Biology Final Exam

Pseudogenes

A DNA sequence similar to a gene but which is not translated May or may not be transcribed May have evolved from original gene by duplication and acquired mutation Crossing over between a pseudogene and functional gene can disrupt gene expression

Point Mutations

A change of a single nucleotide Transition purine replaces purine A to G or G to A or pyrimidine replaces pyrimidine C to T or T to C Transversion purine replaces pyrimidine or pyrimidine replaces purine A or G to T or C T or C to A or G

Hardy-Weinberg equilibrium

A condition in which allele frequencies remain constant

Nonsense Mutation

A point mutation changing a codon for an amino acid into a stop codon Creates truncated proteins that are often nonfunctional Some have dominant effects due to interference with normal functions

Missense Mutation (does not impact protein function)

A point mutation that changes the codon Causes a substitution of an amino acid Missense mutations may affect protein function severely, mildly, or not at all. Example: Hemoglobin mutation Glutamic acid to valine and causes sickle cell anemia

Which of the following is a transition mutation?

A-->G

B is an intron between two exons A and C. Which representation best describes how this region of mRNA will appear after it is transcribed and processed by a spliceosome?

A-C

DNA Bases Pair

Adenine = Thymine (A-T) Guanine(G)= Cytosine (C)

Protein Folding

After synthesis, proteins must be folded into three-dimensional shape Enzymes and chaperone proteins assist Misfolded proteins are tagged and dismantled Proteins can fold in more than one way Misfolded proteins can cause disease

allele frequencies

Allelic Frequency # of particular allele/ total # of alleles in the population Count both chromosomes of each individual Allele frequencies affect the genotype frequencies The frequency of each type of homozygote and heterozygote in the population

Splice Site Mutations

Alters a site where introns are normally removed Intron translated or exon skipped

Developing Prion Diseases

Amino acid in 129th position is key to developing disease Individuals homozygous with valine (VV) or methionine (MM) develop disease Heterozygotes have normal function Position 178 is also important due to the folding of the protein

Repair Disorders: Xeroderma Pigmentosum (XP)

Autosomal recessive, mutation in any of 7 genes Malfunction of excision repair or deficient "sloppy " DNA polymerase Allow thymine dimers to remain and block replication Must avoid UV light Rare, only 250 cases worldwide

mutations in pathogens

Bacteria and viruses undergo mutation Mutation in bacteria can lead to antibiotic resistance Overuse and incomplete course of treatment increases chances of antibiotic resistance Viruses mutate rapidly Influenza vaccines are reassessed each season to accommodate viral changes Rapid mutation of HIV virus makes treatment difficult

Hemoglobin

Four globular proteins surrounding heme group with iron atom: two beta chains and two alpha chains Function is to carry oxygen in red blood cells from lungs to body and carbon dioxide from cells to lungs

phenotype frequencies

Frequency of a trait varies in different populations

Which of the following double stranded DNA segment sequences contains a mutation?

GATA CTCT

In DNA , cytosine binds with

Guanine

Repair Disorders: Inherited Colon Cancer

Hereditary nonpolyposis colon cancer (HNPCC) gene Affects 1/200 individuals Defect in mismatch repair gene is on chromosome 2

DNA is the Genetic Material

Hershey and Chase -Viruses can infect E. coli bacteria -A virus has protein "head" and DNA core -Used radioactive S and P to label protein and DNA -virus injects DNA into a bacterial cell

transcription factors

In bacteria, operons control gene expression In more complex organisms transcription factors control gene expression and link genome to environment Over 2,000 Mutations in transcription factors may cause a wide range of effects including several organ systems

Translation Steps

Initiation Translation begins at start codon (AUG=methionine) Elongation The ribosome uses the tRNA anticodon to match codons to amino acids and adds those amino acids to the growing peptide chain Termination Translation ends at the stop codon UAA, UAG or UGA

Expanding Repeats

Insertion of triplet repeats leads to extra amino acids Some genes are particularly prone to expansion of repeats Number of repeats correlates with earlier onset and more severe phenotype Anticipation is the expansion of the triplet repeat with an increase in severity of phenotype with subsequent generations

population

Is an interbreeding group of the same species within a given geographical area Gene pool - the collection of all alleles in the members of the population Population genetics - the study of the genetics of a population and how the alleles vary with time Gene Flow - alleles can move between populations when individuals migrate and mate

