Bio Study Guide

What Francis Crick and James Watson has discovered in the 1950s?

Midterm 3

1. Chapter 9.1 and 9.2

a. The Structure of DNA

i. Discovered by Francis Crick and James Watson in the 1950s

ii. Nucleotides are the building blocks of DNA

1. Deoxyribose: 5-carbon sugar

2. Phosphate group

3. Nitrogenous base

iii. Double-helix: two strands twisted around each other

1. Purine and pyrimidine pair together

a. AT

b. GC

2. Chargaff’s rule: there is as much A as T and as much G as  

C because they are complementary  

b. The Structure of RNA

i. Does not contain thymine, does contain adenine, cytosine, and  guanine

ii. Single-stranded molecule

iii. Three types:

1. Messenger RNA (mRNA)

2. Transfer RNA (tRNA)

3. Ribosomal RNA (rRNA)  

c. How DNA is arranged in the Cell

i. Twisted in double helix and supercoiled

Double helix

ii. Prokaryotes: single, circular chromosome that is found in the  nucleoid0 Don't forget about the age old question of gea 1000

iii. Tightly packed chromosomes are darker stained and aren’t  active

iv. Loosely packed are lightly stained and are active

d. DNA Replication

i. When a cell divides, each daughter cell receives an identical  copy of the DNA

ii. Occurs during synthesis phase of cell cycle before entering  

mitosis or meiosis

iii. Complimentary strands = having one strand means being able  to recreate the other strand (each strand is a template for the  

complementary strand to be copied)

iv. Semiconservative replication: each new strand of DNA has  one daughter strand and one parent strand

e. DNA Replication in Eukaryotes

i. 3 main stages

1. Initiation

a. DNA is made accessible to the proteins and  

enzymes involved in the replication process

How DNA is arranged in the Cell

b. Origins of replication (specific nucleotide  

sequences)

c. Binds with certain proteins

d. Helicase: enzyme that unwinds and opens up the  DNA helix

e. Replication forks: y-shaped structures that are  formed after DNA opens up

2. Elongation:  

a. DNA polymerase (enzyme) adds DNA to 3’ end of  template

b. Primer sequence is added with complementary  RNA nucleotides

i. Primer is removed later and RNA is replaced  

with DNA

ii. Okazaki fragments: new strand put  

together in short pieceshave repetitive  

sequien

1. Requires primer made of RNA

iii. Lagging strand: strand with the Okazaki  

fragments

3. Termination: primers are removed

a. DNA ligase: enzymes that seal the gaps between  fragments If you want to learn more check out ucla physics 5a

ii. Summary of Steps

1. DNA unwinds at the origin of replication

2. New bases are added to the complimentary parental  strands; one strand is made continuously while other  strand is made in pieces

3. Primers are removed, new DNA nucleotides are put in  place of the primers and the backbone is sealed by DNA  ligase

iii. Telomere Replication

1. Leading strand synthesis continues until end of  chromosome is reached

2. Lagging strand no place for primer to be made for DNA  fragment to be copied at the end of the chromosome 3. End remain unpaired  ends get shorter as they continue  to divide

4. Telomeres: ends of the linear chromosomes  

a. Have repetitive sequences that do not code for  

particular gene

b. Shortened with each round of DNA replication  

instead of genes

5. Telomerase: enzyme, attaches to end of the  

chromosome

a. RNA template is added to DNA strand, successfully  elongated, chromosomes can now replicate

b. Active in germ cells, adult stem cells, and some  Don't forget about the age old question of : abrigo : zapatos de tenis : impermeable : chaqueta : sandalias : bluejeans : gafas de sol : camisetas : traje de baño : botas : pantalones cortos : suéter

cancer cells

c. Discovered by Elizabeth Blackburn in 2009

d. Not active in adult somatic cells

e. Associated with aging

f. Has potential to treat age-related illnesses

f. DNA replication in prokaryotes

i. Prokaryotic chromosome = linear, highly coiled around proteins ii. Eukaryotic chromosome = linear, highly coiled around proteins iii. Prokaryotes replicate much more rapidly

g. DNA repair

i. Most mistakes are corrected

ii. Mismatch repair: enzymes recognize wrongly incorporated  base and excise it from the DNA, replacing it with the correct  base

iii. Nucleotide excision repair: DNA double strand is unwound  and separated, incorrect bases are removed and replaced

1. people with flaws in this system show sensitivity to  

sunlight and develop skin cancers early on in life

iv. Mutation: when a mistake isn’t corrected  We also discuss several other topics like pols 207 smith exam 2

1. Permanent change in DNA sequence

2. Leads to consequences like cancer

2. Lecture 10: DNA Structure and Replication

a. What are genes?  

i. Discovered in late 1800s

ii. Discrete units of heritable information

iii. Chromosomes: threadlike structure in cells that contain: 1. DNA – 4 nucleotides

2. Protein

iv. 50 years ago- are genes made of DNA or protein?

