AP Biology - Big Ideas from Unit #6 Gene Expression and Regulation

(6.1) How is genetic info stored in living organisms?

In living organisms, genetic information is stored in nucleic acids (DNA, RNA, in a sequences of bases).

(6.1) How is genetic info (heritable info) passed from parent to daughter cells?

Genetic info is passed from parent to daughter cells by DNA and packaged into chroosomes.

(6.1) Shape of Chromosomes in Prokaryotic Cells

Prokaryotic organisms generally have circular-shaped chromosomes

(6.1) Shape of Chromosomes in Eukaryotic Cells

Eukaryotic organisms generally have multiple linear-shaped chromosomes

(6.1) Plasmids - What are they?

Prokaryotes and Eukaryotes can contain plasmids, small-extra-chromosomal, double-stranded DNA, circular DNA molecules.

THINK: "Extra DNA"

(6.1) Which molecule can some viruses use to encode genetic info?

RNA.

(6.1) 3 similarities between DNA and RNA.

1) Structurally similar (contain nucleotide monomers, are chain-like molecules, follow base-pairing rules).

2) General purpose (to store genetic information).

3) Consists of sugar, nitrogenous bases, and phosphate backbone.

(6.1) 3 ways in which RNA differs from RNA.

1) RNA has Ribose Sugar, not Deoxyribose.

2) RHA has a nitrogenous base, URACIL, not Thymine.

3) RNA is single strand, not double-stranded.

(6.1) Base Pairing Rules for DNA

(A) Adenine pairs with (T) Thymine

(C) Cytosine pairs with (G) Guanine

A&T, C&G - This base pairing is conserved through evolution

(6.1) Base Pairing Rules for RNA

(A) Adenine pairs with (U) URACIL

(C) Cytosine pairs with (G) Guanine

A&U, C&G - This base pairing is conserved through evolution

(6.1) Pyrimidines

Pyrimidines have SINGLE (1) Ring Structure (Ex. Uracil, Cytosine, Thymine)

THINK: Nucleotides w/ y in their spelling are pyrimidine (Thymine, Cytosine).

(6.1) Purines

Purines have a DOUBLE (2) Ring Structure (Ex. Adenine, Guanine)

(6.1) T/F: A purine base pairs with a pyrimidine.

True.

A (Pyrimidine) pairs with T (Purine) in DNA and U (Purine) in RNA.

G (Pyrimidine) pairs with C (Purine) In DNA and RNA

(6.1) 3 differences between Prokaryotic and Eukaryotic Genomes

1) Shape of Chromosomes (Prokaryotes - Circular, Eukaryotes - Multiple, Linear)

2) Size of Genomes (Prokaryotes - Smaller, Eukaryotes - Bigger)

3) Location of Plasmids (Prokaryotes - Cytosol, Eukaryotes - Nucleus)

(6.1) What is at the 5' end of DNA?

5' - phosphate backbone

(6.1) T/F: DNA is antiparallel.

True.

The base pairings (A&T, C&G) are held together by HYDROGEN BONDS.

Phosphate backbones are held together by phosphodiester COVALENT BONDS.

(6.1) Chargaff's Rules

1) Base composition varies between species.

2) Amount of A = Amount of T; Amount of C = Amount of G

(6.1) Supercoiling

DNA is underwound (less than 1 turn of helix per 10 base pairs) or over-wound (more than 1 turn of helix per 10 base pairs) from normal relaxed double-helix shape.

(6.1) Histones

DNA is wrapped around proteins (histones) to form nucleosomes. Nucleosomes linked to next one with the help of linker DNA.

Histones = Evolutionarily conserved proteins rich in basic amino acids and form an octamer.

(6.1) Transformation

Change in Genotype and Phenotype due to assimilation of external DNA by a cell.

(6.1) Pathogenic

Disease-causing; harmful

(6.1) Non-pathogenic

Harmless

(6.1) bacteriophages

Bacteria-Eaters

(6.2) Purpose of DNA replication

To ensure continuity of hereditary information.

(6.2) DNA Replication is SEMI-CONSERVATIVE - what does that mean?

Each original strand will serve as a template for a new strand of complementary DNA.

(6.2) Direction of DNA Synthesis

DNA is synthesized in the 5' to 3' direction.

