose
glucose + glucose
The muscle prefers glucose over fatty acids because....
glucose can be metabolized anaerobically while fatty acids cannot *Exception - heart muscle
Ketone bodies can be produced to high amounts in insulin-dependent diabetes because ..........
glucose can't be sensed
What are the storage forms of glucose?
glucose polymers, glycogen, starch (amylose, amylopectin), & cellulose
What can do the kidneys filter out
glucose, amion acids, ketone bodies, urea
___ goes to the liver for processing, while __________ go to other tissues for use
glycerol, fatty acids
Adipose releases ___ and __ when signaled by ___ and ___
glycerol, gatty acid-albumin complexis, glucose, VLDL
Immediately after a meal, when glucose and fatty acid levels are high, insulin is secreted and signals tissues to store fuel as...
glycogen and triacylglycerides
Fuel store, Preferred Fuel, and Fuel Sources Exported for skeletal muscle at rest and during exertion.
glycogen, fatty acids, none none, glucose, lactate, alanine
___ can recognize different damaged bases and travel along DNA using ___ to evaluate the status of each base
glycolases base-flipping
Glycerol is made into pyruvate by ____ or into glucose by ____.
glycolysis, gluconeogenesis
conservative genetics
goal: understand, mainatin, and restor pop viability conservation
reading frame
The way a cell's mRNA-translating machinery groups the mRNA nucleotides into codons
trans-acting
These are factors that need not be adjacent to the genes they control. An example would be the lac operon's repressor protein.
Why are inverted repeats needed in the termination sequence?
They help form the secondary hairpin structure which is formed with the H bonds that appear between the inverted repeats.
homeodomain
This conserved region of about 60 amino acids often coincides with the helix-turn-helix structural motif methylated lysines
True or False? Activator GRPs are synergistic.
Treu
______ are the storage form of fatty acids
Triacylglycerols
edward syndrome
Trisomy 18; Caused by nondisjunction during oogenesis; symptoms include clenched fist showing overlapping fingers, rocker bottom feet, congenital heart defects, micrognathia, mental retardation; usually patients die within a few years of life
True or False? A code-reader-writer complex can spread chromatin changes along a chromosome
True
True or False? All mRNA is capped.
True
True or False? All types of RNA are synthesized by bacterial RNA polymerase.
True
True or False? Chain folding and activation of proteins often happen at the same time.
True
True or False? Eukaryote pre-mRNAs can be alternatively splice to yield different protiens.
True
True or False? Nearly all amino acids are chiral compounds
True
True or False? Peptide formation is thermodynamically spontaneous?
True
True or False? The more complex the organism, the more introns per gene.
True
True or False? The ribosome is a ribozyme.
True
True or False? There is never an intron on the ends of DNA.
True
True or False? DNA replication is bidirectional
Ture
agarose gel
Type of Chromatography, used to separate nucleic acids based on size/length of chain. The media serves as the stationary phase and the nucleic acid as the mobile phase. Negatively charged nucleic acids travel toward the anode (positive end). Smaller strands travel faster than larger chains.
snRNA
Type of RNA found only in the eukaryotic nucleus that is involved in processing of initial mRNA transcription products to a mature form suitable for export from the nucleus to the cytoplasm for translation
SDS-PAGE
Type of chromatography used to separate proteins based on mass. SDS binds to the proteins, giving them a negative charge cancelling the effect of charges from the individual amino acids. Lighter proteins travel faster than heavier ones.
E complex
U1, BBP, and U2AF (binds to pyrimidine tract (subunit 65) and 3' splice site (suunite 35))
roles of the specific snRNAs
U1-binds the 5' splice site U2- binds the branch site and forms part of the catalytic center U4-masks the the catalytic activity of U6 U5-binds the 5' splice site and then the 3' splice site U6-catalyzes splicing
A complex
U2 (displaces BBP leaving active A)
U2AF
U2 auxillary factor (attaches after BBP)
B complex
U4:U5:U6 (tri-snRNP particle) comes in, & U2AF leaves -U6 displaces U1 -assembly complete -U 4 leaves, triggering catalysis
When the loop breaks off, which snRNA gets carried aways with the exon before detaching?
U5
Which snRNP displaces the U1?
U6
Electrica potential
U=(1/(4pi*eo)(q/r)
Stop codons
UAA UGA UAG
What are the termination codons?
UAG, UAA, and UGA
How do you determine Ucr
Ucr=Gc*t*da t=thickness a=preexisting crack length da=incremental length Gc=toughness
How do you find Ue
Ue= -pi *sigma^2/(2E)
quantitative genetics
Uses statistical models to describe the heritability of a trait.
concordance value
Values for twins that show the likelihood of sharing phenotype traits. H^2=2(rMZ=rDZ)
VNTR
Variable Number Tandem Repeats. Contains anywhere from 20 to 200 base pairs, comes from parents. ALL humans have VNTRs
component of genetic variance
Vg=Va+Vd+Vi Va=addiive Vd=dominacne Vi=interaction
generalized transduction
Virus moves from cell to cell and carries genetic info
Phenotypic cariance
Vp=Vg+Ve+Vge Vg=genetic Ve=environment Vge=enetice-environment interaction
power=
W/t work/time
What are the 3 different blotting techniques?
Western blotting (aka immunoblotting) -Detecting a specific protein in a sample -Probe: specific antibody that recognizes this protein Southern blotting -Detecting a specific DNA in a sample -Probe: a labeled short stretch of nucleotides that recognizes the sequence in the DNA to be detected Northern blotting -Detecting a specific mRNA in a sample -Probe: a labeled short stretch of nucleotides that recognizes the sequence in the mRNA to be detected
What weakens a H-bond?
When an H bond forms in a non-straight manner, it is weaker than when the H-bond donor and acceptor are aligned, making it highly directional.
catabolite repression
When operons that encode catabolic enzymes are inhibited if the end product of the reaction, the catabolite, is abundant
AMPK
When the cell senses a higher level of Adenosine mono phosphate than Adenosine triphosphate it will activate _____, Triggers fatty acid oxidation and ketogenesis in the liver and skeletal muscles. Upregulates GLUT4
How might overlapping genes occur?
When there are multiple initiation points, multiple reading frames can be produced. Is a select few viruses and bacteria, this has been known to happen.
secondary contact
When two allopatrically speciated populations are brought back together. Can result in a fusion of populations, complete isolation, hybridization,
pol a
Which polymerase polymerizes the lagging strand?
partial diploids
With rare exceptions, after gene transfer occurs through conjugation or transduction in bacteria, the recipient cells become
Most all peptides are trans, except for ___ where trans and cis have the same energy.
X-Pro due to steric hinderances
XIC
X-inactivation center, a short region on the X chromosone
Of the 103,015 protein structures elucidated, how many have been found with X-ray crystallography, NMR spectroscopy, and electron microscopy?
X-rays crystallography: 90% NMR spectroscopy: 10% Electron microscopy: about 100 structures
protenor
XX/XO a butterfly, mode of sex determination: based on how many copies of the X chromosome, two copies indicates female, one copy indicates male
Does attachement of an amino acid to the tRNA attachment site require ATP?
Yes
Does the o- subunit dissociate from the holoenzyme after it has fulfilled its function?
Yes, after a few ribonucleotides have been added, the sigma subunit dissociated and elongation proceeds.
When does pH=pKa?
[A-]=[HA]
List the source and amount of energy stored in your muscles at rest.
[ATP] = 4 mM [ADP] = 0.013 mM [creatine phosphate] = 25 mM [creatine] = 13 mM
Keq
[C]/([A][B])=Keq where C is the product and A&B are the reactants
Which subunit is there more than 1 of in the RNA polymerase?
a (2)
What are the subunits of the E. coli RNA polymerase holoenzyme? Name their known functions.
a (alpha) B, B' (betas)-catalytic bases and active site for transcription o- (sigma factor)-regulatory function in RNA transcription initiation, it recognizes DNA promoters allowing RNA polymerase to bind upstream
heteroduplex
a DNA double helix composed of single strands from two different DNA molecules
merozygotes
a cell with two copies of some genes
dicentric chromosome
a chromosome with two centromeres caused by a terminal break
Histone code is ready by...
a code-reader complex
heli-turn-helix motif
a common motic, 2 a helices lac operon motif
alloploidy
a common type of polyploidy species resulting from two different species interbreeding and combining their chromosomes
heteroduplex
a construct that forms during genetic recombination where one strand from one parent is base paired to the complementary strand of the other parent, a double-stranded region of DNA that contains one or more base mismatches
trans-acting
a diffusible regulatory molecule, ususually a protein, that binds to a specific cis-acting element.
huntington disease
a dominant neurological disorder with onset in middle age, normal individulas have 6-35 CAG repeats. Individuals with this disease have many more....an example of genetic anticipation (onset earlier after each new generation)
copy number variants
a form of structural variation (alterations of the DNA of a genome) that results in the cell having an abnormal number of copies of one or more sections of DNA
FMR-1
a gene code for FMRP that is associated with mental retardation. This is located on the long q arm of the X chromosome recessie sex-linked, triple repeat amlification, fragile x is an x-linked syndrome that causes mental retardation from faulty __ gene in a cgg repeat
one gene, one enzyme hypthesis
a gene contains the information for producing a specific enxyme
Repressible gene
a gene that is repressed when a certain chemical is present
repressible gene
a gene that is repressed when a certain chemical is present
one gene, one polypeptide hypotheses
a gnee contains the information for producina specific polypeptide
operon
a group of contiguous genes that are transcribed into a single mRNA molecule (on a bacterial chromosome)
operon
a group of genes that are regulated together an transcribed as a polycistronic message
population
a group of individulas of the same psecies that live ina defined geopgraphic area and are able to interbreed
fragil x syndrome
a male that has defect in a gene on the X chromosome of hte 23rd pair, leading to a deficiency in a protein needed for brain development, example of genomic imprinting. cells know which parent they came from and react differently based on that; only causes developmental delay when the mother transfers her broken X to son.
sarcoplasmic reticulum
a membrane that loosely surrounds each myfibril, Organelle of the muscle fiber that stores calcium.
interrupted mating
a method used in conjugation experiments in which the length of time that the bacteria spend conjugating is stopped by a blender treatment or other type of harsh agitation
5' cap
a methylated guanine nucleotide added to the 5' end of eukaryotic mRNA. The cap is necessary to initiate translation of mRNA
auxotroph
a microorganism that requires an organic growth factor
trans-acting molecule
a molecule (usually a protein) that regulates gene expression by binding to DNA
trans-acting molecule
a molecule (usually a protein) that regulates gene expression y binding to DNA
bicoid
a morphogen, it affects cell fate in a concentraion-dependient many is necessary for devleopment of the anterior region of the embryo a meternal effect gene-pheotype dep on mom 2 functions-trascription activation and tranlational repression
founder effect
a new population founded by a small number of individuals
Rho-dependent termination involves...
a p (rho) protein that uses ATP and H20
chymotripsin
a pancreatic enzyme that digests proteins.
what's in the attenuator that is inside the leader region
a pause site and a termination site
What does a condensation reaction between two amino acids result in?
a peptide bond
amphiploidy (or allopolyploidy)
a polyploid that originated via doubling of the chromoseomes of a zygote with two unlike chromosome sets usually intially from hybridization between two species (at least 1 diploid set from each parent)
metapopulation
a population composed of spatially separated subpopulations with limited gene flow
Rho-dependent terminatoin
a protein termination factor called p (rho) binds to RNA transcript and causes release of the RNA transcript
antiterminator
a protein that promotes the continuation of transcription by preventing the termination of transcription at specific sites on DNA
identity
a quality that an entity posses which is a by-produce of its origin and its ability to remain distinct from other entites (such as...recognize own species, morphological or behavioral traits, or mix)
attenuator
a region of RNA sequence that forms alternative secondary structures that govern the level of transcription of attenuated operons.
heteroduplex region
a region of double-stranded DNA in which the two strands have nonidentical (though similar) sequences. Heteroduplex regions are formed as intermediates during crossing-over
What happens when a prokaryote reaches a stop codon in the A site
a release factor binds, GTP dependent
Give the genes that code for each subunit.
a rpoA B rpoB B' rpoC w rpoZ o-70 rpoD
inversion
a segment of chromosome is excised and reintegrated at an orientation 180 degrees from the original orientation.
template
a sequence of DNA or RNA that directs the synthesis of a complementary sequence
oligonucleotide
a short DNA fragment that can be synthesized by a machine, are short sequences of nucleotides (RNA or DNA), typically with twenty or fewer bases.
Operator
a short region of regulaotry DNA to which the lac repressor binds
Nilsson-Ehle experiment
good example of polygenic trait -each gene had additive and nonadditive allele, the greater the additive in th egenotype the more intense the red color (assume contribute equally, unaffected by environment)
when a stretche muscle is timulate tanically it produces a force in addtion to passive force, this is called...
active tension
actual vs standard free-energy change
actual: determines the spontaneity or a rxn, its value varying from concentration of reactants and produces standard: free energy difference of reactants under standard conditions (T=25 C, pH=7, C=1M)
unlike neurons, muscles stimuli are __
graded
anagensis
gradual transition from one species to another
Which mRNA group is sliced using a G cofactor?
group I
population
group of individs belonging to the same speciees that live in a defined geographical region
h^2
h^2=(M2-M)/(M1-M)=R/S R=selction response (degree of responce to mating selected parents) S=selection differntial (difference between mean for whole population and mean for selection population
Narrow-Sense Heritabilityp
h^2=Va/Vp
Once the inverted repeats are transcribed they fold into a _____ loop, which causes RNA polymerase to pause.
hairpin
More than ____ of the genome is non-functional.
half
What keeps a fast frature propegating?
having enough energy W>= Ue+Ucr W=work Ue=increase in elastic energy Ucr=energy needed to incrementally increase crack size when inequality is not true the crack stops growing
Tetraploids can arise when after replication the cell fails to divides or can be induced by applying ___ or __ to diploid cells undergoing meiosis or by applying ___ to somatic cells undergoing mitosis
heat, cold shock, colchicine
How do you acomplish denaturing durina a PCR
heating DNA to 95 C
relative refractory period
hen it is possible to tstimulate nerve cell after another action potential has passed through (harder than with resting neuron) lasts about 4 ms
An individual XX chromosome can be completely inactivated by _____ fromation
heterochromatin
methylation on K 9
heterochromatin fomration, gene silencing
How would you distinguish heterochromatin form euchromatin on a microscopic image?
heterochromatin is dark
What is missing from the 5' end that prevent growing from 3' to 5'
high energy phosphate bon
What ionos have a higher concentration in the cytosol than the extracellular fluid and which have alower concentration?
higher: K+ lower: Na+, Cl-, Ca2+
What are the 3 aromatic amino acids?
histidine phenylalanine tyrosine
Explain how histone acetylation affects histone modification
histo acetyltransferases (HATs)-add actyl groups to histones to prome an open chromatin conformation (more gene expression) histone deacetylases (HDACs)-promote closed structure (repress expression)
Triacyl glycerals are hydrolyzed by _____ lipases
hormone-stimulated (under conditions of low glucose epinephrine and glucagon trigger)
Hydrophobic functional groups
hydrocarbon cahings (R-CH3) aromatic
Biomolecules are derivatives of ______.
hydrocarbons Biomolecules: H atoms of hydrocarbons replaced by functional groups
oro's purine synthesis
hydrogen cynide->adenine (forms atp, dna, and rna
RNA polymerase has some proofreading abilities and uses a __ reaction to remove incorrect sequences when it backtracks.
hydrolysis
__ fomrs the C-terminus of the protein
hydrolysis
Unwinding of the DNA involves ATP ___
hydrolysis (for ATP, ATP->ADP)
What caps a fatty acid?
hydrophilic carboxylic acid head
an outward current results from a ____ stimuli
hyperpolarizing
the RNA world
hypothesis: life began as a collection of small number of sell-reproducing catalytic RNA molecules localized withina a small area supportive evidence: -some RNA cna catalzye chemical rxn -some rna can replicate themselves if ribonucleoties are present -explians metabolisma nd geteic cariability
types of sponteaneous mutation
hyrolysis radiation uV light oxidation, etc
Ohm's law for 3 dimensional gradient of currents
i=(z^2e^2C)/B*(-gradV)
oxidative phosphorylation
ion gradients across membranes provide and important ofmr of cellular energy that cen by coupled ot atp synth
ferritin
iron storage protien
problems with iron-sulfur world
iron sulfur world does not explain the generation of genetic material, and does not include reproductino or geetic cariability
amphibolic pathways
irreversible and regulated steps of each pathway are distinct between catabolisma and anabolism
amphiobolic pathways
irreversible and regulated steps of each pathway are distinct between catabolisma nd anabolism
Hunchback protein
is produced from its RNA and then acts as a transcription factor to regulate genes for differentiation in the anterior of embryo (Kruppel for other side)
reduction in gene flow may occur due to ___ and )) of pop resulting from habitat loss
isolation and framentation
activation of muscle can produce force without actually shortening, this is ___ contractions
isometric
What in the inducer used in the lab for the lac operon?
isopropyl-B-D-thiogalactoside (IPTG)
adding membrase area is likened to ...
adding resistors in parallel, thus reducing the overall resistance (remember that conductance, G, add while the inverse of the resistances, 1/R, add)
mRNA processing
addition of 5' cap and 3' tail
polyadenylation
addition of a short sequence or a tail of adenine (poly A-tail) nucleotides to the 3' end of an mRNA molecule. happens during RNA spilcing in eukaryotes.
E1
adds AMP to Ub and forms thioester linkage to Ub
Poly-A-polymerase (PAP)
adds one A at a time
Where is the prach point located and what base is it?
adenine "A" 18~40 nucleotides upstream of 3' spslice sitE
Give the base and nucleoside name for all bases..
adenine---adenosine guanine---guanosine cytosine---cytidine uracil---uridine thymine---thymidine
Glucagon stimulates the .....
adenylate cyclase pathway
Glucose inhibits _____, an enzyme that converts ATP into _____
adenylyl cyclase, cyclic AMP (CAMP)
Advantages and disadvantages of captive breeding
adv-ability to rbuiild a pop disadv-limited pop size lead to reduced heterozygosity in pop, pot loss of good alleles
advatages and disadvantages of gene banks
adv-preserve original genetic diversity disadv -only small selection of pop -storage conditions create selection pressures -favored developed countries but underdeveloped have greatest diversity
How do proteins go from translatio to full functional proteins
after folding, proteins get activated by post-translational modifications the are either resible covalent mod. or irreverible mod.s
glycosylation
aglcosylase=ttachment of carbohydrates
Are anabolic steroid and antagonist or agonist?
agonist
northern blot-rna on gel
agros gel stained with ehtidium bromide radioactie probe too
homologous recombinations
aka General Recombination, refers to recombination between two DNA molecules with extensive regions of sequence similarity (homology)
microsatellite
aka: Simple Sequence Repeats (SSRs) - Polymorphic loci present in nuclear DNA and organellar DNA that consist of repeating units of 1-4 base pairs in length. They are typically neutral, co-dominant and are used as molecular markers which have wide-ranging applications in the field of genetics, including kinship and population studies
what is the issue with chirality?
all 20 amino acids essential for life are L isomers, the amino acids produced in millers experiment lacked chirality
Support for all things came form a single organism?
all organsims today share many common features, proetins,a nd meabolic pathways
what makes up the motor unit
alll muscle fibers inervated by a single motor neuron
What is the lac operon inducer in cells?
allolactase (a disacharide)
GLUT1
allows facilitated diffusion of Glc across BBB
primary antibody
allows the specific detection o the protein of interest
Dietary carbohydrates are first digested by ______
alpha-amylase
post trsncript/transla. control methods
alt splicing and alt polyaden. difference rate mRNA trnasport, translation, degredation protein degredation
point mutation
alteration of single bp (base substitutions, insertion or deletions)
Wht are some other strategies>
alternate corn strains (bt1 and bt1) (could work but cross resistance is a problem, if res to 1 likely res to the other) pesticide pyramids-corn strans that produce mutlitple pesticides crop rotation-if the eggs ar layeed one season and hatcch the next, switch crops so the larvae don't have food
A gene that is constitutive is...
always on
The beginning of a polypeptide chain is the _____ group.
amino
______ tRNA synthetases activate tRNA and attache the amino acids to the tRNA
aminoacyl
What enzyme helps attach amino acids to tRNA
aminoacyl-tRNA synthetase By taking an amino acid and ATP, it attaches AMP to the amino acid and then tRNA comes and attaches to the amino acid.
