BMS 230 - Unit 4

nucleotide changes not in multiples of ___ result in a frameshift mutation

3

DNA polymerase adds to the ____ end only and moves toward the ____ end on the parental template strand, making the new strand in the ___ to ___ direction

3', 5', 5' to 3'

____% of human DNA encodes protein

1.5 (exome)

the average human has about ____ spontaneous mutations in their genome, more common in ____ genes

175, large genes (i.e. CFTR, NF1, dystrophin)

disorder that results in congenital heart disease, cleft lip/palate, facial dysmorphology, learning difficulty, and immune deficiency; mode of inheritance, molecular cause

22q11.2 deletion (DiGeorge or Velocardiofacial), autosomal dominant, deletion of TBX1 gene on q arm on chromosome 22, 3 million base pairs deleted, DNA symmetry between genes causes crossing over between the wrong genes

microRNA's belong to a class of molecules called ________, when they bind to a "target" mRNA, they prevent ________

non-coding RNAs (not part of a protein), translation

two types of excision repair and their differences

nucleotide excision (replaces up to 30 bases, corrects mutations due to carcinogens and UV light exposure), base excision (replaces 1-5 bases, corrects oxidative damage from free radicals)

DNA replication occurs in the _______ during the ______ of the cell cycle, and is _______

nucleus, S phase (prior to cell division), semi-conservative (use one old strand to make a new one)

major DNA repair gene, "guardian of the genome"

p53

cutting the protein after it is already made (after translation) to make different proteins, and an example of this

peptide shortening, cutting DSPP into DPP and DSP

3 types of DNA repair

photoactivation (not in humans), excision, mismatch

a change of a single nucleotide

point mutation

amplifies DNA molecules outside of cells (in a lab not the body), replicates sequence millions of times

polymerase chain reaction

2 methods for amplifying DNA

polymerase chain reaction, recombinant DNA technology

5 components needed for PCR

polymerase, thermocycler, target DNA (specific gene or identified segment, not entire genome), nucleotides, primers (NO primase)

enzyme that adds a short primer (a few nucleotides - RNA) to the template strand so that DNA polymerase can attach

primase

there are cut off of collagen molecules so that they can form tight rope-like structures

propeptide/globular ends

amplifies DNA within cells (in the body) often using sequences from other organisms, utilizes two different species to replicate DNA

recombinant DNA technology

______ is a hot spot that results in mutations because of misalignment during meiosis I, crossing over results in missing genes

repeated genes

50% of the human genome is:

repeated sequences (involved in causing human disease)

in the genomic library _______ enzymes cut the genome into multiple pieces in specific spots, then the DNA fragments are put into _____

restriction, cloning vectors (plasmids and phages)

collagen has a precise structure:

triple helix of 2 alpha 1 and one alpha 2 polypeptides (alternating structure allows stretch); longer precursor procollagen is trimmed to form collagen

should a protein misfold an _______ will occur and _____ molecules will be added - the molecules form a chain (tagging the protein as abnormal) which is signaled for a ____ to get rid of it

unfolded protein response (protein synthesis slows or even stops), ubiquitin, proteosome

the degree that a mutation alters phenotype depends on: (2)

where in the gene the change occurs, how it affects the confirmation or expression of encoded protein

4 examples of ways to get exposure to mutations

workplace, industrial accidents, medical treatments (chemo, x-rays), natural sources (sunlight)

devices that detect and display the mRNAs in a cell to monitor gene expression (see which genes are turned on), piece of glass or plastic, many small pieces of DNA of known sequence are attached to one surface, in a grid pattern; in many applications a sample from an abnormal situation is compared to a normal control

DNA microarrays (gene chips)

enzyme that binds nucleotides to form new strands of DNA during replication; needs a primer, can only add to an existing strand, proofreads and excises mismatched nucleotides, removes RNA primers

DNA polymerase

small segment of DNA that is labeled radioactively or fluorescently so it can be identified; complimentary to one specific gene, made outside of the body

