bio unit 7

nucleic acid elements (5)

C, H, O, N, P

nucleic acid monomer

nucleotide

nucleic acid polymer

polynucleotide

what bond connects nucleic acid monomers

phosphodiester bonds (covalent)

nucleic acid examples (3)

DNA, RNA, ATP (modified)

label the parts

A - ribose sugar

B - phosphate group

C - nitrogenous base (A, T, U, G, C)

what differentiates RNA from DNA structurally

RNA: OH at 2nd carbon

DNA: H at 2nd carbon

where are phosphodiester bonds created (2)

between the 3’ carbon on the sugar of one nucleotide and the phosphate group of the next nucleotide

created by condensation reactions

nitrogenous bases (5)

adenine, cytosine, guanine, thymine, uracil

purine bases (2)

adenine and guanine

pyrimidines bases (3)

uracil, cytosine, thymine

what keeps DNA double helix the same width

purine-pyrimidine pairs

A-T base pairs have ___ hydrogen bonds

two

G-C base pairs have ___ hydrogen bonds

three

DNA replication purpose (3)

process of copying the genome within a cell

creates two identical DNA molecules each with 2 complementary strands

needed for cell division (each cell needs it’s own copy)

meselson and stahl experiment significance (2)

determined how DNA is replicated

replication is semi conservative

meselson and stahl experiment process (4)

1) grew ecoli in N¹⁵ (heavy)

2) switched the ecoli to N¹⁴ (light)

3) round 1 replication: half heavy half light → rules out conservative

4) round 2 replication: half heavy half light, then half light → rules out dispersive

initiation of DNA replication (4)

helicase binds to the origin of replication and unzips the double helix by breaking the hydrogen bonds

creates replication fork (region where original DNA splits into two)

single strand binding proteins bind to the single stranded DNA to keep the strands separate by preventing the bonds from reforming

gyrase/topoisomerase moves in front of the helicase to relieve tension that could damage the DNA

DNA replication synthesizing complementary strand (4)

DNA polymerase III reads the template to build the complementary strand in 5’ → 3’ direction

primase creates an existing strand for DNA polymerase III to add to the 3’end by adding a primer made of a short sequence of RNA nucleotides

after the primer, DNA polymerase III can attach to the next strand

DNA proofreading (2)

can proofread as the new strand is being built (can remove incorrect ones)

not 100% accurate → mistakes are mutations for natural selection

how are primers removed

DNA polymerase I removes the RNA nucleotides and replaces them with the correct DNA nucleotides

leading vs lagging strands (3)

leading needs 1 primer, each Okazaki fragment needs a primer for lagging

leading is synthesized continuously, lagging is synthesized discontinously

leading goes in the same direction as helicase, lagging goes in the opposite direction

which strand has more primase and DNA polymerase I activity

lagging

ligase

catalyzes formation of phosphodiester bonds between the Okazaki fragments forming a continuous bond

polymerase chain reaction (PCR) (2)

used to amplify (create millions/billions of copies) small fragments of DNA

basically DNA replication in a test tube

taq polymerase (2)

DNA polymerase enzyme that’s heat stable

originally found in a prokaryote that lives in hot springs

PCR steps (5)

setup: many free DNA nucleotides, primers, and taq polymerase in test tube

1) denaturation: DNA is heated to break the hydrogen bonds between the strands

2) annealing: sample is cooled to allow primers to bind to the complementary DNA strand

3) extension: at room temperature, taq polymerase replicates the DNA

process is repeated 100 times or so

gel electrophoresis (3)

often done after PCR

uses an electrical current to move DNA fragments through a gel

fragments are separated based on size

restriction enzymes (2)

typically DNA molecules are too long to travel through a gel so they need to be cut into pieces first

restriction enzymes (endonuclease) will cut DNA molecules at very specific sequences

DNA fingerprints

restriction enzymes cut-sites create a unique pattern of bands when a sample is run through a gel “DNA Fingerprint”

SNPS can change cut sites which causes no enzyme activity at the location → changes the bonding pattern

PCR and gel electrophoresis applications

PCR COVID-19 testing, paternity testing, forensic investigations

the central dogma (3)

describes the flow of genetic information from DNA - RNA - protein

DNA is transcribed into mRNA

mRNA is transcribed into a polypeptide chain

transcription (2)

producing mRNA using DNA as a template

allows for only a portion of the genome to be copied (resource efficiency) and DNA to remain protected in the nucleus

where does transcription occur

eukaryotes: nucleus, prokaryotes: cytoplasm

RNA polymerase (2)

performs transcription (elongating mRNA strand) using DNA template as a guide

must synthesize mRNA in 5’ → 3’ direction

phases of transcription (3)

initation, elongation, termination

transcription initation (2)

promoter: non-coding region of DNA in front of the gene of interest that begins with the TATA box

transcription factors (proteins that bind to the promoter) recruit RNA polymerase — begins to temporarily unzip a small section of the double helix to expose the bases

transcription elongation (3)