(6.2) Differentiate between the 5' terminus and the 3' terminus of DNA.

5' - phosphate-terminus

3' - hydroxyl-terminus

(6.2) Anti-parallel meaning

5' -- 3'

3' -- 5'

(6.2) Leading Strand

Since nucleotides can only be added in the 5' to 3' direction, one strand known as the LEADING STRAND, is synthesized continuously

New DNA strand facing Helicase and Replication Fork (1 primer MINIMUM required).

(6.2) Lagging Strand

The other strand of DNA is known as the LAGGING STRAND and is synthesized discontinuously in Okazaki Fragments.

New DNA strand made NOT facing Helicase and Replication Fork.

(6.2) Origins of Replication

Particular sites with short stretches of DNA have specific sequences of nucleotides.

(6.2) Okazaki Fragents

Segments of newly synthesized DNA on the Lagging Strand, welded together by DNA polymerase.

(6.2) Helicase

Enzyme that unwinds the double-helix, untwisting and separating the strands.

(6.2) Single-Strand Binding Proteins (SSBPs)

SSBPS holds the DNA strands apart after unwinding done by Helicase.

(6.2) Topoisomerase

Enzyme that relaxes supercoil @ replication fork. It relaxes the strain caused by unwinding.

(6.2) Primase

Enzyme that synthesizes RNA primer

(6.2) DNA polymerase III

Enzyme that adds DNA nucleotides to new strand REQUIRES RNA primers (synthesized by Primase). Only builds DNA in the 5' - 3' direction. Synthesizes DNA continuously on Leading Strand and Discontinuously in Segments on Lagging Strand.

(6.2) DNA polymerase I

Enzyme that removes the RNA primer and replaces w/ DNA

(6.2) DNA Ligase

Enzyme that joins DNA fragments together on lagging strand.

(6.2) Relation between functons of Helicase and Topoisomerase

Helicase unwinds the original strands as topoisomerase relieves the coiling tension ahead of the replication fork.

(6.2) Steps of DNA Replication

1) Helicase unwinds the parental, template strand @ the double helix

2) SSBPS stabilizes the unwound template strand while topoisomerase relaxes the strain caused by Helicase unwinding the DNA.

3) Leading Strand synthesized continuously in 5' to 3' direction.

4) Primase synthesizes RNA primer for Okazaki Fragment.

5) DNA pol III starts adding DNA nucleotides.

6) DNA pol I removes primer from the 5' end and replaces it with DNA nucleotides.

7) DNA Ligase joins the newly synthesized DNA.

(6.2) Role of DNA pol in DNA proofreading and repair

Proofreads each nucleotides against template strand when covalently bonded to growing strand.

(6.2) Role of Nuclease in DNA proofreading and repair

DNA-cutting enzyme (cuts segment of strand containing errors).

(6.2) Role of Ligase in DNA proofreading and repair

Fills cut-gap w/ correct nucleotides, using the undamaged strand as a template. Seals it up.

(6.2) Role of Repair Enzymes in DNA proofreading and repair

Repairs DNA when mistakes made.

(6.2) Thymine Dimer

Thymine Dimer = Adjacent thymines linked together

Caused by UV radiation, repaired by nucleotide excision.

(6.2) Telomeres

Special nucleotide sequences located ends of eukaryotic chromosomal DNA that don't contain genes but DNA consisting of multiple repetitions of short nucleotide sequences.

Ex. TTAGGG

(6.2) Telomerase

Enzyme that catalyzes lengthening of telomeres.

(6.3) Protein Synthesis

From a Gene to a Protein - Transcription and Translation

(6.3) Central Dogma of Molecular Biology

DNA --> RNA --> Protein

(6.3) Describe flow of genetic info in the cell.

DNA molecules store genetic info. Ribosomes are where proteins are assembled. RNA connects the genetic info in the nucleus to protein synthesis in the Ribosomes.

(6.3) Transcription

The process by which the enzyme directs the formation of a mRNA molecule (messenger RNA).

Production of mRNA (RNA) using info in DNA, carries genetic message from DNA to protein-synthesizing machinery of cell (ribosomes).

(6.3) Location of Transcription

Nucleus

(6.3) Direction of RNA pol for mRNA synthesis

RNA polymerase adds nucleotides in the 5' - 3' direction so it reads the template DNA strand in the 3' - 5' direction.

