Exam II - Nucleic Acids

Nucleic acids

polymers of nucleotides functioning in coding for and synthesizing proteins.

Nucleotide

subunit of a nucleic acid consisting of a five carbon sugar, a base, and a phosphate group.

Nucleoside

subunit of a nucleotide consisting of a five carbon sugar and a base.

Purines

bases used to make up nucleic acids which have two carbon rings. Include Adenine and guanine.

Pyrimidines

bases used to make up nucleic acids which only have one carbon ring. Include cytosine, uracil, and thymine.

DNA

A nucleic acid that preserves the code for making all the proteins needed by the cell. Composed of a deoxyribose sugar, a phosphate group, and a base. Bases include adenine, guanine, cytosine, and thymine.

Hydrogen bonds

bonds holding bases together in double stranded DNA

thymine

Adenine binds with which base in DNA?

cytosine

guanine binds with which base in DNA?

uracile

Adenine binds with which base in RNA?

hydrophobic, inside

Bases are ______ and face the (inside or outside) of the double helix

hydrophilic, outside

Phosphate groups are ______ and face the (inside or outside )of the double helix DNA

A, B, Z

three possible conformations of the DNA of the DNA double helix

Coding strand

strand of DNA containing the code for the synthesis of specific proteins.

Complementary strand

strand of DNA containing the complement of the protein code.

Major groove

large gap in the DNA backbone which allows for the binding of proteins needed for transcription.

Minor groove

small gap in the DNA backbone which has no known significance.

Genetic code

every three bases of DNA in sequence code for a single amino acid in a protein.

46

How many chromosomes do humans have?

Chromosome

a condensed form of DNA found in the nucleus of eukaryotic cells. Consists of two sister chromatids bound at the centromere.

Chromatin

simplest level of DNA which is not condensed

Histone proteins

proteins assisting in the coiled of DNA.

Nonhistone proteins

proteins that are bound to DNA and control DNA and RNA processing.

Nucleosomes

structure formed when is DNA wrapped around either histone proteins about 1.65 times.

Linker DNA

DNA found between two nucleosomes. Where proteins bind to DNA.

Chromatosome

a nucleosome plus a H1 histone protein

Chromatid

super coiled double helix of DNA making up half of the chromosome.

semiconservative

DNA replication is ________, meaning that when replication is complete one strand of the double helix is retained from the old DNA and the other strand is newly synthesized DNA.

Replication fork

the location of active DNA replication

DNA helicase

enzyme that initiates DNA replication by unwinding the DNA double helix at the replication fork. Occurs at multiple points along the length of the DNA. Functions by breaking the hydrogen bonds between DNA bases.

Double helix destabilizing proteins

Proteins that temporarily bind to stabilize the unwound DNA

Upper DNA polymerase III

enzyme that synthesized the leading strand continuously in the 5' to 3' direction

RNA Primase

enzyme bound to DNA helicase that synthesizes a short RNA primer to synthesize the lagging strand discontinuously.

Okazaki fragments

discontinuous fragments of the lagging strand formed during DNA synthesis

Lower DNA polymerase III

enzyme that synthesizes new DNA bound to the RNA primer to form an Okazaki fragment on the lagging strand.

DNA polymerase I

enzyme that hydrolyzes the RNA portion of the primer and completes the gaps between the DNA Okazaki fragments to form a continuous strand along with DNA ligase.

DNA ligase

enzyme that joins the Okazaki fragments in the lagging strand of DNA after the RNA primer is replaced by DNA.

RNA

A nucleic acid that translates the code found in DNA into proteins. Made up a ribose sugar, a phosphate group, and a base. Bases include adenine, guanine, cytoside, and uracil.

RNA polymerase I

RNA polymerase used for rRNA synthesis

RNA polymerase II

RNA polymerase used for HnRNA and mRNA synthesis

RNA polymerase III

RNA polymerase used for the synthesis of tRNA and smaller species of rRNA

Transcription

process of converting DNA to RNA.

Promoter site

only location on DNA where transcription can begin. Contains short sequences of DNA such as TATA or CAAT that do not code for any amino acids. Made up of introns.

Regulatory proteins

proteins that bind to the promoter region on DNA to either support or inhibit the initiation of hnRNA synthesis. Bind at the major groove in linker DNA between nucleusomes.

Upstream promoter element

region of DNA including the promoter site and regulatory proteins.

5' to 3' direction

which direction does transcription occur?

Enhancers

auxillary regions of DNA that have further influence on hnRNA synthesis. Made up of introns.

redundant

Genetic code is ______ meaning multiple codes can equate to the same amino acid.

Stop codes

genetic codes specifying the termination of RNA synthesis. There are 3 of these

Introns

base sequences on DNA and RNA that do not code for amino acids, stop codons, or start codons. Separate exons. Are removed from hnRNA to form mRNA and then proteins.

Spacer molecules

introns that function in connecting coding regions of gene sequences

Telomeres

intron portions at the end of chromosomes that serve as a record for the number of cell divisions and preserved chromosome integrity. Contain highly repeated sequences.

introns

Attach to the centromere during mitosis and meiosis

introns

Serve as promoters and enhancers

Exons

gene sequences that code for either all or part of a protein in both DNA and hnRNA.