F' factor
an F factor that has incorporated part of the bacterial genome
tamoxifen
an antagonist for steroid-hormone receptor binding (raloxifen is too)
What marks the vector
an antibiotic resistance marker that allow for its selection
buffer
an appropriate mixture of weak acid and its conjugate base which generates a powerful solution, resistant to changes in pH
endonuclease
an enzyme that breaks the internal phosphodiester bonds in a DNA molecule.
evolutionary species concept.
an evo species is a lineage evolving spearately from others and with its own unitary evo role and tendencies
fitness
an individulas ability to survive and reproduce
Parallel B-sheet have ___ links and ___ strand links while anti-parallel B-sheets have ___ links and ____ strand links.
angled/hairpin straight/over the sheet
In ion exchange chromatography, ___ exchanger has __ resin the binds ___ molecules, thus allowing the ___ molecules to pass through quicker.
anion/+/-/+
maternal effect genes
anterior, posterior, terminal group
What is the 2 component fo the reaction?
anthranilate
What is the 1 step in the trp pathway catalais?
anthranilate synth. I and II (and glutamate)
trpE
anthranilate synthetase component I
trpD
anthranilate synthetase componets II (PRA sythnetase
dna a strands are arranged ___
antiparallel
protease
any enzyme that catalyzes the splitting of proteins into smaller peptide fractions and amino acids by a process known as proteolysis, An enzyme that digests proteins by hydrolysis.
definition o flife?
any population of entities which has the properties of multiplication, heredity, and variation- John maynard smith life is an expected, collectively self-organized property of catalytic polymers-staurt kauffman life posses the propeties of replication, catalysis, and mutability-norman horowitz life is a self0sustained chemical system capable of undegoing darwinian evolution-gerald joyce
membrane resistance (Rm) depends on ..
area of the membrane
fragile site
areas on chromosome that develop distinctive breaks or gaps when cells are cultures. No relationship to disease (except fragile X)
pseudogene
arise from integration of reverse-transcribed mRNAs, it's a nucleotide sequence of DNA closely resembling that of functional gene but is not expressed
monocistronic mRNA
as a rule....all eukaryotes have mRNAs that encode for only 1 protein
cooperative binding
as one oxygen molecule binds hemoglobin, the molecule changes shape which makes it have a higher affinity for the next oxygen molecul
How is intraspecific diversity measured?
as the frequency of heteroxygosity at a given locus or as the number of different alleles at a locus in the gene pool
What assumptions are made in crack propegation equations
assume material behaves fully linearly elastic, but bone is not elastic bec it depends on the orientation of the bone and water content of the bone
What is the High Dose/Refuge strategy?
assumption: resistance to Bt is recessive, and there are many Bt-sensitive insect for mating heterozygotes may be resistant to low does of toxin but are killed by a high dose of toxin 5-20% refuge depending on location keep plants for them to eat so that they don't evolve a resistance to the bt corn
the reverse citric acid cycle
at hydrothemal vents, there is a constant stream of hydrogen gas and enegy generated from the reation of hydrogen sulfided with iron sulfide. teh reations can be catalyxed by iron sulfide, pyrite, or other iron-sulfur complex in organims, the ractions are catalyxed by enzymes, most enzymes require ionr-sulfur clusters to work
Where is the anti codon located?
at the opposite end of the attachment site
lipidation
attachment of lipids to C- or N- terminus
The tryptophan operon contains a repressor and an ____
attenuator
The Lac genes are only expressed at high levels when lactose is _____ and glucose is ___
available, not
fecundity
avg number of offspring born to a femal with a particular genotype
survival
avg proportion o foffspring that survive to sexula maturity
velocity of the nerve condution is directly dependent ofn ___
axon diameter
highest tesnisle strain on skull a) chewing b)walking c) jumping d) smiling
b) walking
Which of the following is correct about SDS? a.) SDS is a reducing agent that breaks disulfide bonds. b.) SDS is a powerful negatively charged detergent that unfolds proteins and gives proteins extensive negative charges. c.) SDS helps to preserve the 3-dimensional structure of protein. d.)All of the above.
b.) SDS is a powerful negatively charged detergent that unfolds proteins and gives proteins extensive negative charges.
b
b=h^2 regression coefficient the slop of the line tells you how much of the phenotyp can be inherited
What is the simplest life as we know if?
bacteria-single cell organisms with the ability to independly reproduce and generate new bacteria
polycistronic mRNA
bacterial mRNA, it encodes for more than 1 protein. in bacteria, groups of genes whose products are related often clustered along the chromosome. In many such cases, they are contiguous, and all but the last gene lack the encoded signals for termination. The result is that during transcription, a large mRNA is produced that encodes more than one protein.
transduction is mediated by___
bacteriophages
GLUT3
basal glucose uptake for all tissues
Nucleoside vs Nucleotide?
base+sugar=nucleoside bas+sugar+phosphate=nucleotide
A-DNA
bases are more inclined, helix wider, 11 bases pairs per turn. Major (deep) groove is narrow and minor (shallow) is wide
Hfr stain
bateria conjugate with f bacteria, part of bacterial chromosome can be transferred transfer of genes can be used to map genes on the e coli
What bacteriophage did Walter Fiers use to confirm the genetic code studies and what did his experiments show?
bateriophage MS2 (infects E. coli and has 3 genes) He showed colinearity, that is the triplet code matched the amino acids found in the proteins.
mycelogenous luekemia
bcr/c-able onocogen always active c-able: encodes tyrosine kinase bcr: breakpoint cluster region due ot chromosomal mutation--reciprocal translocation between cc-able and bcr gene teh phyiladelphia chromosome
Why is water cohesive?
because of H-bonding
cellulatization
begins with primitive lipids in the surface metabolism..then accumulate
3' polyadenylation
believed to be important for protecting mRNA from exonucleases, serves as handle to deliver mRNA to ribosome
Cleavage:_______________ catalyzes the hydration of the trans double bond between C2 and C3
beta-ketothiolase
ex genetic drift
big horns rock mount sheep,
Cys2His2 zinc-finger domains
bind in tandem along the major goove on DNA
In prokaryotes, GTP is used to..
bind the large ribosomal subunit (50S)
activator preotein
bind to enhancer sequences ex. heat-shock transcription factors bind to heat shock elemnts in yeast
Activators
bind to enhancers and then -recruit chromatin remodelin comlexes (ex HAT) -interact with GTFs -interact with coaactivatorproteins -increase rate of transcription initiation
What do transcription factors bind to and what is their role?
bind to promoter sequences recruit RNA polymerase II mandatory for initiation
Repressors
bind to silencers and then -inhibit formation of PIC -stimulate or recruit chromatin remodelin protiens (HDACs) -block interactions between enhancers and activators -block interactions between promoter elements and the PIC
promoter elements
binding sites for transcription factors; hormone binding sites for thyroid hormones, glucocorticoid hormones and cAMP; increases or decreases transcription
bromodomain
binds to actyllysine; found in many transcription factors
When lactose is absent, the repressor protein...
binds to the operator sequence, resulting in repression of structural gene transcription
poly-A-binding protein
binds to the poly A tail and helps stabilize the process and determine the lenth of the tail
why is conservationgenetics important?
biodiversity depends on genetic diversity
Barrier DNA sequences
block the spread of reader-writer and thereby separating seighboring chromatin domains
On a 2D page, basic to the left and SDS migration top down, where would a small acidic protein end up?
bottom right quadrent
BBP
branchpoint-binding protein
highest comrpessive straing on skull (most negative) a)smiling b) chewing c) heading heavy ball d) wlaking
c) heading heavy bwall (2nd is chewing)
How is cAMP involved in the positive regulation of the lac operon?
it binds the to CAP which then binds to the CAP binding site on the prmoter...as cAMP increases due to low glucose more CAP will be bound to cAMP and more lac genes will be turned on by the promoter
What is the very first precursor for the reaction sequence that makes tryptophan?
chorismate
Each chromosome occupies a discrete domain called a ___ __.
chromatin territory
Histone binding domains are present in ...
chromatin-remodeling and histone-modifying complexes
origin of inversion
chromosome breakage (in two places) -recombination technique
What would havppen without telomere
chromosome fusion and massive genomic instability
Consensus sequences -10 and -35 act in __.
cis
Elements that act in ___ can influence only the expression of adjacent gene on the same DNA molecule.
cis
Enhancers
cis regulatory elements that increase the rate of transcription (position-intependent and orientation -independent
silencer
cis regulatory elements that repress transcription initiation
General (or basal) transcription factors bind ____ elements in eukaryotic promoters.
cis-acting
mutagenesis sreen to locate ____ elements
cis-acting
What are the cis-acting elements and what are the trans-acting elements?
cis-acting-the promoters (-10, -35 consensus sequences) trans-acting the polymerase (simga factor)
__ and __ stimulate in gluconeogenesis
citrate and actyl CoA
isomerization reactions
citrate->isocitrate
primer walking
clone entire fragemnt, sequence from the end and design a new frimer from each new sequence read fo rht enext seq reaction
When there is an ionizable side chain, you find the pI using the two ____ pKa's.
closest
costameres
clusters of structural proteins linking Z disks of sarcomeres to the sarcolemma of striated muscle cells -force tansfer -mechanical support -unifrom spacing
The strand of DNA that as the same sequence as the RNA transcript with T instead of U is called the ____ strand. The RNA transcript is coded from the ___ strand.
coding, template
nonsense
codon for amino acid converted to a stop codon
Fatty acids are linked to _______ before they are oxidized via ________ _____
coenzyme A, acyl CoA synthetase
mutulatism is likely to result from coevoution orcospeciation?
coevolution
contrast coevolution and cospeciation
coevolution->reciprocally induced evelutionary change between two or more species; the gene for gene hypothesis cosepciation:->phylogenetic tracking of host clades by parasite clades; resulting from essentially vicariance among the parsite being induced by a specation event within the host
supraspecific taxa
collectinos of lineages grouped together on the basis of hypthesized past linkages
2^n
combinations possible when chromosomes assort independently where n is halploid number
determination
commitment of a a cell to a specific developmental fate
eupolidy
complete haploid sets of chromosomes are present
How are complex and simple carbohydrates different?
complex->polysaccharides (sucrose, lactose, maltose) simple->(fructose, galactose, mannose, glucose)
Problems with the High Dose/Refuge strategy?
compliance->depends on farmers planting refuge fields (25% farms don't comply with guidlines) bt plants produce fairly low level of toxin->meaning heterozygotes survive..too many survive and reproduce in iowa bt resistant rootworm appears 3 yrs after planting bt corn'l
rRNA
components of ribosome structure
zwitterions
compounds that have a positive charge on one atom and a negative charge on the other
substrate-level phosophorylation
compounds wiht high phyosphoryl-transfer potential can couble with CO2 oxidation to ATP synth (GAP+NAD+HPO42-) (1,3 bisphosphoglycerate+ADP)
A real membrane is not parallel plate capacitor, but a ..
concentric coaxial capaitor
What contributes to IFs leaving and the large subunit associating with the small subunit
confomrational changes and GTP hydrolysis
How are introns and exons distinguished from eachother?
consensus sequences...
Is the protein produced by lacI done constitutively or inducibly?
constitutively
How does allolactase work to help lactose metabolism?
it binds to the repressor protein (chaning its conformation) so that transcription of the structural genes are induced
Genes need for metabolism in E. Coli are transcribed ___. ___ is the preffered carbon source and other varieties of sugar are metabolized by....
constitutively Glucose adjucting gene expression (inducable genes)
genes that are always expressed
constitutively expressed genes
telomere
contain repeated nucleotide sequences that enable the ends of chromosomes to be replicated. Also protect the end of chromosomes from being mistaken by the cell as a broke DNA molecule in need of repair.
davis experiment
continuation of Lederberg-Tatum experiment; constructed U-shaped tube with filter in the middle & two auxotrophic strains on either side; when plated, no bacteria grew on cultures; conclusion was that genetic exchange requires direct contact between cells (conjugation)
eccentric contraction
contraction of muscle causeing lengthening
concentric contraction
contration of muscle that causes shortening
Hormones act as ___ gene regulation.
coordinated.
The RNA polymerase holoenzyme consists of a ___ enzyme and the __ subunit.
core, o-70 (sigma 70) BACTERIAL
specificty o freplication is dictate by _____
corect base-pairing
Tryptophan is the ____ of the repressor protein which can only bind to the operator if it is present
corepressor
What happens when CAP is not bound to cAMP?
it cannot bind to the promoter and cannot activate transcritiption, this happens when glucose is present
What does allolactose do when it is in a cell?
it induces expression of genes necessary for lactose metabolism
Compare youn's moduli and force characteristics of trabecular and cortical bone.
cortical -resists torque -avg. 20.7 GPa tabecular -resists shear and compressive forces -avg. 14.8 GPa
What are the 2 main osseous tissues?
cortical and trabecular (or cancellous)
What fraction of bones are cortical and trabecular? Compare internal surface area of each type.
cortical- .8, 3.5*10^6 mm^2 trabecular- .2, 7*10^6 mm^2
Difference between cortical and trabecular bone tissue?
cortical-compact, high strength, low porosity trabecular-spongy, high porosity, high surface area
The lac repressor is ____ expressed and will always bind the repressor, unless...
costitutively, induced not to (for the lac repressor, its inducer is allolactose a dimer formed from lactose by B-glactosidase)
Major difference between transcription and translation in prokaryotes and eukaryotes.
coupled in prokaryotes because there is no nucleus uncoupled in eukaryotes
Overcome an energetically unforamble rxn (-dG) by..
coupling it with a favorable rxn
What marks the tails where the protein modules of a code-reader complex binds to the nucleosome core?
covalent modification
gene flow
creaded by the dispersal of gametes or by migration of individs introduce new alleles into gene pool->increase genetic variation animals: migration plants: coss pollination and seed dispersal
when ATP is used up in the muscle, ____ ___ acts as a reservoir of phosphoryl gorups that can be transfered to ADP to make ATP
creatine phospahte
unequal crossing over
crossing over between homologs that are not perfectly aligned
stuctural alterations
cuase by leasons such as base mismatcha nd pyrimidine dimer can be easily detected
What two amino acids contain sulfer?
cystine and methionine
Glycolysis occurs in the ___. The krebs cycle occurs in the ____. B-oxidation occurs in the ___.
cytosol, mitochondria, mitochondria
How much of eucaryotic cell is protein by weight? a.) 23% b.) 16% c.) 10% d.) 18%
d.) 18%*
LINEs
long interspersed seq. repeated seq 5k bp long, inerspersed among unique seq DnA up to 35 k bp lone 20% of human genome encode enz. for their own retrotransposition ex. L1
Xist
long ncRNA that facilitates X inactivation
VNTR (minisatalites)
longer than ST not as common as STRs
oxidation
loss of H gain of O part of catabolism
Heritability values are ___ for quantitative traits that are essential survival.
low
What hormones regulate ACC during low and high glucose levels.
low-> glucagon (activate lipolysis) & epinephrine (inhibit fatty acid synth. high-->inu
During lysogenic growth, lambda repressor represses expression o fproteins required for ___ ___
lytic growth
What genes use group II splicing?
mRNA and tRNA of mitochondria
polycistronic mRNA
mRNA that includes coding regions representing more than one gene
RNA Polymerase V
makes longer RNAs that are thought ot pair with the siRNAs at affected chromosomal sites in plants
Which of the following are basic amino acids and carry positive charges at physiologocial pH? a.) valine and leucine b.) glutamate and aspartate c.) cystein and methionine d.) lysine and argine
d.) lysine and arginine
Derive Ficks second law from the continuit eq.
dC/dt=-dJ(x)/dx dC/dt=Dd^2C/dx d being partial derivative
continuity equation
dC/dt=-dJ/dx where d is partial derivative, not derivative this means that that if the concentraction isn't the same evyer where then it is building up or being depleted...matter is convserved
The sigma factor __ the affinity of the polymerase for DNA and is ___ after the promoter is located
decreases, released
compensation loop
deletion loop
How can you get a recessive trait to appear in one that inherited a dominate allele?
deletion of the dominate allele of a heterozygote results in the appearance of the recessive phenotype
What features of trabecular bone affect its mechanical properties?
density and isotropy (vertebrae & tibia- highly oriented, columnar->anisotropic)(bovine humorous-isotropic)
inward current ___ the membrane potential and outward current ___ the membrane
depolarizes, hyperpolarizes
inward current results from ___ stimuli of varying intensity
depolarizing
inward current results from ___ stimuli of varying intensity of the axon membrane
depolarizing
CoA
derived from vit pantothenate CoA is an activated carrier of 2 carbon framents
apomorphic-=
derived or advanced characteristics that arose relatively late in members of a group and therefore differ among them; advanced
epigenetics
describes hertiable changes in gene epression
detection and treatment of fractures
detection -out of place limb or oint -swelling, intense pain -x-ray detection treatmetn -cat/split -eternal fixation -internal fixation
core promoter
determines the site of transcription initiation (Inr element, TATA box, BRE, MRE, DPE)
sequencing
determining linear arrangements of nucleotides by synthesizing a new strand through compl/.. base pairing -need dna sample, primer, and dNTPS adn ddNTPs
bioinformatics
develops hardware and software for processing nucleotide and protein data
Causes of osteoperosis
diet exercise smoking reduction in estrogen genetic
UV radiation ___ the DNA and X-Rays ___
dimerizes pyrimadines (T and c) breaks the backbone
What couldd be the origin of a triploid
diploid mated with tetraploid nondisjucntion in Mi or MII ovum+sperm+sperm
embryonic development of dros
diploid zygote->9 nuc divitions->4 divisions at periphery-?nuclei enclosed in membranes, forming a single layer of cells over embryo surface->embryo ->adult
types of eupoloidy
diploidy 2n polyploidy 3n, 4n, 5n, ... triploidy 3n autopolyploidy - multiples of same genome allopolyploidy - multiples of closely related genomes
___ toxin and __ inhibit elongation of translation
diptheria, ricin
unlike conjugation, transformation does not require___
direct ...but does need free DNA and competent cells
Alternative sigma factors...
direct RNA polymerase to alternative sets of promoters. They control the expression of genese.
bacterial sex requires
direct contact uniddirection tnsfer of fenetic info f factor-contains pilus and origin of replication
methyltransferase is and example of ____
direct repair
DNA photolase is an example of ___ repair and...
direct, fixes pyrimidine dimers
types of damage handled y each type of dna repair
direct-> nucleotide modification, dimers, alyklation base excision->nucleotide modification, dimers nucleotide excision-> nucleotide modification dimers, souble helix distortions
types of selection
directional, druptive, stabilizing
RNA polymerase
directs the synthesis of RNA
Nature exist as a ___ array of species.
discontinuous
transposons
discoverd by barbrara mcclintock mobil genetic elements, or "juming genes" can move around in genome and cause mutations
karyotype
display of 46 human chromosomes
Low FMN, terminator ___, full mRNA __ produced.
disrupted, is
Enhancers can be __ and can be ___.
distal , inverted
cable properties of an axon are dependent on ....
distance and time measure delsewhere
magnitude of hyperpolarization depends on...
distance fromt he stimulating electrode to the recording electrode
Axoplasimic resistance (Ri depends on...
distance, area, and specific resistance (pi)
External resistance (Ro) depedns on ...
distance, area, and specific resistance (po)
interspecific diversity
diversity o fthe number of different pllant and animal species in an ecosystem
intraspecific diversity
diversity within a species
apparent contact zone
does not result from gene flow, but is the result of residual geopraphic variation in ancestral species and is maintained by local selection or chance
SANT domain
domain that recognizes unmodified histone tails
Acids ___ protons and bases ___ protons. Acids ___ electrons and bases ___ electrons.
donate/accept accept/donate
Na+ flux is ___ its concentration gradient
down
Flux moves ___ because it goes from ___ to ___ down a gradiant. A positive flux has a ___ slope.
downhill/high/low/negative
DPE
downstream promoter element
EF-G
drives translocation by stabilizing intermediates in translocatipin
bar phenotype in dros.
duplication of teh 16A gene -heterozygous-smaller -homozygous-even smaller -hterozygous double bar-smallest
When would a diploid individual have a aneuploid cell and why does this matter?
during mitotic nondisjunction and it is significant in tumor biology
regulatory DNA sequence
e.g. promoter, which control the expression level of the gene, DNA sequence to which a transcription regulator binds to determine when, where, and in what quantities a gene is to be transcribed into RNA.
