Week One Objectives Flashcards
What is the chemical make-up of nucleic acids
Nitrogenous Base, Ribose sugar, phosphate (deoxyribose in DNA lacks 2’ carbon hydroxyl group
Watson-Crick Base Pairing
A goes with T (or U)- 2 Hydrogen bonds G goes with C- 3 Hydrogen bonds
Compare/Contrast Eukaryotic and Prokaryotic genomes
Pro circular, Euk linear Pro is tightly coiled, Euk is compacted via histones
What is the semi-conservative model of DNA replication and why is it important for inheritance?
As DNA is replicated a daughter strand is paired with a parental strand (always one old and one new)- this is the way DNA replication ensures duplication of genetic info is passed on
Describe how properties of A.A. affect protein structure
Properities of A.A. (hydrophobicity, polarity, h-bonding ability, etc) affect folding
Primary Structure of Proteins
Amino acids covalently linking through peptide bonds
Secondary Structure of Proteins
Alpha helices, and Beta sheets: form due to hydrogen bonding of backbone (not R groups)
Tertiary Structure of Proteins
interaction of R groups of helices and beta sheets (ion, hydrogen, dipole-dipole, disulfide bridges), can have multiple ways to fold but usually results in lowest energy state
Quaternary Structure
interaction of multiple domains/ tertiary structures
What are some post-translational modifications?
addition of: sugar carbs lipids phosphates acytl group
What do catalysts do to reactions?
lower activation energy to increase the RATE of reaction DOES NOT CHANGE DELTA G (net energy change of reactants to products does not change)
How does substrate and product concentration affect reactions?
Energetically: removing products or adding reactant will make the forward reaction more favorable (makes delta G more negative) Kinetically: increasing [substrate/reactant] will increase rate of rxn
Allosteric activators
-don’t compete with substrate binding site -increasings affinity for substrate -lowers Km (makes enzyme more active) -can increase Vmax
Allosteric inhibitors
-binds at place other than the active site -decreases affinity for substrate -increases Km (makes enzyme less active) -can lower Vmax
Competitive inhibitors
-compete for substrate-binding site in catalytic cleft -prevents substrate from binding -transient interaction :increasing amount of substrate can overcome competitive inhibitor, therefore DOES NOT AFFECT Vmax -Km is INCREASED (need more substrate to get to Vmax)
Non competitive inhibitors
typically binds at catalytic site (ADPspot)/active site, makes COVALENT bond with enzyme CANT OVER COME -Km DOES NOT CHANGE -decreases Vmax
Benefits of enzymes on runs
-lowers activation energy -provides proximity and orientation of reactants -ensures specificity -stabilizing transition complex -can couple energetically unfavorable rxns with favored ones
What is Vmax?
maximum reaction rate at an infinite substrate concentration (where all enzyme is bound to substrate)
Km
Michaelis constant- concentration of substrate at half of Vmax
- Describe the components of the eukaryotic DNA replication complex and their functions
•DNA polymerase- enzyme in replication, copies parental template strand in 3’ to 5’ direction, producing new strands 5’ to 3’ •Primase- makes a RNA primer so DNA polymerase has free 3’ hydroxyl group •SSB Proteins- prevent strands from re-associating and protect them from enzymes that cleave single stranded DNA •Topoisomerases 1- enzymes that break/nick phosphodiester bonds and rejoin them to relieve supercoiling tension •Topoisomerase 2- DNA-helix-passing reaction •Ligase- joins two polynucleotide chains together
- Describe the molecular mechanisms by which eukaryotic cells prevent their genomes from becoming shorter with each cell division, and how this process contributes to normal aging and cancer
• Telomerase adds short piece of DNA (called a telomere) that is lost when cell divides and DNA is replicated • Without this cell progeny will reach Hayflick limit and commit suicide • Aging= somatic cells express telomerase at low levels and decrease expression with time
Describe the structure of a gene, identifying the relative locations and functions of promoters, enhancers, transcriptional start site, introns and exons.
•Promoter (typically upstream of start point) control binding of RNA pol to DNA and identifies the start site and frequency of transcription •Enhancer Frequency of transcription is controlled by cis regulatory sequences (same strand), all regulatory sequences interact with trans-acting proteins that assist in binding and stability of RNA pol •Transcriptional Start Site •Intron/Exons – introns are taken out, exons are spliced together to make protein product
- Compare transcription in prokaryotes and eukaryotes.
Prokaryotic Eukaryotic Transcription occurs is CYTOPLASM Transcription occurs in NUCLEUS Polymerase (with help of sigma) is able to initiate transcription without help of other proteins Requires large set of proteins that must assemble at promoter before RNA Pol can being transcription Core and regulatory elements are adjacent Core and regulatory elements can be VERY far apart Polycistronic (more than one “gene” on mRNA) Cistronic (each mRNA contains only one “gene) Translation of mRNA begins prior to transcription termination (no post transcriptional modifications) Transcription terminates before translation begins (need 5’ cap, Poly A tail, and splicing to occur) No Histones DNA needs to be “unpacked” prior to transcription
Understand the functions, structures, and synthesis of mRNAs, tRNAs, rRNAs, and miRNAs and lincRNAs
• mRNAs- messenger RNA, precursor for protein synthesis • rRNAs- ribosomal RNA, form ribonucleoprotein complexes • miRNAs- small non-coding RNAs, used for other cell processes like regulation • lincRNAs- non-coding RNAs, known functions: gene silencing by affecting chromatin formation or by antisense
Describe relationship between DNA coding strand, DNA template strand, and mRNA
coding strand is compelmentary to template strand, mRNA is complementary to template strand but T’s turn into U’s
Transcription in prokaryotes
1.RNA polymerase holoenzyme forms (core pol plus sigma) 2.RNA pol and Sigma Factor bind to promoter, causing DNA strands to unwind and separate 3.Sigma Factor is release at approx. 10 nucleotides 4.Elongation continues until RNA pol finds termination signal a. Hairpin loop b. Binding of protein Rho c. Note- termination signals are encoded in DNA and many function by forming RNA structure that destabilizes pols grip on RNA
Transcription in Eukaryotes
- transcription factors bind promoter and help RNA pol bind 2. Other factors and RNA pol assemble at promoter 3.TFIIH opens helix, looses transcription factors 4. Elongation factors associate 5. topoisomerases relieve tension in supercoiling 6. Addition of 5’ cap 7. Addition of 3’ poly A tail 8. Introns are spliced out, exons put together 9. mRNA is bound to proteins that stabilize and transport through nuclear pores in cytosol
What are the size of rRNAs?
45S is cleaved to produce 18S, 28S, 5.8S
Given a wild type mRNA sequence, apply an understanding of the codon structure of mRNAs to predict changes in protein structure due to a specific mutation
If there is a mutation that would change the amino acid pair with that codon, it will change the folding of the resulting protein
