BIO 205 Exam 2

Vocab highlighted from PowerPoint from Lecture

Deoxyribonucelic Acid (DNA)

Stores genetic information and is replicated using proteins

RNA world hypothesis

proposes time in evolution where RNA both stored genetic information and catalyzed its own replication

Nucleic Acid

polymer of nucleotide monomers

3 components of nucleotide

1. Phosphate group
2. Five- carbon sugar
3. Nitrogenous (nitrogen-containing) base

Ribonucleotides

monomers of DNA

* Have ribose as their sugar
* Has an -OH group (bonded to 2’ carbon)

Deoxyribonucleotides

monomers of DNA

* Sugar is deoxyribose (=lacking oxygen)
* Both sugars have -OH group bonded to 3’ carbon
* Involved in nucleotide bonding (phosphodiester linkage)

Purines

contain nine atoms in their one ring:

* Adenine (A)
* Guanine (G)

Pyrimidines

Contain six atoms in their one ring:

* Cytosine (C)
* Uracil (U)- only in RNA
* Thymine (T)- Only in DNA

“CUT of Py”

Condensation Reactions

* How Nucleic acids polymerize
* Creates bonds (removes H+ and OH-/H2O and replaces them with new bonds)

Phosphodiester lineage

Join ribonucleotides together

* Phosphate group on 5’ carbon of one nucleotide
* -OH group on 3’ carbon of another
* Polymer produced is RNA/DNA

Sugar-Phosphate backbone

* directional (5’ - 3’ direction)
* one end has unlinked 5’ phosphate group
* one end has unlinked 3’ hydroxyl group

Nucleic Acid polymerization

* Can take place in cells by use of enzymes
* Potential energy raised → 2 additional phosphate group
* Creates nucleotide triphosphates “activated nucleotides”
* ex: Adenosine Triphosphate (ATP)

X-ray cyrstallography

used to measure distances between atoms in DNA

* predicted helical structure

Primary Structure of DNA

written by listing sequences of bases by single-letter abbreviations

* ex: 5’ -ATTAGC- 3’

Secondary Structure of DNA

* DNA polymerized → phosphate groups
* sugar-phosphate backbone
* equal number of purines and pyrimidines

Grooves

attachment sites for enzymes of transcription and replication

Major Groove

backbones closer

Minor Groove

backbones farther

complementary and antiparallel

DNA strands in a double helix are

Tertiary Structure of DNA

* DNA forms compact three dimensional structures in cells
* Compaction
* 2 forms of DNA tertiary structure
* 1. DNA wraps around histones
* DNA twists to form supercoils
* Chromatin form

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Histones

Compact DNA strands and impact chromatin regulation

Supercoils

DNA twists to form

* Have to be untwisted to replicate or create proteins

Chromatin

* material of which the chromosomes of organisms other than bacteria are composed
* supercoiled DNA and is relatively spread out

Euchromatin

loosely packed DNA

Heterochromatin

highly a compacted DNA molecule which only occurs during cell division

Nucleosome

DNA wrapped 8 histones

Arginine and lysine

DNA histones that are positively charged

Phosphates

DNA is negatively charged

Biological reservoir of information

* __***Stores information***__ required for organism’s:
* growth
* reproduction
* Consists of __***sequences of nucleotides***__ in nucleic acid
* 4 nitrogenous bases
* __***Sequence***__ determines everything
* Sequence order is important

DNA Replication

1. 2 strands separated → hydrogen bonds
2. Free deoxynucleotides form hydrogen bonds → ==complementary bases of template strand==
3. Complementary base pairing allows each strand to be copied exactly → ==identical daughter molecules==

Complementary Strand

Phosphodiester linkages form to create new strand

Double Helix Structure of DNA

held together by:

* phosphodiester linkages (backbone)
* hydrogen bonds (bases)
* Hydrophobic interactions (helical structure)

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Functional Group roles in DNA

* makes molecule __***stable and resistant***__ to __**degradation**__
* Stability of DNA key to effectiveness of reliable ==information-storage molecule==

Primary Structure of RNA

* Four Types of nitrogenous bases extending from sugar
* phosphate backbone


1. RNA contains ribose (instead of deoxyribose)
2. RNA contains uracil (instead of thymine)

* Both bind to adenine


3. 2’ -oh group on ribose is ==more reactive== than -H
4. RNA is much ==less stable==

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Secondary Structure of RNA

* results from complementary base pairing: A → U; G → C
* Bases typically form **hydrogen bonds** with complementary bases on same strand
* RNA strand folds over, forming h**airpin structure:**
* Bases on one part fold over and align with bases on other part
* Two sugar-phosphate strands are **antiparallel**