how inditaion factors differ in euk from prok
eIF1, eIF1A, eIF3, eIF5, eIF6 Analogous to IF1 and IF3: block early assembly of ribosome and block other tRNAs from binding eIF2: Analogous to IF2: GTP-bound initiation factor responsible for bringing in initiator tRNA, GTP hydrolysis triggers recruitment of the large subunit eIF4E: binds 5' cap eIF4G: binds eIF4E and 3' poly A binding proteins
dispersive replication
eacch daughter strand contains some old, some new dna segments
Unambigous code
each codon specifies one amino acid
semiconservative replication
each daughter gets old and new
What does it mean to say the genetic code is unambiguous?
each triplet->only 1 amino acid
afferent vs effferent
efferent---signal out (shake) afferent--signal recieved (pain)
What could happen with a monosomic inheritance?
either lethal or turner syndrome if it's a girl it creates a hemizygous state so recessives are expressed
oxidative reduction
electron transfer ex. succinate to fumarate (FAD) matate to oxaloacetate (NAD)
drosophila life cycle
embry0=o->1st instar larva->2nd instar larvae->3rd instar larva->pupa->adult
Wht does the superrepressor (I^s) allele do?
makes the repressor unable to bind to allolactose so that the repressor protein is always bound to the operator sequencce so the structural genes are always repressed (even if lactose is present)
proto-ecological system
martin and russel suggest the first ceullualr lfie was on hydrothermal vents at seafloor spreading zones in deep sea
leucine zipper motif
mediate DNA binding and protein dimerization binds as dimer to consecuitive major gooves, log helic containg hydrophobic residues interact
__ protein allows regulaotry proteins to communicate with the pol II and TFs
mediator (the activaor binds to the mediator complex, fomina a loop with the RNA pol II)
rapid depolarizatio and overshoot in AP= transient increase in _____ accompanied by ___
membrane conductance
What does trisomy 13 do?
mental retardation growth failure cleft palat deafness, among many others
mRNA
messenger RNA, carries information to ribosome (5% of all RNA)
encountering reactive ___ can cause leastions
metabolites (free radials specifically h2o2 and o2-)
Explain how histone methylation and phosphorylation affect gene expression
methylations (repress expression phosphorylation (allows expression)
methylation
methyltransferase=methylate lys or arg demethylase=remove methyl group
M bane
middle line between A band
What introduces alles from other poplations, causing 2 popluations to become more similar to one another as a cnosequenc?
migration
nukker;s experiments produced..
mino acids under possible primitive earth conditions (methane+ammonia+hydrogen (H20)->glycine (an amino acid
homologous rhomologous recombination
mismatch repair
What kind of mutation is responsible for sickle cell anemia?
missense changes glu to val
lygaeus
mode of sex determination: based on Y copy of the chromosome, XX/XY the presence of an x or a y from the male dictates sex humans
codon
more than one nucleotide A sequence of three nucleotide bases on mRNA that refers to a specific amino acid.
ways of distinguishing evolutionary division
morphology allozymes dna seq
B dna
most stable configuration for a random sequence of nucleotides under physiological conditions, alpha helix (right handed
high heritabilty means
mostly do to genetic inheritance
increaste in the muscle twitch will increase recuitment of ...
motor fibery by increasing the strength of the the external stimulus
Difference between glucocgon and epinephrine in fuel mobilization?
muscle Ep->increasy glycogenolysis adipose glu&Ep->increase lipolysis liver glu&Ep->decrease glycogen synthesis and increase glycogenolysis Ep->increase gluconeogenesis
What creates new alleles
mutation
Which gene mutation be the one to only make the lac operon constitutive?
mutation in the operator (mutation in the repressor could make it repressed or consititutive diepending on have the gene muation affects the repressor)
What else, besides a mutation in the lacI, cause the lac operon to be constitutive?
mutation in the operator where the repressor binds
frame shift mutation
mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotides
___ create new alleles in gene pool
mutations
without repair, spontaneous changes in DNA can produce __
mutations
How do you determine whether the regulatory elemts act in cis or in trans?
mutations in the repressor gene, the operator, and the promoter are combined with the structural mutatnts
polar mutations
mutations that disrupt expression of downstream genes
mutualism between populations
mutualistic relationship between pop of the involved species rather than between individ (ex. pollination)
myoblast aggregate to form ___, through __,
mycytes, myogensi
mycytes contain __
myfibrils
Does the change in Gibbs free energy need to be positive or negative in order to occur spontaneously?
negative
contrast action potential on motor neurson vs muscle cell membranes
neurons: (1-3 ms) muscle: (3-5 ms)
pI is the average of the pKa values of the two dissociation events that determine if the polypeptide stays ____ or not
neurtral it's the pKa's on either side of the ) charge
HW modle can be used to identify __ aleles that are not subject to selection
neutral
sodium bicarobonate
neutralizes pH to allow digestive enzymes to function
Nicotinamide is derived from the vitamin _____, and is the electron acceptor and donor
niacin
What are the two diff ways to repair double stranded breaks?
nonhomologous joining (doesn't need sister chromatid) homologous (sister chromatid)
Water-soluble proteins fold into compact structures with ____ cores.
nonpolar
Why kind of mutation causes cyctis fibrosis? is there another disease you can name that has this mutation type?
nonsense muation duchenne muscular dystropy
typical bone design
not designed to resist fracture tries to maintain balance between strength and weight dynamically adapt to stresses and strains reg applied
What would make CdRP?
nothing..mutation would prevent creation
what are the 4 types of muscle fiber orientation
parallel (layrngeal, sartorius) fusiform (biceps) pinnate (reduce distance that muscle can contract, deltoid) bipennate
portal vein
part of systemic veins return the venous bloof from the spleen and viscera of digestion to the liver
merozygote
partial diploid, a partly diploid E. coli cell formed from a complete chromosome (the endogenote) plus a fragment (the exogenote)
meterozygotes
partial diploids with a chromosomal copy of the lac operon and a second copy on a plasmid (mutations of lac Operon studied inn merozygotes)
intial depolariation is ____ and spreads out from the origin of depolarization in all directions
passive
electrotonic
passive spread of changes in membrane potential, a local change that decays over a short distance and can be caused by ion flow, and is governed by V = IR, once depolarization reaches threshold, and action potential is triggered and the depolarization switches to tthe all or none response (now it doesn't disperse, it keeps the charge) and is then conducted in only one direction
Give the zymogen and site of synthesis for the following active enzymes. pepsin chymotrypsin trypsin carboxypeptidase
pepsinogen->stomach chymotrypsinoge->pancreas trypsinogen->pancreas procarboxypeptidase->pancreas
the ___ ___ center catalyzes peptide formation
peptidyl transferase
What is the primary function os fthe RNA molecules of the ribosome?
performing catyltic functions
types of inversion
pericentric-includes centromere -paracentric-doesn't include centromere
How can you tell if amutation is a large-scale chromosome change or a change in one gene
phenotype -organismal or cellular level -molecular level (proteins, mRNA, DNA_
Which are bond angles are t phi and psi of the peptide bond?
phi->N(-H)-C (front end of a residue) psi->C(-H)-C(=O) (back end of a residue)
How do you keep the the donor and the vector from re-ligating?
phosphatase can be used
Capping provides protection from ___ & ___, and enhances ___.
phosphatases & nucleases translation
What contributes to the buffering in cytoplasm?
phosphate with pKa=7.2 at its isoelectic point histidine side chains (imidazolium ion->imadazole) rxn at pKa=6.5
histone phosphorylation
phosphate groups are added next to a methylated amino acid on the histone tail can loosen chromatin
F-2,BP simulates ___ and ___, inhibits ____.
phosphfructo kinase, pyruvate kinase, fructose 1,6 biphosphatese
As the RNA strand grows, it forms ___ bonds where the 3' OH attacks the __ phosphate groups of the ribonucleotide.
phosphodiester, a (alpha)
What are some phosphoryl group carriers that have a higher energy release than ATP? Give the amount.
phosphoenolpyruvate (PEP) -14.8 kcal/mol 1,3-biphosphoglycerate -11.8 creatine phosphate -10.3
ATP is a very efficient carrier of...
phosphoryl groups
How do you measure pKa?
pka=-log Ka = -log [H+][A-]/[HA] [A-] base [HA] acid
detection and teatment on fatigue fractures
plain film, bone scan, mri (left to right increase in detection) treatment -depends if fracture is complete -change in behavior or activity
the peptide bond is rigid and ___.
planar
It takes ___ to read some marks on nucleosome.
plant homeodomain
loci
point on the chromosome where the gene is found
what diseases are associte with thicker membraes and surface area
polumonary fibrosis-thicker memb emphysems-reducctions in surface area
Termination occurs when ___ __ is added to the transcript.
poly A tail
CPSF and CstF attract ___ and __ proteins
poly-A-polymerase, poly-A-binding protins
A single mRNA that encodes more than one seperately translated protein is referred to as _______________.
polycistronic mRNA
Which is more deadly aneuploidy or polypoidy?
polyploidy
what cause fatigue fractures in runners?
poor training and bad footwear
assumptions of hardy weingberg law
pop large, random mating, no mutatio, no migration, no natural selection allelic frew do not change gentotypic few stabilize
founder effect
pop orignates from small number of founders ex. navajo albanism
incipient species
populations undergoing the speciation process
How does positive and negative regulation happen?
positive-activator binds to operator negative-repressor binds to operator
RNA Polymerase II
pre-mRNA, snoRNAs, some miRNAs, and some snRNA nucleoplasm
transacetylase
precise role unknown, may help neutralize toxic by- products of lactose metabolism or assist permease. Co-regulated by lac operon.
negative assortative maing
preference for dissimilar genotypes
positive assortative mating
preference for similar genotypes
Contrast premating isolating mechanisms and postmating isolating mechanisms.
premating-isolation: waste less time and energy, no gametes wasted (habitat isolation, ethological isolation, mechanical isolation) postmating-isolation: wast cosiderable time, energy, and gametes, energetically very inefficient (hybrid sterility, hybrid inviability, zygotic mortality, gametic mortality)
PEST sequences
present in short-lived proteins (<2 hrs half life)
gametic mortality
prezygotic isolation mechanism; sperm are immobilized/destroyed before fertilization (immune system)
In a Western-blot, which comes first, primary or secondary antibody application?
primary
transfection
process of infecting useing olu viral nucleic acid
alternative splicing
produces different mRNAs from the same gene
semisterility
production of unbalanced gametes in meiosis because an organism that is heterozygous for a reciprocal translocation usually produces half as many offspring as normal
Name 3 intercalating agents. What do they do?
proflavin acridine orange ICR-191 can cause single nucleotide pair insertion or deltion
As they emerge from ribosomes, proteins fold by...
progressive stabilization of intermediates (secondary folds, tertiary folds, then quaternary, finally disulfide bonds form
How does the initiator codon differ between prokaryotes and eukaryotes?
prokaryotes use fmet which loses its formyl group upon protein synthesis completion eukaryotes do not have fmet, only met
Phosphorylation of teh CTD allows for...
promoter escape
__ often contian __ islands
promoters, CpG
The lac operator overlaps the ___, causing the lac repressor, when bound, to physically prevent RNA polymerase form binding its promoter.
promtoer
incorectly folded proteins get digested by.
proteasome
Moleculear chaperones assist protein folidng, mainly by...
protectig exposed hydrophobic patches
role of polyadenylation
protects the 3' end aids in transport to cytoplasm
What role does the 5' cap play?
protects the 5' end from nuclease, helps export mRNA to cytoplasm, in translation it binds mRNA to ribosome
cohesin
protein complex which holds sister chromatids together
The use of recombinant DNA technology significantly facilitates _____ ______ Recombinant DNA technology allows ____ and easy manipulation of genes that encode _____ of interest. Expressing cloned genes in a suitable host can lead to production of very large amount of ______ of interest. Recombinant DNA technology allows the addition of _______ ____ to proteins of interest, which enable affinity purification of the proteins.
protein purification cloning/protein proteins affinity tags
ribonucleoproteins
proteins that assemble around the rRNA to form the large and small subunits of ribosomes
activators
proteins that increase the rate of trranscription initation
repressors
proteins that reduce the rate of transcription initiation
transcription factors
proteins that regulate transcritpition (may be expressed only at certain times; may be reugulated by phosphorylationo r binding of another molecule)
Western Blot
proteins, reveal protein size and levels with differens samples or tissues
Lysogenic induction requires ___ cleavage of lambda repressor
proteolytic
Gene Banks
provide long term storage of reproductive components of animals or plants
enzyme-linked secondary antibody
provides a means or detecton of the complex of primary antibody and protein of interest (ex. HRP-linked secondary antibody)
The pKa of an acid can be if a another group is...
pulling charge away from it. So a carboxylic group is more acidic when it is attached to a carbon with an amine across from it, pulling away some of the negative charge.
Nucleotide incorporation followed by ______ dissociation, which triggers the release of the _____ and translocation of the DNA by one nucleotide.
pyrophosphate, fingers
ligation reactions
pyruvate + CO2 + ATP +H2O---> oxaloacetate + ADP +Pi + H+
Alaniene inhbits ___
pyruvate kinase
ligation rxn involed in formation of cov bonds
pyruvate->oxaloacetate (uses ATP)
threshold characteristics
quantitative but only present or absent, below a certain value is no, above is yes
What gene uses group 1 splicing?
rRNA
rRNA, mRNA, sn, RNA, 5S rRNA, tRNA...which is not formed in the nucleoplasm?
rRNA
What are ribosomes made of?
rRNA and proteins 2 subunits: large and small
___ and __ are modified in bacteriea, but not __ (types of RNA)
rRNA, tRNA, mRNA
Genetic drift leads to ___ changes in allele freq.
random alleles become more fixed or lost due to change -likelihood that allele is related to pop size
shot gun sequencing
random cuts and puting into vectors, sequence from vector-nbase primer and then enter data into computer, seq deried from overlapping fragmen
genetic drift
random freq changes in allele affect small pop (alleles become fixed in small pop)
isomerization
rearrangement of atoms to form isomers citrate-isocitrate
CCR5
receptor on immune cells chemokine (C-C motif) receptor 5 expressed in t-cells and macrophges recp for inflammatory cc-chemokine transduces intracell signal y increasin ca ion levels in cyto (CCR%-d322 homozy are resistant to HIV...HIV uses CCR5 to enter and infect hsts
coevolution
reciprocally induced evolutionary change between two or more species or population
Robertsonian translocation
recirprocal translocation between chromosomes 14 and 21, responsibel for familial Down Syndrome
reproductive commuities
recognize and seek out members of their own species to reproduce
CAP site
recognized by activator protein called CATABOLITE ACTIVATOR PROTEIN (CAP
Tudor domain
recognizes Methylated histones
bromodomain
recognizes and interacts with acetylated lysine residues
The more ______ a carbon is to begin with, the more free energy is released by its oxidation.
reduced
what leads to speciation
reduced gene flow, selection, and genetic drift
Why does trabecular bone strength decrese with age?
reduction is stiffness, loss of elasticity -less calcium and phosphorus
NADPH is used for
reductive biosynthesis
While NAD+ and FAD are activated carriers for e- for oxidation of food molecules, NADPH is used for _____ ______
reductive biosynthesis
trans acting elements
refers to DNA sequences encoding diffusible proteins (transcription factors, transcription activators and repressors).
cable properties
refers to ability of axon to conduct current; cytoplasm has high resistance, resistance decreases as axon diameter increases, current leaks out through ion channels
unlikke crossing over, bacterial recombination refers to____
refers to the replacement of one or more genes present in the chromosome of one cell with those from the chromosome of a genetically distinct cell
What happens to the conformation of trp operon in abunent trp?
region 3 and 4 bind causing termination because the ribosome does not pause because the trp codon is quickly coded since there is an abundunce of trp tRNAs
proximal promoter elements
regulate the rate of transcription initioation (CAAT box, GC box)
GLUT2
regulates insulin in pancrease B cells in the liver removes excess glusoe from blood
attenuator
regulation at the level of termination (while repressor acts at transcription initation)
Gene expression is controlled by ___ proteins (GRPs)
regulatory most activators and repessors act at the level of transcritipn intiation structure-recognize specific short stretches of DNA, DNA-binding regions on GRPs ar called motifs
cis-acting site
regulatory region on a DNA molecule that affects expression of a gene or gene cluster located near it on the same DNA molecule
cis-acting site
regulatory region on a DNA molecule that affects expression of gene or gene cluster located near it on the same DNA molecule
riboswitch
regulatory segment of a messenger RNA molecule that binds a small molecule, resulting in a change in production of the proteins encoded by the mRNA, Regulatory sequences in an RNA molecule. When an inducer molecule binds to this, it changes the configuration of the RNA molecule and alters the expression of the RNA, usually by affecting termination of transcription or affecting translation.
When CAP is bound to cAMP, it binds to a ___ ___ in the promotoer of the lac operon and stimulates transcription.
regulatory site
CCAAT box and the GC box are located in __ promoter region and the TATA box is located in the ___ promoter region
regulatory, core
Quorum sensing
release chemical signals that regulat gene expresssion in other cells
DNA topoisomerases
relieve winding and DNA tagling
RNAse H
remove RNA primer
mismatch repair
removes the leasion from the newly sythn strand by to the parental strand
homologous joining
repairs double breaks -cannot use complemnt as template since both damaged->error prone -use of sister chromatid in cell division removes error prone
A rho-independent erminator contains ____ repeat followed y a string of approximately 6 ____ nucleotides.
repeat (ex. ACCC...GGGT) ( TGGG...CCCA) adenine
Replication slippages is a possile mechanisme for___
repeat expansion which may create a single stranded loop leading to a double stranded product with a heteroduplex wihtin the repats repair result in incorporation of slipped region and repeat expansion
nucelotide
repeating monomers in DNA and RNA; consist of a phosphate group, 5-carbon sugar, and a nitrogen base
transesterfiation
replace the O-R2 of the phosphate with the O-R3 of R3-OH
Chromatin remodeling
repositioning and removal of nucleosomes affects chromatin structure and gene expression
When is the lac Operon induced and when is it repressed?
repressed-lactose absent induced-lactose present
tryptophan operon
repressible operon---when trp is absent, the repressor is inactive-----when trp is present and there is enough of it, the trp binds to the repressor and activates it to stop producing
Inducible genes are expressed only in the absence of a ____ and/or presence of an ____ molecule.
repressor effector/inducer
What are the 2 mechanism fo the trp operon?
repressor-operator interaction--uses tryptophan as a corepressor termination of transcription before genes are reached -max gene transcription when trp starved -mild transcription if trp in low levels -done by changing secondary structure of mRNA transcript
lytic growth
reproduction of phage in the cell leads to cell bursting
agamic systems
reproductive sstems that result in immediate isolation form the parental species, independent divergance of the resultling lineages, and thuse emergance of ne species. This is driven by lac of gamete fusion. offspring arise asexually or throughapomicitc reproduction (no fertilzation of the egg) occurs in both plants and animals
general transcritpion factors
required for basel trranscriptioni
auxotroph
requires nutrients from external environment (medium_ ex leuc-
opening of the inactivation happens after ___, following ___, continues through ____ and ends when ___
reset, upstroke of the eaction potential, repolarization of the membrane, resetting of the resting conditions
cable properties depesn on ___ to __ flow
resistance to current flow ristance increase with increased myelin thickness (larger space constant) increase in cross-sectional area of the axon, reduces Ri, (increasing space constant) the larger the space constant, the loger the depolarization will be maintained as it goes over longer distances
viscosity
resistance to flow (measure in centipoise cP)
Paralog
result from ducliatevolve new functions
actual contact zone
results from gene flow between differentiated population
allele flow
results from migration of individuals
genetic drift
resutls in random changes in allele frequenceis due to samlin error. it can lead to allele fixation or lass (risk of this decreases with increase in pop size) (can be due to founder effect ofr genetic bottle neck
complementation testing
reveals whether two mutations are in teh same or different gene
denrites ___ the signal axons __ the signal
reveive, transmit
The flavin's isoalloxazine ring is derived from the vitamin ______, and is the electron acceptor and donor
riboflavin
What enzyme cleaves the transcript after the poly-A is added?
ribonuclease
rRNA
ribosomal RNA, makes up ribosomes (80% of all RNA molecules)
What happens to the shape of the trp operon when starved of trp?
ribosome pauses at region 1 while 2 and 3 bind forming the antitermination conformation
___ are another way to induce transcription attenuation
riboswitches (stop when high, start when low)
origin of fmailial down syndrome
roberttsonian translocation between chrom. 14 and 21
variance
s^2=sum(x-X)^2/(n-1) x=sample X=mean
terminal cisternae
sacs that make contaact with the t-tubles
What are saltatory conduction and electotonic conduction?
salatatory-leap electrotonic-dributes charge
autopolyploidy
same chromosome set is double, tripled, or
functional unit of contraction
sarcomere (extends from one z line to the next)
Ames Test
screen new drugs to reduce possible adverse effects
DNA ligase
seale Okazaki fragments
BLAst
searches can be ued to search data bases to find alignment between newly sequenced genome ang genes tha hve already been identified in the same of different species (finding genes of relatedfunctions)
Give examples of reproductive isolating mechanisms.
seasonal isolation habitat isolation ethological (behavior) isolation mechanical isolation gametic mortality zygotic mortality hybrid inviability hybrid sterility
zygotic gense
segementation genes, homeotic genes
gene
segment of DNA that contains the instructions for making a particular protein
ex of gene regulatory networks
segmentation in drosophila..postion at about 4.5 hrs after fert is when cells determined
isoelectric focusing
separating proteins based on their isoelectric points when the pH o the gel region equal the pI of the protein, the gel stops
structural genomics
sequenceing genomse and analyzing nucleotide sequences to id genes, gene regulatory elements, etc. process called annotation
consensus sequences
sequences of DNA that are similar in different genes of the same organism or in one or more genes of related organisms (ex. TATTAA and TTGACA)
open reading frames
sequences of triplet nucleotides that, after transcription and mRNA splicing, are translated into the amino acid seq of a protein begins at ATG initiation that transcribes AUG found in protein-coding genes
cell cycle
series of events that cells go through as they grow and divide
Hox gene
series of genes that controls the differentiation of cells and tissues in an embryo
microRNAs
serve as a guid RNA that determine the specificity of argonaute complex
Paul Berg
set of 3 genes responsible for metabolizing galactose in the bacterium E. coli insrted int .... genome
Assumptions of the probabilty of diffusion
seventeen slide
splicesosome
several snRNPS and proteins that completes cut and splice
non-newtonian blood viscosity depends on
shear rate which is determed by blood platelets, red cells, etc. shear stress changes become greater as hematocrit increases ..at low shear stress the hematocrit induces greater changes in blood vescosity
stress rate relation
shear stress (t) and shear rate (y) relation t=K*y^n n<1 highest stress n=1 linear n>q lowest stress
Where does the ribosome bind in prokaryotes?
shine dalgano box (AGGAGG)
SINE
short interspersed sequ 100- 400- bp repeated seq interspered betweend unique seuence DNA 1k-2k long 10% human genome ex. Alu
operator
short region of regulatory DNA of defined nucelotide sequence that is recognized by a repressor protein
tRNA
short-chain RNA molecules present in the cell (in at least 20 varieties, each variety capable of combining with a specific amino acid) that attach the correct amino acid to the protein chain that is being synthesized at the ribosome of the cell (according
anfinsen experiment
showed: -a protein can self-assemble into its functional confomrtion -folding information is contained in the sequence , An intact protein folding ribonuclease, treat with urea will denature the protein and betamercapta will reduce the disulfide bond. the denature structure then can be reformed with the removal of the urea and oxidize by b mercapta. This experiment show that proteins can be denatured reversibly and renature spontaneously.
