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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
Q

Replication, DNA Sequencing and the Human Genome Project:

A

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
Q

polymerase chain reaction process

A
  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
Q

CENTRAL DOGMA OF BIOLOGY:

A

CENTRAL DOGMA OF BIOLOGY: DNA → RNA→ Protein

28
Q

RNA PROCESSING/SPLICING:

A

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
Q

transcription process

A

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
Q

Nucleoside triphosphates (NTP’s)

A

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
Q

promoter region

A

: 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
Q

terminator region

A

sequence of nucleotides that cause RNA polymerase to detach from DNA.

33
Q

antisense strand

A

Template strand: ANTISENSE STRAND, strand used as template to create mRNA

34
Q

sense strand

A

Coding strand: SENSE STRAND, same sequence as the mRNA strand but with Thymine instead of Uracil

35
Q

how are dna sequences copied for transcription?

A

HOW ARE THEY COPIED? Codons are specific for amino acids, to stop and start codons are used to decide which strands are used

36
Q

transcription and replication similarities

A

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
Q

METHYLATION AND GENE EXPRESSION:

A

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
Q

EPIGENETICS:

A

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
Q

Proteins and Gene Expression:

A

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
Q

rRNA

A

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
Q

mRNA

A

mRNA: messenger RNA

strand of genes carries to cytoplasm for protein synthesis

42
Q

tRNA

A

tRNA: transport RNA. Consists of anticodon and protein attachment site
carries AA to mRNA/rRNA using anticompletmatry base pairing rules

43
Q

Translation: initiation

A

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
Q

Translation: Elongation

A

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
Q

Translation: Termination

A

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
Q

POLYSOMES

A

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
Q

prokaryotic protein synthesis

A

Translation and transcription occur at the same time because there is no nuclear envelope
Use ribosomes

48
Q

eukaryotic protein synthesis

A

mRNA has to travel out of the nucleus in order for translation to happen
Use ribosomes

49
Q

primary protein structure

A

Straight, linear sequence of amino acids
Peptide bonding
Not found in nature

50
Q

secondary protein structure

A

When a primary sequence folds to form alpha helix or beta pleated sheet structures
Hydrogen bonding
Silk (transthyretin)

51
Q

tertiary protein structure

A

Secondary structure fold to form 3D globular proteins
Hydrogen bonding
Disulphide bonding
Weak ionic bonds
Hydrophilic and hydrophobic and R group interactions

Enzymes

52
Q

quaternary protein structure

A

Multiple polypeptide chains form a singular structure
Hydrogen bonding
Disulphide bonding
Weak ionic bonds
Hydrophilic, hydrophobic and R group interactions

Haemoglobin

53
Q

Haemoglobin

A

Haemoglobin: a protein that transports oxygen from the lungs

54
Q

Actin and myosin

A

Actin and myosin: proteins that interact for muscle movement

55
Q

Insulin

A

Insulin: hormone that maintains glucose levels

56
Q

immunoglobulins

A

Immunoglobulins: group of proteins that act as antibodies to fight bacteria and virus

57
Q

Amylase

A

Amylase: a digestive enzyme that catalyzes the hydrolysis of starch

58
Q

Fibrous protein

A

composed of many polypeptide chains, long and narrow shape, insoluble in water. E.g.g collages, actin

59
Q

Globular protein

A

3D proteins. Soluble. Very reactive. E.g. insulin, haemoglobin

60
Q

Polar and nonpolar amino acids:

A

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
Q

EXPERIMENTS + what they were

A
  • 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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