Chapter 16 - C+G Biology (exam 4)

central dogma overview

DNA —> mRNA —> protein

(transcription). (translation).

DNA polymerase

synthesizes DNA in only the 5’ to 3’ direction

• cannot start de novo you can’t start from nothing (you need a primer)

proofreading ability

DNA Polymerase does this as it is adding more bases it can check to make sure they’re correct (it can backtrack/delete/restart)

exonuclease

enzyme that removes nucleotides one at a time - break/chew up ends of nucleotides/DNA

3’ to 5’ backspaces in opposoite diretion 

10-⁶ error rate 

chances that DNA polymerase will make a mistake while/after proofreading (NOTICE THAT ITS WHILE OR AFTER PROOFREADING)

1 in a million error

super efficient 

3 main type of DNA polymerase (subtypes/isoforms)

alpha, delta, epsilon

DNA replication - semi conservative

each cell gets 1 new stand and 1 old stand (this reduces chances of mutations) this is after S phase 

origin =

start site of replication

we have thousands of origins or replication (faster)

(+) MCMs

recruited (called) protein that will open up the bubble 

MCMs = mini-chromosome maintenance 

BIND TO THE ORIGIN AND OPEN UP THE BUBBLE

(-) Geminin

(antagonists) stop MCMs, stop the opening of the bubble

replication bubble - draw this

every bubble has 2 replication forks

think sandwich 

helicase

takes double stranded DNA and makes it single stranded

(breaks down hydrogen bonds between base pairs)

single stranded binding proteins 

(SSBP) binds single strands and keeps them single

the strands are attracted to each other but this keeps them single and seperate 

topoisomerase

cleave DNA, release torsional strain, and put it back together

torsional strain

as we pull the DNA helix tighter and apart, the ends tighten and break off (DNA breaks)

the 3 that are a part of the replication bubble:

helicase, SSBP, topoisomerase

primase

creates primer (RNA) base/foundation (can work de novo)

polymerase

makes DNA (both leading and lagging works 5’ —> 3’)

the strand that goes into the fork

leading strand

continuous replication into the fork 

making way from the fork is the…

lagging strand 

the lagging strand makes fragments of DNA called…

Okazaki fragments 

DNA polymerase Alpha (A)

STARTS lagging strand

DNA polymerase delta (D)

finishes lagging strand

epsilon

starts leading strand (enzyme)

DNA ligase

fuse okazaki fragments together (fragments from lagging strand)

transcription

where a gene (DNA sequence) is copied into mRNA (messenger RNA)

translation

where mRNA sequence is read by a ribosome to build a protein (chain of amino acids) 

End-replication problem 

when we get to the ends of chromosomes 

• need to remove RNA primer and fill it with DNA

on the lagging strand we will loose…

50-200 bp each division (shorten) (removing the primer means we can’t add on to it anymore so we just loose this DNA) 

telomeres

protective caps/repeating unit attached to the ends of chromosomes

• are how we solve the end replication problem (so we don’t loose chromosomes) 

• we are degrading telomeres and not chromosomes

what is the sequence that will repeat tons (thousands of times) at the ends of our chromosomes

TTAGGG

telomerase 

enzyme that places telomeres at the end of our chromosomes

• these are only active in fetal development (silenced after birth)

if telomerase is active after birth/fetal development…

this causes cancer

90% of al cancer patients have active telomerase

active telomerase allows indefinite cell division (bypassing normal limits) that usually prevent tumor growth

purines

double-ring

adenine, guanine

pyrimidines

single-ring

thymine, cytosine

**in RNA instead of thymine its uracil 

mutation

change in the genetic code

• we can classify mutations by their effect 

• if we change DNA there is the potential for changing the resulting protein

point mutation is when 

1 nucleotide changes

transition

1 nucleotide base changes but class did not change

ex) purines —> purines

ex) pyrimidines —> pyrimidines

ex) A —> G

nucelotides

A nucleotide is the basic building block of nucleic acids — DNA and RNA.

Each nucleotide has 3 parts:

1. Phosphate group (PO₄³⁻)
   → Links nucleotides together to form the backbone of DNA/RNA.

2. Pentose sugar (5-carbon sugar)

   • Deoxyribose in DNA

   • Ribose in RNA

3. Nitrogenous base

   • Adenine (A), Guanine (G), Cytosine (C), Thymine (T) (DNA only), or Uracil (U) (RNA only)

transversion

nucleotide changes and class changes

ex) purine —> pyrimidine 

ex) C —> A

silent mutation

change to genetic code, no change to protein/amino acids

best possible mutation option for patients

missense mutation

change in genetic code, 1 amino acid is different

nonsense mutation

change in genetic code resulting in a stop codon (has the biggest effect on structure of proteins)

there are 3 stops/stop codons

UGA

UAA

UAG

if we change to one of these we stop

mutations happen when…

in s phase but you find out about them when cell tries to do its function and it messes up or can’t 

insertion/deletion

insert or delete a base pair

this shifts the reading frame (bc/ we read by 3s) and this is called FRAMESHIFT

1 codon is 

3 nucleotides (CCC) 

we read by 3s

normal pairs in DNA

A — T

C — G

Mismatched Repair Pathway

(MMR)

mismatch is being corrected

DNA polymerase messes up in HIGHLY REPETITIVE REGIONS = mismatch

detects mismatched base pairing

what is mismatched pairing repaired by

polymerase delta (mismatched bases fixed by Delta)

the defect related to MMR

lynch syndrome

• MSH 2/6 missing 

• they can’t fix errors and this leads to the accumulation of mutations really fast = cancer

• having this increases risk of certain cancers

base excision repair

chemically altered/disturbed base is fixed

• detects distorted bases

• this is caused by carcinogens/mutagens

• small chemical changes, 1 base is chemically altered

base excision repair repairs with

polymerase Beta

if you’re missing polymerase Beta this leads to

cognitive decline and the asge effect is cancer/cognitive decline

nucleotide excision repair

repair process that removes large, bulky damage affecting the DNA double helix (affecting multiple bases)

• detect DNA adducts (chemicals that can bind DNA) or bulky damage from UV light 

nucleotide excision repair repairs with

polymerase Delta or Epsilon

not having nucleotide excision repair leads to the defect of

xeroderma pigmentosum

skin cancer “vampire disease” can’t go out in the sun 

Homology-directed repair

• repairs double stranded breaks (when 2 strands are not connected)

• can ONLY occur when sister chromatids are present (late S phase, G2, early M phase)

what are sister chromatids used for in homology-directed repair

used as a template to fill in parts of damaged DNA sequence 

in homology directed repair there is no loss of genetic material because

undamaged sister chromatid is used to accurately copy the damaged DNA sequence 

a defect in homology directed repair would be

BRCA 1 / 2 (genes that increase risk of developing breast or ovarian cancer)

Non-homologous end joining

• repairs double stranded breaks 

• will occur of HDR is unavailable 

• there WILL be loss of genetic material (because it fixes the double stranded breaks without a template)

the defect in non-homologous end joining is

SCID (severe combined immunodeficiency)

a messed up, almost nonexistent immune system