___ combine with proteins to form ___ (RNA transcriptional silencing complex) which attracts proteins that methylate histone and repress transcription.
siRNA RITS
RNA Polymerase IV
siRNAs in plants that specify the silencing of matching DNA sequneces
laplace's law
sigma (o)=in-wall hoop stress p=ressure r=redius t=wall thickness o=(pr)/(2t)
The lag gene provides and exampel fo ___ ___ in that their expression is controlled by 2 signals, regualted sepreataely
signal integration
___ ___ mark proteins for translocation across the ER
signal sequences (SRPs
DNA methylation __ gene expression
silences
methylation on K 27
silencing of Hox genes, X chromosome inactivation
reasons to stuyd bacteria
similar to own haploid-maning all mutations expressed -factory for recombinant DNA
oparin-haldane hypothesis
simple organic compounds were changed by heat and solar radiation into more complex organic compounds
Ricin cleaves..
single adenine base from 28S
one gene one enzyme hypothesis
single gene controlled the synthesis of a single enzyme. Discovered by Beadle and Tatum
xeroderma pigmentosum
skin damage
B is the __ clamp and t is ___ core complex
sliding, simerizes
At what pH does enzyme activity switch from pepsin to chymotrypsin?
slightly less than 5
Which are innervated first, large or small motor units/
small because they are more readily excitable (delicate movements or fine motor control
plasmid
small independent circular DNA, which carries genes that confer desirable traits to the bacteria
snRNA
small nuclear RNAs
snRNPs
small nuclear ribonuclear proteins
vectors
small pieves of dna with essential characteristics endogenous, in lab used in lconing and dna analysis
microRNA
small single stranded RNA molecules that bind to mRNA and can degrade mRNA or block its translation produced by RNA polymerase II, cleaved from larger precursors
the slow twitch has a ___ maximum velocity and a maximum force that is ____ to the fast twitch
smaller, equal
Degenerate code
some amino acids are specified by two or more codons
What assay do you use ot diag. sickle cell
southern blo
wdistinguish what each blot shows
southern-which samples (or parts of) have the DNA you want northern-tell you what tissue a gen is expressed western-preotein size and leve in different sample so ftissue
homodomains
special class of heliz-turn-helix motifs held together by hydrophobic interactions typically bind as dimers, and interact with the major groove (recognition heliz) and minor goove (Arg)
centromere
specialized DNA sequence that allows one copy of each duplicated chromosome to be apportioned to each daughter cell
secondary speciation
speciation due to interspecific hybridation or polyploidization
orthogolog
speciation event, retain function
contrast speciation and anagensis
speciation-lineage splitting -anagensis-character evolution
CAP site
specific activator binding site to which the activator, CAP binds
replication origin
specific sequence of DNA at which DNA synthesis begins
Hoaw are introns removed?
spliceome machiner
nuclear-derived mRNA uses __ to splice
spliceosomes (used with multiple or long introns_
How are the exons joined with such high precision?
splicing enhancers
second law of thermodynamics
spontaneous processes always increase the entropy of the universe
Which snRNA binds at the start of the intron? Which binds at the branchpoint?
start- U1 branch point-U2
Paris' law
steady grow of fatigue fracture da/dN=C(deltaK)^m
___ prevent DNA polymease from using rNTP precursors
steric constrains
___ and related hydrophobic molecules pass through membranse and bind to DNA-binding receptors
steroids ex nuclear hormone receptor regulate transcription by recruiting coactivators to the transcrioption complex
secretin
stimulates production of sodium bicarbonate
cholecystokinin (CCK)
stimulates release of digestive enzymes for proteins, lipids and carbohydrates also stimulates gall bladder to release bile salts for lipid digestion
activated carriers
store energy in an easily exchangable form, either as a readily transferable chemical group of as high-energy electrons
Fatuigue fracture iss like a cycle where __ varies with sigma max and simga mine and __ varies with sigma.
stress, stress intensity (K)
__ result from highly organized arrangements of proetins in the muscle fiber
striationss
5S rRNA
structural component of the prokaryotic ribosome.
the high energy of the Atp results from..
structural diff between ATP and its hydrolisis products electrostatic repulsion->ADP and resonace stabilized Pi
lac A
structural gene of lac operon, gene that encodes for the enzyme transacetylase, which may be involved in the removal of toxic by-products of lactose digestion from the cell
leucine zipper motif
structural motif in many DNA binding proteins in which two alpha helices from separate proteins are joined together in a coiled coil.
conservation genetics
study o f genetic ffactors that contribute to species decline and ways that genetics can be used understand, maintain, and restor population viability
functional genomics
study of gene function based on resulting rnas or possible proteins they encode based on similariity in homologous genes or protein domains or motfs
Oxidation-reduction reactions
succinate + FAD--> Fumerate +FADH2 malate +NAD---> oxaloacetate + NADH + H+
molecular markers
such as SNPs, that dont produce visible phenotypes. use to locate genes of interest in the genome through linkage. localize disease genes: test for association between any SNP marker and the presence/absence of disease
Give the enzymes that break down sucrose, lactose, and maltose.
sucrose---sucrase lactose---lactase maltose---maltase
temporal summation
sum with succession of time
spacitla summation
summ over the space same space in time
muscle forces ___ with repetitive stimulation
summates
_____ _____ is a recurrin theme in protein-DNA interaction
symmetry matching
phototroph
synth the essential nutrients ex leuc+
gluconeogenisis
synthesis of glucose from noncarbohydrate sources, such as amino acids and glycerol; canoccur in the liver and kidneys when the carbohydrate intake is insufficient to meet the bodies needs.
____ are transverse tubles that transmit action potential form sarcolemma to the interior of the cell
t-tubles
newtonian fluid stress
t=u*du/dy du/dy=shear rate 9u is velocity and y i radius) u=kinetic viscocity
The attenuation sequence responds to concentrations of __. When a leader peptide is complete __ occurse. When it is incomplete __ occurs.
tRNA, nothing (bc of high tryptophan, transcription (low trypt)
RNA Polymerase III
tRNA, some snRNA, 5S rRNA, some miRNAs nucleoplasm
release factors mimic ___, and thus fit in the A site
tRNAs
How mich free radicals alter G?
takadd another keto
What does snRNA U4 do?
takes U5 and U6 to replace U1
tandem vs nontandem duplication
tandem-on same side of centromere nontandem-duplication moved to otherside of the centromere
Bacterial ___ is a target for antibiotics.
target ex. rifampicin
deletion mapping
technique for determining the chromosomal location of a gene by studying the association of its phenotype or product with particular chromosome deletions
recombinate DNA technology
techniques for obtaining amplifying and manipulating specific DNA fragments
oxidaiton of what realses more energy
teh more reduced carbon
Northern Blot
tells in what tissue a gene is expressed and how much is expressed, useful in detecting splice variants
What 3 uniquie sequence elements are required for the maintenance and replication of chromosomes?
telomere, replication origin, and centromere
melting profile
temp at which dsDNA/RNA is half disassociated into ssDNA/RNA
Which strand is the RNA sequence taken from, the DNA template or coding strand?
template
The newly synthesized mRNA is complementary to the ___ strand, and identical to the __ strand (U instead of T).
template, coding
genetic bottle neck
temporary, drastic reduction o fpop size
__ base pairees per 360 turn
ten
skeletal muscles transfer force via __
tendons
fertility factor
term given to the pili that forms the conjugation tube through which donor DNA is passed on to recipient.
In addition to the promoter site, the template strand also contains a ___ sequence.
terminator
What is the quaterenary structure of Hemoglobin? How many subunits are there?
tetramer 4
What toxins can block ion channels? Give specifics and which they block
tetrodotoxin (TTX) for Na channel tetraethylammonium (TEA) for K channel
What does positive control ensure?
that the lac operon will be expressed when there is no glucose and only lactose...so that when it is on the B-galactosidease will breakdown the lactose into glucose and galactose
What is the attachment site of the amino acid?
the 3' end...always CCA (AAC on the tRNA)
Which bands make up the striations
the A and I bands
Which band has no thin fillaments
the H zone
self-slicing
the RNA molecule itself has catalytic activity (no proteins required)
tRNAs are charged by...
the attahcment of an amino acid tot he 3' terminal adenosine nucleotidee via a high energy acyl linkage
absolute finess
the avg reprodguction rate of individulas wiht the same genotype
z disk
the black line
genomics
the cloning and molecular characterization of ent
exon
the coding sequences in a gene
genome
the complete set of information in an organism's DNA
chromatin
the complex of DNA and protein that makes up chromosomes
How is the Na+ flux stopped
the concentration gradient brings Na+ into the cell, which carries a charge that builds and eventually opposes further flux
Wallace effect
the concept that reprouctive isolation between two incipient species is reinforced due to hybrid inviability
What part of the RNA polymerase is responsible for elongating the RNA product?
the core enzyme, aBB'w subunits
A bands
the dark broad band between the black lines
typological species concept
the discredited, pre-Darwinian notion that species are classes defined by the presence of fixed, unchanging characters shared by all members
sympatric speciation
the establishment of specific status amon two or more subsets of a single ancestral species while these subsets remain in geographic contact.
relative fitness
the ftiness of particular genotype relative to tother genotype int he pop (the most fit is assigned 1)
How can variegation in flies occur?
the gene is closer to the heterochromatin in translocation heterozygote
gene pool
the genetic information carried by memebrs of a population (all alleles and their relative frequencies)
phyletic speciation
the gradual evolution of a single species into an entirely new species than that of its ancestors
A thermodynamically unfavorable reaction sequence can be converted into a favorable one by coupling it to...
the hydrolysis of ATP molecules in a new reaction
Wobble Hypothesis
the hypothesis that some tRNA molecules can pair with more than one mRNA codon, tolerating some variations in the third base, as long as the first and second bases are correctly matched proposed by Francis Crick
How do you tell which pair is base is mismatched?
the incorrect strand is identified by the ABSENCE of methylation mismatch repair complex (MutS, MutL, and MutH) hind new strand with err and endonucleas nicks the ackone near unmethylated GATC seq
intron
the intervening non-coding sequences in a gene
I band
the light bands that encompass the black line
replicationn origin
the location at which duplication of the DNA begines
genetic erosion
the loss of previously existing genetic diveristy from a population of species
histone code
the many variations of histone modifications
genntic load
the number of deleterious alles in the gene pool of apop
effective population size
the number of individuals in a population who have and equal probabilyt of contributing gametes to the next generation
Twist Number (Tw)
the number of times one strand completely wraps around the other strand
minimal media
the nutrients required for the growth of wild-type bacteria - varies with species. Typically need a carbon source (a sugar), some salts, and trace elements
How were the trp operons decifered?
the operons produce amino acids that are not found in the media (environment)...so by filling the media with specific amino acids you and determine which amino acid codes for it because it will typically be attenuated (turned off) by the abundance of the amino acid it codes for.
primary speciation
the originationof new species from one common ancestral species
What is the equilibrium potential
the potential at which the electrical force exactly balance diffusion so that the net flux of ions is 0 the 0 charge membranes do not exist though
inbreeding coefficient (F)
the prob that an individ inherits two allels that are idential by desent F=(2pq-H)/2pq increases proportion o fhomozygotes in pop
coefficient of inbreeding (F)
the prob that an individula has two allels that are identical by descentj
tRNA
transfer RNA, binds to amino acids and carries them to the ribosome (15% of all RNA)
group transfer
transfer of a functional group from one molecule to another glucost to glucose 6-phosphate (uses ATP)
transformation
transfer of extracellular DNA into cells
iron transporting proetins
transferring & transferrin receptor
E2
transfers Ub thioester linkage from E1 to E2
___ plays a critical role in recominat dna tech
transformation
The formyl group on N-formlmethioin is added after charging of the tRNA, by an ezyme (______) that recognizes the particular tRNA^fMet and transfers a formyl group form 10-formyltetrahydrofolate
transformylase 50% proteins retain the formylmethionine others clip it of after ~10 a.a. are added
transitions vs transversions
transistion-substituting a purine base with another purine base..same for pyr. trnasversion-substituting a purine for a pyrimidine and vise versa
GTP drives _____ of tRNA and mRNA after peptide bond fomration
translocation
__ __ carry cargo proteins to their final destination
transport vesicles
What happens when there is high levels of tyrptophan?
transription does not occure
When there is no iron to bind to cytosolic aconitase, ____ ___ are made. In excess, iron binds toe cyt. acon. adn __ is made.
trasferrin receptor, ferritin (iron storage molec)
Where are triacylglyerols, protein and glycogen stored?
triacylglycerols (adipose tissue) protein (muscle) glycogen (muscle and liver)
in skeletal muscle, the junction of T-tuble and SR forms a ___
triad (composed of terminal cisternae from the SR and the t-tuble_
At 35 the chances of having a downs kid is 3/1000, by 40 the rate has more than ___. At 45 it is 1/___ and at 50 it is 1/__.
triples, 30, 15
genetic code
triplet code in which each three nucleotide condon in an mRNA specifies one amino
"seedless" fruits are ___. strawberries are an example of __ These are ___, which are benificial in horticulture. Done so __
triploids, octaploid, autopolyploids, asexually
What would make lnGP?
trp B or trp A mutation and/or lack of serine
What would make PRA?
trp C mutation
trpL
trp leader controls the expression of genes. contains a stop signal, an attenuator. When trp is high then leader slows it down
LNP to tryp?
trp synth B and tryp synth a (and serine)
What would make chorismate?
trpE or trp D and/or lack of glutamine
True or False? tRNA is single stranded
true
True or false DNA ligase rquires ATP
true
cloned dna can be sequence, if if the sequence of the insert is completly unknone \ t or f
true
trpB
tryptopahn synthetase B
trpA
tryptophan sythetase a
Structural genes encode proteins that synthesize ___; the structural genes are transcribed whe __ is asent but are repressed when __ is present
tryptophan x3
True or Fale? muslce cells are mutlinucleated
ture
True or false Spontaneous loss of purines and deamination of certain bases can occure
ture
How does a tetraploid pair and which is inviable
two bivalents - viable 2n one quadrivalent - viable 2n univalent+trivalent - inviable gametes
recombination
two daughter DNA molecules are formed by the exchange of segment between two partne dna
ethological isolation
two similar species do not form hybrid due to differences in mating behavior
UV light cause __ dimers
typmidine
___ tags prteins for destruction
ubiquitin`
postreplication repair
undamge region of complementary parental strand is used homologous recomination
___ fats have double bonds in the hydrocarbon chain. ___ fats have no double bonds in the hydrocarbon chain.
unsaturated, saturated
What region would a rho bind to during termination?
unstructured RNA, moving toward the 3' end...it then encounters a terminator sequence, pauses, and rho unwinds the DNA-RNA hybrid using helicase activity
pre-initiation complex (PIC)
unwinds promoter DNA, and transcription is ninitiated...after which RNA Pol II continues elongation; some GTFs remain at the promoter
FMR-1 gene
upstream from this gene is a CpG island which can be methylated and decreased transcription of the gene. Within the gene there is a region that contains a variable number of trinucleotide repeats (CGG); this is the fragile site. There are normally 28 CGGs with 2 AGGs thrown in to break them up. This region is normally transcribed into mRNA but not translated. Individuals with fragile X have >230 repeats; this is associated with an over-methylation of the CpG island and reduced transcription of this gene. Function of this gene is not yet known.
A string of what base follows the inverted repeats on the hairpin structure?
uracil
What 6 bases follow the hairpin?
uracil (transcribed from adenine)
What enzymes are used in base excision repair?
uracil DNA removed with glycosylase the AP endonuclease and phosphodieterase remove the surage phosophat eleasveing a single bp break dna poly and dna lig fix it
Termination in the RNA occurs immediately upstream from a run of ___ that follow the stem loop formed from inverted repeats.
uracils
miller experiment produce what important amino acids?
urea, acetic acid, lactic acid if no oxygen,...then these would condense into a thick "soup" in small pools
chromatin remodeling complex
use energy from ATP hydrolysis to catalyse changes in the structure of nucleosmes allow greater access to the DNA
bioinformatic
use of computerm nathematic, and computer programing -based approaches to orgaize, share, and anzalyse data related to...
solve end-prelication problem
use telomeres
balancer chromosome
used in lab studies, it contains inversions and is nice control to prevent cross overs
what is patch-clamping membranes do
used to study the behavior of single channels using a patch clamp technique where on clamps the voltage across the patcha nad measures current across it
deletion mapping
uses the presence or absence of expected banding patterns on a chromosome to determine chromosomal location of a gene
hydrolitic rxn
uses water to cleave bonds
variegation
variability in coloration
Explain how Nucleosomoe composition affects gene expresseion.
variant nucleosomes H2Az and H3.3 substitue H2 and H3, preventing repression
aneuploidy
variation in the number of a particular chromosome within a set generally leads to an abnormal condition because it leads to an imbalance in amount of gene products (too much or too little) trisomy (2n + 1), monosomy (2n - 1)
methylated C nucleotide are common sites for mutation in ___ DNA
vertebrate
Allospatric speciation is most commonly experienced by ...
vertebrate carnivores, birdes, reptiles, amhibians, and most fishes a fairly slow process, speed dictated by how large the newly subdivided population is and how quickly mutations arise large animal species with poor movement are restricted to this model (chromosomal rearrangemenst are minimal in these sorts of animals)
What types of organismss undergo sympatric speciation
very common among parasites of plants and animals, demonstrating this is very difficult
How do nucleotides link?
via a phosphodiester linkage, the 3' OH is lost and the O from the phosphate binds to the phosphate
lysogenic growth
viral genome is incorperatated into the cell's genome and is reproduced when the cell divides
Fick Dilution Principle
volume=amount/concentration=m/c
work=
w=f*d force*distance
iron slfur world from?
wachtershauser from munich and karl popper proposed pioneer organism originated from volcainit hydrothermal flow reaction of CO and H2S with nickle sulfide and iron sulfide generates methyl thioester of acetic acid, and tioacetic acid the activated acteic acid analogues of acetyl-Coa phosophoanhydridge compounds alba amino acids
Hydrophobic Effect
water excludes non-polar substances and forces them to associate with each other
A strong acid has a ___ conjugate base and vice versa.
weak
When would the lac gene not be expressed?
when glucose is present and lactose isn't
When does lactose get used by E. coli?
when glucose is unavailable and lactose is present, lactose may be used as a carbon source instead
When is the lac operon repressed?
when lactose is absent
passive force
when muscles cells are stretche d passively they produce a passive foree due to elastic properties of the muscle material
When are pseydogenes made?
when reverse transcriptase is present in a cell, mRNA molecules can be copied into double-stranded DNA. In rare instance, these DNA molecules can integrate into the genome, creating pseudogenes.
