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IB BIOLOGY 2017 EXAM > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

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1
Q

Alfred Hershey and Martha Chase Experiment 1952

A

They carried out experiments to confirm DNA as genetic material
Use radioisotopes in their experiment
Bacteriophage viruses were used with isotopes of the radioactive phosphorus and sulfur

Phosphorus is found in the DNA of the Virus and Sulfur is found in the protein coat.

Bacteriophage consist of a protein outer coat and an inner core o DNA which infect cells and take over their metabolism

The bacteriophages with the radioactive sulfur and phosphorus was then allowed to infect E.Coli bacteria

The phage with sulfur didn’t affect the E.Coli’s next generation, whereas the phage with phosphorus did, as its genetic material was implanted into the E.Coli

=This proved that that DNA is the genetic material

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2
Q

DNA STRUCTURE:

A

Double stranded molecule in the shape of an helix
Sugar-phosphate backbone of DNA

Two molecules are held together by a covalent bond called a phosphodiester bond (which forms between a hydroxyl group of the 3’ carbon and the phosphate group of the 5’ carbon of deoxyribose)

The bond between nucleotides is composed of hydrogen bonding

DNA strands are antiparallel in a 5’ to 3’ orientation

Nitrogenous bases: adenine, thymine, guanine and cytosine

Pyrimidines: Thymine and Cytosine

Purines: Adenine and Guanine

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3
Q

Thymine and Cytosine

A

Pyrimidines: Thymine and Cytosine

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4
Q

Adenine and Guanine

A

Purines: Adenine and Guanine

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5
Q

DNA PACKAGING

A

Eukaryotic DNA molecules are paired with histone proteins which package the DNA into a nucleosome

Eight histones make up the nucleosome core which DNA wraps itself twice around

Looks like beads on a string

Fifth nucleosome leads to further wrapping or supercoiling of the DNA

When DNA is wrapped around the histones, it is inaccessible to transcription enzymes, which is why they have to be unwound for protein synthesis to occur

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6
Q

HIGHLY REPETITIVE SEQUENCES OF DNA

A

Satellite DNA or Junk DNA
Dispersed throughout genome, they are transposable (can move)
They are referred to as jumping genes as they can change positions with a chromosome without detaching from the DNA molecule

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7
Q

PROTEIN CODING GENES

A

A base sequences of codons can code for an amino acid
Genes are made up of numerous fragments of protein encoding information interspersed with non condition fragments (EXONS AND INTRONS)

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8
Q

STRUCTURAL DNA

A

Highly coiled DNA that doesn’t have a coding function
Usually around a centromere or at a telomere
Have lost their function possibly due to mutation?

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9
Q

SHORT TANDEM REPEATS

A

STR are used during DNA profiling

The polymorphic sequences of DNA are short repetitive sequence of DNA at 13 different locations in the loci

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10
Q

DNA PROFILING:

A

DNA PROFILING: process of obtaining a specific DNA pattern from an organism such as a human from it body tissue

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11
Q

exons

A

coding region of a gene

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12
Q

introns

A

noncoding region of a gene (removed during RNA splicing)

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13
Q

NONCODING DNA sequences

A

Non coding regions of DNA (Introns) contain telomeres, regulators of gene expression, transfer nucleic acid encoders, etc.

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14
Q

what do we know through the human genome project?

A

Through the Human Genome Project, we know that less that 2% of human DNA is actually used for protein synthesis

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15
Q

DNA replication

A

DNA Replication is Semiconservative

Meselson and Stahl confirms this through radioactive nitrogen isotopes used as radioactive markers on a DNA strand

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16
Q

DNA replication steps

A

Helicase uncoils the DNA

RNA primase adds short sequences of RNA to both strands (the primer)

The primer allows DNA polymerase III to bind and start replication

DNA polymerase III adds nucleotides to each template strand in a 5’→3’ direction

These nucleotides are initially deoxyribonucleoside triphosphates but they lose two phosphate groups during
the replication process to release energy

One strand is replicated in a continuous manner in the same direction as the replication fork (leading strand)

The other strand is replicated in fragments (Okazaki fragments) in the opposite direction (lagging strand)

DNA polymerase I removes the RNA primers and replaces them with DNA

DNA ligase then joins the Okazaki fragments together to form a continuous strand

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17
Q

helicase

A

Unwind double helix at replication fork

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18
Q

primase

A

Synthesize RNA primer

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19
Q

dna polymerase I

A

Removes the primer and replaces it with DNA

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20
Q

dna polymerase III

A

Synthesized new strand by adding nucleotides onto the primer in a 5’ to 3’ direction

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21
Q

dna ligase

A

Joins the end of DNA segments and Okazaki fragments

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22
Q

Single-stranded binding protein: k

A

Single-stranded binding protein: keeps the separated DNA strands apart during replication

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23
Q

leading and lagging strands?