Replication 0.2

Meselson and Stahl, 1957 Labeled newly synthesized DNA with heavy nitrogen (15N) Density shift experiments with bacteria Traced replicating DNA Determined DNA replicates semiconservatively

SIckle Cell Anemia

Mutation encodes valine in place of glutamic acid Phenotype associated with homozygotes Altered surface of hemoglobin allows molecules to link in low oxygen conditions Creates sickle shape of RBC Sickling causes anemia, joint pain, and organ damage when RBC become lodged in small blood vessels

Alzheimer Disease

Mutations in presenilin1 cause early onset autosomal dominant Alzheimer disease Found on Chromosome 14 Presenilin protein is a receptor anchored in the Golgi membrane Monitors beta amyloid usage 30+ missense mutations in presenilin result in beta amyloid accumulation.

somatic mutation

Occur in cells of the body, excluding the germline Affects subsequent somatic cell descendants Not transmitted to offspring

transcription steps

Occurs in three steps: •Initiation •Elongation RNA polymerase adds nucleotides to growing RNA •Termination Sequences in the DNA prompt the RNA polymerase to fall off, ending the transcript

Replication

Production of new copies of the DNA molecules occurs in interphase prior to cell division Potential mechanisms: organization of DNA strands Conservative ( old/old + new/new) Semiconservative (old/new + new/old) Dispersive mixed (old & new)

Transcription

RNA is synthesized from DNA

transcription

RNA is the bridge from DNA to protein mRNA is synthesized from the template strand of DNA The complementary strand is the coding strand of DNA Requires enzyme RNA polymerase and transcription factors

transcription initiation

RNA polymerase reads the nucleotides on the template strand from 3' to 5' and creates an RNA molecule that looks like the coding strand

Spontaneous Mutation Rate

Rate differs for different genes Vary by size Sequence dependence Hot spots Table 12.3 lists rates for several genes On average, 1/100,000 each round of replication Each individual has multiple new mutations Most by are not in coding regions of genes

Central Dogma

Replication->DNA->Transcription->RNA->translation->protein

Mutational Hot Spots

Short repetitive sequences Pairing of repeats may interfere with replication or repair enzymes Palindromes Often associated with insertions or deletions Duplications of larger regions Mispairing during meiosis

Watson and Crick's Model of DNA

Sugar and phosphate "backbone" Two nucleotide chains in a helix. Hydrogen bonds hold the two strands together DNA strands are antiparallel

The DNA template ATGCGTTA is transcribed into an RNA strand with the sequence:

UACGCAAU

rRNA (ribosomal RNA)

With associated proteins make up ribosome Two subunits that join during protein synthesis Provides structural support and some are a catalysis (ribozymes)

Exposure to Mutagens

Workplace Industrial accidents Chernobyl Medical treatments Weapons Natural sources

somatic mutation:

affects a particular subset of cells

Ames Test

an in vitro test of the mutagenicity of a substance

Transcription and replication are alike in that both ...

are guided by complementary base pairing.

Silent Mutations ( does not impact protein function)

are mutations that do not alter the amino acid encoded Example: A mutation from AAA to AAG alters the DNA, the protein sequence remains unchanged AAA and AAG both encode for lysine These codons are called synonymous codons

Which of the following is considered "junk" DNA?

introns

Which is not true about the genetic code?

it is different for humans and bacteria

A codon consists of 3 consecutive

mRNA bases

RNA processing

mRNA transcripts are modified before use as a template for translation: Addition of capping nucleotide at the 5' end Addition of polyA tail to 3' end Important for moving transcript out of nucleus and for regulating when translation occurs Splicing occurs, removing internal sequences Introns are sequences removed Exons are sequences remaining

Major types of RNA

mRNA, tRNA, rRNA

A retrovirus contains an enzyme called reverse transcriptase that copies its RNA genome into DNA. This is opposite the central dogma because:

of the retrograde flow of genetic information

Sickle cell disease is caused by a(n):

point mutation

The DNA of a cell is like a library. The books of a library are analogous to genes, and the sections of a library are analogous to chromosomes. Which of the following would NOT be a library activity analogous to a function of biotechnology?

returning books that had been checked out

What are the four roles DNA must have for being a genetic material?

eplication, encoding information, mutation or recombination, and gene expression.

