Biology 1406
Exam 2 Notes
Structure of DNA
Ch. 10
Genetic information (DNA) determines structure of proteins
DNA → RNA → proteins → cell structure
3.11 – 3.15
→ enzymes control cell chemistry ( metabolism )
Proteins - made of monomers called amino acids
- polypeptide chain
- many different proteins
- each with unique shape and unique function
- 20 different amino acids
- basic chain with different “R” groups
Levels of structure:
primary - amino acid sequence
secondary - regular coils and pleats
tertiary - loops and bends in polypeptide
quaternary - linking of polypeptides
sequence → final protein shape ( in chemical environment )
and
shape determines function (good and bad examples)
*What causes secondary, tertiary and quaternary levels?
*A genetic mutation can change the function of a protein. How?
*What is denaturation?
What causes it?
*How does it affect the function of a protein?
Proteins have many functions – determine structure and function of organisms :
-enzymes
- regulate and speed up chemical reactions
- very specific (one enzyme for each reaction)
- structural proteins
- contractile proteins
- antibodies, hormones
- transport proteins
- plasma membrane proteins (receptors, channels, markers, attachment)
- transcription factors (regulate gene expression)
Protein Synthesis
10.1 – 10.16
The genetic code is a code to build proteins, determines amino acid sequence (primary structure)
Chromosome - one very long DNA molecule with supporting (histone) proteins
Gene - a section of the DNA molecule that codes for one polypeptide chain.
A single chromosome contains thousands of genes.
Locus - the particular location on a chromosome where a gene is located
8.11
Allele – different forms of a gene due to mutations
9.3
Nucleic Acids
Ch 10 , 3.15
2 types : Ribonucleic Acid (RNA) and Deoxyribonucleic Acid (DNA)
DNA and RNA are polymers made of nucleotides
Each nucleotide is made of:
- a sugar (ribose in RNA, deoxyribose in DNA)
- a phosphate (same in RNA and DNA)
- a nitrogen base:
- adenine, guanine, cytosine and thymine in DNA
- adenine, guanine, cytosine and uracil in RNA
(adenine and guanine are double C-N ring molecules)
(cytosine, thymine and uracil are single C-N rings)
Polymer is a long chain sugar phosphate “backbone” with nitrogen bases to the side
- nucleotides can link in any sequence
- sequence of nitrogen basis is information
- sequence of nucleotides has a 3’ and a 5’ end
- nucleotides added at 3’ end only
RNA is a single chain of nucleotides
DNA is a double chain of nucleotides cross-linked by nitrogen bases (“double helix” or “twisted
ladder”)
-nitrogen bases always link a certain way:
- adenine to thymine ( or uracil ) and guanine to cytosine
*Why? Give 2 reasons based on the structure of these molecules.
- nitrogen bases link by weak hydrogen bonds.
*Why is this important?
- each sugar-phosphate has 3’ and 5’ ends
- cross-linked chains are antiparallel (opposite ends)
*Why is it important that the polymer have distinct ends?
*Describe three differences between DNA and RNA
*What does the term “complementary” mean?
*Why are nucleic acids said to have a sugar – phosphate backbone if each nucleotide
monomer is made of three parts?
DNA Replication: forming duplicate copies of DNA
10.4 -.5
- complex series of reactions directed by enzymes to uncoil helix, break hydrogen bonds
between bases, join new nucleotides
- possible because nitrogen bases are complementary
Guanine ↔ Cytosine
Adenine ↔ Thymine
*Why is DNA important to living organisms?
*Why is DNA replication important?
- new polymer 5’ → 3’ (new nucleotides added at 3’ end)
- “bubbles” form as DNA is replicated
10.5
*What are these and why do they occur?
*What is the function, or job, of DNA polymerase?
*What is the function, or job, of DNA ligase?
*What is the primary trait of DNA that makes replication possible?
*Describe another trait of DNA that is important to this process.
The genetic code:
Chemical language of DNA into chemical language of proteins
- plan to describe amino acid sequence in proteins
- 4 nucleotides (nitrogen bases) in DNA - therefore 4 letter alphabet
- 20 different amino acids make up all proteins - therefore 20 things to describe
If 1 nitrogen base coded for 1 amino acid – 4 possible 10.7
If 2 nitrogen bases coded for 1 amino acid – 16 possible
If 3 nitrogen bases coded for 1 amino acid – 64 possible
- 3 nucleotides in sequence code for 1 amino acid ( = codon or triplet code)
- 64 codons - 20 amino acids, therefore several codons code for the same amino
acid.