Tertiary Structure of RNA

* Forms when secondary structures fold into more complex shapes
* RNA shapes are more diverse in shape, size and reactivity than DNA
* Can have ==enzymatic function==

DNA Polymerase

* Enzymes that catalyzes DNA synthesis
* Several types
* Works in one direction
* Add deoxyribonucleotides only in 3’ end of a growing DNA chain
* DNA synthesis always proceeds in 5’ → 3’ direction

Endergonic

DNA polymerization requires input of energy

Deoxyribonucleoside triphosphates (dNTPs)

* Have 3 phosphates
* high potential energy b/c of their closely packed __***phosphate groups***__
* have enough potential energy to make formation of __***phosphodiester bonds exergonic***__

Replication Bubble

an unwound and open region of a DNA helix where DNA replication occurs

* Forms when DNA is being synthesized


* Origin of replication:
* Bacteria → one and form only one
* Eukaryotic cell have many on each chromosome

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Replication Forks

Structure that forms within the long helical DNA during DNA replication.

* Synthesis is __**bidirectional**__
* replication bubbles grow in __**2 directions**__

DNA helicase

Highly conserved group of enzymes that unwind DNA

* Breaks hydrogen bonds between two DNA strands to separate them
* Single-strand DNA-binding proteins (SSBPs) attach to separated strands to prevent closing

Topoisomerase

* makes single-stranded cuts in DNA
* cut and pass double stranded DNA

Primer

short stretches of DNA that targets unique sequences and help identify a unique part of genome

* Serve as a starting point for DNA synthesis


* 10 to 25 nucleotides long

Lagging Strand

* discontinuous strand
* Strand synthesized away from replication fork
* Occurs because DNA synthesis must proceed in 5’ → 3’ direction

Discontinuous replication hypothesis

* Primase synthesizes new RNA primers on lagging strand as replication fork opens
* DNA polymerase synthesizes short fragments of DNA along lagging strand
* Fragments are linked into continuous strand

Okazaki Fragments

short sections of DNA formed at the time of discontinuous synthesis of lagging strand during replication of DNA

Telomeres

region at the end of eukaryotic chromosome

* do not contain genes

Telomere Replication

1. 3’ end of lagging strand forms single-stranded “overhang”
2. Telomerase binds to overhand → uses RNA as template for DNA synthesis
3. As telomerase move down the new strand, it adds more short DNA sequences at the end of parent strand
4. Once overhang is long enough, normal DNA synthesis can occur

Exonuclease active site

* Mismatched deoxyribonucleotide moves to site where it does fit
* Site catalyzes removal of incorrect deoxyribonucleotide

Mismatch repair

occurs when mismatched bases are corrected after DNA synthesis is complete

Nucleotide excision repair

* similar details to the mismatch repair above
* protein complex *recognizes* kink
* *removes* damaged single-stranded DNA
* Uses intact strand as *template* for new DNA
* **DNA** **ligase** *links* repair strand to original undamaged DNA

Gene Expression

the process of converting information in DNA into functioning molecules within the cell

Central Dogma

DNA → RNA → Proteins

* ==Genes== → stretches of DNA that code for proteins
* **DNA sequence** codes for RNA sequence
* **RNA sequence** codes for sequence of amino acids in protein

Transcription

process of using DNA template to make complementary RNA

* making a copy of information

Translation

process of using information in mRNA to synthesize proteins

* interprets nucleotide “language” to amino acids

Reverse transcriptase

Some viruses never go through a DNA stage

* Synthesizes DNA from an RNA template
* Gene flow is RNA → DNA

Genetic Code

specifies how a sequence of nucleotides codes for a sequence of amino acids

Codon

* mRNA
* Group of three bases that specifies particular amino acid
* Distinguish from DNA triplets

Redundant code

All but two amino acids are encoded by more than one codon

Unambiguous Code

One codon never codes for more than one amino acid

Non- overlapping Code

Codons are read one at a time

Universal Code

All codons specify the same amino acids in all organisms (with minor exceptions)

Conservative Code

If several codons specify the same amino acid, the first two bases are usually identical

Mutation

any permanent change in an organism’s DNA:

* Modification in cell’s information archive
* New alleles
* Change in its genotype

Point Mutation

mutations result from one or a small number of base changes

Chromosome- level Mutation

* mutations are larger in scale
* may change chromosome number → polyploidy or aneuploidy → or structure

Missense Mutation

Point Mutation

* mutations change an **amino acid** in protein

Silent Mutation

Point Mutation

* mutations do *not change amino acid sequence* due to **redundancy** in the code