The human genome codes for 30,000 to 40,000 proteins, but any given cell might produce only 5,000 to 20,000 different proteins. How is this possible?

genes are regulated so that not all genes are transcribed in all cells

mRNA Nucleotides and the Amino Acids in a Protein

•Proteins are formed from 20 amino acids in humans Codons of three nucleotides: AAA AGA ACA AUA AAG AGG ACG AUG AAC AGC ACC AUC AAU AGU ACU AUU GAA GGA GCA GUA GAG GGG GCG GUG GAC GGC GCC GUC GAU GGU GCU GUU CAA CGA CCA CUA CAG CGG CCG CUG CAC CGC CCC CUC CAU CGU CCU CUU UAA UGA UCA UUA UAG UGG UCG UUG UAC UGC UCC UUC UAU UGU UCU UUU Allows for 64 potential codons => sufficient!

Misfolded Proteins Are Destroyed

•Ubiquitin tags misfolded proteins •Transports it to a proteasome

Protein Synthesis

Transcription production of mRNA in the nucleus mRNA processing and mRNA exits the nucleus Translation Production of amino acid chain within ribosome

Role of Genetic Material

"A genetic material must carry out two jobs: duplicate itself and control the development of the rest of the cell in a specific way."

Repair Disorders : trichothiodystrophy

- Five genes - Symptoms reflect accumulating oxidative damage - Faulty nucleotide excision repair or base excision repair or both - Dwarfism, mental retardation, premature aging, scaly skin (ichthyosis)

Friedrich Miescher (1871)

- Isolated white blood cell nuclei from pus - Found an acid substance with nitrogen and phosphorus - He called it nuclein - Later, it was called nucleic acid

Archibald Garrod (1902)

-Linked inheritance of inborn errors of metabolism with the lack of particular enzymes -First described the disease alkaptonuria

Gene Expression

-Production of protein from the instructions on the DNA -Proteins have diverse functions in the body examples are listed in Table 10.1 -Protein synthesis requires several steps including: Transcription - production of mRNA RNA processing Translation - production of protein using mRNA, tRNA, and rRNA

deoxyribonucleic acid (DNA)

-Subunits are deoxyribonucleotides -composed of: -Sugar-deoxyribose -Phosphate group -Base -one of four types adenine (A), thymine (T) guanine (G), cytosine (C)

Molecular definition of a gene

-a gene is a segment of DNA -it directs the formation of RNA to produce protein -the protein (or functional RNA) creates the phenotype -information is conveyed by the sequence of the nucleotides

If the sequence of one strand of DNA molecule is 5' ATGGCAT 3', the sequence of the complementary strand is

3'TACCGTA5'

germline mutations

•Mutations that occur in the germline cells •Possibility of transmission to offspring

If a DNA sequence reads GTCCAG, what RNA will it encode, and what amino acids does it encode (from left to right)?

CAGGUC, gln-val

mRNA (messenger RNA)

Carries information from DNA to ribosome Produced in the nucleus Transported to the ribosome A three nucleotide Codon specifies a particular amino acid

Thalassemia

Caused by another beta hemoglobin mutation Too few beta hemoglobin molecules Excess of alpha hemoglobin leads to iron release, which destroys RBC, damages heart, liver, and endocrine glands. Thalassemia minor (heterozygous) Thalassemia major (homozygous for mutation and more severe)

induced mutations

Caused by mutagens, many are also carcinogens and cause cancer Examples: Alkylating agents remove a base Acridine dyes add or remove base Xrays break chromosomes delete few nucleotides UV radiation creates thymidine dimers

Prion Disorders

Caused by mutation in the prion gene Leads to an abnormally shaped prion protein The mutant form converts normal prion proteins to mutant protein shapes Can be inherited or transmitted like an infection from tissue with the mutant protein -Creutztfeldt-Jakob Disease (CJD) -Mad Cow Disease (vCJD) -Fatal Familial Insomnia

genetic code

Codons are the triplet code groups of three RNA nucleotides used to encode one amino acid The genetic code refers to which codons encode which amino acids, one start codon, and three stop codons Non overlapping Genetic code is universal - evidence of a common ancestor The genetic code is degenerate - some codons encode the same amino acid

Collagen

Comprises 60% of protein in bone and cartilage A significant proportion of skin, ligament, tendon, tooth dentin, and connective tissue Has a precise structure Triple helix of two alpha1 and one alpha 2 proteins Longer precursor, procollagen is trimmed to form collagen

conditional mutations (does not impact protein function)