When does tRNA become charged?
when the amino acid is finally attached to it
What does it mean to say the positive regulation of the lac operon is catabolite repression?
when the catabolite, glucose, is in high levels (and of course lactose is available) then CAP does NOT become bound...it does not prevent translation but it prevents CAP from binding to the promoter and initiating tranlastion
The promoter determines..
where transcription begins
cis-acting elements determine...
where transcription start, down to exact nucleotide
mutualisms between organisms
whole organisms are free living associat in mutualistic realsitionships (ex inset-fungus muti, ant plant mut)
hagan pouisseuille equ
y=8u/d y=32Q/(pi*d^3) u=average velocity Q=mean volumetric flow d=diameter assume parabolic veocity profile, straight vessle, cylindrical, ineleastic, blood is newtonian,flow is steady and laminar)
shear rate, assuem velocity of flued is zeros (no-clip condition)
y=du/dr u=fluid velocity r=radius
can more thatn one ribosome work on the same mRNA?
yes
Are chromatin structures hertiable?
yes, at least in certain types of chromatin
when there is no overlap of thick and thin filament, the force is ___
zero
What does a mutation in the lacI gene do?
makes the lac gene constitutive...always on because the repressor cannot be correctly formed OR...it will make it so the lactose can't bind to the repressor..thus making the gene repressed
polymorphism
- Any trait that has two or more alleles that occur at appreciable frequencies, at a given genetic locu
origin of duplication
-unequal crossing over -chromosome breakage
reversion
., Alteration in DNA that reverses the effects of a prior mutation
3' to 5' direection
...
Blast stands for...Basic Local alignemnt search tool
...
By drawing the compounds, show the difference between ribose and deoxyribose.
...
Draw glycolysis, the structures of the compounds, and name the enzymes.
...
Draw out a nucleotide structure.
...
Draw the H bonds linking each base pair.
...
Draw the base pairs that pair together, showing their H bond links.
...
Draw the purine bases.
...
Draw the pyrimidine bases.
...
Draw the structure for GTP. What base is attached to the sugar?
...
Draw the structures of the purine and pyrimidines.
...
Know how the 3 forms of DNA differ in structure.
...
Know the 20 ammino acids, abbreviations, and letters.
...
Show how the edges of the base pairs relate to the major and minor groove.
...
Show the major and minor groove of each base pair.
...
What patters are seen for the major and minor grooves?
...
When does ligase use pyrophosphate
...
a dna
...
activator
...
argonaute
...
autoinducer
...
beta strand motif
...
combinatorial control
...
dna finger prints based on...PCR-nased assys of variable number tandem repeats (VNTR) polymorphisms (7 looked at)
...
dna polymerase III
...
draw the circuit model for the membrane
...
expec to designe
...
guanidinium
...
imidazole
...
lyases add or remove funct. groups
...
pold
...
soluble protein factors in translation
...
theory of emergence
...
NMR spectroscopy
..., A concentrated solution of pure protein is placed in strong magnetic field & hit w/radio waves of different frequencies.The 'H' nuclei in the protein generates an NMR signal; used to determine distances bet/amino acids & bet/different parts of the protein. Computes a 3D model of the protein
aminoacyl tRNA sythetase
..., attaches amino acid to tRNA
How long is a H-bond?
.2 nm
base pares are ___ nm aprat
.34...3,4 for a complete turn
maximum velocity occurs at __force, and maximum velocity occurs at ___ velocity
0, 0
how many cell layers thick are blood vessls
1
Show how the oxidation of acyl CoA becomes involved in the electron transport chain. List the enzymes involved in each step
1 - Acyl CoA dehydrogenase (E) 2 - Electron-transferring flavoprotein (ETF) 3 - ETF:ubiquinone reductase (Fe-
What does nondisjunction during mieosis II result in?
1 monosomy (monosomic) 1 triosomy (trisomic) 2 normal gametes (aka disomic)
How many different start and stop signals are there in the genetic code?
1 start (AUG) and 3 stop (UAA, UAG, and UGA)
The probability of forminga protein with no errors depends on..
1) # of amino acids 2) frequency (E/epsilon) of inserting of a wrong a.a.
Give the 8 traits of the genetic code.
1) 3 nucleotide/codon->1 amino acid 2) unambiguous 3) degenerate 4) 1 start, 3 stop codes 5) commaless 6) linear 7) nonoverlapping 8) universal
What are the 4 steps of RNA processing?
1) 5' cap added (7-meG) 2) 3' Polyadenylation tail 3) splicing (removal of introns) 4) RNA editing
Give the sequence of mRNA processing.
1) 5' cap is added after transcription begins 2) Introns are spliced out as they are synthesized 3) 3' end is cleaved by an endonuclease and a poly A tail is added
List the 3 requirments for RNA polymerase.
1) A template. 2) Activated precursors in the form of the 4 ribonucleoside triphosphates. 3) Divalent metal ions, Mg2+ or Mn2+
classes of transpoable elements
1) DNA seq encodes proteins that move the Dna elemtns directly toa new postionm (prok and euk) 2) related to retrovirus, encode a revers transcriptase for making dna copies of their rna transcripts with subs integrate at new sites in the genome (euk only)
What does nondisjunction in meiosis I result in?
2 monosomy & 2 triosomy
High ____ will lower lipolysis
Acetoacetate
_____ is the ketone body that can be used as fuel when glucose isn't available
Acetoacetate
Energy from the oxidation of food occurs in what 3 stage?
1) Digestion 2) Formation of key metabolites (glycolysis) 3) ATP producetion (Krebs)
dna polymerase III
-uses RNA primer, An enzyme that catalyzes the elongation of new DNA at a replication fork by the addition of nucleotides to the existing chain.
nominalistic species concept
(attrib to Lamrak and Buffon) denies existence of real universal entities and maintains tha tonly individual organisms exist. That is species are simply man made constructs and species names only apply to similar type individuals
How was one gene one enzyme hyptheses tested
(beadle and tatum )mutant enduced nutritional gene showed no growth in minimul medium...break down complete medium showed groth would occur in minimul medium + amino acid mix...if the mutation affected tyrosine instead of amino acid synthesis, then addition of tyrosine to the minimul was needed
western corn rootworm
(beetle larvae) damage to corn plants in US...they damage the plants directly and create conditions making fungal infection more likely
DNA
(biochemistry) a long linear polymer found in the nucleus of a cell and formed from nucleotides and shaped like a double helix
RNA
(biochemistry) a long linear polymer of nucleotides found in the nucleus but mainly in the cytoplasm of a cell where it is associated with microsomes
mutant
(biology) an organism that has characteristics resulting from chromosomal alteration
polymorphism
(biology) the existence of two or more forms of individuals within the same animal species (independent of sex differences)
evolution
(biology) the sequence of events involved in the evolutionary development of a species or taxonomic group of organisms
Holiday Junction
(cross-strand exchange) a special DNA intermediate that contains 4 DNA trands sharedbetween TWO DNA helices
typological species concept
(dates to Plato times, Linnaeus adhered to this) Species were similar individuals that shared the same essence. One species was separted from another by sharped differences in morphology, behavior, etc. Species were immutable (constant through time) Varitons thought to be infrequent and range for it was very limited.
southern blot
(edward southern 1975) 1) degest D with RE and sepoarate iagarose gel elct. 2) stain with ehtidium bromide 3) dee with UV light smear 4) denature DNA with NaOH 5) transfer DNA to nitocellulose or nylone membrane 6) expose to UV to crosslink dna to blot 7) incubate with radioactive probe 8) wash blot to remove excess probe 9) expose to x-ray film 10)bands on film represne sites where the probe annealed
Core promoter
(eukaryotic) the site to which the basal transcription apparatus binds, contains one or more consensus sequences (TATA box)
core promoter
(eukaryotic) the site to which the basal transcription apparatus binds, contains one or more consensus sequences (TATA box)
inversion
(genetics) a kind of mutation in which the order of the genes in a section of a chromosome is reversed
haploid
(genetics) an organism or cell having only one complete set of chromosomes
mutation
(genetics) any event that changes genetic structure
meiosis
(genetics) cell division that produces reproductive cells in sexually reproducing organisms
transformation
(genetics) modification of a cell or bacterium by the uptake and incorporation of exogenous DNA
position effect
(genetics) the effect on the expression of a gene produced by changing its location in a chromosome
transcription
(genetics) the organic process whereby the DNA sequence in a gene is copied into mRNA
transduction
(genetics) the process of transfering genetic material from one cell to another by a plasmid or bacteriophage
translation
(genetics) the process whereby genetic information coded in messenger RNA directs the formation of a specific protein at a ribosome in the cytoplasm
phyletic species concept (PSC)
(joel cracraft) species is the smallest diagnosable cluster within which there is a pattern of ancestry and descent (implicate diag. clusters defined by uniquely derived characters> (modified by McKitrick and Zink with add it si is the smalles diagnoable cluster and is monophyletic) (operational concept, definition..not as theoretically as good as ESC thoguh)
miRNA
(micro RNA) regulate gene expression typically by blocking translation of selective mRNAs
Nicotinate
(niacin) - vitamin B, Vitamin precursor of NADH or NADPH
How is does direct repair act on UV damage?
(not in humans) light >300nm onto CPP photolyase
What's the Wobble Hypothesis?
(pattern of degeneracy in the 3rd position) the 1st two are nucleotides are more critical in attracting the correct tRNA during translation the the 3rd (why triplet codes share the same first two for an amino acid typically when degeneracy is present)
cospeciation
(phylogenetic tracking) results whenn the speciation patterns in a host are reflected in the speciation pattern of that hosts parasites
smRNA
(small RNA) general term to include all small regulatory RNAs
siRNA
(small interfering RNA) turn off gene expression directing degredation of selective mRNAs
snRNA
(small nuclear RNA) RNA processing Found only in the nucleus of Eukaryotes and functions to remove introns from mRNA
lacA
(thiogalactoside transacetylase)-detoxifies biproducts of the permease
the inside of the neuron is ___ and the outside is __
+, -
The first nucleotide transcribed is designated __. Downstream DNA is _____ while upstream DNA is ___ and is not transribed like downstream DNA.
+1 positive negative
varying what will change the twitch force?
-voltage, -duration -delay -frequency
3 principle ways metabolic processes are regulated.
-amount of enzymes (rate of transcription) -catalytic activity is regulated (reversible allosteric control, feedback inhibition, reversible covalent modifications, hormones, energy charge) -accessibility of substrate is regulated (compartmentalization segregates opposed reactions, controlling flux of substrates)
types of DNA repair systems
-base-excision repair -nucleotide excision repair -mismatch repair -homologoust recombination and NHEJ (double breaks) DIrect repair (DNA photolyse, demethylates)
How do Eukaryotes regulate genes?
-chromatin structure (heterochromatin, euchromatin) -splicing and polyadenylation -export of mRNA from the nucleus -turnover of mRNA -reuglation of protein synthesis and degreadtion -posttranslational regulation of protein activity
main forces applied to the EC
-circuferential distention of blood pressure (due to pules pressure variation inside vessel) -shear stress (due to blood flow)
Give 7 traits of the genetic code.
-colinear -triple code, reading frame -unambiguous -degenerate -directs initiation and termination of translation -nonoverlapping -universal
What factors make eukaryote transcription highly regulated?
-complex transciptional regulation -nuclear membrane -RNA processing -transport of mRNA
Name the forces that stabilize the structure of biomolecules and maintain biological orders.
-covalent bonding -non-covalent bonding -H-bonding -hydrophobic/hydrophilic interaction
mechanisms o fgene duplicatoin?
-crossing over -breakage and fusion during meisosis -segmental -retroposition (MRNA to DNA via reverse transcriptase) -chromosomal or genome duplication
what do base and nucleotide excision epair hav in vommon
-cut to remove -use other strans as template -seal dsDNA back up
large scale changes in chromosome arrangement and/ or content
-deletion -inversion -duplication -nonreciprical translocation -uneven translocation
types of ionophores
-diffusable ionophore: binds ligand and carries across -channel-forming ionophore: provides aqueous path
List the 7 assumptions of the Hardy Wiegnberg model
-diploid organisms and sexual reproduction -nonoverlaping generations -random mating -large populations (no genetic drift) -no mirgartion (no gene flow) -no new matations arise -no selection (all have same fitness)
Mechanisms of DNA repair
-direct reversal of DNA damage -base excision repair -repair involving excision of nucleotides -repair of double stranded breaks
problems with inversions
-drisrup genes in cell of prigin depending on break points -position effect (on/off with heterchromatin, eucromatin) -fertility problems because of pairing problems in meiosis -prevent future crossovers -balancer chromosome
how did scientists discover genes are mad e of dna
-dye stains dna -intensity of dy in mitosis stges -used evidence of dna distribution -frederic griffith pneumonia experiment
nucleotide excition repair
-endonuclate nicks large chunk with damage -dna polym fills in -ligase seals.
Function of 5' cap
-facilitate bind of 5' end to ribosome -increase mRNA stability -enhance RNA splicing
What does the binding of OR1 do?
-facilitate tetrramerization -prevent Cro transcription
What are some of the processes tha could contrib to generation of complex genome?
-gene duplication -gene conversion
What is Matt's Method for estimating pI of a polypeptide?
-identify all ionizable groups and copy down their typical pKa values -add H to any group that is not protonated and write down the fully protonated peptide charge -Count the positve charges -order the pKa from lowest to highest -starting with the positive charge, deprotonate, writing the pKa from lowest to highest for the steps taken until all species have been deprotonated -then average the two pKa's around the 0 -
mechanisms of mutation
-incorportiaon of error in replication -rare base forms -strand slippage and unequal crossing over -spontaneous chemical changes -inudced chemical changes
population augmentation strategy
-increase numbers of declineing pop by transplanting individs of the same species from other locations adv -increase gene flow -ptential for improved fitness disadvant -genetic swamping-loss of specied id as a result of the blending -outbreeding depression-reduce fitness in prgenyof matings exex florda panther
Function of 3' poly-A tail
-increase stability of mRNA -facilitate binding to ribosome
What mutations can occur in regulatory elements (promoter, operator)?
-interfere with expression of all 3 genes -cis-acting
What are the 4 types of non-covalent bonds? Rank them from highest strength to lowest.
-ionic interaction: attraction or repulsion due charge (20-40 kJ/mol) -hydrogen bonds (20 kJ/mol) -hydrophobic interaction (8 kJ/mol) -van der Waals: when two atoms are in close proximity (4 kJ/mol)
Why do constitutive mutations occur?
-lac operator sequence (lacOc) mutated so the repressor can't bind to it -the lac repressor (I)--nonfuctional due to a mutation that renders it unable to bind to the DNA of the operator sequence
What two reactions does B-galactosidase catalyze?
-lactose->glalctose+glucose -lactose->allolactose
Name the 6 traits of the genetic code.
-linear and commaless -read as triplet condons -unambiguous (1 triplet->1 amino acid) -degenerative (1 amino acid can be made by more than 1 triplet) -nonoverlapping -nearly universal
effects of genetic erosion
-lloss of favorable alleses -reduced heterozygosity
What two factors influence all chemical reactions?
-tendency to achieve the most stable bonding states -tendency to achieve the highest degree of randomness (net effect of the two being free-energy)
types of point mutaitons
-location: germline vs somatic, autosome vs. sex chomosome -affect to DNA seq.-substitution, insertion, deletion -affect on polypeptide: silent, missense, non-sense, gain of function, loss of function, null -affect on organism: neutral, lethal, conditional, mutant vs wild type
What are the 7 requirements for initiation of translation in E. coli.
-mRNA -initiator tRNA (tRNA^(fMet)-->UAC complement of AUG) -small ribosomal subunit -GTP -Mg2+ -3 initation factors -large ribosomal subunit
adenylate cyclase pathway
-makes cAMP, which binds to regulatory subunits of PKA tetramer & allows catalytic subunits to break off, phosphorylation of cellular target activate gluconeogenisis, glycogenolysis, lipolysis inhibit glycolysis and glycogen synthesis
3 reasons living organisms need energy?
-mechanical work -active transport -synthesis of biomolecules
Characterisitics of trabeulae?
-microscopic rod or plate shapes -positionaed along stress lines -irregularly shaped
types of DNA damage
-mis-incorporation of a single base -cheical modification bases -chemical cross-linke between the two strands of the double helix -breaks in one or both of the phosphodiester backbones
What are the positive aspects of BSC that nominclastic and typological lack?
-more evo explination of what species is -stresses genetic cohesion (species' reality from the historically evolved, shared info contents of genetic pool. -species form repoductive communities, ecological units, and genetic units
Name 4 things that lead to the discovery of the genetic code.
-mutations affecting the reading frame -RNA homopolymers (nirenberg and Matthei) -the triplet binding assay (Nirenber and Leder) -confirmaion by sequencing studies
Casues of population bottlenecks
-natural disaster or disease -captive breeding pprograms -founder effect caused by mirgration of samll number of individs
How is eukaryot transcription different from prokaryotes?
-occurs in the nucleus -requires chromatin remodeling -more extensive interactions between cis-acting DNA sequences (promoters, enhancers, silencers) and trans-acting proteins (transrciption factors) -extensive RNA processing -3 RNA polymerases
incomplete penetrance
-person has genotype for a disorder but doesn't not display the phenotype (or clinical manifestations) of the disorder (CAN PASS ON TO CHILDREN 30% female 80 male
What causes loss of genetic diveristy?
-pop fragmentation-disrupts gene flow -agricultural practices -consumer demand-pref for certain varieties less div in because of artificial selection leads to less resistance to disease, cold, or drought
non-random mating types
-positive assortive mating: tend of simliar genotypes to mate -negative assortive mating -inbreeding (coeff of inbreeding F)
in situ conservation strategy
-preserve pop size and biological diverity in original habitat -id of biodiversity hot spots to target spots for conservation -"on-farm" preservation-maint of trad crp vaieties and livestock
What is the process of transcription?
-promoter recognition -initiation -elongation -termination
telomeres
-protect eukaryotic chromosomes
What do we need to purify a protein of interest?
-protein source -separation methods -an assay
Steps of rec and rad catalyzis
-recA interwines the DNA single strand and DNA duplex -DNA single strans search the duplex for homologous sequ -strand invasion: single strnad froms bp with complement in heteroduplex
E3
-recognizes target prteins -ligates Ub to Lys on target, forming isopeptide bond
inbreeding depression
-reduced fitness and lower survival in inbred pop -result of increased homozygosity for bad alleles
Give some more mechanisms the regulate gene expression
-regulate mRNA half-life -regulation of translation -posttranslation regulation (regulate protein stability (ubiquitination) and activity (phosphorylation))
functions of lymph system
-removal of interstitial fluid from tissues -absorms and transports fatty acids and fats from digeston -transports white blood cells to and from lymphs into bones -transport antigen-presenting cells (APCs), such as endritic cells, to the lymph nodes where an immune response is stimulated
What are the 3 units formed by a species?
-reproductive communities -ecological units -genetic units
What components are necessary for traslation?
-ribosomes -charged tRNAs -mRNA transcript -amino acids
components of selective channel
-selectivity filter -activation gate (volate dependent) -inactivation gate (voltage and time dependent, must be reset and open before anothe raction poetnetial) -blocked by toxins (tetrodotozin fro Na, tetraethylammonium for K_
problems with RNA world
-self-replicaitn RNA only up to 14 nucleotides long, catalytic RNAs estimated to require 50 nucelotides -no known physical encouragement for meultiple self-replicating RNA molecules ot colelct in the same local area
Most genetic differences in humans result from...
