2.4: The central dogma

central dogma

the source and order of ALL genetic information into function in organisms

DNA defintion

it is the carrier of genetic information

DNA association to central dogma

• DNA is replicated to pass on the information

  • DNA is transcribed into mRNA

mRNA definition

the chemical messenger of information

• It is the RNA product of transcription of DNA coding strand

• mRNA is translated into protein

Protein defintion

functional units of life (structure, carriers, and enzymes) that maintain it.

• final product of central dogma

where are each components of the central dogma located?

dna: nucleus

rna: cytosol

protein: cytosol

where is DNA located in bacteria

nucleoid region

examples of proteins

• muscle

• skin, hair, fingernails, and claws

• pepsin

• insulin

how many amino acids are there

20 (naturally occurring)

how many essential amino acids are there

9

• they are obtained from your diet

what reaction joins amino acids

dehydration synthesis

what kind of bond forms within different amino acids

peptide bond

what two parts of an amino acid are involved in a peptide bond

the amino group of one amino acid and the carboxylic acid of the other AA

primary structure

the particular sequence of amino acids that are the backbone of a peptide chain or protein

what are the two main types of secondary structures

alpha helix

beta pleated sheet

alpha helix (represented by a spiral)

three dimensional arrangement of amino acids with the polypeptide chain in a corkscrew shape

what holds the alpha helix structure together?

it is held by H bonds between the —NH group and the —C=O

Beta pleated sheet (represented by large arrows)

polypeptide chains arranged side by side

• hydrogen bonds form between chains

• R groups extend above and below the sheet

• typical of fibrous proteins such as silk.

tertiary structure

Specific overall shape of a protein due to functional group interaction from each chain

• cross links between R groups of amino acids in chain

• Looks like a blob full of arrows and spirals

disulfide bond

—S—S—

• Located in cystine AA

ionic bond

—COO- - - - - +H3N—

H bonds

C=O ------ HO—

T or F: function determines shape of protein

False

• the shape dictates the function!

quaternary structure

protein assembly with two or more chains

e.g. hemoglobin (has 4 polypeptide chains)

• not all proteins need to do this

globular proteins

spherical

• examples:

  • insulin

  • hemoglobin

  • enzymes

  • antibodies

they typically end up being more active or enzymatic/signals

fibrous proteins

long, thin fibers

• examples:

  • hair

  • wool

  • skin

  • nails

• there’s a strong correlation with these being more structural.

Denaturation of proteins

disruption of secondary, tertiary, and quaternary protein structure

what are the different ways to denature a protein

1. heat/organics

2. acids/bases

3. heavy metal ions

4. agitation

heat/organics denaturation

breaks apart H bonds and disrupts hydrophobic interactions

acids/bases denaturation

breaks apart H bonds between polar R groups and ionic bonds

• since they are a little electric, they disrupt any ionic interactions.

heavy metal ions denaturation

react with S-S bonds to form solids

agitation denaturation

stretches chains until bonds break.

nucleic acids

the genetic material of the cell and are composed of recurring monomeric units called nucleotides.

• the nucleic acids DNA and RNA are polymers of nucelotides.

gene

portion (sequence) of DNA nucleotides that are the blueprint for one protein.

genome

collection of genes of an organism

genotype

specific gene “type”

phenotype

observable, physical, or functional traits for a genotype.

how does DNA determines traits?

DNA contains specific sequences of bases.

• Genes use this information to direct protein synthesis, which helps determine traits.

what is the relationship between genotype, proteins, and phenotype?

proteins linke genotype (genetic makeup) to phenotype (observable traits) by helping produce those traits.

inheritance

How traits (proteins and genes) are passed on in subsequent generations.

components of nucleotides

3 parts:

• nitrogenous base

• carbohydrate

  • 3x phosphate

how many cells does each human have

40-80 trillion

• and they all carry the exact same info

each human cell contains…:

• 23 chromosome pairs

• 2m of DNA

• 3 billion DNA subunits

• about 25,000 genes coding for proteins to perform all life functions

how many chromosomes do bacteria carry

1 chromosome

we can form 150,000 proteins, but we only have 25,000 genes. How is that?

25,000 genes can come in variations which leads to a greater variety of proteins.

the sugar of dna

Deoxyribose

• pentose = 5 C

• there is no room for O on 2’ carbon

to which carbon do the phosphate groups attach?

5’

to which carbon do the nitrogenous bases attach?

1’ C

what are the two types of bases

purines and pyrimidines

purines

have a double ring structure

• adenine

• guanine

Pyrimidines

single ring structure

• cytosine

• thymine

DNA NTP

deoxyribonucleoside triphosphate

• when you have the phosphates attached, they get renamed into the name + the phosphate

  • 1 = monophosphate

  • 2 = diphosphate

  • 3 = triphosphate

DNA properties

1. polarity

2. strandedness

3. antiparallelicity

4. complementarity

polarity

DNA has a direction because the sugar-phosphate backbone has two different ends: the 5′ end and the 3′ end.

• 5′ end: Has a phosphate group attached to the sugar's 5′ carbon (often).

