B/B biomolecules Flashcards
- functional RNA
- not translated
non-coding RNA
the study of heritable changes in DNA activity that are not caused by changes in DNA sequence
- main mechanisms: DNA methylation and histone modification
Epigenetics
all ____ amino acids are optically _____
chiral, active
what type of amino acids are found in proteins?
L-aminio acids
nonpolar amino acids. categories include AAs with alkyl or aromatic R groups
Hydrophobic
polar amino acids. categories include neutral, basic, and acidic R groups
hydroPHILIC amino acids
What are the hydrophobic/nonpolar alkyl amino acids?
- G - glycine
- A - alanine
- V -valine
- L - leucine
- I - isoleucine
- M - methionine
- P - proline
what are the hydrophobic/nonpolar aromatic AAs?
- W - Tryptophan
- F - Phenylalanine
- Y - Tyrosine
aromatic groups can absorb UV light. The more protein the more UV stored.
what are the hydrophilic neutral AAs?
- S - Serine
- T - Threonine
- N - Asparagine
- Q - Glutamine
- C - Cysteine
every AA in this group has an OH or SH in the side chain and are able to form hydrogen bonds
what are the hydrophilic basic AAs?
- R - Argenine
- K - Lysine
- H - histidine
All have a Nitrogen in the side chain
what are the hydrophilic acidic (negatively charged) AAs?
Aspartate/Aspartic acid (D)
Glutamate/Glutamic Acid (E)
both have a second carboxyl (-COOH) group in the side chain
what is pI?
isoelectric point
- the point along the pH scale where the amino acid has a net charge of 0 (zero)
what type of bonds join amino acids together?
Peptide bonds (which are essentially amide bonds)
how can a peptide bond be cleaved by hydrolysis?
via a strong acid or proteolysis (protease cuts a specific bond)
What bonds are present in primary protein structure?
Since the primary structure is just the sequence of amino acids, covalent bonds link amino acids together. The types of covalent bonds used are peptide and disulfide bonds.
How is the secondary structure of a protein formed?
- 2’ structure is formed due to the attractive and repulsive forces of interactions between main chains of neighboring amino acids. This forms recurring structural patterns.
- 2’ structure depends primarily on H bonds
- structural pattern examples: a helix and b-sheet.
- B-sheet occurs with H bonding between neighboring chains rather than within the same polypeptide (like a-helix).
- parallel B sheet = H bonded strands run in same direction forming bent/weaker H bonds
- antiparallel B-sheets = H bonded strands that run in opposite directions forming linear/stronger H bonds
what type of bonds are depended upon by 3’ and 4’ protein structure?
- peptide bonds of AA sequence & H-bonds of 2’ structure
- Ionic and hydrophobic interactions and disulfide bonds ***
explain the special properties of Histidine (H)
- found in both protonated and unprotonated forms in the body
- useful around the sites of enzymes to stabilize or destabilize a reaction
explain the special properties of glycine (G)
- NOT chiral
- NOT optically active
- very small and flexible
- acts as a helix breaker bc the small R group supports other confirmations
explain the special properties of Cysteine
- forms a reversible disulfide bond upon oxidation and becomes cysTINE
- CystEine is ~oxidized~ (LEO) to become cysTINE (TINEy –> loss of electrons makes it smaller) -S-S-
what is an opetator?
- a SEQUENCE of DNA
- bound by a transcription factor protein
what is a promotor?
- a SEQUENCE of DNA
- bound by a RNA polymerase
what are general transcription factos (GTFs)
- class of proteins that bind to specific DNA sites to ~activate~ transcription
what are activators?
a type of DNA binding PROTEIN that enhances the interaction between RNA polymerase and a [articular promoter by encouraging transcription
what is an enhancer?
- a DNA SITE bound by activators in order to loop the DNA to bring a specific promoter to the initiation complex
- cis-acting : act on the same chromosome as they are located
- don’t act on promoter regions themselves
what is a repressor?
- PROTEIN that binds to the operator that stops RNA pol. movement and stop transcription/gene expression
- if inducer is present, can react with repressor to make it detach from operator and let gene be transcribed
what is a silencer?
- region of DNA bound by repressor proteins to silence gene expression
what must happen during Post-Transcriptional Regulation?
- pre-mRNA is modified before it leaves the nucleus
- only EXONS are present in finished mRNA
- introns are spliced out since they are non-coding RNA segments via a spliceosome
- 5’ cap that protects mRNA from exonucleases, promotes ribosome binding, and regulated nuclear export of mRNA
- poly A tail on 3’ end to help with transcription termination
What is non-coding RNA (ncRNA)?
- a functional RNA molecule that is not translated into protein.
- has vital functions in the cell as RNA (many participate in transcription/translation)
what is Ribosomal RNA (rRNA)?
- help make up the ribosome, used in translation
what is MicroRNA (miRNA)
- functions in transcriptional and post-transcriptional regulation of gene expression by base pairing with complementary sequences within mRNA molecules
what are transfer RNAs (tRNAs)
- link codons in mRNA strand with corresponding amino acids for polypeptides
what are small nucleolar RNAs (snoRNAs)?
- small RNA molecules that guide covalent modifications of rRNA, tRNA, and snRNA through methylation or pseudouridylation
what are small nuclear RNAs (snRNAs)?
- main function: processing of the pre-mRNA in the nucleus
- also aid in regulation of transcription factors or RNA polymerase II and maintaining telomeres
Oncogenes
- proto-oncogenes code for proteinst aht normally detect cell growth & differentiation then something happens to make them oncogenes via:
1. deletion or point mutation 2. gene amplification/increased mRNA stability 3. chromosomal rearrangement
What are tumor supressors?
genes whose protein products either have a halting effect on the regulation of the cell cycle or can promote apoptosis
- act as big stop signs/safety checks to stop mistakes in cell division
- Two types: DNA repair proteins and Cell Cycle Repressor proteins
ex of tumor supressor: p53 protein (holds cell hostage between G1–>S)
What is a point mutation?
when one DNA base is replaced with another which leads to a change in one RNA nucleotide and sometimes a change in an amino acid
what is a frameshift mutation?
- when a DNA base is added to or removed from the gene sequence. Shifts the translational reading frame
- have the most significant effect on the final protein
what is a nonsense mutation? a missense mutation?
nonsense: when the mutation leads to the RNA sequence codon being a STOP codon
missense: changes one amino acid to another. can either be consercative (AA is same type as original) or non-conservative
What is the difference between a transition point mutation and a transversion point mutation?
transition: substituting purine for purine or pyrimidine for pyrimidine (ex: A–> G or C—> T)
transversion: switiching a purine for a pyrimidine or vice versa