Conditional mutations produce a phenotype under particular conditions or environments G6PD enzyme responds to oxidants, chemicals that strip electrons from other molecules High levels of oxidants occur when eating fava beans or taking antimalarial drugs Conditions Individuals with mutations in G6PD Low oxidants no phenotype High oxidants red blood cells burst, anemia

Failure of DNA Repair

Fewer mutations are corrected Increase in mutations in the genome The protein p53 monitors repair of DNA If damage is too severe, the p53 protein promotes programmed cell death or apoptosis Mutations may occur in genes encoding DNA repair proteins Lead to overall increase in mutations

macroevolution

Formation of new species

Which od the following best illustrates the central dogma of biology

DNA -> RNA -> protein

two types of nucleic acids

DNA and RNA

What is the function of DNA in translation?

DNA is not directly involved, it just contains information

Spontaneous Mutation

De novo or new mutations Not caused by exposure to known mutagen Errors in DNA replication DNA bases have slight chemical instability Exist in alternating forms called tautomers As replication fork encounters unstable tautomers, mispairing can occur

Frederick Griffith (1928)

Diplococcus pneumoniae infects mice mice develop pneumonia and die Two types of bacteria -r bacteria rough coat (no pneumonia) -s bacteria smooth coat -pneumonia Coat type is associated with virulence

DNA repair

Errors in DNA replication or damage to DNA create mutations Most errors and damage are repaired Type of repair depends upon the type of damage or error Different organisms vary in their ability to repair DNA In humans, mutations in DNA replication occur in 1 / 100 million bases

determining mutation rate

Estimates of spontaneous mutation rate can be derived from observation of dominant traits. For autosomal genes, mutation rate = # of cases/ 2 (# of individuals)

Insertions or Deletions

The genetic code is read in triplet nucleotides Addition or subtraction of nucleotides not in multiples of three leads to a change in the reading frame Causes a frameshift and alters amino acids after mutation Addition or subtraction of nucleotides in multiples of three leads to addition or subtraction of entire amino acids

Translation

The process of reading the RNA sequence of an mRNA and creating the amino acid sequence of a protein Occurs within the ribosome

DNA forms a

double helix

microevolution

enetic change due to changing allelic frequencies in populations Allelic frequencies can change when: Nonrandom mating Gene flow Genetic drift Natural selection (unequal reproductive success)

A point mutation alters:

single base

Structure of DNA

sugar, phosphate, base (3 parts of a nucleotide )

A(n) ________ molecule carries amino acids to the ribosomes where they are joined to form a polypeptide.

tRNA

Orientation of DNA

the 5' and 3' hydroxyl groups attach phosphate groups -the directionality of a DNA strand os due to the orientation of the phosphate-sugar backbone

If the structure of a TV show is analogous to the structure of a gene, then the introns of a gene would be analogous to

the commercials between segments of the show

the "transforming principle"

treated type r bacteria with protease and DNase DNase prevented transformation

Mismatch Repair

• Enzymes detect nucleotides that do not base pair in newly replicated DNA •The incorrect base is excised and replaced •Proofreading is the detection of mismatches

Mutation

•A change in the nucleotide sequence of a gene •May occur at the molecular or chromosomal level •The effect of mutations vary •Mutant refers to an unusual phenotype •Mutations are important to evolution

tRNA (transfer RNA)

•Cloverleaf shape •Anticodon of tRNA forms hydrogen bonds with the mRNA codon and a specific amino acid at the other end

Chromatin

•Composed of DNA and associated proteins •DNA winds around histone proteins (nucleosomes) •Other proteins wind DNA more tightly to form a chromosome •During mitosis, replication and mRNA production DNA is unwound

Excision Repair

•Damaged DNA is removed by excision of the bases •Bases are replaced by a DNA polymerase Nucleotide excision repair •Replaces up to 30 bases •Used in repair of UVB and some carcinogens Base excision repair •Replaces 1-5 bases •Repairs oxidative damage

Replication as a process•

•Double-stranded DNA unwinds. •The junction of the unwound molecules is a replication fork. •A new strand is formed by pairing complementary bases with the old strand. •Two molecules are made. •Each has one new and one old DNA strand •Two sister chromatids are formed