Finals DNA replication, Protein synthesis, VIruses

DNA/Deoxyribonucleic acid

made up of nucleotides, which consist of a phosphate group, 5 5-carbon sugar, and a nitrogen base (A, T, C, G)

Purines

Double-ring structure of bases; Adenine and Guanine

Pyrimidines

single-ring structures; Cytosine and Thymine

Double Helix

structure of DNA as described by Watson and Crick, where 2 strands of DNA wrap around each other

Hydrogen bond

a bond that holds base pairs together

Erwin Chargaff

the person who discovered that the amount of A and T bases and the amount of G and C bases in any sample of DNA are equal, which supports the idea that they are complementary pairs

Covalent Bond

a bond between the nitrogen base and the phosphate

Adenine and Thymine

In this base pairing, 2 hydrogen bonds form

Guana and Cytosine

In this base pairing, 3 hydrogen bonds form

Replication

the process by which a DNA molecule builds an exact duplicate

Helicase

Breaks the hydrogen bonds between nitrogen bases and untwists DNA strands at the replication fork, separating the 2 parental strands

DNA polymerase

adds the new nucleotides to the existing chain, also proofreads new bases to ensure accuracy

DNA Ligase

forms h-bonds between the new nitrogen bases

Semi-conservative

each replicated DNA strand is attached to one original DNA strand

3’-5’

leading strand, fewer mistakes

5’-3’

lagging strand, greater mistakes, done in okasaki fragments

Origins of replication

stretches of DNA that have a specific sequence of nucleotides, which proteins recognize and initiate DNA replication by attaching to the DNA at these sites and separating the strands

Replication Bubble

the result of the proteins separating DNA, creating a bubble-like structure

Replication forky Y-shaped region at the end of each replication bubble, where the new strands of DNA are elongating

Repairing damaged DNA

enzyme nucleases cut off damaged DNA, DNA polymerase fills in new nucleotides, ligase enzymes create new bonds

Gene expression

the process by which DNA directs the synthesis of protein, occurring in 2 steps

Codon

a portion of 3 nucleotides that calls for a specific amino acid

Start and Stop Codons

codons that do not signal for any amino acids

RNA

carries the messages from the DNA (in the nucleus) to the ribosomes (in the cytoplasm) and tells the ribosomes which proteins to make and how to make them

Messenger RNA

travels from the nucleus to the cytoplasm (ribosomes) with the instructions for making proteins; instructions carried in the form of codons

Transfer RNA

reads the message by mRNA, and gathers the amino acids for making the protein; transfers amino acids from the cytoplasmic pool of amino acids to a ribosome

Ribosomal RNA

found in the ribosome; used to bind the mRNA and tRNA to the ribosome; allows all components required for the synthesis of proteins to be held together

Transcription(DNA→ mRNA)

RNA polymerase binds to the site of DNA called a promoter, using one strand of DNA as a template. New nucleotides are inserted according to RNA base pairing rules until the terminator is reached. The mRNA molecule is made in the nucleus and is sent to the ribosomes in the cytoplasm to tell them what to do.

Promoter

DNA sequence where RNA polymerase attaches and initiates transcription

Terminator

DNA sequence that signals the end of transcription

Translation (mRNA→ Proteins)

mRNA attaches to the ribosome, the proper amino acid is brought to the ribosome by tRNA, the ribosome hitches the amino acid together with peptide bonds, and proteins are made.

Anticodon

3 3-nucleotide sequence that the tRNA molecule binds to the complementary codon on the mRNA molecule during protein synthesis

Ribosome

site of protein synthesis, made up of two subunits (small and large); has one binding site for mRNA, and 3 binding sites for tRNA

Mutations

changes in the genetic material of a cell

Gene mutation

a mutation that occurs within a single gene

Chromosome mutations

mutations that produce changes in the whole chromosome

Mutagens

agents in the environment that can change DNA (Radiation, chemicals, infectious agents)

Germ Cell Mutations

a change that occurs in an organism's gametes, affecting the offspring (occurs during meiosis)

Somatic cell mutations

changes occurring in an organism's somatic cells affecting the organism (occur during mitosis)

Letal Mutations

mutations that cause death before birth

Point mutations

changes in just one base pair of a gene (including base pair substitutions and base pair insertions or deletions)

Base Pair substitutions

replacement of one nitrogen base with another; would affect the coding of one singular amino acid

Substitution in the 3rd position

point mutation that mostly won't affect the outcome of an amino acid, as codons are redundant in some of the third position bases

Base pair insertion or deletion/ Frameshift mutations

addition or deletion of a nucleotide leads to disastrous effects, leading to improperly grouped codons

Deletion

chromosome mutation resulting from a loss of a piece of a chromosome due to breakage

Inversionacchromosomalme mutation where a chromosomal segment breaks off, flips around backward, and then reattaches

Translocation

a chromosome mutation where a piece of one chromosome breaks off and reattaches to a nonhomologous chromosome

Nondisjunction

chromosomal mutation where a chromosome fails to separate from its homologue during meiosis; one gamete receives an extra copy of the chromosome, while the other gamete receives no copy

Virus

A virus is a nonliving infectious particle made of nucleic acid (DNA or RNA) enclosed in a protein coat called a capsid; some viruses also have an outer lipid envelope. Viruses cannot reproduce or carry out metabolism on their own—they must infect a host cell and use its machinery to replicate.

Bacteriophage (phages)

viruses that attack bacteria

Prophage

viral DNA of a bacteriophage inserted into a bacterial chromosome during the lysogenic cycle that is copied along with the host DNA

Enveloped Virus

a virus that possesses a lipid membrane surrounding its capsid; typically derived from the host cell membrane. Envelope proteins help viruses enter host cells. Examples include influenza, HIV, mumps, and herpesviruses.

Retrovirus

RNA virus that uses reverse transcriptase to convert its RNA to DNA once inside a host cell (EX., HIV)

Viroids

Small, circular RNA molecules that infect plants

Prions

misfolded form of brain proteins that induce other proteins to misfold, leading to brain damage

Emerging Virus

An emerging virus is a virus that has suddenly appeared in a population or is rapidly increasing in incidence. Emerging viruses often arise due to mutation, contact with new host species, or environmental changes. Examples

Lytic cycle

Virus attaches to host and injects genetic material→ host produces viral proteins and genomes→new viruses assemble→ host cell bursts→ rapid cell destruction

Lysogenic Cycle

Viral DNA integrates host chromosome, forming a prophae→. Viral and host DNA are copied when the cell divides→. No immediate destruction of the host • environmental factors can cause a prophage to switch to the lytic cycle

General structure of a virus

Genome (DNA or RNA) + protein coat (capsid); some have a lipid envelope with glycoprotein spikes

Structure of Tobacco Mosaic Virus

Helical, rod-shaped virus with an RNA genome.

RNA virus structure

RNA genome, helical capsid, lipid envelope with spike protein

HIV virus structure

Two RNA strands, enzymes (reverse transcriptase, integrase, protease), icosahedral capsid, lipid envelope with glycoproteins

Enveloped virus reproductive cycle

Attach → enter → replicate genome → assemble virions → exit by budding with envelope

HIV nucleic acid behavior in a cell

HIV RNA → converted to DNA → viral DNA integrates into host genome → host makes viral RNA and proteins → new viruses assemble.

Anti-HIV drug categories

Reverse transcriptase inhibitors (RTIs) and protease inhibitors.