ANTI-PARALLEL

(6.3) Other names for Template DNA Strand

Template DNA Strand, Noncoding strand, Minus Strand, Antisense Strand

(6.3) mRNA

Messenger RNA.

Carries genetic info from DNA to ribosomes. Info used to direct protein (polypeptide) synthesis.

Carries genetic message of DNA as RNA to translation - produced during transcription.

(6.3) tRNA

Transfer RNA.

RNA recruited by ribosomes to help create specific polypeptide sequences, as directed by mRNA.

Transfer amino acid from the cytoplasmic pool of amino acids to growing polypeptide in the ribosome.

BIG IDEA: tRNA translates mRNA into adding amino acids with the help of rRNA to growing polypeptide chain in ribosome.

(6.3) rRNA

Ribosomal RNA.

Functional units of ribosomes responsible for protein synthesis.

Attaches Amino Acids to polypeptide chain

(6.3) Codon

3-base sequence in mRNA. Each codon codes for a specific Amino Acid. Multiple codons can code for the same amino acid as the genetic code is redundant but not amiguous.

(6.3) Anticodon

3 base sequence in tRNA that complements mRNA codon base pairing.

(6.3) In Eukaryotes, what is pre-mRNA called?

Primary transcript.

(6.3) # of Amino Acids

20.

(6.3) Of the 64 possible codons, how many code for amino acids?

61 code for amino acids, 3 code for STOP(ing) Transcription and Translation.

(6.3) What is the start codon?

AUG - codes for Methionine Amino Acid - initiates translation

(6.3) Reading Frame

Correct reading of Codons

(6.3) RNA polymerase (or RNA pol II in Eukaryotic Cells)

Enzyme that uses DNA template strand to transcribe a new mRNA strand. Note that it doesn't require a primer to build in the 5' - 3' direction.

(6.3) Promoter

Site of Initiation of Transcription - DNA sequence where RNA pol. attaches and initiates, starts transcription.

(6.3) Terminator

Sequence that signals end of transcription.

(6.3) Transcription Unit

Stretch of DNA transcribed into RNA molecule downstream from promoter.

(6.3) Transcription Factors

Collection of proteins that help binding of RNA pol to promoter and initiation of transcription.

(6.3) Start point

Specific nucleotide where RNA pol starts synthesis of mRNA.

(6.3) Stages of Transcription

1) Initiation

2) Elongation

3) Termination

(6.3) Step #1 of Transcription

1) Initiation

After RNA pol. binds to the promoter, RNA pol unwinds DNA, initiates (starts) RNA synthesis at the start point on template strand in antiparallel 5' - 3' direction.

(6.3) Step #2 of Transcription

2) Elongation

RNA pol. moves downstream and expands (elongates) mRNA 5' - 3' direction. Post-transcription, DNA strands return back to double-helix form.

(6.3) Step #3 of Transcription

3) Termination

Newly synthesized RNA transcript (mRNA) is released, RNA pol. detaches from DNA.

(6.3) Promoter and RNA pol. in Eukaryotes and Prokaryotes

1) In prokaryotes, part of RNA pol itself specifically recognizes and binds to promoter.

2) In eukaryotes, transcription factors (collection of proteins) helps guide the binding of RNA pol. and initiation of transcription.

(6.3) Transcription Complex

Prokaryotes - A single type of RNA polymerase that synthesizes several types of RNA with functions in gene expression (ex. mRNA, rRNA)

Eukaryotes - Minimum of 3 types of RNA pol in Nuclei. For the pre-mRNA synthesis (primary transcript), RNA pol. II does mRNA synthesis.

(6.3) TATA Box

Nucleotide sequence w/ TATA ~25 nucleotides upstream from the start point.

(6.3) T/F: RNA processing only occurs in eukaryotic cells.

True. RNA processing only occurs in eukaryotic cells. Primary transcript altered at both ends, sections in middle removed.

(6.3) What happens @ 5' end of mRNA?

Receives a 5' GTP Cap

(6.3) What happens @ 3' end of mRNA?

3' poly-A tail added.

(6.3) 3 important functions 5' cap and poly-A tail

1) Facilitate export of mature mRNA from Nucleus through nucleopore

2) Protect mRNA from degradation by hydrolytic enzymes

3) Help ribosomes attach to 5' end of mRNA once it reaches cytoplasm.