Frameshift Mutation

Point Mutation

* mutations shift reading frame, altering meaning of **all** subsequent codons

Nonsense Mutation

Point Mutation

* mutations change codon that specifies an amino acid into **stop codon**

Inversion Mutation

Chromosome Mutation

* segment of chromosome breaks off, flips around, and rejoins

Translocation Mutation

Chromosome Mutation

* section of chromosome breaks off and becomes attached to another chromosome

Deletion Mutation

Chromosome Mutation

* segment of a chromosome is lost

Duplication Mutation

Chromosome Mutation

* segment of chromosome in present in multiple copies

Karyotype

complete set of chromosome in cell

Genetic Screen

Method of identifying organisms with mutations in genes that produce a product of interest

* Assumption: mutate an enzyme, **you will not get the molecules** produced by the enzyme

RNA Polymerase

synthesizes an RNA version of the instructions stored in DNA

* Uses ribonucleoside triphosphates (NTPs)
* Matches complementary bases to one strand of DNA
* perform template-directed synthesis in **5’ → 3’ direction**
* does not require a primer to begin transcription
* Cannot initiate transcription on its own

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Bacterial Promoters

40-50 base pair long and contains **two sites** which are recognized by sigma

* -10 box and -35 box

Termination

occurs when RNA polymerase transcribes a signal

* Codes for RNA that forms a **hairpin structure**
* Causes the RNA polymerase to separate from the RNA transcript

Elongation

RNA polymerase reads the DNA template:

* Nucleotides are added to the 3’ end of the RNA

Transcription in Eukaryotes

* 3 RNA polymerase
* Larger promoters, including TATA Box
* General transcription factors
* At termination: poly (A) signal is transcribed (rather than a hairpin)

Poly A signal Sequence

The end of the transcript

* Transcribed in Eukaryotes during termination

snRNPs

Small nuclear ribonucleoproteins

RNA Splicing

Form of RNA processing in Eukaryotes:

Allows different mRNAs and proteins to be produced from a single gene

* Cut out: introns
* Kept: exons
* Catalyzed by snRNPs

4 Steps of RNA Splicing

1. __snRNPs__ bind to 5’ exon -intron and 3’ intron - exon boundaries and to an A near the end of intron
2. Other snRNPs join complex to form a **spliceosome**
3. The intron forms a single- stranded __stem plus a loop__ (lariat)
4. The lariat is cut out and 2 exons are linked. Intron → degraded

Caps and Tails

Pre- mRNA are processed by 2 events:


1. ==5’ cap==: modified guanine nucleotide **enables ribosomes to bind and protect from degradation**
2. ==Poly (A) tail:== 100-250 adenine nucleotides **needed for translation and protect from degradation**
3. Product → mature mRNA

Template

* read by RNA polymerase
* mRNA will have a **complementary sequence** to this strand
* Does **NOT carry the “code” to** create a protein

Non-template

* not read by RNA polymerase
* Complementary to template
* mRNA will have **same sequence**
* **Carries the “code”** for making a protein

Transcription and Translation in Eukaryotes

* mRNAs are **synthesized and processed** in nucleus
* **Mature** mRNAs are transported to cytoplasm for translation by ribosomes and polyribosomes form

Transfer RNA (tRNA)

Adapter molecule used in translation

* Ex: aminoacyl tRNA → linked to its amino acid

Structure of tRNA

* short: 75 - 95 nucleotides long
* form secondary structures by folding into a **stem-and-loop**

Aminoacyl-tRNA synthetase

“charge” the tRNA using ATP

* Catalyze the addition of amino acids to tRNA

Wobble Pairing

hydrogen-bonded pairing between two nucleotides generally occurring between two RNA molecules that does not follow the Watson-Crick base pair rules

* The anticodon’s third position can form a nonstandard base pair

A site

Acceptor or aminoacyl → tRNA carries an amino acid

* remains if there is a codon-anticodon match

P site

Peptidyl → holds growing peptide chain

* peptide bond forms between the amino acid on the A-site tRNA and the polypeptide on the ___ tRNA
* the ribosome moves down the mRNA by one codon and all three tRNAs move down one position

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E site

Exit → tRNAs without amino acids exit the ribosome

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Initiation in Bacteria

* begins near the AUG start codon
* small ribosomal subunit binds to the ribosome binding site → Shine-Dalgarno sequence
* 3 step process:


1. mRNA binds to a small ribosomal subunit
2. Initiator tRNA bearing f-Met binds to the start codon
3. Large ribosomal subunit binds so that the initiator tRNA is in the P site

Initiator tRNA

first tRNA in initiating translation

* carries a modified methionine (f-Met) in bacteria

Initiation in Eukaryotes