-single nucleotide polymorphisms (SNPs)-single base changes in the geome -copy number variations (CNVs)-segments of DNA taht are duplicated or deleted
What 4 properties of a protein can be exploited for separation?
-size -charge -hydrophobicity -binding properties
Factors that influence Glaucoma
-stiffnes of sclera -radius of eye -stiffness of lamina cribrosa -intraocular pressure -thickness of scleral shell
design factors for irrecuglar bone?
-strength to resis diff. load -stiffness -light wight -fatigue fract resitanc =absorb energy during impact -sel-repairing -ability to dynamically adapt
genomics encompasses
-structural genomics\ -functional genomics -comparatic genomics -metagenomics
What are the 4 main points on which the eukaryotes and prokaryotes differ in transcription?
1) Eukaryotes have 3 (instead of 1) forms of RNA polymerase and transcription occurs inside the nucleus. 2) Eukaryotes require chromatin remodeling, the unwinding of the chromatin. 3) Eukaryotes have more extensive pre-intiation components, such as transcription factors, enhancer, and silencers that are needed for proper transcription. 4) Eukaryotes require mRNA processing, where RNA becomes mRNA.
What are 4 methods of gene regulation?
1) How long mRNA is stable and available for translation 2) control efficiency of translation 3) control how long the protein is stable before degradation 4) regulate initiation of treanscription
How did Nirenber and Mattaei decifer the genetic code inorder to determine non-specific triplet code assignments?
1) Sythesizing polpeptides in Cell-Free system Using an invitro mixture of ribosomes, tRNAs, amino acids and other molicule, radioactivally tagged amino acids were used to follow the protein synthesis. The mRNA was added with the enzyme polynucleotide phosphorylase which catylzed the formation of RNA in the presence ofhigh concentrations of ribonucleoside diphosphates. The probability of insertion of a particular ribonucleotide was proportional to the availabilty of the molecule relative to tother available ribonucleotides. 2) Homopolymers By making homopolymers (UUUU..., AAA..., GGG.., CCC...) and labeling particular amino acids, the triplet condon assignments for the homopolymers was elucidated. 3) Mixed Copolymers By putting two different ribonucleosides in at different ratios, it was possible ot anylze te resulting ratio of amino acids and match up their ratios to the probability of its triplet.
Give the sequence of transcription factor binding.
1) TFIID (TBP included) 2) TFIIA 3) TFIIA 4) RNA pol II with TFIIF, TFIIE, & TFIIH
How does evo species concept explain hybridization?
1) a retrianed trait from primative anscestores 2) the 2 species are each other's closest relatives -if zone of contact bn them is narrow and old, then good species -if zone of contact is wide, not good species -contact zone may only be apparent, not actual
Name 4 corolaries of evo species concept.
1) all organisms, past and present, belong to some evolutionary species. (oragisms derive from liniages) 2) species repr isolated to the extent that this is required for maintaining their separte identies, tendencies and fates ( the interbreeding criterion) 3)evo species may or may not exhibit recognizable phenetic differences (over or under estimate # of lineages) 4) no presumed separate, single evo lineage may be subdivided into a series of ancestral and descendent species. phylletic spciation
What are the 3 reasons to reject phyletic speciation
1) arbitrary as to where we draw the line between species 2) arbitrays spsecies produce arbitrary mechanisms 3) phyletic speciation has never been adequeately demonstrated
What are some post-translational modification to proteins that may occure?
1) cleavage removes a protein (such as fMet) 2) cleavage may split a polyprotein 30 addtion of chemical constituent may modify a protein (ex. phosphorylation)
What are the 4 cis-acting DNA elements that regulate the initiation of transcription by RNP II?
1) core promoter 2) proximal-promoter elements 3) enhancers 4) silencers 1-determines whre RNP II binds and begins to copy 2, 3, and 4-efficiency of the rate of transcription
What are 3 possible outcomes of second contact?
1) if reproductive isolation is complete and anagenesis had proceeded to where new species are now eocologically segregated from one another, then both species can occupy the same space without causing evolutionary changes in the other 2) If, however, reproductive isolation is complete but geographic isolation hasne't been long enough or anagenesis hasn't been quick enough then the species are still ecologically segregated and when they are reintroduced into the same space there will be competition, causing mutally induced divergence, called character dispacement. (doesn't have to be morphological, can be behaivoral, habitat use, food choice, etc., 3) If reproductive isolation is not complete, hybridization between the tow incipient species may occur. Potentilly resulting in introgression where the incepient species lose distinctivness and meld back into a form that may or may not be like it was previously. Or, the hybrids may have lower fitness and introgression would not occure and natural selection might improve reproductive isolations so that hybrids don't form...leading to speciation completion in a Mayrian sense (called the Wallace effect), or anagensis may continue, ultimately leading to speciation
2 criteria for a pathway?
1) individual reactions must be specific 2) entire set of reactions must be energetically favorable
2 criteria of a pathway
1) individual rxns must be specific 2) entire set or rxns must be energetically favorable
4 factors that contribute to natural selection
1) individulas of the same species exhibit variation in phenotype 2)many variations are heritable and passes on to offspring 3)reproduction produces more offspring than can survive with limited resources, individuals must compet for resources and mates and must avoid predators 4) some phenotypes are more successful than others, leading to greater survival and reproduction success
4 types of mutualism?
1) intracellular mutualism 2) intraorganismal mutualism 3) mutualisms between organisms 4) mutualism between populations
making a genomic library
1) isolate genomic dna 2) framgent into smaller pieces (restrition digest) 3) ligate ach segment into avector 4) transform into host cells to create a lirary respresneting all genomic r
What are the minimal elements of life?
1) life must be chemical (no artificial computer intellegence) 2) life sustians itself by gathering atoms and energy from its environment (doesn't eat=not alive) (requires metabolism) 3) living organisms must display variation
3 stages of fatty acid processing
1) lipids broken down to fatty acids and glycerol 2) fatty acids are activated and transported into mitochondria 3) fatty acids are oxidized in a step-by-step process to obtain molecules of acteyl CoA
3 ways of regulating development
1) localization of maternal molecules 2) cell signaling 3) gene regulatory networks
steps in bacterial translational initiation
1) mRNA and ribosome must come together 2) charged tRNA must find P site 3) ribosome must be in proper position over start codon
5 gener principles and motifs of metabolism
1) meabolic pathways -fueld degraded, large molecules constructed 2) ATP in ATP yielding and consuming pathways -energy currency 3) oxidation -formation of ATP 4) key intermediate -shared among many metabolic pathways 5) highly regulated -allows efficient use of fuels and coordination
3 factors interbreeding depends on
1) mode of reproduction 2) devleopmental plasticity 3) geographic position
Give the function of the mouth, stomach, pancreas, gall bladder and intestine.
1) mouth: homogenization of food 2) stomach: denature (low pH) and degrade (pepsin) of protein 3) pancreas: releases enzymes of proteins, lipids, and carbs; releases sodium bicarbonate to neutriaize pH 4) gall bladder: release bile salts 5) intestine: peptidases further degrade proteins
Reasnos the typological species concept was rejected
1) now way to objectively determine what the essence of a species is 2) applications allos you to have members fall into different species groups based on differences in sex or age 3) sibling species, species tha look the same but do not funcation the same 4)degree of difference between 2 forms is not a decivsive criterion when ranking taxa as species
3 steps of capping reaction
1) phosphatase removes P from 5' end of RNA 2) guanyl transferase adds GMP in a reverse linkage 3) methyltransferase adds methyl groups
roles of the snRNP's
1) recognize 5' splice site & branch site 2) bring the 5' splice site & branch sit together as required 3) catalyze the RNA cleavage and joining reaction (specifically snRNA)
What are the important features of a plasmid vector?
1) small, circular molecule 2) origin of replication 3) polylinker (multiple cloning site) with unique restrition sites 4)seletable marker 5) reporter gene
problems with interbreeding criterion?
1) some want to view specieation as incomplete until both have sypatric distribution 2) prejudice to describes new species and not sympatric to its closest relative 3)95% of specieation occurs in allopatry
Aside from ecological model of sympatric speciation, what are other models for sympatric speciation?
1) speciation by hybridization--in bisexual organisms, the origin of hyrbid species is usually sympratric 2) speciation of apomixis--asexual species derived from bisexual ancestors may arise in place and there is no reason to beleive that suce speciation must involve geographic barrier because instance speciation is thought to be instantaneous
How are lipids digested?
1) stomach: emulsion (miscelle formation) 2) intestine: bile salts 3) pacrease: lipases
What 3 criteria for id of coevolved systems
1) traits involved int 2 interactin populations or species are genetically determined 2)where variation in these traits occur, the 2 taxa vary in tandem 3) the traits and the variation are mutually induced. taht is the getic traits do not occure in areas where the other interactive species is absent or rare, and each trait is specific to that species or population and no other.
5 weakness of BSC
1) what about asexual species? (instead of repro. isolated-> that occupies specific niche in nature, but this still would allow for recognition of each separate species 2)How do you measure reproductive isolation? No introgression, some, how much/ 3) What about allopatric populations? Can't test repro isolation. 4)is repro isolation imortant, because some may retain compatibility primatively 5)fossils don't fit definition (can measure repro isolation)
What is the stomach pH?
1-2
How frequent is down syndrome?
1/800 births; 4000 - 5000 births annually.
-_ and -_ sequences affect transcription
10, 35
10% solutions of NaCl is...
10/100mL
percentage of spontanous abortions
15%
Mutations affecting splicing have been estimate to cause __% of all genetic disease.
15% ex. Breast&ovarian cancer (BRCA1), cystic fibrosis (CFTR), Lesch-Nyhan syndrome
What is the precursor for the small and large ribosomal particle units?
15S rRNA, it is transcribe in nucleolus...continas spacers between units...requires processing to remove spacers
What makes up the small ribosomal particle?
18S unit combine with polypeptides encoded by other genes
Who is credited with the theoretical elucidation of the triplet nature of the genetic code? Explain the reasoning.
1960s Sidney Brenner (4 bases) 4^2=16 too few for 20 4^3=64 just right for 20 with degeneracy accounting for extra 4^4=256 way too many for 20 amino acid
Who first postulated the existence of mRNA?
1961 Jacob and Monod
composition of porteasome
19S cap onboth sides of 20S catalytic core (acts like a protein shredder)
What atomic magnetic moments is the NMR based on?
1H, 13C, 15N, 31P
trisomy 21
1st most common cause of mental retardation-down syndrome-etiology(cause): chromosomal nondisjunction during meiosis; an increased risk of having child with DS in older mothers > 45 yrs; mental retardation, IQ 30-70, flat nasal bridge, epicanthal folds, low set ears, short stature, short neck, hypotonia, protruding tongue, congenital heart disease, increased respiratory infections, alzheimers, most males are sterile, some females can reproduce
How is hemaglobin made up>
2 B globin and 2 a-globin with 4 heme groups
How many H-bonds are involved in each of the DNA base pairs? Can you draw out the base pairs?
2 for AT 3 for GC
Discuss the transesterfications that occur to form the lariat and spliced product
2' OH on intron A transesterfies with the P between G of teh e5' exon and the G of the intron the now 3' OH of the 5' exon transesterfies with the G and G of 3' exon P, joining the exons and cleaving the lariat
Each round of oxidation shortens the fatty acid by __ carbons, and produces __ each: FADH2, NADH, and acetyl CoA
2, 1
During translation the __ unit ribosome pairs the synthetic RNA triplet in the __ unit to the charged tRNA anticodon in the __ unit, forming the RNA triplet-tRNA-ribosome complex.
2, small, large
__ synthetases charge 31 tRNAs that base pair with 61 codons
20 (b/c 20 amino acids)
About how many adnenines are int the poly a tail?
200
RNA pol II produces ~_ nucleotides (nt) and then is capped
25
Approximately how many genes are there on the human genome?
25,000
Approximately how many different proteins are in our body? Of those, how many are unclassified?
25,000 30.6%
results fo F+XF- HfrXF- F'XF-
2F+ one Hfr, and one F- (no change 2 F'
types of aneuploidy
2n+/- x chromosomes monosomy 2n-1 disomy 2n trisomy 2n+1
trisomy
2n+1; less drastic phenotype for sex chromosomes than autosomes but are often lethal
_ h bonds in G C pair
3
codon
3 nucleotide sequence that specifies one amino acid
Amino acid binds to the _' end of the tRNA, opposite to the anticodon fo the tRNA.
3' end
laggin strand goes from __ to __ direction
3' to 5'
about __% of cytosines are methylated in verebrate DNA and is repaired by...
3, special DNA glycosylase that recognizes a mismateched TG
slow myosin twitch is __/sec fast myosin twitch is __/sec
3, 10
How many Baise pair? genes? how much repeat?
3.2 Billion 25,ooo 50%`
How many base pairs long is the DNA?
3.2 billion
There are ___ residues per turne with a pitch of ___ nm.
3.6/0.54
How strong is a C-C bond?
350 kJ/mol
The pI of arginine is about 10.5. What will be its charge at pH 3, 7, and 10.5?
3: pH<pI positive 7: pH<pI positive 10.5: pH<pI negative
H-bonding occurs between the carboxyl end of a residue and the amino end of a residue every ___ residues.
4 (i+4)
how old is the earth?
4.5 billion
Muscle can exert about ___ ___ force during an eccentric contraction compared to maximul isometric force
40% more
How many atoms are on the peptide bond plane?
5
Eukaryotic ribosomes are recruited to the mRNA byt eh...
5' cap
For the exons sandwiching the intron (these are consensus sequences), what is on the 5' and 3' end?
5' consensus sequence: GU(A/G)AGU splice site 3' consensus sequence: CAGG
What are the Wobble rules?
5' end of anticodon---->3' end of codon G--->U or C C---->G A--->U U--->A or G I--->U, C, or A (inosine, modified from A)
How many genes are there on the trp gene? What do they code for?
5, 5 different enzymes
What makes up the large ribosomal particle?
5.8S, 28 S unit plus a 5S unit-combine with polypeptides encode by other genes
threshold to elicit the action potential is the Em ___% of the time
50%
What conditions would result from nondisjuction in meiosis II?
50% change of the male or female being normal 25% change of a having either a Klinefelter boy with the trisomic or lethal boy with monosomic 25% change of 47, XXX female for trisomic or turner for monosomic overall less chance of death than with meiosis I nondisjucntion, plus half are normal
The human cell DNA loses __ purines everyday.
5000
At what temp do primers anneal
55 C
What part of the large ribosomal unit is made outside the nucleolus?
5S unit
Splicomes use __ snRNAs, rich in uradine.
6
myosin has __ proteins with __ heavy chaing + __ pairs of light chaing
6, 2, 2
avogadro's number
6.2*10^23 number of particles in a mole
The brain uses ___% of glucose. It can oly use ___ or __ as energy sources.
60-70, glucose, ketone bodies
early atmposphere
74% co2 15% wat vapor, 10% nitrogen now 78% nitrogen, 21% o2, 1% argon and .03% co2
How long is tRNA and what is its secondary structure? What charges this molecule?
74-90 nucleotides cloverleaf adding an amino acid
___% od Down's cases are due to nondisjunction in meiosis ___, almost always (95%) in ovum.
75, I
How many exons exist for the following introns: 79, 81, 23?
80, 82,24
SNPs
90-95% of seq. varitation 1/350 bp freq most in non-coding region->affect expression those in coding->missence deteced in southern blot with RFLPs
coefficient of coincidence
=(# of observed doubles)/(# of expected doubles)
How much purified protein is needed for crystallography?
>2 mg
cDNA
A DNA molecule made in vitro using mRNA as a template and the enzyme reverse transcriptase. A cDNA molecule therefore corresponds to a gene, but lacks the introns present in the DNA of the genome.
recombinant DNA
A DNA molecule made in vitro with segments from different sources.
TATA box
A DNA sequence in eukaryotic promoters crucial in forming the transcription initiation complex.
enhancer
A DNA sequence that recognizes certain transcription factors that can stimulate transcription of nearby genes
parapatric speciation
A branching of population lineages to form seperate species in which the diverging lineages are mostly nonoverlapping in geographic distribution but make contact on a narrow borderline
nucleotide
A building block of DNA, consisting of a five-carbon sugar covalently bonded to a nitrogenous base and a phosphate group.
cap 0
A cap at the 5' end if mRNA that has a methyl group only on 7-guanine.
cap 1
A cap at the 5' end of mRNA that has methyl groups on the terminal 7-guanine and the 2'-O position of the next base.
cap 2
A cap that has three methyl groups at the 5' end of mRNA
cyclin
A cellular protein that occurs in a cyclically fluctuating concentration and that plays an important role in regulating the cell cycle. Rises from the end of mitosis to the end of the next mitosis.
trait
A characteristic that an organism can pass on to its offspring through its genes.
covalent bond
A chemical bond that involves sharing a pair of electrons between atoms in a molecule
exergonic
A chemical process in which there is a net energy release
What would you expect about the formation of an a-helix for a segment of a protein chain that contains lysine approximately every fourth residue with all other residues being mostly hydrophobic? A) Helix formation would be favored at neutral pH. B) Helix formation would be favored at low pH. C) Helix formation would be favored at high pH. D) Helix formation would never occur regardless of pH.
A) Helix formation would be favored at neutral pH.
Once the RNA polymerase pauses, the hydrogen bonds in ____ ___ __ break and the RNA transcript separtes from the template, terminating transcription
A-U base pairs
vitamins that don't function as coenzymes
A-vision, growth, repro C (asorbic acid)-antiox D-calcium met E-antiox K-blood coagulation
chargaff's rule
A=T, G=C
Acetyl CoA carboxylase (ACC) is regulated by the conditions of the cell Explain further.
ACC is inactive when glucose levels are low if citrate is high, suggests CoA & ATP are high, so ACC will get partially activated by citrate
substrate-level phosporylation
ADP gains a phosphate from a high-energy organic material such as 1,3-Bisphosphoglycerate or phosphoenolpyruvate
Which releases more energy? ATP->ADP or ADP->AMP
ADP->AMP -10.9 kcal.mol (ATP->ADP -7.3 kcal/com)
What does oxidation of carbon fuels in catabolism create?
ADP->ATP oxidation reaction
____-dependent protein kinase is the cell's fuel gauge; it responds to energy charge
AMP
What is AMP, ADP, and ATP? Which is found in the DNA backbone?
AMP-adenosine monophosphate ADP-adenosine diphosphate ATP-adenosine triphosphate AMP, there is one phosphate group between each sugar
____ mactivates catabolic pathways that generate ATP, while inhibiting anabolic pathways so as to conserve ATP for more vital processes
AMPK
contrast action potential and electrotonic potential that hasn't reached threshold
AP: unidirectional, all-or-none EP: bidirection, gradded
What makes anthrailate to PRA?
AS I and II (and PRPP-->phosphorilbosyl pyrophosphate)
SWI, SNF proteins remodel nucleosomes and require..
ATP
hyrolisis of ___ coupled to thermo. unforable reaction can drive it forward
ATP
List the groups carried by the following: ATP NADH and NADPH FADH2 FMNH2 Coenzyme A Lipoamide Thiamine pyrophosphate Biotine Uridine diphosphate glucose Nucleoside triphosphate
ATP (phosphoryl) NADH and NADPH FADH2 FMNH2 (electrons) Coenzyme A Lipoamide (Acyl) Thiamine pyrophosphate (Aldehyde) Biotin (CO2) Uridine diphosphate glucose (glucose) Nucleoside triphosphate (Nucleotides)
___ catylzes the formation of aminoacyle tRNA
ATP hydrolysis
go through the proces of ubiquitin taging
ATP+Ub->Ub bound to E1->Ubbound to E2->E3->substrate with Ub->->-> afte enough tags it is degraded by prteasome
How are snRNPs released from the mRNA after splicing?
ATP=powered helicases unwind RNA duplex intermediates that facilitate catalysis and induce the release of snRNPs from the mRNA
What is the base pairs the recruit the small subunit of the ribosome, initating translation.
AUG, preceeded by the Shine-Dalgarno sequence
philidelphia chromosome
Abnormal chromosome produced by a translocation bt 9 & 22, Chronic Myelogenous Leukemia
histone modifications
Ac, Me, P
competence
Acceptable levels of achievement, Basic need to be effective in dealing with the environment.