RNA polymerase “reads” the template strand (antisense strand) to synthesize the mRNA in 5’ → 3’ direction

as its synthesized, the RNA nucleotides will temporarily hydrogen bond with the template strand

the growing mRNA strand exits RNA polymerase and the DNA rezips

template strand

antisense stand, RNA polymerase reads it

coding strand

sense strand, complementary DNA strand

transcription termination

signals for RNA polymerase to release the mRNA and detaches from the DNA → transcription now finished

regulation of transcription (4)

noncoding regions of DNA that don’t code for a protein

some parts help with regulation

enhancers: increases rate of transcription

silencers: decrease rate of transcription

non-coding DNA regions (3)

telomers: repetitive sequences at the end of linear (eukaryotic) chromosomes → protects the ends of the chromosomes

genes for rRNA and tRNA: RNA is synthesized from these genes, but they don’t code for proteins

introns: base sequences that get removed from the mRNA after transcription (only in eukaryotes)

mRNA processing (3)

done in eukaryotic cells after transcription and before it leaves the nucleus

converts pre-mRNA into mature mRNA

includes mRNA splicing and addition for the 5’ cap and poly-A tail

5’ cap (3)

modified nucleotide that is added to the 5’ end of mRNA

helps with ribosome binding during translation

aids in the export of the mature RNA from the nucleus and protects the mRNA from degradation in the cytoplasm

poly-A tail (2)

string of adenines attached to the 3’ end of mRNA

aids in the export of the mature of mRNA from the nucleus and protects the mRNA from degradation in the cytoplasm

mRNA splicing (4)

pre-mRNA has exons (expressed base sequences) and introns

introns are removed from the mRNA during splicing (stays in the nucleus)

snRNPs bind to either side of the introns and then assemble into spliceosomes

spliceosomes remove the introns and ligate the exons together

snRNPs

small nuclear ribonucleoproteins

alternative splicing (2)

different introns are removed creating unique mature mRNAs — creating unique polypeptides

one gene (and so one pre-mRNA) can provide instructions for several different polypeptides due to alternative splicing

elements in proteins (4)

C, H, O, N

proteins monomer

amino acid

how many amino acids to proteins have

20 bc 20 different side chains

proteins polymer

polypeptide

protein bond

peptide bond (covalent)

protein structure levels (4)

1^o: polypeptide chain

2^o: local folding (alpha helics and beta pleated sheets)

3^o: 3D structure determined by side chains

4^o: 2+ polypeptide chains interacting

protein synthesis in prokaryotes (2)

translation can occur immediately after transcription

causes protein synthesis to be faster than in eukaryotes

protein synthesis in eukaryotes (3)

transcription occurs in the nucleus

mRNA processing occurs before the mature mRNA can leave the nucleus

transcription occurs in the cytoplasm either by free or attached (on the rough ER) ribosomes

codon (2)

mRNA is ready in triplets of bases

each codon codes for a specific amino acid

start codon

AUG

stop codons (3)

UGA, UAA, UAG

characteristics of genetic code (3)

universal - basis of several biotechnology techniques (ex GMOs)

redundant/degenerate - some condones code for the same AA

unambiguous - no codon specifies more than one AA

implications of universal genetic code (2)

allows for genetically modified organisms

splice the gene(s) of interest into another organism - allows for protein synthesis of the gene(s) of interest by the new organism

uses of genetically modified organisms (2)

insulin gene in bacteria → allows for mass production of the insulin protein

pesticide gene in crops → allows for the crops to produce a protein that acts as a pesticide so bugs don’t eat them

genetic modification process (5)

A - isolate gene of interest and amplify it using PCR

B- isolate bacterial plasmid and amplify it using PCR

C - use a restriction enzymes to cut the gene of interest and then insert it into plasmid (creating a recombination plasmid)

D - insert recombinant plasmid into host organism: creating a transgenic organism