• 3′ end: Has a free hydroxyl (–OH) group on the sugar's 3′ carbon.

strandedness

This refers to how many strands make up DNA.

• DNA is usually double-stranded, meaning it consists of two nucleotide chains.

  • The two strands are held together by hydrogen bonds between complementary bases.

  • provides stability and protection

antiparallelity

The two DNA strands run in opposite directions.

• One strand runs 5′ → 3′.

  • The other runs 3′ → 5′.

• template strand and coding strand

complementarity

The nitrogenous bases pair in a specific way:

• A (adenine) pairs with T (thymine) in DNA.

• G (guanine) pairs with C (cytosine) in DNA.

what type of reaction bonds nucleotides

dehydration synthesis

chargoff’s rule

#’s A = #’s T

C = G

counts how many A, T, G, and Cs there are in DNA

properties:

• interact → H-bonds

• complementary

why is important to learn about DNA and its properties in micro?

helps us understand the stability of DNA

GC content

checks the organisms that have a higher amount of GC vs a lower amount

• it can help identify and characterize microorganisms.

helix formation of dna

when they base pair, they start coiling around each other

Eukaryotic chromosome characteristics

• is linear

• has 2 copies present = diploid

• the double stranded helix is extremely long

• they have positively charge proteins called histones

why is it important that histones are positively charged

because it binds to DNA which is negatively charged (bc of all the phosphates it has)

extra nuclear DNA (5%)

DNA that is used to do other things for the cell.

inactive DNA

• Activated by complexes with nuclear DNA products

used for replication of organelles

• mitochondria

• chloroplasts plasmids

  • fungi

  • protista

  • proks

histone-like proteins

what prokaryotes use to DNA around to compact it

prokaryote chromsome shape

circular

• they usually only have one chromosome.

exceptions regarding prokaryote chromosomes

• multiple copies of chromosomes

• separate chromosomes (circular + linear)

plasmids

found in PROKS

• Independently replicate

• they are small portions of DNA

  • compose up to 5% of the entire genome.

• non essential

• advantgeous

F plasmids

The F stands for fertility

conjugation

• bacteria that have an F plasmid can interact with other bacteria either very closely related or identical to them and pass on the genes.

R plasmids

R stands for resistance

• antibiotic resistance conferral

B plasmids

B stands for bacteriocin

• a protein that destroys other bacteria/competitors

V plasmids

V stands for virulence

• transfers ability to become pathogenic

• ex: capsules

what happens when an organism has multiple plasmids and starts trading these?

gains abilities

why must each daughter cell receive a complete copy of the chromosome?

to ensure each daughter cell has the genetic info needed to carry out essential cellular functions and survive.

what happens if there are missing genes?

cell death

parent dsDNA

Each original strand is a template

• produces two new alternating complementary strand

• each daughter inherits one new strand, one old strand

  • semi conservative replication

the overall process of DNA replication

duplicates the DNA blueprint (both strands) so that daughter cells can obtain the exact same genetic material.

1. unwind

2. unzip

3. prime

4. replicate

• bidirectional

• no end

where does DNA replication start?

origin of replication

tools for dna replication

• dna strands

• dna topoisomerase + gyrase

• dna helicase

• rna primase

• dna polymerase

• dna nucelotides

DNA gyrase + topoisomerase

unwinds dsDNA templates

• reduces coiling

DNA helicase

opens dsDNA: physically separates the 2 DNA strands by breaking the hydrogen bonds between the bases.

Melts DNA

• replication fork

leading strand

dna is synthesized continuously

• follows replication fork

lagging strand

discontinuous

• goes in the opposite direction of replication fork

• okazaki fragments

dna polymerases (2)

reads opened strands

• DNApol catalyzes synthesis of new strands

• 5’ to 3’

DNA replication errors

dNTPs bind complementary

• DNA polymerases builds polymers @ 1,000 NTs/s

  • Errors occur every 100,000 nucleotides

  • they proofread to remove any mistakes; however, it might make a mistake every 3 cell divisions.

which is faster at replicating: eukaryotes or prokaryotes?

prokaryotes

• only one origin of replication

transcription

RNA polymerase uses DNA blueprint and transcribes the info into a language the ribosomes can understand.

• it only read individuals genes, not the entire code.

tRNA

Transfer RNA

• functions as a helper to bring correct amino acids to ribosome to build new protein.

rRNA

ribosomal RNA

• part of the structure of ribosome (protein enzyme used to build protein)

RNA structure

• nitrogenous base (T → U)

• sugar (ribose)

  • phosphate groups

Why is the sugar for RNA not deoxyribose?

There is an O an the second carbon.

what is transcription in gene expression?

the process of using a DNA template strand to synthesize a single, complementary strand of RNA (mRNA).

• decodes DNA blueprint

tools involved in transcription

• DNA template strand

• RNA polymerase

• RNA nucleotides

Promoter

start site of transcription

terminator

signal for RNA polymerase to stop process.

what are the steps for transcription

• initiation

• elongation

• termination

post transcriptional modification

primary to mature mRNA

EUKs ONLY

• process of changing or processing an RNA molecule after transcription so it can function properly.

Exons

regions of DNA expressed