Sickle-cell anemia
An autosomal recessive disorder characterized by a single nucleotide mutation in chromosome 11 that leads a defect in the β-globin gene in which glutamic acid is substituted for by valine at position 6. Hemoglobin with this mutation is referred to as HbS, as opposed to the normal adult HbA. Under conditions of low oxygen concentration, the HbS polymerizes. The deoxy form of haemoglobin exposes a hydrophobic patch on the protein between the E and F helices. The hydrophobic residues of the valine at position 6 of the beta chain in haemoglobin are able to associate with the hydrophobic patch, causing haemoglobin S molecules to aggregate and form fibrous precipitates.
reverse transcriptase
An enzyme encoded by some certain viruses (retroviruses) that uses RNA as a template for DNA synthesis.
DNA polymerase
An enzyme that catalyzes the elongation of new DNA at a replication fork by the addition of nucleotides to the existing chain.
dna polymerase II
An enzyme that catalyzes the elongation of new DNA at a replication fork by the addition of nucleotides to the existing chain.
dna polymerase III
An enzyme that catalyzes the elongation of new DNA at a replication fork by the addition of nucleotides to the existing chain.
telomerase
An enzyme that catalyzes the lengthening of telomeres. The enzyme includes a molecule of RNA that serves as a template for new telomere segments.
exonuclease
An enzyme that cleaves nucleotides from either the 3' or the 5' ends of DNA or RNAd
ligase
An enzyme that connects two fragments of DNA to make a single fragment; also called DNA ligase. This enzyme is usedd during DNA replication and is also used in recombinant DNA research.
holoenzyme
An enzyme that consists of an apoenzyme and a cofactor.
primase
An enzyme that joins RNA nucleotides to make the primer.
kinase
An enzyme that phosphorylates something else. Kinases are frequently used in regulatory pathways, phosphorylating other enzymes.
helicase
An enzyme that untwists the double helix of DNA at the replication forks.
metaphase plate
An imaginary plane during metaphase in which the centromeres of all the duplicated chromosomes are located midway between the two poles
autopolyploidy
An individual that has more than two chromosome sets that are all derived from a single species
anfinsen experiment
An intact protein folding ribonuclease, treat with urea will denature the protein and betamercapta will reduce the disulfide bond. the denature structure then can be reformed with the removal of the urea and oxidize by b mercapta. This experiment show that proteins can be denatured reversibly and renature spontaneously.
paracentric inversion
An inversion where both breaks are on the same side of the centromere. Crossed over strands are directed into polar bodies in egg formation.
genetic map
An ordered list of genetic loci (genes or other genetic markers) along a chromosome.
genotype
An organism's genetic makeup
phenotype
An organism's physical appearance, or visible traits.
Traits of downs
Associated with several medical problems • hearing and vision defects • heart abnormalities • increased susceptibility to infection • Leukemia (20-fold risk) • thyroid disorders • Alzheimer-type dementia in later life. • Associated with developmental difficulties • delayed motor skills • delayed cognitive skills •Variable expressivity of symptom
imprinting
At a single locus, only 1 allele is active. The other is inactive (via methylation). Deletion of the active allele = disease
What are the largest subunits for RNA polymerase? The smallest?
B (151 kd) and B' (155 kd) w (10 kd)
What strong reducing agent breaks disulfide bonds or subunit analysis?
B-mercaptoethanol
Thiamine
B1, Aldehyde carrier precursor
Riboflavin
B2 precursor for FADH2 and FMNH2, electon carriers
Pantothenate
B5, precursor of CoA
Biotin
B7, CO2 carrier precursor
--- ARE VEHICLES FOR TRNSDUCTION
BACTERIOPHAGES
Name the various cis-acting elements of the RNA pol II promoter region.
BRE: TFIIB binding element TATA box: consensus sequence Inr: Initiator DCE: downstream core element DPE: downstream promoter element
F+ cell
Bacterial cells that possess a plasmid called the F factor, which includes a gene for a sex pilus.
CDK
Cyclin-dependent kinases. A protein kinase that is active only when attached to a particular cyclin. Activity rises and falls depending on the concentration of the cyclin partner. Regulates cell cylce.
centriole
Cylinder structures that are composed of microtubules, Are located near the nucleus and help to organize cell division.
ribosome
Cytoplasmic organelles at which proteins are synthesized.
Name the 4 DNA and the 4 protein elements that reuglate genes in eukaryotes.
DNA -core promoter -proximal promoter elements -enhabcers -silencers Proteins -transcription factors -general transcription factors -activators -repressors
central dogma
DNA -> RNA -> Protein
heterochromatin
DNA that is densely packed around histones. The genes in heterochromatin are generally inaccessible to enzymes and are turned off.
heterochromatin
DNA that is densely packed around histones. The genes in heterochromatin are generally inaccessible to enzymes and are turned off. Ex. telomeres and centromeres
euchromatin
DNA that is loosely packed around histones. This DNA is more accessible to enzymes and the genes in euchromatin can be activated if needed.
The Law of LaPlace
DP=T/r cylinder DP=2T/r sphere T=P in tubing/sphere
cockayne syndrome
Defective DNA repair (BER/NER) associated with neurodegeneration but no increase chance of cacer; defective excision repair associated with small stature, premature aging and sun sensitivity
cru-du-chat syndrome
Deletion of part of the short arm of chr. 5. Children are severely mentally delayed, have a number of physical abnormalities, and cry similar to the mew of a kitten
genetic variation
Differences among individuals in the composition of their genes or other DNA segments
Besides forming the phospholipid bilayer, what other important biological function does the hydrophobic effect serve?
Hydrophobic effects drive a protein to fold into a compact conformation where polar groups are outside the inner non-polar groups.
Wallace effect
Hypothesis that natural selection can contribute to the reproductive isolation of incipient species by encouraging varieties to develop barriers to hybridization, If hybrids show a reduced viability or fertility - NS will favor genetic variants which promote mating between individuals of the same population
How does a-amanitin affect the different types of RNA polymerase?
I High Km, insensitive II Low Km, strongly inhibited III Med Km, inhibited by high concentrations
Name the 3 types of RNA polymerase for eukaryotes. Give their location and cellular transcripts.
I Nucleolus 18S, 5.8S, and 28S rRNA II Nuceloplasm mRNA precursors and snRNA III Nucleoplasm tRNA and 5S rRNA
Which has more 0 n gametes, nondisjunction in I or II?
I has 2 0 n gametes which would bind and make monosomic
polymerase I vs II
I invitro dna synt III invivo dna synt
Give the product and location.
I rRNA Nucleolus II mRNA, snRNA Nucleoplasm III 5S rRAN, tRNA Nuceloplasm
What are the 3 initation factors that direct the assembly of the initaiton complex that contains mRNA and the intitator tRNA? Give specific functions for each.
IF1-prevents tRNAsf rom binding A IF2 -GTPase -Interacts with: small subunit, IF1, and charged initator tRNA -facilitates binding of intiator tRNA IF3 -prevents 50S from prematurly associating with 30S
Give the role of the 3 inititation factors
IF1-stabilizes 30S subunit IF2-binds fmet-tRNA to 30S-mRNA complex, binds to GTP IF3-binds 30s subunit to mRNA
Explain what happens if tryptophan is absent or present
If tryptophan is absent then the repressor alone cannot bind to the opertor If it is presnet then it binds
gene duplication
Instances in which a particular section of DNA, chromosome segment, chromosome or entire genome occurs more than once (Hall and Hallgrimsson 714) Can result in new genes that come from pre-existing genes (Futuyma 465) Leads to the formation of gene families, or gene clusters: Globin, Lactate Dehydrogenase, Esterase
____ gradients across membranes provide an important form of cellular energy that can be coupled to ATP synthesis
Ion
What are the 4 types of chromatography?
Ion-exchange chromatography -Fractionation based on charge; Gel-filtration chromatography -Fractionation based on size; Affinity chromatography -Fractionation based on specific binding; Hydrophobic chromatography -Fractionation based on hydrophobicity.
genomics
Is the study and comparison of genomes both within and across species.
What is the significance of the RNA having secondary and tertiary structures?
It allows for the creation of active sites.
What is an amino acid?
It is a hydrocarbon derivative with 1 H, 1 a-amino (+) group, 1 a-carboxyl group (-), and a side chain, most of which exist as zwitterions at physiological pH.
Is RNA single or double stranded? What structures does it form?
It is single stranded and can H bond with itself to form secondary and tertiary structures.
Fick's First Law of Difusion
J = -D(dC/dx)
pressure-driven flow
J=-L(dP/dx)
Fourier's Law of Heat Transfer
J=-L(dT/dx) L=lambda
Ohm's current law
J=-s(dw/dx) s=sigma w=trident=>psi
Michealis-Menten formulat of enzyme kinetics
J=Jmaz[S]/(Km+[S])
What methods were used to determine the specific triplet assignments?
Nirenberg and Leder-Triplet Binding Assay -Particular triplets were synthesized and bound to ribosomes. The tRNA bound to the triplet RNA-complex was determined by labeling the amino acid tested for and filtering the mixture. -lead to concultion that the genetic code was degenerte and unambiguous Khorana-Repeating Copolymers -Di, tri, and tetra repeats were made into long chains and joined enzymatically. The different triplet combos resulted in different amino acids depending on the start point. Then, the di, tri, and tetra chains were used to determine which had the same amino acid, providing a specific assignemnt.
Does the promoter get transcribed into the RNA?
No
Are operons common in eukaryotes?
No..they are rare
With saltatory conduction, the action potential only occur at...
Noes of Ranvier where the Na and K channels are
Rank the following bonds according to strengh. C-C C-O O-H C-H N-H S-S
O-H (470) C-H (414) N-H (389) C-O (352) C-C (348) S-S (214)
In aerobic organisms, the ultimate e- acceptor is ___. The ultimate oxidation product is ___.
O2, CO2
In absence of a catalyst: -NADH, NADPH, and FADH2 react slowly with __ ATP and acetyl CoA are _______ slowly
O2, hydrolyzed
rank affinity of the lambda to the operators from highest to lowest
OR1>OR2>OR3
What enzymes do snakes have in their venom?
Phospholipases: digest cell membranes (loss of cellular components) & lyse blood cells Collagenase: digests collagen (component of connective tissue) Hyaluronidase: digests hyaluronidate (glycoasminoglycan, component of connective tissue) Proteolytic enzymes: degrade basement membranes and extracellular matrix (tissue damage) Neurotoxins: immobolize prey
chiasmata
Point where two chromatids are intertwined, Molecular markers (scars) that prove crossing over has occurred - hold together sister chromatids from mom and dad.
What is the difference between polar and non-polar covalent bonds? Give examples of each.
Polar: electrons are shared unequally -O-H -N-H Non-polar: electrons are shared equally -C-H
habitat isolation
Populations live in different habitats and do not meet
ubiquitination
Post-translational regulation of gene expression: modification of protein product by attachment of ubiquitin to other proteins for degradation
base pair
Principle that bonds in DNA can form only between adenine and thymine and between guanine and cytosine
Explain how it wasm shown that DNA was the genetic material.
R strain (rough nonpathogenic mutant bacterium) grow in presence of S strain (smooth pathogenic baterium which causes pneumonia) cell-free extract or heat-killed S strain cells. R stain was observed to transform to S strain, with pathogenic daughter cells, leading to the conclusion that the S strain carries heritable information. The S strain was then fractioned into part RNA, protein, DNA, lipid, and carbohydrate of purified molecules. Testing for the transformation of the R strain to S strain, it was concluded the DNA carries the heritable information.
aldhyde
R-(C=O)-H
carboxyl
R-(C=O)-OH
keto
R-(C=O)-R
amino
R-NH2
phosphate
R-O-(P=O)(-O)(-O)
hydroxyl
R-OH
sulfhydrul
R-SH
Axon membrane can be modeld as a __ circuit
RC
What are the 3 termination of translation factors and their roles?
RF1- catalyzes release of peptid chaing from tRNA and dissociation of tanslocation complex; specific for UAA and UAG termination codons RF2-behaves like RF1 but only for UAA and UGA RF3-stimulates RF1 and RF2
Release factors
RF1-recognizes UAG, UAA RF2-recognizes UGA, UAA RF3-stimulate dissociation of RF1 & RF2
transcritipion couled repair involve __ polymerase that stalls at the site of dama
RNA
What transcribes mRNA?
RNA Polyerase II
What transcribes rRNA?
RNA Polymerase I
What transcribes tRNA?
RNA Polymerase III
Besides alternative splice, what is another way of altering the sequence of an mRNA?
RNA editing
What makes the structure of RNA different from DNA?
RNA has a 2' OH
RNAi
RNA interference; stops gene expression at transcription by using a short interfering RNA to make double-stranded RNA., RNA interference; injecting double stranded RNA into a cell turns off expression of a gene with the same sequence as the RNA
messenger RNA
RNA molecule that carries copies of instructions for the assembly of amino acids into proteins from DNA to the rest of the cell
What syntesizes RNA?
RNA polymerase
What eukaryotic RNA polymerase is responsible for transcription?
RNA polymerase II
___ and __ are localized in certain areas within the nucleus.
RNA polymerase II and trascription factors
Anions of ____ bind to main chains of polypeptides at a ratio of ___ ___ anion for every two amino acid residues. Consequently, all proteins carry a large net _____ charge that is roughly proportional to the ___ of the protein. The rate of migration is now strictly determined by the mass of the proteins: smaller ones travel faster.
SDS/one/SDS negative/mass
3 types of DNA polymorphism
SNPs STRs-short tandem repeats (microsatelites VNTRs-variable number tandem repeats (Iminisatelites)
Transfer NRCs?
SWI/SNF and CHD which are both also slide
genetics
Scientific study of heredity
genetic code
Set of rules that determine how a nucleotide sequence is converted into the amino acid sequence of a protein.
__ factor binds to the promoter.
Sigma
possible out omes of gene duplication
Similar Functionality LDH (A and C) and Globin Genes Pseudogene Genes that no longer function Functionally Distinct Lactate Dehydrogenase (LDH) converted to Malate Dehydrogenase (MDH) Are duplicated genes under selective pressure?
SNP
Single Nucleotide Polymorphism , DNA sequence variation occurring at a single nucleotide in the genome snp 1/35 bp genet div estimate
heritability
The proportion of variation among individuals that we can attribute to genes. The heritability of a trait may vary, depending on the range of populations and environments studied., A statistical estimate of the extent to which variation in a trait within a population is due to genetic factors
chromosomal aberration
The rearrangement of genes within chromosomes or a change in the total number of chromosomes
secondary structure
The second level of protein structure; the regular local patterns of coils or folds of a polypeptide chain.
gene amplification
The selective synthesis of DNA, which results in multiple copies of a single gene, thereby enhancing expression.
X chromosome
The sex chromosome found in both men and women. Females have two X chromosomes; males have one. An X chromosome from each parent produces a female child.
Y chromosome
The sex chromosome found only in males. When paired with an X chromosome from the mother, it produces a male child.
pre-initiation complex
The structure comprising the small subunit of the ribosome, the initiator tRNA plus ancillary factors that forms the initial association with the mRNA during protein synthesis in eukaryotes. Also the structure that forms at the core promoter of a gene transcribed by RNA polymerase II.
bivalent
The structure formed by the pair of homologous chromosomes during crossing over. Also called a tetrad because it consists of four chromatids.
Holliday structure
The structure that forms during the intermediate stage of crossing over where a branch migration occurs and generates unique gametes. A key intermediate of recombination.
holliday structure
The structure that forms during the intermediate stage of crossing over where a branch migration occurs and generates unique gametes. A key intermediate of recombination.
population genetics
The study of genetic changes in populations; the science of microevolutionary changes in populations.
C terminal domain
This must be phosphorylated by TFIIH kinase to initiate transcription. This phosphorylated tail provides a binding site for factors involved both in processing the transcript and in regulating the activity of promotor and transcription unit chromatin. It in an integrator and coordinator of the gene expression machinery
rRNA
a significant component of the ribosome. rRNA fabricates the polypeptides and provides a mechanism for decoding mRNA into amino acids and interacts with the tRNA during translation. rRNA was once known to be the key component of the structural of ribosomes, but its actually found to be a catalytic element for protein synthesis.
terminal deletion
a single break in a chromosome. The piece without the centromere will be lost.
chromosome
a single large macromolecule of DNA plus the DNA-bound proteins which serve to package and manage the DNA
RNA interference
a small fragment of dsRNA with seq similarity to a gene interferes with the express of that gene
the minor pathway
a small group of introns is spliced by an alternative spliceosome composed of a different set snRNPs
correpressor
a small molecule that affects gene expression; when the appropriate corepressor is present, a repressible gene is turned off
inducer
a small molecule that affects gene expression; when the appropriate inducer is present an inducible gene is turned on
inducer
a small molecule that affects gene expression; when the appropriate inducer is present, and inducible gene is turned on
corepressor
a small molecule that affects gene expression; whne the appropriate corepressor is presnet, a repressible gene is tunred off
codon
a specific sequence of three adjacent bases on a strand of DNA or RNA that provides genetic code information for a particular amino acid
helix-turn-helix motif
a structure found in transcription factor proteins that promotes binding to the major groove of DNA
sigma factor
a sub-unit of the polymerase (in bacteria) which is responsible of recognizing the promoter. after the creation of approximately 10 RNA nucleotides the ___________ ___________ disengages from the polymerase allowing it to continue transcription and to reach the terminator. it latches back on once the polymerase leaves the DNA strand.
RNase
a transferase that catalyzes the hydrolysis of ribonucleic acid
founder effect
a type of allopatric speciation mechanism in which a very small subsample of a population founds a new populaition in a geographically isolated area...probably a faster process than large scale allopatric model since genetic novelities can be fixed (homozygous in the populaition) in the small population
What are the 5 subunits of the RNA polymerase? Give their functions.
a-assembly of core enzyme; interacts with regulatory factors B-all stages of catalysis B'-bind to DNA; takes part in catalysis w-required to restore denatured polymerase to its native form o-70 (sigma 70)-promoter recognition
Which of the following is correct? a.) It is the actual free-energy change (i.e., DG) that determines whether a chemical reaction can occur spontaneously. b.) DG stays the same even if the concentration of reactants and products changes. c.) Reaction reaches equilibrium when standard free-energy change (i.e., DG0') equals 0. d.) All three statements above are correct
a.) It is the actual free-energy change (i.e., DG) that determines whether a chemical reaction can occur spontaneously.