E - (optional) if the goal was to create/harvest a protein, allow the transgenic organism to grow in culture, then extract the protein of interest

types of RNA (3)

mRNA: messenger - takes the message from DNA and brings it to the ribosomes

tRNA: transfer - carries amino acids to the ribosomes

rRNA: ribosomal - structural component of ribosomes

tRNA structure (5)

single strand folded into 3D structure

2D representation resembles clover

held together by hydrogen bonds

anticodon: group of 3 bases in the tRNA that will bind to the mRNA codon

amino acid binding site: where the amino acid gets attached

tRNA enzyme and function (3)

aminoacyl-tRNA synthetase

attaches the correct amino acid to the tRNA

the tRNA brings the amino acid to the ribosome and binds to the mRNA codon

ribosome structure (4)

made of rRNA and proteins

2 subunits: small and large

mRNA attaches to the small subunit

large subunit has 3 binding sites for tRNA (A, P, and E sites)

ribosome APE binding sites (3)

A site: aminoacyl-tRNA binding site (for incoming tRNA)

P site: peptidyl-tRNA binding site (for tRNA “holding” the growing polypeptide chain)

E site: exit site (for discharging/”empty” tRNA to leave)

ribosomes facilitate binding of ______________ with _______ AND the formation of the __________________ between amino acids and the peptide chain

mRNA codon, tRNA, peptide bond

RNA translation initiation (4)

5’ end of the mRNA binds to the small ribosomal subunit

subunit moves from 5’ to 3’ and scans for the start codon

at the start codon, the initiator tRNA binds to the start codon

large ribosomal subunit assembles, placing the initator tRNA into the P site

RNA translation elongation (2)

the ribosomes begins to read the mRNA in codons

cycle repeats until the stop codon is reached

RNA translation elongation codon recognition (2)

incoming tRNA’s anticodon binds to the mRNA’s codon in the A site

ensures that the correct amino acid is added

RNA translation elongation peptide bond formation (2)

peptide bond is formed between the polypeptide chain and the new amino acid

transfers the chain from the P site to the A site

RNA translation elongation translocation (3)

ribosome shifts over one codon

discharged tRNA moves to the E site and exits, tRNA in the A site moves into the P site

the A site is now empty for the next tRNA

translation termination (4)

when a stop codon is in the A site, no new tRNA will enter

release factor will enter and perform a hydrolysis reaction to break the bond between polypeptide chain and tRNA in the P site

after the polypeptide chain is released, the translation complex dissolves

the polypeptide chain will then be modified and folded into its final structure/functional form

RNA post-translation modifications (2)

often occurs in the golgi

can involve adding chemical groups (phosphates or sugars) or cleaning specific peptide bonds

pre-proinsulin to prosulin

in the RER, the signal peptide is removed → proinsulin

pre-proinsulin (2)

110 amino acid length

4 sections (signal peptide, A chain, B chain, C-peptide)

proinsulin to insulin (3)

in the RER: form disulfide bridges between the A chain and B chain

the bridges are packaged into vesicles to move to the golgi

in the golgi: removed C-peptide → insulin

preteomes (3)

the total of all proteins made and used by the body

dynamic: constantly synthesizing and hydrolysing proteins

done by proteasomes

proteasomes

protein complex that hydrolyzes damaged or unused proteins

cell differentiation/specialization (3)

all cells in the body have the same DNA

cells have differentiated into different types (ex muscle cells, neurons, heart cells, skin cells, etc.)

different genes are expressed (proteins produced) in those different cell types → one major thing making them different

mutations (2)

structural changes or alterations in the DNA sequence of an organism

have zero impact, decrease, or increase fitness (adaptation)

types of mutations (4)

substitutions (point mutations): single nucleotide is changed (SNPs)

synonymous mutation (silent) amino acid stays the same

non-synonymous mutation: amino acid is changed

insertions or deletions: one or more nucleotides are added/removed → results in a frameshift mutation where the reading frame is altered, drastic impact bc all codons are changed

synonymous mutations _______ impact the polypeptide while nonsynonymous mutations _______ impact the polypeptide

do not, can

causes of mutations (2)

errors in DNA replication/repair (DNA polymerase III or breakdown in repair process)

exposure to mutagens (chemical mutagens and radiation)

which base is more likely to be mutated

cytosine (into uracil)

consequences of mutations in somatic cells

causes issues to the individual but is not passed on to offspring

somatic cells

all the cells in the body excluding germ cells

germ cells

cells that produce sperm and eggs

consequences of mutations in germ cells

can be passed on and inherited

impact of mutations on fitness (3)

neutral/silent mutation: doesn’t change fitness (ex synonymous or non-coding regions)

harmful mutation: reduces fitness and selected against (ex causes disease)

beneficial mutation: increases fitness and selected for (adaptation)