DNA probe

______ is a mutation hot spot that causes single-stranded DNA to pair with itself (called a hair pin), preventing accurate replication - DNA skips it

DNA symmetry

three steps of PCR

Denaturation (heat is used to separate the two strands of target DNA), Annealing (two short DNA primers bind to the DNA at a lower temp), Extension (the enzyme taq1 DNA polymerase adds bases to the primers

disorder that results in the clinical symptoms of progressive muscle weakness, heart problems, and developmental delay; mode of inheritance, and molecular cause

Duchenne muscular dystrophy (DMD), X-linked recessive, nonsense mutation in the DMD gene on the X-chromosome, not enough dystrophin protein is made (lack of connection between cell membrane and sarcolemma = muscular weakness)

disorder that results in early onset colon cancer (30-40), increased sensitivity to other cancers, develops without polyps, and affects the proximal colon (difficult to diagnose); mode of inheritance and molecular cause

HNPCC or Lynch syndrome, autosomal dominant, mutation in 1 of the 7 mismatch repair genes

disorder that has these clinical symptoms: motor, cognitive, psychiatric disturbances, age of onset 35-44, survival is 15-18 years; its disorder type, gene affected, and mode of inheritance

Huntington's disease, trnucleotide repeat disorder (CAG), HTT gene autosomal dominant

alternate splicing occurs during ______ and in the _____

RNA processing (between transcription and translation), nucleus

8% of the human genome is derived from ______, this is evidence of past infection, sequences tend to increase over time because all of this DNA is passed to offspring

RNA viruses (retroviruses)

copy number variants correlated to ______ might be used to give medical advice

cholesterol levels (increased number of genes involved = more intervention - exercise, diet, drugs)

adding methyl groups, acetyls, and phosphates; epigenetic changes that can be passed on; chemical groups allow chromatin to open or close, controlling gene expression

chromatin remodeling

a protein-encoding gene contains some control over its own expression level through two general processes:

chromatin remodeling (effects transcription), microRNAs (effects translation)

goal of this repair is to remove and replace pyrimidine dimers and surrounding bases

excision repair

mutations caused by UV light are repaired via:

excision repair

main con of recombinant DNA technology

expensive

different types of mutations can cause the same single-gene disorder, an example of this is:

familial hypercholesterolemia

2 things that cause mutations

errors in DNA replication, damage to the DNA

more than ___ collagen genes encode more than ___ types of collagen molecules; mutations in these genes lead to a variety of medical problems

35, 20

Human DNA replicates about ____ bases/sec, which is pretty fast so it can lead to errors

50

there are over ____ genes dedicated to repair

50

example of a positive mutation in the body:

a positive mutation in CCR5 receptors does not allow HIV to bind to lymphocytes - these people cannot contract HIV; helps us to create treatments

what happens when acetyls and phosphates are added, and removed

added: chromatid unwinds, transcription is on, gene is expressed; removed: chromatid packs, transcription is off, gene is not expressed

what happens when a methyl group is added, and removed

added: gene is not expressed, removed: gene is expressed

clumping of abnormal proteins; can be toxic in the brain when they gather on nerve cells

aggregation

the "genes in pieces" pattern of exons and introns and ______ help greatly expand the gene number - skipping spice sites to create new proteins; 1 gene makes multiple proteins by cutting it in different ways

alternate splicing

expansion of the triple repeat with an increase in severity of phenotype with each generation - increased repeats = earlier onset and increased severity; and two examples of this

anticipation, huntington's disease, myotonic dystrophy

when the DNA is damaged there are 3 possible outcomes:

apoptosis (damage is beyond repair, so cell death), repair, cancer or passage of mutation (mutation doesn't get corrected, replication = cancer, germline = passed on)

mutations are more likely to occur in these 3 hot spots:

areas of DNA symmetry, repeated genes, large genes

disorder that results in poor balance, telangiectasias (abnormal tangles of blood vessels, commonly in the eye), increase risk for cancer, diabetes, and infection; mode of inheritance and molecular cause