- DNA code is redundant but not ambiguous
- no punctuation between codons – depends on starting point
ATCGCCTAGCAACTGCTT
-------- ------- ------- ------- ------- start and stop codons (mRNA) : AUG = “start here”
UAG, UAA, UGA = “stop” (5’ → 3’)
- DNA and RNA constructed and translated 5’→3’
- codons are universal; they code for the same amino acid in all living organisms; suggests
that all living organisms are from a common ancestor
- “Recombinant DNA” possible because of this.
→
mRNA →
Protein
↑
↑
transcription
translation
DNA
Transcription DNA → mRNA
- messenger RNA (mRNA) along DNA
- only along “sense strand” of DNA (template strand or transcribed strand)
- formed in nucleus, translated in ribosomes in the cytoplasm
- complementary RNA nucleotides are assembled along DNA by RNA polymerase
- RNA polymerase attaches at promoter and releases at terminator
- the mRNA is modified before it leaves the nucleus
Examples:
Translation mRNA → protein ( protein synthesis)
- occurs in ribosomes in the cytoplasm of the cell using mRNA as a
template
10.11-10.16
- transfer RNA (tRNA) carries amino acid molecules to the ribosomes to be assembled into
protein
- tRNA has 2 specific binding sites:
- anticodon nitrogen bases (1 of 64)
- amino acid (1 of 20)
Steps in protein synthesis:
- begins at the 5’ end of mRNA
- translation begins at first “start” codon (AUG) on mRNA
- tRNA molecule with anticodon that matches codon of mRNA is placed in active site of
ribosome
- amino acid is bonded to amino acid chain and released from tRNA
- proceeds one codon at a time until a “stop” codon (UAA, UAG, or UGA) is reached (these
do not have a tRNA molecule)
Mutations – random changes in DNA that are copied during replication
- change the nitrogen base sequence
- mutations within a gene produce alleles
- can be base substitution (“point”) mutations
or
- base insertions or base deletions (“frame shift”) mutation
*Which is most likely to cause the most severe change in the nucleotide sequence, a frame shift or a
point mutation? Explain why.
*What are the variations of a gene, which are caused by mutations, called?
- mutations can cause larger changes
- relocating genes within chromosomes, or breaking chromosomes, forming new
chromosomes
- gene duplication is important source of new genes
- “junk” DNA thought to be genes that are no longer expressed and randomly
duplicated sections ( 95% of our DN
Biology 1406
Exam 2 Review
Why are proteins important to cells and organisms? What do they do?
What are the monomers that form proteins?
How many different monomers form the hundreds of thousands of polymers that make up organisms? How can so
few monomers make so many polymers?
How are amino acid sequence, protein shape and protein function related?
What are the two types of nucleic acids and what monomers make up these molecules?
Using the symbols D (=deoxyribose sugar), R (=ribose sugar), P (=phosphate) and A,C,G,T,U (=nitrogen bases)
draw all of the possible nucleotides.
List three differences between RNA and DNA.
Using the symbols above draw a nine nucleotide section of DNA. Clearly indicate the location of the weaker
hydrogen bonds and distinguish between the 5’ and 3’ ends.
Describe two reasons why the nitrogen bases are complementary - always C to G and A to T or U.
Specifically what information is stored in DNA?
Define the terms chromosome and gene. Which is larger?
What is an allele? What is a locus?
What is DNA replication? What is produced by this process?
What roles do the enzymes DNA polymerase and DNA ligase play in this process?
Why is DNA replication important to living organisms?
Describe two features of the DNA molecule that make this process possible.
Compare the genetic code to a language. What are the letters are what are the words?
What do these words describe?
How are words distinguished from other words?
How are sentences punctuated?
What is the difference between the 3’ and 5’ ends and how is this used in the genetic code?
Explain what is meant by the phrase “the genetic code is redundant but never ambiguous”.
What is meant by the phrase “the genetic code is universal”. Why is this important to biologist?
Describe the process of transcription. What is produced by this process?
How does the “sense” strand (also called template or transcribed strand) of DNA differ from the “nonsense” strand?
Which is the longer?
If the “nonsense” strand is not transcribed what is its value? Is nature wasteful?
What role does the enzyme RNA polymerase play in this process and what are promoters and terminators?
Describe the process of translation. What is the product of this process?
What cell organelle assembles protein?
What molecule transports amino acids to the ribosome to be assembled?
Describe the two binding sites of tRNA. Why is this important to the process of translation?
Follow the steps in translating a six amino acid protein from start to finish.
Define the term mutation.
Distinguish between a point (base substitution) and a frame shift (base deletion or insertion) mutation.
How are the resulting proteins affected by these mutations?
What is the term for variations of a gene caused by mutations?