CH 13 GEN BIO 2

All of the work in cell is done by

Proteins

What makes cells different

Expression of those proteins; cells MAKE own proteins

# of amino acids

Only 20; the "-ases"

Relationship between allele and sex ratio

Allele doesn't affect sex ratio

Protein function "depend chain"

PROTEIN FUNCTION depends on AMINO ACID SEQUENCE depends on ALLELES (GENES) depends on DNA SEQUENCE

Central dogma of biology

DNA -> RNA -> Protein

Meselson and Stahl

Determined that DNA replication is semiconservative

Erwin Chargaff

Determined that amount of purines & pyrimadines is equal (A&Ts are equal, C&Gs, whole sum is =)

Rosalyn Franklin

Came up with the double helix

Watson and Crick

Stole the double helix image (from Rosalyn) and presented it; THEY came up with the LADDERS

Transcription

DNA --> RNA

Translation

RNA --> protein

Retrovirus

Virus that contains RNA as its genetic information; flips normal DNA --> RNA to RNA --> DNA

Examples of protein complications

Post-trans modifications, prions

Prions

Infectious proteins that are misfolded

Example of an RNA virus

Ebola, COVID

DNA vs RNA

DNA is double-sided, ACGT; RNA is single-stranded, ACGU

Both DNA and RNA is made from

Monomers of nucleotides (polymers)

DNA is a

Polymer of nucleotides

Hydrogenous pairing:

G = C, A = T

Chargaff's Rule

The amount of purines must equal the amount of pyrimidines

(ex. 15%G = 15%C, so A&G would have to both be 35% to equal 100%)

Purines & pyrimidines will be in PAIRS because

of the way the H bonds can form on the sides with the purines

Nitrogenous bases have a lot of

Nitrogen

Nucleoside

Pentose sugar + nitrogenous base

Order of Cs on a nucleoside

(STARTS ON RIGHT, clockwise) Base, 1', 2', 3', 4', 5'

Base

First position, DOES NOT CHANGE

1'

On the carbon between between O and H

2'

in RIBOSE, contains OH group (OXYribose)

in d + DEOXYRIBOSE, contains just H (DEOXYribose)

3'

IMPORTANT!! OH group where the molecule can GROW; present in both ribose and deoxyribose

Absence of 3'

Occurs in dideoxyribose; only an H here instead of OH, so this molecule cannot grow, making it a TERMINATOR protein

4'

Creates helix shape and bond angles

5'

Phosphate; "TIDE" part of nucleotide

Nucleotide

Pentose sugar + nitrogenous base + phosphate

The base can be either

A purine or pyrimidine

Precursors (2)

Nucleotide triphosphate (NTP); need 3 phosphates because energy comes from 2 of them

OR deoxynucleotide (dNTP)

ddNTP

dedioxynucleotide triphosphate; is a terminator

RNA vs DNA vs terminator molecule

Difference is in the 2':

RNA has OH, which is very reactive and unstable

DNA has H

Terminator has H, and 3' is ALSO H (hence cannot grow)

Stability of RNA with transport of it

Its reactivity and instability is why RNA vaccines need to be shipped on ice at -80 because it degrades at room temp

Polynucleotide precursors

Go in either 5' -> 3' OR 3' -> 5' direction

# of H bonds between T and A

2

# of H bonds between C and G

3

Sense direction

5' to 3'

Antisense direction

3' to 5'

Creator + meaning of antiparallel theory

Watson & Crick; realized that each strand has to be going in OPPOSITE DIRECTIONS

DNA structure (2)

Double-stranded antiparallel

Complementary base pairing

Using H-bonds and Chargaff’s rule; 1 = (A+T)+(C+G)

What molecule needs to grow

3’ endof the DNA strand, which is necessary for DNA polymerase to add new nucleotides during replication.