ataxia telangiectasia (AT), autosomal recessive, mutation in ATM gene - directly involved in cell cycle checkpoints, specifically recognize double-stranded breaks

disorders that result from mutations in repair genes are mostly ________ (mode of inheritance), ______ individuals are often severely affected, and ______ individuals have increased sensitivity to environmental mutations

autosomal dominant, homozygous, heterozygous

why would Huntington's disease alter the expression of other genes

because proteosomes are overwhelmed with the abnormal proteins

enzymes that stabilize separate DNA strands

binding proteins

____ tests are used to look at different protein concentrations (changing conditions cause a change in the protein conc.) because plasma contains about 40,000 different types of proteins; ______ is shedding light on how genes are turned on and off

blood, stem cell biology

set of bacteria that are protein encoding genes (only the genes that are turned on) produced by extracting mRNA and using reverse transcriptase to make DNA

cDNA library

keep the amino acid strand linear (prevent folding) until the entire strand is made to ensure it can fold into the correct shape

chaperone proteins

another "tool" used in creating recombinant DNA molecules is a ______, it carries DNA from the cells of one species into the cells of another, the most common type is ______, as well as what other two

cloning vector, plasmids (circular DNA), bacteriophages, disable retroviruses

a major component of connective tissue - bone, cartilage, skin, ligament, tendon, and tooth dentin

collagen

DNA that is not naturally occurring, laboratory generated using mRNA

complimentary DNA (cDNA)

sequences that vary in number from person to person; differences between populations - people in Africa have millions more base pairs than Americans; what causes these

copy number variants; deletions, insertions, tandem duplications

UV light exposure results in _____ bonds between ______, which creates ______, which kink the DNA resulting in replication errors

covalent (usually ionic bonds, covalent are much stronger), pyrimidines, thymine dimers

male infertility is a common example of a _______ on the Y chromosome

deletion

removing genetic material v. adding genetic material; they both do not always cause disease - depend where they are located and how big; which one is more severe

deletion, insertion; deletion is more severe bc having less genetic material is usually more severe than having more

disorder where the enamel doesn't form properly so it breaks down quickly; what proteins are deficient

dentinogenesis imperfecta, DPP and DSP (DSPP isn't cut properly to create these 2)

why do we have different gene expression throughout our lives, what is an example of this

different genes have to be turned on at different times to meet changing protein needs; i.e. hemoglobin - different chains during embryonic period, fetal period, and adulthood because of different oxygen sources, need more O2 in embryonic period bc everything is developing; adults can only survive with fetal hemoglobin up to a certain concentration

different amino acid sequence that causes multiple beta-pleated sheets, altering the tertiary structure

disease-associated protein

repair that fixes mutations caused by ionizing radiation (X-rays)

double-stranded break repair

disorder that has the clinical symptoms of joint laxity (double-jointed) and increased skin elasticity that results in lasting damage; mode of inheritance, molecular cause

ehler-danos syndrome, autosomal dominant, mutation in collagen 5 alpha 1 (globular heads are not removed, can't pack at tightly, can't maintain form gets too stretched)

changes to the chemical groups that associate with DNA that are transmitted to daughter cells after cell division, do not actually change the DNA sequence

epigenetic changes

mutations that affect the amino acid where the mutation occurs and every amino acid after it

frameshift mutation

collections of recombinant DNA that contain pieces of the genome; set of bacteria that contains the whole genome

genomic library

mutations that originate in meiosis when forming sperm or egg, affect all cells of an individual, passed on to future generations

germline mutations

enzyme the unwinds the parental DNA double helix

helicase

the new strand of DNA binds to an old strand of DNA during replication via ______ bonds

hydrogen

mutations caused by mutagens, many are also carcinogens and cause cancer; most of these mutations are random; examples: chemotherapy removes nucleotide bases, X-rays break chromosomes, sunlight creates thymine dimers

