REVIEW 2 Flashcards
Structure of DNA
Nucleic Acid (4 different nucleotides)
Each is made of a phosphate group covalently bonded to a pentose sugar (deoxyribose) bonded to a nitrogenous base
Adenine, Thymine, Cytosine, Guanine
Direction of Bonded nucleotides
5’-3’
How are Nucleotides linked
Phosphodiester bonds
What forms the double strand?
Hydrogen bonds
Number of H-bonds between different bases and base pairs
2 h-bonds: Adenine to Thymine
3 h bonds: Guanine to cytosine
AND VICE VERSA
How are DNA strands made?
ANTIPARALLEL
Discovery of DNA structure
Rosalind Franklin
Photo 51 showed that DNA is a double helix with phosphate groups on the outside and nitrogenous bases on the inside
How is DNA packaged?
Nucleosomes
- Core = 8 histone proteins (positively charged) with DNA molecule (negatively charged) wrapped twice around
- DNA and histone proteins form chromatin (one extra histone protein)
This allows supercoiling into chromosomes
DNA sequences
2% is unique (these are genes and can be transcribed)
5-45% is highly repetitive
20% is structural sequences
Hershey-Chase Experiments
Determined that DNA, not proteins, was the genetic material
- Put radioactive phosphorus (DNA material) and sulfur (protein material) into a virus
- New viruses that were created had radioactive phosphorus, NOT sulfur in the pellet
DNA Replication Steps
- Helicase unzips parental DNA molecule (Breaking the Hydrogen Bonds between the double helix)
Gyrase stabilizes the unizipped molecules - Primase adds sequence of RNA bases (primer) to each parental DNA molecule at the replication origin
- DNA Polymerase III adds new nucleotides (deoxynucleoside triphosphates) to the RNA primer (at 3’ end only) to create a new complementary strand. This is continuous in the leading strand, but not in the lagging strand which is formed with Okazaki fragments later filled in by ligase (5’ to 3’ direction)
- DNA Polymerase I removes RNA primers and replaces them with DNA nucleotides
OVERALL, process is semi-conservative; each daughter molecule is half old and half new.
Meselson and Stahl experiment
Showed that DNA replication is semi-conservative.
How is DNA used to make proteins
Central dogma: DNA -> transcription -> RNA -> translation -> protein
DNA vs RNA
DNA | RNA
Double strand | Single Strand
Deoxyribose | Ribose
Thymine | Uracil
DNA Transcription Steps
- Initiation - RNA polymerase unwinds (breaks H bonds) strands and bands to a promoter on the antisense DNA strand.
- Elongation - RNA polymerase adds RNA nucleotides (two phosphates lost to provide energy) to 3’ end of growing mRNA strand based on code
- Termination - RNA polymerase continues until the terminator sequence is released
What happens post-transcription
In eukaryotes, introns (non-coding regions) are removed to form mature mRNA (only exons remain to be translated into amino acids/proteins
Alternative RNA splicing by spliceosomes creates the possibility for MANY polypeptides from one gene.
Ribosome structure
rRNA in nucleolus and proteins
Small/large subunit
Large subunit has A, P and E binding sites
tRNA structure
T shpaed
Contains Anti-codons and amino acid binding site (the 3’ end @ sequence CCA)
Translation steps
- Initiation - the small subunit of the ribosome binds to the mRNA at the start codon (AUG), tRNA (With correct anticodon) binds to mRNA, large subunit binds (1st tRNA in P site)
- Elongation (and translocation) - second tRNA comes into A site (complementary base pairing). Moves into P site, peptide bond formed, moves into E (exit) site
- Termination - STOP codon is reached, polypeptide chain released from tRNA in P site, ribosome disassembles
What does differentiated mean in a cell?
Different genes turned on/expressed, meaning there are different proteins
Epigenome
A collection of all the factors that modify/impact the activity/expression of genes without altering DNA sequences
1. Nucleosomes - more nucleosomes = more DNA packaged more tightly together, less transcription.
2. Methylation - methyl groups cause more tight coiling
3. Proteins - Transcription factors (act on RNA polymerase), activators and repressors
4. Environment - changes methylation, affects proteins
Primary Protein Structure
Sequence and number of amino acids - linked by peptide bonds
Secondary Protein Structure
Folding pattern: alpha helix or Beta pleated sheets (linked by Hydrogen Bonds)
Interaction between amino and carboxyl groups
Tertiary Protein Structure
Folding pattern into 3D shape
Interactions between R groups (Disulfide bridges, Ionic bonds, Hydrogen Bonds, Van der Waals (hydrophobic) interactions
Quaternary Protein Structure
NOT IN ALL PROTEINS
Links several polypeptide chains together (same binding as tertiary)
Linking prosthetic group to polypeptide
KNOW HOW TO DRAW PEPTIDE BOND
Drawing here
How is polarity of proteins determined?
R Groups
Polar proteins functions
Form inner proteins and cytoplasm/extracellular portions of membrane proteins, active sites on enzymes
Non polar proteins function
Outer portions of membrane proteins (toward phospholipid tails), embedded in cell membrane, active sites on enzymes.
Protein functions
THMEDS
Transport (hemoglobin)
Hormonal communication (insulin, LH)
Movement (actin, myosin)
Enzymes/catalysts (catalase, amylase, lipase)
Defense (immunoglobulin, antibodies)
Structure (collagen, elastin, keratin)
Fibrous vs globular proteins
Fibrous | Globular
Long, narrow | Rounded, spherical
Repetitive (no 3° structure) | Irregular
Structure/ support | Enzymes/ metabolism
Insoluble (in water)| Soluble (in water)
Actin, myosin, keratin, collagen | Hemoglobin, insulin, amylase
Endergonic reactions
Anabolic
More energy IN (energy stored in products)
condensation (builds bonds)
Example: photosynthesis
Exergonic reactions
Catabolic
More energy released
Offer involves hydrolysis
Example: cellular respiration
Competitive inhibitors
Shape similar to substrate
Binds to active site
Increased substrate concentration reduces inhibition
Reversible inhibition
Non-Competitive inhibitors
Shape NOT similar to substrate
Binds to other side (changes enzyme shape so regular substrate can’t bind)
Increased substrate concentration has no effect on inhibition
Usually irreversible inhibition
How is lactase used in industry?
Lactase can pre-digest lactose in milk for lactose intolerant individuals