Heterogenous nuclear RNA (HnRNA)

the initial coding RNA product made from DNA. A precursor to mRNA. Differs from mRNA because it contains introns. Contains two or more exons separated by one or more introns.

GTP cap at the 5' end and a poly adenosine tail at the 3' end

two modifications mad eto HnRNA to form mRNA that help in preventing the degradation of RNA.

Transesterification reactions

reactions that facilitate the looping out of introns by breaking the intron exon phosphate bonds and forming new exon exon phosphate bonds.

Nuclear RNA (nRNA)

RNA which facilitates the looping out of introns from hnRNA to form mRNA.

Messenger RNA (mRNA)

a cellular refinement of hnRNA made in the nucleus. Formed when the introns are removed from hnRNA. Carries the exact code for protein sequencing. Comprises only 3% of the total RNA. Indicated strict control for the rate of protein synthesis.

Translation

process of converting mRNA to protein.

Transfer RNA (tRNA)

a short chain RNA that attaches to specific amino acids and transports them to ribosomes where proteins are synthesize. Has extensive base pair binding, an acceptor stem that binds the amino acid, and an anticodon region that minds mRNA

Anticodon region

region of tRNA that binds to mRNA.

Acceptor stem

region of tRNA at its 3' ends that binds the amino acid.

Guanine

the base that facilitates the twisted conformation of tRNA and helps to carry its amino acid to a codon site on a ribosome.

Ribosome

a two subunit structure made up or rRNA which works in junction with tRNA to build proteins. Multiple ribosomes move along a single mRNA at a time.

40s subunit

subunit of a ribosome that houses the mRNA

60s subunit

subunit of a ribosome that houses the incoming tRNAs and their amino acids.

Ribosomal RNA (rRNA)

the most abundant RNA (75%) and 66% of the ribosomal mass. Plays a specific role in protein synthesis that is not well understood. Possibly a catalytic role.

10

how many proteins can be formed from a single mRNA molecule per minute?

12

how many proteins are required for the initiation of translation in eukaryotes?

Peptidyl site

site on the 40 s subunit of the ribosome where tRNA binds and mRNA start codon AUG is read

60s subunit binds (full ribosome is formed)

what happens in response to tRNA binding to the peptidyl site of the 40s subunit?

GTP

acts as an energy source for initiation to occur

Aminoacyl site

site adjacent to the peptidyl site on the ribosome where a second tRNA delivers the proper amino acid.

GTP

acts as an energy source for elongation I

Peptide bond formation and the release of the amino acid in the P site

what two events occur during the elongation II stage of translation?

23s rRNA

rRNA located in the 60s ribosomal subunit that forms a peptide bond via catalytic activity.

elongation III

-initial tRNA is removed and the ribosome continues along the mRNA

-Dipeptide is moved from the A site to the P site using GTP

-Elongation is repeated until there is no more code to be read from the mRNA

Releasing factor

protein that binds to the termination code on the mRNA at the ribosomal A site

ribosome and peptide

what two structures are released fromt eh mRNA at the termination stage of translation?

freely in the cytoplasm or attach to the rough ER

Inactive ribosome can exist in these two locations after the termination of translation

rough ER

Ribosomes attached to the _______ make proteins that will be used for cellular membranes as well as proteins needed for extracellular function.

Sickle cell anemia

condition which occurs due to a genetic code change in DNA. A substitution of valine for glutamine in hemoglobin. Red blood cells then develop a sickle like shape resulting in blocked vessels and early destruction of the red blood cells.

valine for glutamine

what amino acid substitution occurs in hemoglobin to produce sickle cell anemia?

Cancer

uncontrolled cell division

-cells lose control over division

-excessive protein synthesis

-inactivation of tumor suppressor genes

three changes in cells having cancer

oncogenes

genes that make an excessive amount of protein which binds to promoter regions and signals the cells to divide continuously

tumor suppressor genes

genes that suppress division

UV radiation

damage by this element induces a bond to form between adjacent pyrimidines in DNA. DNA is then distorted and replication cannot occur beyond the dimer formed. DNA replication does not continue beyond the dimer. Ie) skin cancer

Low

levels of uv radiation that inhibit cellular mitosis in the cornea

Moderate to high

levels of uv radiation that result in swollen nuclei and cell death in the cornea

Extreme

levels of uv radiation that result in complete sloughing of corneal epithelial cells

Photokeratitis

corneal injury due to exposure of the cornea to UV radiation

290

uv light levels below _____ nm damage only the corneal epithelium. Higher wavelengths damage deeper layers of the cornea, lens, and retina

UV B (280 to 320 nm)

UV light levels that induce damage to the lens epithelium and are linked to the formation of cortical and posterior subcapsular cataracts.

Xray and gamma rays

higher energy rays than UV radiation that produce more damage to the lens

Alkylating Agents

chemical substance that can produce DNA damage. Form covalent alkyl bridges between bases on different chains of double stranded DNA. Used in the treatment of cancer to target cancerous cells, but damage normal cells to an extent as well.

2-naphylamine

agent used in the manufacture of dyes known to cause bladder cancer after chronic exposure.

Excinuclease

enzyme which breaks 5' to 3' bonds approximately 5 to 8 bases on both sides of the pyrimidine dimer formed by UV radiation.