A

Leading strand is assembled continuously towards the progressing replication in a 5’-3’ direction whereas the lagging strand is assembled by fragments moving away from the process also in a 5’ to 3’ direction

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24
Q

Speed and Accuracy of Replication:

A

4000 nucleotides are replicated per second
Speed essential, such as bacteria who divide every 20 min

Eukaryotic cells contain huge numbers of nucleotides compared with prokaryotic cells, so multiple replication areas are needed

Mutations however can occur due to this

REPAIR ENZYMES exist to identify and correct errors

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25
Replication, DNA Sequencing and the Human Genome Project:
DNA profiling is a reliable mean of identifying personal charceteirts Human Genome Project requires actual representation of nucleotide sequence in humans Frederick Sanger developed the first sequencing procedure using the polymerase chain reaction
26
polymerase chain reaction process
1. Single-stranded fragments placed into four different test tubes with primers, DNA polymerase and DNA nucleotides 2. Each tube contains a dideoxynucleotides, which prevents further nucleotide addition to chain after being added itself (four different types in existence) 3. Each tube contains a different type of dideoxynucleotide (ATCG) 4. Synthesis of each new DNA strand continues until DDON is added 5. DNA from each tube is separated on electrophoresis gel to determine exact sequence of the particular fragment of DNA
27
CENTRAL DOGMA OF BIOLOGY:
CENTRAL DOGMA OF BIOLOGY: DNA → RNA→ Protein
28
RNA PROCESSING/SPLICING:
When non coding regions of DNA (introns) are removed to make pre-mRNA into mRNA to be used during translation Spliceosomes are composed of small nuclear RNA’s that removed the introns Introns are formed into Lariat loops by spliceosomes and then cut out by snRNPS (small nuclear ribonucleoproteins)
29
transcription process
RNA polymerase (unwinds the strand and using the antisense strand as a template, synthesis the mRNA Transcription Factors (recruit RNA Polymerase) at the Promoter region (beginning of gene) During mRNA synthesis, uracil is used instead of thymine in the new strand RNA polymerase adds nucleoside triphosphates to the enlarging mRNA molecule. As they are added, phosphates are released which produce the RNA nucleotides. They are added at the 3’ end of the growing mRNA strand Terminator region: end of the gene, signals for the mRNA and RNA polymerase to detach
30
Nucleoside triphosphates (NTP’s)
contain three phosphates and the 5-carbon sugar ribose and are paired with exposed bases of antisense strand. Polymerization of the mRNA occurs with the help of RNA polymerase and energy provided by phosphate release in the NTP’s
31
promoter region
: short sequence of bases that aren’t transcribed however recruit transcription enzymes Promoter region of a gene determines which DNA strand is the antisense strand
32
terminator region
sequence of nucleotides that cause RNA polymerase to detach from DNA.
33
antisense strand
Template strand: ANTISENSE STRAND, strand used as template to create mRNA
34
sense strand
Coding strand: SENSE STRAND, same sequence as the mRNA strand but with Thymine instead of Uracil
35
how are dna sequences copied for transcription?
HOW ARE THEY COPIED? Codons are specific for amino acids, to stop and start codons are used to decide which strands are used
36
transcription and replication similarities
Both processes involve the unzipping of double helix and a complementary strad being used to synthesize a new strand RNA polymerase works in 5’-3’ direction
37
METHYLATION AND GENE EXPRESSION:
Inactive DNA is usually highly methylated compared with DNA actively being transcribed In females, one X chromosome is usually inactive as it is highly methylated Methylation causes a section of DNA to wrap more tightly around histones, thus preventing transcription of that particular allele Once a gene has been methylated, it stays that way through cell divisions
38
EPIGENETICS:
EPIGENETICS: the study of how DNA interacts with smaller molecules that can activate genes. Methyl groups inhibit gene expression by causing DNA to coil tightly. It's important because it mediates a lifelong dialogue between genes and the environment and can explain origins of conditions. Example: himalayan rabbits
