Exam 1: Biomolecules and Enzyme Kinetics Flashcards
Name the four macromolecules (biomolecules) within the cell and their building blocks:
Sugars (glycans), Fatty Acids (lipids), Amino Acids (proteins), Nucleotides (Nucleic Acids) FANS
Give examples of biomolecules
Fatty Acids: Fats
Amino Acids: Enzymes
Nucleotides: RNA, DNA
Sugar polysacchrides
Describe central dogma of biology
DNA creates RNA through transcription, RNA creates proteins through translation
About DNA (macro view)
Deoxyribonucleic Acid, instructions for creating proteins, inherited instructions, made of nucleotides
Components of nucleotides
5-carbon sugar (deoxy), phosphate, and nitrogenous base
How can you distinguish between rna and dna
Deoxyribose vs ribose sugar, DNA is missing an OH group on the second carbon of the ribose sugar (2-deoxyribo)
Categorize the nitrogenous bases which make up DNA
Purines: Adenine and Guanine
Pyrimidines: Cytosine, Uracil (RNA), Thymine (DNA)
About nucleoside and naming
Nucleosides= Nucleobase + sugar
if base is purine: ending is -osine
if base of pyridine: ending is -idine
if deoxy sugar, add deoxy-
ex: adenosine, deoxyadenosine, cytidine
Two types of nucleotides
ribonucleosides, and deoxyribonucleosides
Impossible nucleosides
Thymidine, Thymidine monophosphate, deoxyuridine, deoxyuridine monophosphate
Purpose of phosphate group in DNA
serves as linkers to form nucleic acids, provides polarity (5’ vs 3’) end, base sequences can vary, phosphodiester linkage
Alternate functions of nucleotides other than forming nucleic acids
carrying energy of hydrolyzes phosphoanhydride bonds (ATP), forming coenzymes, acting as signaling molecules
Forming dsDNA
hydrogen bonding holds two nucleotides together, two h-bonds between T/U-A and three between G/C (G/C is a stronger and shorter bond)
About dsDNA structure
two interconnected, right handed double helix structure, antiparallel strands
How many base pairs in the human genome?
3,000,000,000
How is the genome organized, start from DNA
DNA is organized intro strings of chromatin, which are wrapped around histones to form nucleosomes, these nucleosomes continue to bind into two chromatids held together by a centromere to form a chromosome
Name DNA replication enzymes
DNA helicase, RNA primase, DNA polymerase I, II, III, ss-binding proteins, DNA ligase, Sliding clamp, topoisomerase
DNA replication: purpose of DNA helicase
unwinds DNA double helix
DNA replication: purpose of RNA primase
builds RNA primer
DNA replication: purpose of DNA polymerase I, II, III
removes RNA primer, adds nucleotides, repairs
DNA replication: purpose of ss-binding proteins
prevents DNA unwinding
DNA replication: purpose of DNA ligase
seals gaps in okazaki fragments
DNA replication: purpose of sliding clamp
keeps DNA polymerase in place
DNA replication: purpose of topoisomerase
keeps DNA flexible throughout process
Describe process of DNA replication
1: Helicase unwinds DNA
2: ss-binding proteins stabilize strands
3: leading strand synthesized in 5’-3’ direction using DNA polymerase guided by sliding clamp
4: lagging strand is synthesized discontinously, RNA primase synths a RNA primers which the DNA polymerase binds to to form an okazaki fragment
5:DNA ligase joins okazaki fragments to growing strand
About RNA (generic)
RNA acts a messenger to create proteins
highlights of RNA transcription (enzymes, somponents)
RNA polymerase- unwinds dsDNA and copies one strand as RNA
Promoter DNA sequence- binding site for RNA polymerase
Transcription factors- help RNA polymerase find promoter
Termination- releases RNA polymerase and mRNA strand
types of RNA
mRNA- messenger to encode proteins
rRNA-ribosome components
tRNA- transport amino acids to ribosome
ncRNA- non coding RNA
Translation overview
Ribosomes read genetic material within mRNA and produce proteins, protein building blocks are amino acids, tRNA transfers amino acids to ribosome
About amino acids
Codons, or three nucleotides, code for 20 amino acids , many doubles (start codon AUG, stop codons: UAA, UAG, UGA
Translation steps
initiate, elongate, terminate
Components of ribosome
large subunit and small subunit, large subunit houses R, P, and A sites
How to regulate transcription
gene expression refers to mRNA production within the cell, Gene regulation refers to modulating gene expression (transcription factors, activators, enhancer sequences)
Two types of genetic mutations
SNPs and insertions/deletions
what results from SNPs + description
Silent- no effect on amino acid sequence
missense- changes amino acid code
nonsense- creates stop codon
what results from insertion/deletion and description
base pair insertion- frameshift causes entensive missense
frameshift causes immediate nonsense (stop codon)
insertion of deletion of 3 nucleoides-no entensive frameshift
define epigenetics
changing gene expression in an organism without changing genetic code- environmental factors, methylation, acetylation, phosphorylation
describe protein structure/folding
proteins develops its structure in 3-4 stages
1: primary protein structure- regular chain
2:secondary- sequence of amino acids is linked by weak hydrogen bonds for fold beta sheets or alpha helixes
3-ternary-when attractions between alpha and beta sheets produce 3-d structures
4-quaternary- a protein of more than one acid chain, consisting of subunits
Post translational modifications of proteins
chemical groups (methylation, acetylation, phosphorylation), complex grounds (sugars), polypeptides, peptide cleavage, deamidation, can alter protien chanrge hydrophobicity and conformation
Enzyme basics
large proteins, named by adding -ase to the catalyzed thing, substrate specific, lower activation energies
enzyme-substrate interaction
bind by weak forces, like hydrogen bonds and vander waals, substrate binds to the active site of the enzyme (lock and key model), maye require co factor or coenzymes
what are cofactors and coenzymes
grounds added to substrates/proteins, cofactors are ions and coenzymes are proteins
what are “Michaelis-Menten” kinetics
describe rate of enzymatic reactions, S+E=SE