induced mutations

DNA strand that is made in the direction that the helicase is unwinding is the ______ strand, while the strand that is made in the opposite direction of the helicase is the ______ strand (DNA is made in fragments)

leading/continuous, lagging/discontinuous

steps to make cDNA

mRNA is isolated, reverse transcriptase is added (makes mRNA-cRNA hybrid), mRNA-degrading enzymes are added (mRNA goes away, single strand of cDNA), DNA polymerase is added (makes 2nd strand of cDNA)

the main application of recombinant DNA

mass-produce proteins (i.e insulin, surfactant for premature infants' lungs)

______ turns genes off, pharmacogenetics (drugs) not well studied in this area

methylation

repair that corrects errors due to DNA replication (nucleotides are unstable, DNAP puts in wrong base, repair removes only the incorrect nucleptide and replaces it with the correct one)- corrects de novo/new mutations

mismatch repair

consequence of a point mutation where one amino acid is replaced with another v. a codon for an amino acid is changed to a stop codon

missense mutation, nonsense mutation

a change in the DNA sequence, present in <1% of the population, effects may vary - positive, negative, silent

mutation

disorder that results in the clinical symptoms of extreme muscle weakness, cardiac abnormalities, and cataracts; mode of inheritance, molecular cause

myotonic dystrophy, autosomal dominant, triple repeat in DMPK gene (CTG's repeated)

a specific set of three nucleotides gets reinserted into the gene over and over forming the wrong amino acids, the protein cannot function properly because it cannot fold properly

trinucleotide repeat disorder

manufacturing recombinant DNA requires ____ enzymes that cut donor and recipient DNA at the same sequence; these enzymes cut DNA at sites that are _____; the cutting action of many of these enzymes results in single-stranded extensions called _______

restriction, palindromic (read same forward as backward), sticky ends (DNA does not like to be single-stranded so it tries to stick to other strands)

enzyme that takes RNA and makes a complimentary single-strand of DNA; in a lab, not in the body

reverse transcriptase

mutations that do not alter the encoded amino acid

silent mutations

a human chromosome replicates ______ at _____ points along its length; a site where DNA is locally opened is called a _________

simultaneously, hundred, replication fork

changes a gene in a desired way

site-directed mutagenesis

acetyl groups are added by a __________, and make the histone _____ so the DNA opens up

small protein complex, negative (histones are usually positive and DNA is negative)

mutations that originate in mitosis, affect cells other than gametes, affect only cells that descend from changed cell, not passed on

somatic mutations

mutations that alter a site where an intron is normally removed from mRNA; can affect the phenotype if: (2)

splice site mutations; intron is translated or skipped, exon is skipped

mutations that are by chance, most happen due to DNA replication errors - DNA polymerase makes mistakes because nucleotides are unstable

spontaneous mutations (de novo or new)

silent mutations are ______ while missense mutations are ______, regarding the encoded amino acid

synonymous (replaces the sequence with a codon for the same amino acid), non-synonymous (replaces the sequence with a codon for a different amino acid, changes the protein)

type of insertion, repeated base right next to each other

tandem duplication

nucleotides can change shape so they are _____; one nucleotide change can cause disease

tautomeric

a plant or animal that is produced by genetically altering a gamete or a fertilized ovum by adding foreign DNA

transgenic

point mutation where a purine replaces a purine (A and G) or a pyrimidine replaces a pyrimidine (C and T) v. a point mutation where a purine replaces a pyrimidine or a pyrimidine replaces a purine

transition, transversion

protein folding begins as ______ proceeds; _____ and _____ assist

translation, enzymes, chaperone proteins

disorder that results in painful blistering of the skin when exposed to sun (can't repair thymine dimers that form due to UV exposure), increased risk of skin cancer and other cancers; mode of inheritance and molecular cause

xeroderma pigmentosum (XP), autosomal recessive, mutation in nucleotide excision repair gene - thymine dimers persist and block replication