39
Proteins and Gene Expression:
Gene expression is regulated by proteins called transcription factors that regulate transcription by binding the RNA polymerase at the promoter region of a gene Transcription activators cause looping of DNA which result in shorter distance between promoter and activator regions of DNA Repression proteins bind to segments of DNA called silences that prevent transcription of that particular region
40
rRNA
ribosomal RNA. Composed of a small subunit that binds to the mRNA during translation and a large subunit that consists of A, P, and E sites A site= attachment site P site= parking site E site= end site Can be seen with electron microscope
41
mRNA
mRNA: messenger RNA | strand of genes carries to cytoplasm for protein synthesis
42
tRNA
tRNA: transport RNA. Consists of anticodon and protein attachment site carries AA to mRNA/rRNA using anticompletmatry base pairing rules
43
Translation: initiation
Initiation: rRNAs small subunit binds to mRNA, moving in a 5’-3’ direction down the strand until it's reached the start codon. First tRNA brings Methionine to the P site of the large subunit of the rRNA.
44
Translation: Elongation
Elongation: a second tRNA brings another AA and attaches to the A site. Peptide bond forms between the AA’s. The rRNA shifts down the mRNA in a 5’-3’ direction, causing Met to be in the E site, the 2nd mRNA to be in the P site. Third tRNA carries another AA to the A site. This process continues until termination.
45
Translation: Termination
Termination: the process ends when the rRNA reaches a stop codon. A release factor then fills the A site which catalysis the hydrolysis of the bond linking the tRNA in the p site, which release the polypeptide chain from the ribosome. The mRNA, rRNA and tRNA then disassemble into smaller subunits to be used again.
46
POLYSOMES
POLYSOMES: are a group of ribosomes riding along the same mRNA to cause simultaneous translation This speeds up the rate of translation and amount of proteins produced
47
prokaryotic protein synthesis
Translation and transcription occur at the same time because there is no nuclear envelope Use ribosomes
48
eukaryotic protein synthesis
mRNA has to travel out of the nucleus in order for translation to happen Use ribosomes
49
primary protein structure
Straight, linear sequence of amino acids Peptide bonding Not found in nature
50
secondary protein structure
When a primary sequence folds to form alpha helix or beta pleated sheet structures Hydrogen bonding Silk (transthyretin)
51
tertiary protein structure
Secondary structure fold to form 3D globular proteins Hydrogen bonding Disulphide bonding Weak ionic bonds Hydrophilic and hydrophobic and R group interactions Enzymes
52
quaternary protein structure
Multiple polypeptide chains form a singular structure Hydrogen bonding Disulphide bonding Weak ionic bonds Hydrophilic, hydrophobic and R group interactions Haemoglobin
53
Haemoglobin
Haemoglobin: a protein that transports oxygen from the lungs
54
Actin and myosin
Actin and myosin: proteins that interact for muscle movement
55
Insulin
Insulin: hormone that maintains glucose levels
56
immunoglobulins
Immunoglobulins: group of proteins that act as antibodies to fight bacteria and virus
57
Amylase
Amylase: a digestive enzyme that catalyzes the hydrolysis of starch
58
Fibrous protein
composed of many polypeptide chains, long and narrow shape, insoluble in water. E.g.g collages, actin
59
Globular protein
3D proteins. Soluble. Very reactive. E.g. insulin, haemoglobin
60
Polar and nonpolar amino acids:
R Groups often decide the properties of the amino acids, including polarity Polar amino acids: hydrophilic properties Polar and nonpolar amino acids are important to determine specificity of enzymes (active site determination)
61
EXPERIMENTS + what they were
- hershey chase; proving DNA as genetic matieral using phage viruses and E.Coli - watson crick franklin; DNA structure + X-Ray Crystallogrophy - singer nicolson; structure of the phospholipid bilayer fluid mosaic model of the membrane - meselson stahl; thoery of semi-conservative replication

IB BIOLOGY 2017 EXAM (11 decks)

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