Which of the following amino acids has NO chiral carbon? a.) glycine b.) alanine c.) proline d.) serine
a.) glycine
How does aminoacyl tRNA sythetases activate tRNA
a.a.+ATP=aminoacyl-AMP+PPi aminoacyl-AMP+tRNA=aminoacyl-tRNA+AMP a.a+ATP+tRNA+H2O=aminoacyl-tRNA+AMP+2Pi
DNA poluymerase holoenzyem pars?
a: DNA polymerase e: 2' to 5' proofreading exonuclease B: he dimeric sliding clamp
sequence the stages of an actin potension what is the overshoot and hyperpolization onthe line?
abs refractory perison (stimulate response is the first hump) followed by relative refractory period overshott is the part of the signal that goes over ) (usually is 39) hyperpolarization (amount that goes below resting potential which is about -66)
specification
acquisition of cells' spetilly distinct identiy
acetylation
acteyltransferase=acetylate lys (histones) or N-terminus deacetylase=remove acetyl group
each myofibril is composed of thin (___ bases) and thick ___ based) filaments
actin, myosin
the change in membrane potential caused by depolarization is the ____
action potential
excitation-contraction coupling
action potential on the surface of the muscle fiber signal muscle contraction
Ca transients follow the ___ but preceeds the __
action potiential force exertion
glucagon
activate lipid synthesis sitmulate fatty acid synthesis
The formation of an __ ___ is coupled to an energetically favorable reaction in order to drive a ___ ___.
activated carrier energetically unfavorable
What does binding of OR2 do?
activates lambda transcription
Enzyme change the ___ ___ of a reaction but not the ___ ___.
activation energy/equilibrium point
Rb phosphorylation
activation of early G1 CDKs leads to activation of late G1 CDKs through Rb phosphorylation; the degree of Rb phosphorylation increases as cells progress through the cell cycle; Rb is like a clock, you can tell where cells are in the cell cycle by Rb phosphorylation
Repressors bind operators. Activators bind..
activator binding sites (sometimes called enhancers)
trans-acting transcription factors
activators (DNA binding domain binds to enhancer) and repressors
multi factor gene regulation
activators can bind to enhancor cites for different genes and the genes have different combination of activators needed for it
What would the be if a specific sigma subunit of bacterial RNA polymerase were mutated? a. Nothing would result; sigma is not essential b. RNA polymerase would still bind DNA at specific sites, but will fall off after joining together only a few RNA nucleotides c. RNA polymerase would initiate transcription at random on the DNA d. the core enzyme would bot be as stable as usual
c. RNA polymerase would initiate transcription at random on the DNA
Calculate pI (isoelectric point) of the following amino acid. The pKa values of a-carboxyl group, a-amino group, and e-amino group (i.e., side chain) are 2.2, 9.1, and 10.5, respectively. a.) (2.2 + 9.1) / 2 = 5.6 b.) (2.2 + 10.5) / 2 = 6.4 c.) (9.1 + 10.5) / 2 = 9.8 d.) (2.2 + 9.1 + 10.5) / 3 = 7.3
c.) (9.1 + 10.5) / 2 = 9.8
How much of eucaryotic cell is water? a.) 80% b.) 90% c.) 70% d.) 60%
c.) 70%
Which of the following amino acid residues has an ionizable side chain with a pKa value close to physiological pH so it can contribute to buffering inside the cells? a.) Glycine b.) Alanine c.) Histidine d.) Glutamine
c.) Histidine
Which of the following amino acids have two chiral carbons? s.) Leucine and tyrosine b.) Leucine and serine c.) Isoleucine and threonine d.) Valine and serine
c.) Isoleucine and threonine
subunits of troponin
c: binds to calcium t: binds to tropomyosin i: inhibit the interaction en the thick and thin filamnets that cause force development
No glucose means there is high ___.
cAMP
With the lac operon, what would be the positive regulation?
cAMP binding to CAP on the promoter
When glucose levels are low, ___ is produce by adenylate cylase, ___ binds CAP, inducing CAP to bind the DNA.
cAMP, cAMP
the space constant and time constant arethe ___ __ of the action
cable properties
Quantitative Trait Loci (QTLs)
can be mapped and id.ed not responsible for phenotype, markers for nearby loci that do influence it
RFKOs (restriction Fragment Lenth Polymorphisms)
can be useful markers for genetic variants or diseae digest genomic DNA with enzyme E, run on gel, probe
What are the 3 types of caps?
cap 0 cap 1 cap 2
Why do the 5' cap and 3' tail matter once the mRNA reach the ribosome
cap binding proteins around the ribosomes bind to them, helping form the initaiton structures during translation
____ can release energy even in low conditions of oxygen.
carbohydraes
Compounds with high phosphoryl-transfer potential can couple ________ ________ to ATP synthesis
carbon oxidation
tRNA
carry amino acids to translation site
Which is energetically favorable? Catabolism or anabolism?
catabolism
lipid catabolism and anabolism
catabolism (oxidative) -lipolysis -fatty acid oxidation anabolism (reductive -fatty acid synthesis -triacylglycerol synthesis
What kind of reactions are catabolism and anabolism?
catabolism->oxidation (loss of H, gain of O) anabolism->reduction (gain of H, loss of O)
cAMP binds to the _____ protein
catabolite activating protein (CAP_
ribozymes
catalytic RNA, RNA molecules that are capable of catalyzing specific biochemical reactions
Sigma factors act ___.
catalytically
RNA polymerase ___ the transcription process.
catalyzes
At very acid pH most amino acids exist as ____ and at very basic pH most amino acids exist as ___.
cations (NH3 pKa=10) anions (COO pKa=2)
DNA polymerase
catylze the elongation of the DNA strand
DNA primase
catylze the fomration of RNA primer
trinucleotide repeat
caused by slippage during replication. Leads to Huntington's disease., 3 nucleotides in tandem repeats with an abnormaly large number of insertion and causes diseases.
F- cell
cell during conjugation that is the recipient of genetic plasmid
cotransformed
cells that are transformed by two or more genes
competent cells
cells that can take up
competent cells
cells that can take up DNA
transformants
cells that recieve genetic material
transformant
cells the reveive genetic materil
What happens if the functio of the Hox gene is lost?
cells will assume different fate
cotransformed
cellst that atre transformed by two or more genes
discontinuous variation
characteristics that have either one phenotype or another eg tongue rolling, eye colour etc.
capcaitative current
charge that builds up or depletes from a capaccitor
ex bottle neck
cheetahs exhbit abnormal spermatozoa and poor reproductive rate
humans are ___trophs and plants are __trophs
chemo, photo
How would sympatric speciation occur?
if a biological barrier to interbreeding arose within the confines of a panmictic (random breeding) population without spacial segregation of the incipient species. Possible due to ecological specialization in two or more incipient species accompanied byrapid reproduction isolation. Introgression first prevented by ecological factor such as shift in food source or host, ad that prevents incipient species from coming into contact with on another occurs frequenltly in insect groups
Corollary to the assumptions at life arose from a sinlge organsim?
if multiple types of organisms developed simultaneously (or nearly so), one type dominated and eliminated the others
What is Hardy-Weinberg Equilibrium?
if pop is not evolving, then freq of alles p and q have genotypic frequencies of 2 homozygous genotypes are p^2 and q^2 and the frequency of the heterozyous genotyp are 2 pq a pop in HW equilibrium, thes freq will not change over time p^2+2pq+q^2=1
CENP-A (a H3 variant)
important for centromere function. CENP-A allows the attachment of the mitotic spindle to the kinetochore.
H2A.X
important histone variant for DNA repair; H2A.X becomes phosphorylated upon DNA break, which helps to recruit DNA repair enzymes.
___ paterns are established in the male and female germline
imprenting -metylation=imprinting=silencing
SOS repair system
in E. coli, sps system allow dna replicatio to occure depite errors as an alternative to cell death
Where is the double helix most vulnerable to acid-base reaction, disruptions?
in GC pairing between N-H bonding to N The N-H will lose its H if the pKa=9.7
complete media
in addition to the minimal media ingredients, includes vitamins, amino acids, etc.
semi-conservative replication
in each new DNA double helix, one strand is from the original molecule, and one strand is new
Fahrenholz's Rule
in groups of permanent parsites, the classification of the parasites usually compares directly wiht the natural relationship of the hosts. The more specific it is to its host-?the phylogenetic moe tracking
transcription bubble
in prokaryotes, when the RNA polymerase holoenzyme binds to the promoter, the complex opens and RNA is synthesized TBP bound to the TAT box is the heart of the intiation complex
When does the lacI repressor bind to the operator?
in the absence of lactose (negative regulation)
What component of the selective channel is responsible for the refractory period?
inactivation gat
What mutations typically occure in structural genes of the lac Operon?
inactivation of one of the 3 enzymes (permease, B-galactosidase, or transacetylase) gene expression is usually not changed, although nonsense mutations may disrupt expression of downstream genes (polar mutations)
introgression
incorporation of genes of one species into the gene pool of another
euploidy
increase in number of complete sets of chromosome occurs frequently in plants, rarely in animals can lead to formation of new species diploid, triploid, tetraploid 2n, 3n, 4n odd numbers are usually sterile
recruitment
increase in the force resulting in increasing number o fmotor units
inbreeding
increases numb of homozygous individ
fitness
individ genetic contrib to future generations (w)
For the lac operon, lactose acts as an ____ that binds the repressor, preventing the repressor binding to the operator.
inducer
gene conversion
info on 1 locus is transfered unidirectionally to other members of the gene family, so all acqu smae sequ usually after duplication
Phosphorylation of CTD marks the ransition from...
initatio to elongation
The sigma subunit regulates...
initiation but is not required for elongation
framshift
insertion or deltion of bp alter grouping of nucleotide into codons
Sanger sequencingd
insulin
ecological units
interact among themselves and with other species in environment
activator GRPs
interact with other proteins, including mediator recruit the transcriptional machinery tothe mene
ethidium
intercalating agent which can bind with DNA and slip into the space between tis base pairs
Genes that are transcritiptionally active tend to be near the edges of chromosome territories bordering ___ ___.
interchromosomal doains
ubiquinone
intermediate carrier, carries the electron and hands it over (Q)
2 levels of genetic boidiversity
interspecific diversity-number of diff plant and animal specianin an ecosyst intraspecific diversity-diveristy within a speces
Introns are __ sequences, exons are __ sequences
intervening, expressed
primer
intitial segment o fpolymer that is to be extended on which elongation depends
intra diversitnpopy vs interpopulation diversity
intrapopulation diversity-genetic diversity wihtin individuals with a given pop interpop div-genetic div among diff pops of the same species
RNA processing involves the removal of...
intron regions
The termination sequence has DNA with ___ ___ that form hair pin structures in the RNA transcript.
inverted repeats
CoA is derived from the vitamin _______, and is an activated carrier of two-carbon fragments
pantothenate
Why do scientist study meozygotes for lac operon mutations?
it's dipoid with a chroosome copy and a plamsmid copy. The chromosome has mutaion in one of the structural genes. The plasmid has a mutation in the operon. epression of the structural gene reveals which copy of the operon are active
wHY IS THE NOMINALISTIC SPECIES CONCEPT REGJUECTED
it's juveniile says mayr
What happens to the lamina durnig glaucoma?
its strain is large as it gets stretched by the expansion of the scleral canal
sliding clamp
keep DNA polymerase firmly on the DNA
SSB
keep single strand DNA in extedn inflexible confromation
phosphorylation
kinases=phosphorylates Ser, Thr, Tyr phosphatases=remove phosphate
What is lacI?
lacI is the repressor gene that precedds the lac Operon, it encodes the repressor protein which binds to the operator to block gene expression
What are the structural genes of the lac operon and baterial cells what are their function?
lacZ-encodes B-galactosidase, which breaks down lactose into glucose and galactose lacY-encodes lactose permease, which facilitates entry of lactose into bacterial cells lacA-encodes transacetylase (role in lactose metabolism is unclear)
DNA methylation
lack in expressed, heaveily methylated genes are not expressed tissue specific/differentiation heritable
What wold make anthranilate?
lack of PRPP
How does the lac operon get expressed at different levels of glucose and lactose?
lactose absent and glucose high or low-->lac operon repressed lactose absent, glucose high->no cAMP binding to CAP binding site, so low gene expression lactose and glucose absent-->lac operon highly expressed
__ phage uses alternative patterns of gene exrpression control lytic and lysogenic growth
lambda
___ repressor binds to operators cooperatevely
lambda
___ and ___ reviprocally regulate each other by binding to operators in the regulatory region
lammbda repressor and Cro
5S rRNA is only in the ___ subunit of ribosomes.
large
lampbrush chromosomes
large bivalent chromosomes in the germinal vesicle of an amphibian oocyte, highly active in gene expression
gneetic ottle nex
large pop get small fast
RNA Polymerase I
large rRNA, nucleolus
with saltatory conduction Rm is ___, Cm is __, and Ri is -__
large, small, small
translocations
large-scale mutations with a change in position of chromosome segments. Usually no gain or loss of genetic material.
What rRNAs are used in prokaryotes for the large and small subunits?
large: 23S rRNA, and 5S rRNA small 16S rRNA (uses less proteins too)
composition of large and small subunit of ribosome
large: peptidyl transferase center (euk-5.8S rRNA, 5S rRNA, 28S rRNA+49 proteins=60S) (prok-5S, 23S-34 proteins=50S) small: decoding center (16S rRNA) (euk-18S-33 proteins=40S) (prok-16S+21 proteins=30S)
What loop forms when U2 binds with U5 and U6?
lariat loop
saltatory conduction
leap conduction
Z DNA
left handed helix; may regulate of eukaryotic gene expression.
Z DNA
left-handed helix, backbone appears to zigzag slightly, bases substantially tilted relative to central axis, occurs at hight salt concentration, alternates between prymidines and purines
the relation between active force and muscle length is the ___ curve
length-tension
how long does ATP in a mucle last?
less than 1 second
human genome project
less than 2% of genome codes for proteins (about 20,000 genes) 99.9% the same (regardless of race or ethnicity)
How long does ATP last in the muscle?
less than a second
Iron-sulfur world hypothesis
life began at hydro thermal vents at hte bottom of hte ocean, fed by a a constant stream of hot volanic gas Fe+H2S-> FeS_H2+energy FeS+H2S->FeS2+H2+energy
H band
lighter section and M band that is in the middle of the A band
Steady-state flows require _____ gradients.
linear
polypeptide
linear sequence of amino acids (primary structure) which determines its Secondary, Tertiary, and Quaternary structures
proteins are ____ polymers of ____
linear/amino acids
clamp loader
load sling clamp
deme
local, stable populaiton
Location of cortical bone?
long bones and surrounding trabecular bone
Location of trabeular bone?
long bones, flat bones, and vertebrae
intraspecif diversity
nuclear, mitochondrial, and chloroplast DNA analyzed short tandem repeats (STRs) or microstellite variation among individs within pop are used as an indirect estimate of overall genetic diversity DNA profiling by DNA fingerpringtin
What enzymes are envoleved in nucelotide excision repair?
nuclease DNA helicase which removes a large section that DNA polymerase and ligase fix
What are the 4 macromolecules tha make up bacteria?
nucleic acids (DNA, RNA) protiens polysaccharides (polymers of sugars) lipdis
Name 3 histone modicifications.
nucleosome composition histone acetylation histone methylation an d phosphorylation
chromatin remodeling
nucleosome repositiong
loss/gain function
nucleotide seq causes reduced or lost function or increased of novel function
nuetral/silent
nucleotide seq of condon change to another codon for the same amino
missense
nucleotide sequence change to a sequence for a differnt am
mutation rate
number of new mutant alleles per given number of gametes
Linking Number (Lk)
number of times one strand would have ot be passed through the other strand in order for the two strands to be entirely separated from each other
Writhing Number (Wr)
number of times the long axis of the double helix crosses over tiself or is wound in a cylindrical manner
sigma factors and the promoters they recognize
o-70 most genes o-32 genes induced by heat shock ...more
b dna
observed at high humidity, most closely corresponds to the average structure of DNA under physiological conditions. it has 10 base pairs per turn, and a wide major groove and a narrow minor groove.
Give some examples of geographic barriers.
oceans, high moutain ranges, glaciers, deep river valleys, wied rivers, deserts, waterfalls, salt water all environmental properties that prevent gene flow
cistrons
often used in place of a gene. It is a short length of DNA which codes for a polypeptide
In the luminal phase, HCL denatures proteins and activates pepsin, pepsin hydrolyzes proteins into poly peptides, and pancreatice endo and exopeptides hydrolyze polypeptides into what?
oligopeptides
gene conversion
one allele direts the conversion of a partner to its own form
What does it mean to say the genetic cod is degenerate?
one amino acid can be coded from different triplets
About __ cytosines are converted to uracil via deamination
one hundred
biparental inheritance
one member of each homologous pair of chromosomes is derived from the maternal parent and one is derived from the paternal parent
How many copies of the lac operon does a merozygote have?
one on the chromosome and one on the F' plasmie
lineage
one or a series of demes that share a common history of descent not shared by other demes
intraorganismal mutualism
one org liven intrercellularly or in special orgass (ex. lichens, termites, roaches,)
intracellular mutualisim
one org lives inside the cell of another org (ex. mitochondiria within prokaryotic cells to form eukaryotic cellls)
semisterility
only some fertilizationevent produce viable progey
familial mediterranean fever
onset 10 variable expressivity and variable penetrance , Autosomal recessive dysfunction of neutrophils that presents with fever and acute serosal inflammation. The ^SAA will deposit as AA amyloid. Mefv gene
Acytlations promotes an ___ chromatine sturtuer as opposed to one with __ islands and __ histonse (___ between nucleoseomse).
open CpG,deacytlated, H1
Dna helicase
open up the DNA helix
development at orgnaismal level vs cellular level
org -growth -differentiation-specialization of a group of cells -morphogenesis-development of a pattern shape or form cellular -specification-spatially distince identity -determination -differentiation
What organisms typically undergo parapatirc speciation?
organisms are fairly sedentary...progen thoguht to move o more than 1000 meters from the original location..need be no spatial isolation with respect to parental species plants, terrestrial snails, flightless insects, some small mamamlas, and certain lizards
conservative rplication
oricinal dna molecule remains, new dna molecule two new strands
What is the main disease that impacts trabecular bone?
osteoperosis
epigenetic reprogramming
other genes are regulated through in early embryonic develpment
phosphates on the -___ and bases on the __
outside, inside
Lipids require ___ to yield biologically useful energy.
oxygen
isoelectric point
pH at which a particular molecule carries no net electrical charge. pI=(pK1+pK2)/2
How does pH relate to pKa?
pH=pKa + log([A-]/[HA])
genotypic freq
p^2-homoztg dominant allele pair frew q^ homo recess 2pq hetozy allele frew p^2+2pq+q^2=1
proteolytic cleavage
the process of breaking peptide bonds between amino acids in proteins. Carried out by enzymes called peptidases, proteases or proteolytic cleavage enzymes. Proteins often undergo proteolytic cleavage before final maturation of the protein. It is irreversible.
Genetic engineering
the process of producing modified DNA in vitro and intorducing the recombinant DNA into host organisms
differentiation
the process through which a cell develops its final specialized adult forma nd function
reproductive isolating mechanisms
the properties of individuals, populations, and species, that constrain gene flow between populations and species. These are not environmental factors, but properties of the organisms themselves These isolating mechnisms evolve during geographic isolation to prevent interbreeding of populations that are sympatric (overlapping, share same area)
genotypic frequency
the proportion of individula in a population wiht a particula genotype (combination of two alleles)
allelic frequency
the proportion of one allele of a gene out of all of teh alleles of the gene in the population (a sinlge allele); the probabilty that a random gamete from the population will contain a particular allele
proximal promoter elements
the proximal sequences right before the TATA box that are binding sites for transcription factors associated with RNA polymerase.
what does the promoter and operator make up?
the regulatory region of an operon
What is the negative regulation with the lac operon?
the repressor binds to the operator
microscopy
the science that studies microscope techniques
Rho-independent (intrinsic) termination
the secondary structure of the RNA transcript causes release of the RNA transcript
amphidiploid
the state of an organism produced by two diploid parental species; they contain two diploid genomes, each one derived from each parent
transformation
the transfer of genetic material in the form of DNA fragments from one cell to another organism to another, The genetic alteration of a bacterial cell by introduction of DNA from another cell or from a virus.
developmental genetics
the use of genetic analysis to study development
What happens when lactose and glucose are present?
there is a basal level of transcription
How does proofreading work in tRNA
there's an editing site where rapid hydrolyis fixes "mischarge"
-dG is ___ favorable 0 G is ___ +dG is...
thermodynamically reversible; at equilibrium thermodynamically unfavorable; rever process is favorable
What's wrong with triploids in meiosis?
they either pair as bivalent+univalent or a trivalent, so most of the resulting gametes won't have anormal n or 2n chromosome numbers
If B-galactosidase fails to be produce due to a nonsense mutation, what will happen with the lacY and lacA genes?
they will not be coded because the ribosomal subunits will dissociate prior to translation...
Which bands are the thick (myosin) and thin (actin) filament?
thick-A band thin-start at Z disk
What factors affect diffusion capacity
thickness of membrane surface area
longitudinal SR
thin tubes of membrane that connect terminal cisternae from one side of sarcomere to the other
parapatric speciation
this model defines the mechanism involved in the speciation process of closely related species that have narrow zones of overlap, when ecological factors limit the rance of a species a new chromosomal rearrangement or gene combination is adaptive in homozygous condition, allowing those with this novel genotype to colonize previously unexploited habitat where heterozygous cannot inhabit either and get selected out of the population
reductive biosynthesis
this process includes reducing CO2 using reduced coenzyme (NADPH) to synthesize c- fuels such as carbohydrates
action potential is triggered by depolarizing the membrane to ___
threshold
absolute refractory period
time at which another action potential cannot fire (approx.=1-2ms)
___ muscle has constant force and ___ muscles have phases of force
tonicc, phasic
amanitin
toxin from mushroom, binds to huma RNA polymerase, blocks transcription
Proteins that act in ___ can diffuse through the cytoplasm and act at target DNA sites on any DNA molecule in the cell.
trans
What mutations occur in the lacI gene?
trans-acting
maternal-effect genes
transcibed from the mother's diploid genome gene products (mRNA & protein) are deposited in the egg prior to fertilization
how do you make cDNA libraries
transcribe digest parent strand (RNase H), leaving behind specific regions transcribe
zygotic genes
transcribed in embryponic nuclei after fertilization
most regulation in gene expression for eukaryotes is at the level of _____ ___ while in prokaryotes it's at ___ __
transcriptional control, transcriptional initiation
___ and __ can be used to map chromsome
transduction and transformation
The intron is removed through 2 succesive ______ reaction in a forma called a ___ as the flanking exons are goined
transesterfication, lariat