b. Fredrick Griffith (1928)  

i. Researching a vaccine for bacterial pneumonia  

ii. S Strain (smooth) - virulent

iii. R Strain (Rough) – nonvirulent

iv. Transformation: Transfer of one or more genes from one  organism to another

v. Conducted an experiment with the bacteria, killing it rendered it  unable to cause disease

1. R-Strain picked up genes from heat- killed S-strain  Don't forget about the age old question of chem 222 uiuc

bacteria and were able to kill

2. Did it pick up DNA or proteins?  

c. Avery McCarty, MacLeod (1944)

i. Determined that DNA is the transformation molecule

d. Hershey and Chase (1952)

i. DNA is the hereditary Molecule

ii. Bacteriophage: Virus that infects bacteria

1. Radiolabeled bacteria, sulfur labeled protein and  

phosphorous labled DNA  

e. Genes are made of DNA

i. Nothing is really known about it yet

f. DNA Nucleotides

i. 3 parts

1. Phosphate

2. Deoxyribose sugar

3. Nitrogen base

ii. 4 different bases

1. Cytosine- single-ring, pyrimidine

2. Thymine- single-ring, pyrimidine

3. Guanine- double-ring, purine

4. Adenine- double ring, purine

g. Erwin Chargaff

i. A = T

ii. C = G  

h. Pioneering Scientists

i. James Watson and Francis Crick

ii. Maclyn McCarty

iii. Rosalind Franklin

i. DNA Double Helix

i. Watson and Crick Model

ii. Double-stranded (Chains of DNA Nucleotides)  

1. Sugar phosphate backbone; covalent bonds

iii. Bases have hydrogen bonds If you want to learn more check out nas1882

iv. Two strands are complementary

1. one sequence of bases can be used to create the correct  sequence of bases for the other strand

a. strands are antiparallel

2. complementary base pairing

3. 3’ strand and 5’ strand run opposite from one another j. DNA Replication

i. All cells come from pre-existing cells

ii. DNA must be accurately copied

iii. Semiconservative replication: part of parent DNA is  conserved in each new DNA molecule

iv. Replication fork: formed by opening of the origin of  replication

v. Helicase: unzips DNA strands

vi. RNA primer: synthesized and elongated by DNA polymerase  (synthesizes in 5’3’ direction)

vii. Leading strand: DNA is synthesized continuously

viii. Lagging strand: synthesized in short stretches

1. Okazaki fragments: joins the DNA fragments

2. Synthesis has to go in opposite directions

k. Telomeres and Telomerase

i. Telomeres: ends of eukaryotic chromosomes; non-coding  repetitive sequences

1. The ends of linear chromosomes are maintained by the  telomerase enzyme

a. Active in most cells of embryos and during  

childhood development  

b. Activity is low in adult somatic cells

ii. Cancer cells show activation of telomerase

iii. Elizabeth Blackburn – discovered telomerase, 2009 Nobel Prize iv. Primase and DNA polymerase synthesize the complementary  strand

l. DNA Proof reading and repair

i. Proofreading by DNA polymerase corrects errors during  

replication

ii. Mismatch repair the incorrectly added base is detected after  replication. The mismatch repair proteins detect this base and  remove it from new strand. The gap is filled with correct base.  3. Chapter 9.3: Transcription

a. Functions of DNA

i. Replication

ii. Provide info needed to construct necessary proteins necessary  for cells to perform functions

iii. mRNA: transcribed from DNA, provides code to form a protein  by a process called translation

b. The Central Dogma: DNA encodes RNA; RNA encodes Protein i. Genes specify sequences of mRNAs  

ii. mRNAs specify the sequences of proteins

iii. Nucleotide is added to mRNA strand for every complementary  nucleotide read in the DNA strand

iv. Groups of 3 mRNA nucleotides correspond to one amino acid of  the protein sequence

c. Transcription: from DNA to mRNA

i. Eukaryotes genes bound in nucleus  transcription occurs in  nucleus, mRNA must be transported to cytoplasm

ii. Prokaryotes transcription occurs in the cytoplasm

iii. Three stages of transcription

1. Initiation

a. DNA double helix partially unwinds in the region of  

mRNA synthesis

b. Transcription bubble: region of unwinding  

c. Promoter: DNA sequence which proteins and  

enzymes involved in transcription bind to initiate  

the process

i. specific sequence is important because it  

determines if corresponding gene is  

transcribed all the time, some of the time, or  

hardly at all.

2. Elongation

a. Template strand: one of the two DNA strands  

where Transcription always proceeds from

b. Non-template strand: mRNA product  

complementary to the template strand, almost  

identical to the other DNA strand

i. Contains uracil in place of thymine

c. RNA polymerase: proceeds along DNA template  

adding nucleotides by base pairing with the DNA  

template, except RNA is being synthesized  

i. DNA is continuously unwound ahead of the  

core enzyme and rewound behind it.  