(6.3) Introns vs. Exons

Intron = Area of mRNA not expressed, noncoding segments of nucleic acids.

Exons = Areas of mRNA expressed, coding sequence of nucleic acids.

In gene expression, only exons are expressed. Ex = expressed.

(6.3) snRNPS

Small nuclear ribonucleoproteins particles that recognize splice sites.

RNA and protein molecules make up snRNPS.

(6.3) Ribozyme

RNA molecules that function as enzymes.

(6.3) 3 properties of RNA that allow it to function as an enzyme

1) RNA is single-stranded.

2) Some bases in RNA contain functional groups that can participate in catalysis.

3) Ability of RNA to hydrogen-bond w/ other nucleic acid molecules.

(6.3) Alternate Splicing

Process of splicing introns and connecting retained exons in mature mRNA transcripts.

(6.3) How does alternate splicing lead to different proteins from the same gene?

Many different exons on primary transcripts. Different mRNA transcripts can be synthesized from 1 primary transcript. Different variations in exon order or amount of exons lead to different mRNA transcripts, yielding different proteins.

(6.4) Translation

Production of polypeptide (protein synthesis, amino acid sequence) using info in mRNA.

template: mRNA

product synthesized: polypeptide amino acid sequence

location: cytoplasm & ribosomes

(6.4) tRNA structure

1 end - specific amino acid

1 end - specific set of nucleotides that complement base pairing of mRNA (anticodon).

tRNA originates from inside nucleus and travels to cytoplasm. tRNA is reusable.

(6.4) Aminoacyl-tRNA synthases

20 present, one for each amino acid.

(6.4) Wobble

Rules for base pairing between the 3rd nucleotide base of codon and the corresponding base of tRNA anticodon are relaxed compared to other codon positions.

ex. U @ 5' end of tRNA anticodon can pair w/ A or G in 3rd position @ 3' end of mRNA codon.

(6.4) Process of Specific Amino Acid being joined to tRNA

1) Amino Acid and correct tRNA enter active site of specific synthetase.

2) ATP loses 2 phosphate groups, bonding to amino acid as AMP.

3) Correctly-labeled tRNA bonds covalently to Amino Acid, displacing AMP.

4) Charged tRNA w/ Amino Acid released by enzyme.

(6.4) Structure of Eukaryotic Ribosome

Slightly larger and differ somewhat from prokaryotic ribosomes in molecular composition.

Composed of large and small subunits. Has E, P, and A, sites.

(6.4) E site of Ribosome (Exit site)

Exit for discharged tRNA from Ribosomes.

(6.4) P site of Ribosome (peptidyl-tRNA binding site)

Holds tRNA carrying growing polypeptide chain.

(6.4) A site of Ribosome (aminoacyl-tRNA binding site)

Holds tRNA carrying NEXT amino acid to be added to chain.

(6.4) Stages of Translation

1) Initiation

2) Elongation

3) Termination

(6.4) Step #1 of Translation

1) Translation

1.1) Small ribosomal subunits bind to both mRNA and specific initiator tRNA carrying Methionine. base pairing

1.2) Arrival of large ribosomal subunit completes initiation complex. Initiation factors (proteins) required to bring all translation components together. Hydrolysis of GTP provides energy for assembly. Initiator tRNA in P site. A site open to tRNA bearing next Amino Acid.

(6.4) Step #2 of Translation

2) Elongation

2.1) Codon Recognition: Anticodon of incoming aminoacyl tRNA base-pairs w/complementary mRNA codon in A site. Hydrolysis increases the accuracy and efficiency of this step. Many different aminoacyl tRNAs present, but only one with appropriate anticodon will bind.

2.2) Peptide Bond Formation: rRNA molecule of large ribosomal subunit catalyzes formation of peptide bond between carboxyl end of growing polypeptide in P site and amino group of new amino acid in A site. Removes polypeptide from tRNA in P site, attaches to Amino Acid on tRNA in A site.

2.3) Translocation: Ribosome translocates tRNA in A site to P site. Simultaneously, empty tRNA in P site moved to E site to be released. mRNA moves along its bound tRNAs brinding next codon to be translated in A site.