Alphaphosphates

Phosphate groups attached to 5’ end of molecule, are what are between nucleotides

DNA packaging negatively charged

Is negatively charged due to negative backbone (will be attracted to POSITIVE histones)

DNA polymer pH

Is acidic due to released protons

DNA polymer ionization

Is polyanionic BECAUSE of ions become the phosphodiester backbone (bonds between phosphate groups)

Polyamines

Small, positively-charged organic molecules that counterbalance negative charge of DNA backbone by binding to phosphate groups

Histones

Large proteins that are wrapped with DNA to form nucleosomes; positive charge

Five elements needed for DNA polymerization

• Precursors

• Energy

• Enzymes

• Template

• Primer

Precursors

The building blocks (dNTPs) that DNA polymerase uses to make a new strands

SSBP

Single-stranded binding proteins; protect the ladder by holding it in place to reduce stress as unzipping occurs

Example of a cofactor & function

Mg2+ ions; enable enzyme activity

Energy in DNA polymerization

Comes from gamma (y) and beta (B) nucleotides (phosphates); these bonds are very unstable and have a lot of energy

4 enzymes in DNA polymerization

Helicase; primase; DNA polymerase; DNA ligase

Helicase

Breaks (“unzips”) H bonds between nucleotides; dsDNA → ssDNA

Primase

Makes short RNA primers that will allow a 3’OH to grow

DNA polymerase

Catalyzes formation of phosphodiester bonds, so rate goes from 1000 nucleotides/second → 100 nucleotides/second (adds complementary base to new DNA)

thing that ACTUALLY COPIES THE DNA

DdDp

DNA-dependent DNA polymerase; different name for DNA polymerase

DNA ligase

Combines polymerase fragments together (lagging)

Template

The original DNA copy needed for replication

Primer

Made from RNA, allows a 3’ to grow a NEW STRAND (2’ OH is only a temporary primer)

Semiconservative replication

“One old, one new”; build a NEW strand off of each of the split PARENT strands (half of each of the split cell’s DNA came from the parent cell)

3 ingredients of semi-conservative DNA replication

Helicase, DNA polymerase, replication fork

Leading strand follows

The fork

Fork quantity

Can have multiple; formed when helicase unzips the DNA

Helicase unzipping

is PERMANENT; will be doing this in 2 directions at a time, as there is no difference in directionality for them

Distinction between leading and lagging strand

Leading strand follows the form and is synthesized CONTINUOUSLY in direction of fork; lagging strand going AGAINST the grain and being synthesized in FRAGMENTS

Okazaki fragment

In LAGGING strands, how the strand is synthesized due to DNA polymerase having to STOP & RESTART at each DNA primase, creating the fragments

POINT of lagging process

To minimize the amount of ssDNA (don’t want a super-long single strand waiting to be read)

What is ALWAYS present on template leading strand

Free 3’ nucleotide; there in order to make the phosphodiester backbone (help the molecule grow)

Parent DNA ploidy

2n

Replicated DNA ploidy

2n+

Key piece of info needed for labeling leading/lagging

DIRECTION of the fork

Role of DNA ligase in Okazaki fragments

Seal the fragments together to make one long, continuous diester backbone by filling in spaces in the backbone

Proofreading rate

Human DNA polymerase synthesizes 50 bases/second; is relatively slow due to exonuclease

Exonuclease

Repair enzyme that finds errors in proofreading process and repairs them (ex. when wrong base is put in)

Initial error rate

1 per 100,000 bases (would cause 60,000 mutations per cell division)

if we DIDN’T have any repair enzymes

Proofreading enzyme

Special kind of DNA polymerase that finds wrong/extra bases as it is reading; reduces error rate to 1 in 10^10 bases

3 things that protect your DNA

Untranslated regions; “junk” regions; noncoding

Depurinated base

Sugar & phosphate but no carbon; also targeted by proofreading enzymes

Wrong/broken base in DNA proofreading

Will cut that section out, synthesize new replacement section, then ligate

What wrong base will normally cause

Would normally cause synthesis to grind to a halt, but rarely we just incorporate them into DNA

Telomeres

ENDS of chromosomes; go to the end and start adding a whole lot of bases, which protects the ends

Why is end protection necessary

Every round of replication would otherwuse lose about 50-100 nucleotides, which would accumulate into numerous genes/actual coding info over generations

Telomerase

Adds DNA bases to ends to maintain them; essentially protects the ends with “junk”

TTAGGG frequency on ends

Around 2500 times

Sheltrin 6-protein complex

Special knot at the end that regulates telomere length and protects ends; if you give to mice, will start living for YEARS longer than they should

Relationship between aging and telomeres

As you age, telomeres will shrink (nobody knows why)

T-loop

Protect the ends from fraying, like a “cap” on the end of your chromosomes to keep them from fraying apart

THINK AGLETS ON SHOELACES