3. Termination

a. Prokaryotic polymerase needs to leave DNA  

template and free the new mRNA  

b. Uses two different termination signals

c. Process of transcription is now complete  

iv. Eukaryotic RNA processing

1. Creates a molecule that is much more stable than a  

prokaryotic mRNA

a. Eukaryotic mRNAs last for several hours

b. Prokaryotic mRNAs last no more than 5 seconds  

2. mRNA transcript is coated in RNA stabilizing proteins  

a. prevents it from degrading while being processed  

and exported out of nucleus

3. Elongation is complete enzyme adds string of 200  

adenine residues to 3’ end (poly-A tail)

a. Protects mRNA

b. Signals to cell that transcript needs to be  

transported to cytoplasm

4. Exons: expressed protein-coding sequences in eukaryotic genes

5. Introns: intervening sequences in eukaryotic genes

a. Don’t encode functional proteins  

b. Removed from pre-mRNA during processing  

i. Must be completely removed to exons can  

code the correct amino acids

6. If one single nucleotide is screwed, the protein is  

nonfunctional

7. Splicing: process of removing introns and reconnection  

exons

a. Occurs while pre-mRNA is still in the nucleus  

4. Chapter 9.4: Translation

a. Synthesis of protein is a cell’s most energy-consuming metabolic  processes

b. Translation involves decoding on mRNA message into a polypeptide  product

c. The Protein Synthesis machinery

i. rRNA: ribosomal RNA

ii. translation requires the input of an mRNA template, ribosomes,  tRNA, and various enzymatic factors  

iii. ribosomes are complex macromolecules composed of structural  and catalytic rRNA, and many distinct polypeptides

1. eukaryotes nucleolus specializes for synthesis and  

assembly of rRNA

iv. ribosomes located in cytoplasm for prokaryotes  

v. ribosomes located in cytoplasm and ER for eukaryotes

1. made up of small and large subunits

vi. tRNA: bound sequentially by large subunits of ribosomes, brings amino acids to growing chain of the polypeptide

1. 40 to 60 types may exist in cytoplasm

2. Translate the language of RNA into the language of  

proteins

d. The Genetic Code  

i. Triplet codon: three-nucleotide sequence that defines each  amino acid

ii. Genetic code: the relationship between a nucleotide codon and its corresponding amino acid

iii. Combos of nucleotides correspond to single amino acids  

(encoded by more than one nucleotide triplet)

iv. Stop codons: 3/64 codons that terminate protein synthesis and release the polypeptide from the translation machinery

v. Start codon initiates translation

1. Ex) AUG – also specifies the amino acids methionine

2. Starts near 5’ end of the mRNA  

vi. Genetic code is universal  

1. Proves that all life on earth shares a common origin

e. The Mechanism of Protein Synthesis

i. 3 phases

ii. Similar in prokaryotes and eukaryotes

1. Initiation

a. Formation of initiation complex

b. Initiator tRNA interacts with AUG start codon and  

links to special form of amino acid methionine that  

is removed from the polypeptide after translation is

complete

2. Elongation

a. Same for both prokaryotes and eukaryotes  

b. With each step, a charged tRNA enters the  

complex, the polypeptide becomes on amino acid  

longer, and an uncharged tRNA departs  

3. Termination  

a. Occurs when a stop codon (UAA, UAG, UGA) is  

encountered

b. Growing polypeptide is released and the ribosome  

subunits dissociate and leave the mRNA  

c. mRNA is degraded so the nucleotides can be  

reused in another transcription after many  

ribosomes have completed translation  

5. Chapter 9.5: How Genes Are Regulated

a. Gene expression: process of turning on a gene to produce RNA and  protein

b. Cells in multicellular organisms are specialized  

i. Consequence of different genes in each cell

c. Each cell has certain functions they must perform

d. Each cell has genes that are not expressed

e. Cells will turn on and off genes at certain times in response to  changing environments

f. Malfunctions in gene expression can lead to diseases like cancer g. Prokaryotic vs. Eukaryotic gene expression

i. Prokaryotes  

1. lack a cell nucleus

2. Transcription and translation occur almost simultaneously  3. Protein is no longer needed transcription stops  4. Regulation on DNA transcription into RNA is the primary  method to control the creation of proteins

5. Gene expression is at transcription level  

6. Lac operon: strand of DNA with three adjacent genes that  code for proteins that participate in the absorption and  metabolism of lactose

a. Contains a promoter sequence where RNA  

polymerase binds to begin transcription  

b. Operator- area between promoter and three genes  ii. Eukaryotes  

1. Have intracellular organelles and are much more  complicated

2. DNA is in nucleus where it is transcribed in mRNA transported to cytoplasm ribosomes translate it into  proteins

3. Transcription and translation are separated by nuclear  membrane

a. Transcription in nucleus 

b. Translation in cytoplasm 

4. Gene expression can occur in all stages of the process a. Epigenetic level: when gene expression occurs  when DNA is uncoiled and loosened from  

nucleosomes to bind transcription factors 

b. Transcription level: when RNA is transcribed  

c. Post transcription level: when RNA is processed  and exported to the cytoplasm after it is  

transcribed 

d. Translational level: when RNA is translated into  protein 

e. Post translational level: after protein has been made

5. Includes addition of 5’ cap, poly-A tail, and excision of  introns and splicing of exons